diff --git a/dev/index.html b/dev/index.html index 08b457ac8..509bf850b 100644 --- a/dev/index.html +++ b/dev/index.html @@ -134,48 +134,48 @@

Install or update #> ✔ Got pkgconfig 2.0.3 (source) (6.08 kB) #> ✔ Got glue 1.6.2 (source) (106.51 kB) #> ✔ Got lifecycle 1.0.3 (source) (106.85 kB) -#> ✔ Got magrittr 2.0.3 (source) (267.07 kB) #> ✔ Got fansi 1.0.4 (source) (482.06 kB) #> ✔ Got cli 3.6.1 (source) (567.29 kB) -#> ✔ Got utf8 1.2.3 (source) (241.41 kB) +#> ✔ Got magrittr 2.0.3 (source) (267.07 kB) #> ✔ Got tibble 3.2.1 (source) (565.98 kB) #> ✔ Got pillar 1.9.0 (source) (444.53 kB) -#> ✔ Got rlang 1.1.1 (source) (762.53 kB) +#> ✔ Got utf8 1.2.3 (source) (241.41 kB) #> ✔ Got vctrs 0.6.3 (source) (967.34 kB) +#> ✔ Got rlang 1.1.1 (source) (762.53 kB) #> ℹ Building cli 3.6.1 #> ℹ Building fansi 1.0.4 -#> ✔ Built fansi 1.0.4 (5.7s) +#> ✔ Built fansi 1.0.4 (4.5s) #> ℹ Building glue 1.6.2 -#> ✔ Built glue 1.6.2 (2.2s) +#> ✔ Built glue 1.6.2 (1.7s) #> ℹ Building magrittr 2.0.3 -#> ✔ Built magrittr 2.0.3 (1.7s) +#> ✔ Built magrittr 2.0.3 (1.4s) #> ℹ Building pkgconfig 2.0.3 -#> ✔ Built pkgconfig 2.0.3 (1.2s) +#> ✔ Built pkgconfig 2.0.3 (910ms) #> ℹ Building rlang 1.1.1 -#> ✔ Built cli 3.6.1 (13.4s) +#> ✔ Built cli 3.6.1 (10s) #> ℹ Building utf8 1.2.3 -#> ✔ Built utf8 1.2.3 (11.9s) -#> ✔ Installed cli 3.6.1 (51ms) -#> ✔ Installed fansi 1.0.4 (64ms) -#> ✔ Installed glue 1.6.2 (32ms) -#> ✔ Installed magrittr 2.0.3 (32ms) -#> ✔ Installed pkgconfig 2.0.3 (25ms) -#> ✔ Installed utf8 1.2.3 (33ms) -#> ✔ Built rlang 1.1.1 (16.8s) -#> ✔ Installed rlang 1.1.1 (57ms) +#> ✔ Built rlang 1.1.1 (12.5s) +#> ✔ Installed cli 3.6.1 (39ms) +#> ✔ Installed fansi 1.0.4 (1s) +#> ✔ Installed glue 1.6.2 (26ms) +#> ✔ Installed magrittr 2.0.3 (28ms) +#> ✔ Installed pkgconfig 2.0.3 (27ms) +#> ✔ Installed rlang 1.1.1 (54ms) #> ℹ Building lifecycle 1.0.3 -#> ✔ Built lifecycle 1.0.3 (2s) -#> ✔ Installed lifecycle 1.0.3 (27ms) +#> ✔ Built utf8 1.2.3 (13.4s) +#> ✔ Installed utf8 1.2.3 (28ms) +#> ✔ Built lifecycle 1.0.3 (1.4s) +#> ✔ Installed lifecycle 1.0.3 (23ms) #> ℹ Building vctrs 0.6.3 -#> ✔ Built vctrs 0.6.3 (25.8s) -#> ✔ Installed vctrs 0.6.3 (70ms) +#> ✔ Built vctrs 0.6.3 (19.7s) +#> ✔ Installed vctrs 0.6.3 (60ms) #> ℹ Building pillar 1.9.0 -#> ✔ Built pillar 1.9.0 (4.8s) -#> ✔ Installed pillar 1.9.0 (40ms) +#> ✔ Built pillar 1.9.0 (3.5s) +#> ✔ Installed pillar 1.9.0 (34ms) #> ℹ Building tibble 3.2.1 -#> ✔ Built tibble 3.2.1 (4.4s) -#> ✔ Installed tibble 3.2.1 (45ms) -#> ✔ 1 pkg + 10 deps: added 11, dld 11 (4.52 MB) [1m 16.6s] +#> ✔ Built tibble 3.2.1 (3.3s) +#> ✔ Installed tibble 3.2.1 (36ms) +#> ✔ 1 pkg + 10 deps: added 11, dld 11 (4.52 MB) [59.7s] @@ -194,11 +194,11 @@

Install packages from GitHubℹ No downloads are needed, 1 pkg is cached #> ✔ Got tibble 3.2.1.9005 (source) (1.32 MB) #> ℹ Packaging tibble 3.2.1.9005 -#> ✔ Packaged tibble 3.2.1.9005 (683ms) +#> ✔ Packaged tibble 3.2.1.9005 (471ms) #> ℹ Building tibble 3.2.1.9005 -#> ✔ Built tibble 3.2.1.9005 (4.2s) -#> ✔ Installed tibble 3.2.1.9005 (github::tidyverse/tibble@4de5c15) (34ms) -#> ✔ 1 pkg + 10 deps: kept 10, upd 1, dld 1 (NA B) [7.5s] +#> ✔ Built tibble 3.2.1.9005 (3.1s) +#> ✔ Installed tibble 3.2.1.9005 (github::tidyverse/tibble@4de5c15) (27ms) +#> ✔ 1 pkg + 10 deps: kept 10, upd 1, dld 1 (NA B) [6.3s] @@ -269,11 +269,11 @@

Install a local package an #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got cli 3.6.1 (source) (567.29 kB) #> ℹ Packaging cli 3.6.1 -#> ✔ Packaged cli 3.6.1 (1.1s) +#> ✔ Packaged cli 3.6.1 (792ms) #> ℹ Building cli 3.6.1 -#> ✔ Built cli 3.6.1 (12.2s) -#> ✔ Installed cli 3.6.1 (local) (47ms) -#> ✔ 1 pkg: upd 1, dld 1 (567.29 kB) [14.4s] +#> ✔ Built cli 3.6.1 (9s) +#> ✔ Installed cli 3.6.1 (local) (50ms) +#> ✔ 1 pkg: upd 1, dld 1 (567.29 kB) [10.7s] diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml index 562aca41f..d2664e18d 100644 --- a/dev/pkgdown.yml +++ b/dev/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: internals: internals.html -last_built: 2023-07-17T09:40Z +last_built: 2023-07-17T11:42Z urls: reference: https://pak.r-lib.org/reference article: https://pak.r-lib.org/articles diff --git a/dev/search.json b/dev/search.json index f9483db27..24113074c 100644 --- a/dev/search.json +++ b/dev/search.json @@ -1 +1 @@ -[{"path":"https://pak.r-lib.org/dev/articles/internals.html","id":"the-embedded-library","dir":"Articles","previous_headings":"","what":"The embedded library","title":"pak internals","text":"pak bundles dependencies installed package, user’s cache directory. can happen several ways: running inside R CMD check, R CMD INSTALL installs dependencies installing package data, /library within installed package. Downloading installing (currently) 37 dependencies takes 1-1.5 minutes platforms binaries, 4 minutes platforms compile everything source (measured Linux). goal create self-contained binaries CRAN. main advantage data step can show progress /messages user. bundling fails, pak errors. avoid creating non-functional binary package. Hopefully CRAN just try creating binary , later. also works well platforms (yet) binaries, e.g. M1 macs, Linux new experimental Windows platform. running inside R CMD check, pak bundle dependencies, make checks faster. Unlike traditional R CMD check setup, CRAN install package check. Instead, pre-install , refer install log check. set env vars pre-install, pak still bundle dependencies case. pak installed GitHub, using remotes::install_github() similar, dependency bundling happens. nice platforms build self-contained binary. see also next item. DESCRIPTION Remotes field, pak bundle dependencies, emits message suggests using create_dev_lib(). can’t easily install GitHub using base R functions . running R CMD check, pak uses testthat.R bundle dependencies temporary installation used check. However, pak copies dependencies case, make check faster. copying dependencies fails, pak skips test suite. reason copying testthat.R instead install time way avoid check warning large /library directory. pak installation currently tested bundled dependencies, setup.R bundles , user’s cache directory. make sure can still use devtools::test() alike development. developing pak interactively, e.g. using load_all(), use create_dev_lib() copy dependencies user’s cache directory. summary, various bundling modes: install.packages() binary pkg CRAN → pak ready use install.packages() source pkg CRAN → install /library R CMD INSTALL CRAN (build binaries) → install /library R CMD INSTALL (CRAN) R CMD check → bundle R CMD check → copy /library, ignore errors remotes::install_github() without Remotes → install /library remotes::install_github() Remotes → bundle devtools::test() similar → copy user’s cache directory","code":""},{"path":"https://pak.r-lib.org/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Gábor Csárdi. Author, maintainer. Jim Hester. Author. . Copyright holder, funder.","code":""},{"path":"https://pak.r-lib.org/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Csárdi G, Hester J (2023). pak: Another Approach Package Installation. R package version 0.5.1.9000, https://pak.r-lib.org/.","code":"@Manual{, title = {pak: Another Approach to Package Installation}, author = {Gábor Csárdi and Jim Hester}, year = {2023}, note = {R package version 0.5.1.9000}, url = {https://pak.r-lib.org/}, }"},{"path":"https://pak.r-lib.org/dev/index.html","id":"pak","dir":"","previous_headings":"","what":"Another Approach to Package Installation","title":"Another Approach to Package Installation","text":"Fresh Approach R Package Installation pak installs R packages CRAN, Bioconductor, GitHub, URLs, git repositories, local files directories. alternative install.packages() devtools::install_github(). pak fast, safe convenient. 🚀 Short tour 🔗 Quick links (start doubt!) ✨ Features ⬇️ Installation 📘 License","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/index.html","id":"install-or-update-packages-from-cran-or-bioconductor","dir":"","previous_headings":"🚀 Short tour","what":"Install or update packages from CRAN or Bioconductor","title":"Another Approach to Package Installation","text":"","code":"pak::pkg_install(\"tibble\") #> ✔ Updated metadata database: 2.53 MB in 3 files. #> ✔ Updating metadata database ... done #> #> → Will install 11 packages. #> → Will download 11 CRAN packages (4.52 MB). #> + cli 3.6.1 [bld][cmp][dl] (567.29 kB) #> + fansi 1.0.4 [bld][cmp][dl] (482.06 kB) #> + glue 1.6.2 [bld][cmp][dl] (106.51 kB) #> + lifecycle 1.0.3 [bld][dl] (106.85 kB) #> + magrittr 2.0.3 [bld][cmp][dl] (267.07 kB) #> + pillar 1.9.0 [bld][dl] (444.53 kB) #> + pkgconfig 2.0.3 [bld][dl] (6.08 kB) #> + rlang 1.1.1 [bld][cmp][dl] (762.53 kB) #> + tibble 3.2.1 [bld][cmp][dl] (565.98 kB) #> + utf8 1.2.3 [bld][cmp][dl] (241.41 kB) #> + vctrs 0.6.3 [bld][cmp][dl] (967.34 kB) #> #> ℹ Getting 11 pkgs (4.52 MB) #> ✔ Got pkgconfig 2.0.3 (source) (6.08 kB) #> ✔ Got glue 1.6.2 (source) (106.51 kB) #> ✔ Got lifecycle 1.0.3 (source) (106.85 kB) #> ✔ Got magrittr 2.0.3 (source) (267.07 kB) #> ✔ Got fansi 1.0.4 (source) (482.06 kB) #> ✔ Got cli 3.6.1 (source) (567.29 kB) #> ✔ Got utf8 1.2.3 (source) (241.41 kB) #> ✔ Got tibble 3.2.1 (source) (565.98 kB) #> ✔ Got pillar 1.9.0 (source) (444.53 kB) #> ✔ Got rlang 1.1.1 (source) (762.53 kB) #> ✔ Got vctrs 0.6.3 (source) (967.34 kB) #> ℹ Building cli 3.6.1 #> ℹ Building fansi 1.0.4 #> ✔ Built fansi 1.0.4 (5.7s) #> ℹ Building glue 1.6.2 #> ✔ Built glue 1.6.2 (2.2s) #> ℹ Building magrittr 2.0.3 #> ✔ Built magrittr 2.0.3 (1.7s) #> ℹ Building pkgconfig 2.0.3 #> ✔ Built pkgconfig 2.0.3 (1.2s) #> ℹ Building rlang 1.1.1 #> ✔ Built cli 3.6.1 (13.4s) #> ℹ Building utf8 1.2.3 #> ✔ Built utf8 1.2.3 (11.9s) #> ✔ Installed cli 3.6.1 (51ms) #> ✔ Installed fansi 1.0.4 (64ms) #> ✔ Installed glue 1.6.2 (32ms) #> ✔ Installed magrittr 2.0.3 (32ms) #> ✔ Installed pkgconfig 2.0.3 (25ms) #> ✔ Installed utf8 1.2.3 (33ms) #> ✔ Built rlang 1.1.1 (16.8s) #> ✔ Installed rlang 1.1.1 (57ms) #> ℹ Building lifecycle 1.0.3 #> ✔ Built lifecycle 1.0.3 (2s) #> ✔ Installed lifecycle 1.0.3 (27ms) #> ℹ Building vctrs 0.6.3 #> ✔ Built vctrs 0.6.3 (25.8s) #> ✔ Installed vctrs 0.6.3 (70ms) #> ℹ Building pillar 1.9.0 #> ✔ Built pillar 1.9.0 (4.8s) #> ✔ Installed pillar 1.9.0 (40ms) #> ℹ Building tibble 3.2.1 #> ✔ Built tibble 3.2.1 (4.4s) #> ✔ Installed tibble 3.2.1 (45ms) #> ✔ 1 pkg + 10 deps: added 11, dld 11 (4.52 MB) [1m 16.6s]"},{"path":"https://pak.r-lib.org/dev/index.html","id":"install-packages-from-github","dir":"","previous_headings":"🚀 Short tour","what":"Install packages from GitHub","title":"Another Approach to Package Installation","text":"","code":"pak::pkg_install(\"tidyverse/tibble\") #> #> → Will update 1 package. #> → The package (0 B) is cached. #> + tibble 3.2.1 → 3.2.1.9005 [bld][cmp] (GitHub: 4de5c15) #> #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got tibble 3.2.1.9005 (source) (1.32 MB) #> ℹ Packaging tibble 3.2.1.9005 #> ✔ Packaged tibble 3.2.1.9005 (683ms) #> ℹ Building tibble 3.2.1.9005 #> ✔ Built tibble 3.2.1.9005 (4.2s) #> ✔ Installed tibble 3.2.1.9005 (github::tidyverse/tibble@4de5c15) (34ms) #> ✔ 1 pkg + 10 deps: kept 10, upd 1, dld 1 (NA B) [7.5s]"},{"path":"https://pak.r-lib.org/dev/index.html","id":"look-up-dependencies","dir":"","previous_headings":"🚀 Short tour","what":"Look up dependencies","title":"Another Approach to Package Installation","text":"","code":"pak::pkg_deps_tree(\"tibble\") #> tibble 3.2.1 [new][bld][cmp] #> ├─fansi 1.0.4 [new][bld][cmp] #> ├─lifecycle 1.0.3 [new][bld] #> │ ├─cli 3.6.1 [new][bld][cmp] #> │ ├─glue 1.6.2 [new][bld][cmp] #> │ └─rlang 1.1.1 [new][bld][cmp] #> ├─magrittr 2.0.3 [new][bld][cmp] #> ├─pillar 1.9.0 [new][bld] #> │ ├─cli #> │ ├─fansi #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─utf8 1.2.3 [new][bld][cmp] #> │ └─vctrs 0.6.3 [new][bld][cmp] #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ └─rlang #> ├─pkgconfig 2.0.3 [new][bld] #> ├─rlang #> └─vctrs #> #> Key: [new] new | [bld] build | [cmp] compile"},{"path":"https://pak.r-lib.org/dev/index.html","id":"explain-dependencies","dir":"","previous_headings":"🚀 Short tour","what":"Explain dependencies","title":"Another Approach to Package Installation","text":"","code":"pak::pkg_deps_explain(\"tibble\", \"rlang\") #> tibble -> lifecycle -> rlang #> tibble -> pillar -> lifecycle -> rlang #> tibble -> pillar -> rlang #> tibble -> pillar -> vctrs -> lifecycle -> rlang #> tibble -> pillar -> vctrs -> rlang #> tibble -> rlang #> tibble -> vctrs -> lifecycle -> rlang #> tibble -> vctrs -> rlang"},{"path":"https://pak.r-lib.org/dev/index.html","id":"install-a-local-package-and-its-dependencies","dir":"","previous_headings":"🚀 Short tour","what":"Install a local package and its dependencies","title":"Another Approach to Package Installation","text":"","code":"pak::local_install(\"cli\") #> #> → Will update 1 package. #> → The package (0 B) is cached. #> + cli 3.6.1 → 3.6.1 [bld][cmp] #> #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got cli 3.6.1 (source) (567.29 kB) #> ℹ Packaging cli 3.6.1 #> ✔ Packaged cli 3.6.1 (1.1s) #> ℹ Building cli 3.6.1 #> ✔ Built cli 3.6.1 (12.2s) #> ✔ Installed cli 3.6.1 (local) (47ms) #> ✔ 1 pkg: upd 1, dld 1 (567.29 kB) [14.4s]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/index.html","id":"how-do-i--","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"How do I … ?","title":"Another Approach to Package Installation","text":"Start Get Started pak solve specific issues.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"faq","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"FAQ","title":"Another Approach to Package Installation","text":"Check list frequently asked questions.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"reference","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"Reference","title":"Another Approach to Package Installation","text":"complete reference pak functions complete source information pak.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"i-have-another-question","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"I have a(nother) question","title":"Another Approach to Package Installation","text":"Don’t hesitate ask RStudio Community forum. Use pak tag.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"i-would-like-to-report-a-bug","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"I would like to report a bug","title":"Another Approach to Package Installation","text":"Head pak issue tracker.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"sparkles-features","dir":"","previous_headings":"","what":"✨ Features","title":"Another Approach to Package Installation","text":"⚡ Fast - parallel downloads installation, caching, etc. 🦺 Safe - dependency solver, system dependency solver, etc. 🏪 Convenient - packages multiple sources, time travel, etc. See complete list awesome features.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/index.html","id":"pre-built-binaries","dir":"","previous_headings":"⬇️ Installation","what":"Pre-built binaries","title":"Another Approach to Package Installation","text":"Install binary build pak repository GitHub: supported following systems: macOS support official CRAN R build. builds, e.g. Homebrew R, supported.","code":"install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch))"},{"path":"https://pak.r-lib.org/dev/index.html","id":"install-from-cran","dir":"","previous_headings":"⬇️ Installation","what":"Install from CRAN","title":"Another Approach to Package Installation","text":"Install released version package CRAN usual: potentially needs C compiler platforms CRAN binaries packages .","code":"install.packages(\"pak\")"},{"path":"https://pak.r-lib.org/dev/index.html","id":"other-platforms-and-nightly-builds","dir":"","previous_headings":"⬇️ Installation","what":"Other platforms and nightly builds","title":"Another Approach to Package Installation","text":"See installation page!","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"blue_book-license","dir":"","previous_headings":"","what":"📘 License","title":"Another Approach to Package Installation","text":"GPL-3 © RStudio","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Package cache utilities — cache_summary","title":"Package cache utilities — cache_summary","text":"Various utilities inspect clean package cache. See pkgcache package need control package cache.","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Package cache utilities — cache_summary","text":"","code":"cache_summary() cache_list(...) cache_delete(...) cache_clean()"},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Package cache utilities — cache_summary","text":"... cache_list() cache_delete(), ... may contain filters, argument name column name. E.g. package, version, etc. Call cache_list() without arguments see available column names. call cache_delete() without arguments, delete cached files.","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Package cache utilities — cache_summary","text":"cache_summary() returns list elements: cachepath: absolute path package cache files: number files (packages) cache size: total size package cache bytes cache_list() returns data frame data cache. cache_delete() returns nothing. cache_clean() returns nothing.","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Package cache utilities — cache_summary","text":"cache_summary() returns summary package cache. cache_list() lists (default), subset packages package cache. cache_delete() deletes files cache. cache_clean() deletes files cache.","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Package cache utilities — cache_summary","text":"","code":"cache_summary() #> $cachepath #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/pkg\" #> #> $files #> [1] 483 #> #> $size #> [1] 654662486 #> cache_list() #> # A data frame: 483 × 11 #> fullpath path package url etag sha256 version platf…¹ built #> #> 1 /Users/gaborc… arch… NA http… \"\\\"1… 0c8f0… NA NA NA #> 2 /Users/gaborc… bin/… evalua… http… \"\\\"1… 08a39… 0.17 aarch6… NA #> 3 /Users/gaborc… bin/… crayon http… \"\\\"2… 1e6d5… 1.5.2 aarch6… NA #> 4 /Users/gaborc… bin/… common… http… \"\\\"4… 47b4a… 1.8.1 aarch6… NA #> 5 /Users/gaborc… bin/… curl http… \"\\\"b… 7b8ba… 4.3.3 aarch6… NA #> 6 /Users/gaborc… bin/… tinytex http… \"\\\"2… 7e9ba… 0.42 aarch6… NA #> 7 /Users/gaborc… bin/… jsonli… http… \"\\\"1… 68e59… 1.8.2 aarch6… NA #> 8 /Users/gaborc… bin/… lifecy… http… \"\\\"1… 7ce27… 1.0.3 aarch6… NA #> 9 /Users/gaborc… bin/… vctrs http… \"\\\"1… c3a69… 0.4.2 aarch6… NA #> 10 /Users/gaborc… src/… pkgcac… NA NA 9b70a… NA NA 0 #> # … with 473 more rows, 2 more variables: vignettes , #> # rversion , and abbreviated variable name ¹​platform cache_list(package = \"recipes\") #> # A data frame: 1 × 11 #> fullp…¹ path package url etag sha256 version platf…² built vigne…³ #> #> 1 /Users… bin/… recipes http… \"\\\"1… e281e… 1.0.2 aarch6… NA NA #> # … with 1 more variable: rversion , and abbreviated variable #> # names ¹​fullpath, ²​platform, ³​vignettes cache_list(platform = \"source\") #> # A data frame: 69 × 11 #> fullpath path package url etag sha256 version platf…¹ built #> #> 1 /Users/gaborc… src/… crayon http… \"\\\"9… 70a9a… 1.5.2 source NA #> 2 /Users/gaborc… src/… zip http… \"\\\"1… 14873… 2.2.1 source NA #> 3 /Users/gaborc… src/… curl http… \"\\\"a… 3567b… 4.3.3 source NA #> 4 /Users/gaborc… src/… rlang http… \"\\\"b… e6973… 1.0.6 source NA #> 5 /Users/gaborc… src/… openssl http… \"\\\"1… 7cde9… 2.0.3 source NA #> 6 /Users/gaborc… src/… tinytex http… \"\\\"8… 205f7… 0.42 source NA #> 7 /Users/gaborc… src/… evalua… http… \"\\\"6… 49c74… 0.17 source NA #> 8 /Users/gaborc… src/… Rcpp http… \"\\\"2… 807ce… 1.0.9 source NA #> 9 /Users/gaborc… src/… knitr http… \"\\\"d… 9b8f9… 1.40 source NA #> 10 /Users/gaborc… src/… lpSolve http… \"\\\"7… f7258… 5.6.17 source NA #> # … with 59 more rows, 2 more variables: vignettes , #> # rversion , and abbreviated variable name ¹​platform cache_delete(package = \"knitr\") cache_delete(platform = \"macos\") cache_clean()"},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":null,"dir":"Reference","previous_headings":"","what":"Frequently Asked Questions — FAQ","title":"Frequently Asked Questions — FAQ","text":"Please take look list asking questions.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-reinstall-a-package-","dir":"Reference","previous_headings":"","what":"How do I reinstall a package?","title":"Frequently Asked Questions — FAQ","text":"pak reinstall package, version already installed. Sometimes still want reinstall, e.g. fix broken installation. case can delete package install , use ?reinstall parameter:","code":"pak::pkg_install(\"tibble\") #> #> → Will install 13 packages. #> → All 13 packages (7.68 MB) are cached. #> + cli 3.3.0 #> + crayon 1.5.1 #> + ellipsis 0.3.2 #> + fansi 1.0.3 #> + glue 1.6.2 #> + lifecycle 1.0.1 #> + magrittr 2.0.3 #> + pillar 1.7.0 #> + pkgconfig 2.0.3 #> + rlang 1.0.2 #> + tibble 3.1.7 #> + utf8 1.2.2 #> + vctrs 0.4.1 #> ℹ No downloads are needed, 13 pkgs (7.68 MB) are cached #> ✔ Got utf8 1.2.2 (aarch64-apple-darwin20) (209.24 kB) #> ✔ Installed cli 3.3.0 (76ms) #> ✔ Installed crayon 1.5.1 (87ms) #> ✔ Installed ellipsis 0.3.2 (97ms) #> ✔ Installed fansi 1.0.3 (103ms) #> ✔ Installed glue 1.6.2 (111ms) #> ✔ Installed lifecycle 1.0.1 (153ms) #> ✔ Installed magrittr 2.0.3 (158ms) #> ✔ Installed pillar 1.7.0 (162ms) #> ✔ Installed pkgconfig 2.0.3 (87ms) #> ✔ Installed rlang 1.0.2 (39ms) #> ✔ Installed tibble 3.1.7 (41ms) #> ✔ Installed utf8 1.2.2 (39ms) #> ✔ Installed vctrs 0.4.1 (32ms) #> ✔ 1 pkg + 12 deps: added 13, dld 1 (209.24 kB) [1.8s] pak::pkg_install(\"tibble?reinstall\") #> #> → Will install 1 package. #> → The package (724.32 kB) is cached. #> + tibble 3.1.7 #> ℹ No downloads are needed, 1 pkg (724.32 kB) is cached #> ✔ Installed tibble 3.1.7 (42ms) #> ✔ 1 pkg + 12 deps: kept 11, added 1 [343ms]"},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-install-a-dependency-from-a-binary-package","dir":"Reference","previous_headings":"","what":"How do I install a dependency from a binary package","title":"Frequently Asked Questions — FAQ","text":"Sometimes suffifient install binary package older version dependency, instead newer source package potentially needs compilers, system tools libraries. pkg_install() lockfile_create() default upgrade = FALSE, always chooses binaries source packages, use pkg_install() need anything extra. local_install_* functions default upgrade = TRUE, pak() pkf = NULL, need explicitly use upgrade = FALSE.","code":""},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-install-a-package-from-source-","dir":"Reference","previous_headings":"","what":"How do I install a package from source?","title":"Frequently Asked Questions — FAQ","text":"force installation source package (instead binary package), use ?source parameter:","code":"pak::pkg_install(\"tibble?source\") #> #> → Will install 1 package. #> → The package (672.34 kB) is cached. #> + tibble 3.1.7 👷🏼‍♀️🔧 #> ℹ No downloads are needed, 1 pkg (672.34 kB) is cached #> ℹ Building tibble 3.1.7 #> ✔ Built tibble 3.1.7 (3.1s) #> ✔ Installed tibble 3.1.7 (35ms) #> ✔ 1 pkg + 12 deps: kept 11, added 1 [4.1s]"},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-install-the-latest-version-of-a-dependency-","dir":"Reference","previous_headings":"","what":"How do I install the latest version of a dependency?","title":"Frequently Asked Questions — FAQ","text":"want always install dependency source, want latest version reason, can use source parameter = form: =?source. example install tibble, cli dependency installed source write:","code":"pak::pkg_install(c(\"tibble\", \"cli=?source\")) #> #> → Will install 1 package. #> → The package (540.04 kB) is cached. #> + cli 3.3.0 👷🏽🔧 #> ℹ No downloads are needed, 1 pkg (540.04 kB) is cached #> ℹ Building cli 3.3.0 #> ✔ Built cli 3.3.0 (4.5s) #> ✔ Installed cli 3.3.0 (68ms) #> ✔ 1 pkg + 12 deps: kept 11, added 1 [4.9s]"},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-ignore-an-optional-dependency-","dir":"Reference","previous_headings":"","what":"How do I ignore an optional dependency?","title":"Frequently Asked Questions — FAQ","text":"syntax Note can ignore optional dependencies, .e. packages Suggests Enhances.","code":"pak::pkg_install( c(\"tibble\", \"DiagrammeR=?ignore\", \"formattable=?ignore\"), dependencies = TRUE ) #> #> ℹ No downloads are needed #> ✔ 1 pkg + 12 deps: kept 12 [583ms] =?ignore"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-can-i-use-pak-with-renv-","dir":"Reference","previous_headings":"","what":"How can I use pak with renv?","title":"Frequently Asked Questions — FAQ","text":"currently, keep eye issue: https://github.com/r-lib/pak/issues/343","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":null,"dir":"Reference","previous_headings":"","what":"A list of the most important pak features — Great pak features","title":"A list of the most important pak features — Great pak features","text":"list important pak features.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"parallel-http","dir":"Reference","previous_headings":"","what":"Parallel HTTP","title":"A list of the most important pak features — Great pak features","text":"pak performs HTTP queries concurrently. true downloads package metadata package repositories, resolves packages CRAN, GitHub, URLs, etc, downloads actual package files, etc.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"parallel-installation","dir":"Reference","previous_headings":"","what":"Parallel installation","title":"A list of the most important pak features — Great pak features","text":"pak installs packages concurrently, much dependency graph allows .","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"caching","dir":"Reference","previous_headings":"","what":"Caching","title":"A list of the most important pak features — Great pak features","text":"pak caches metadata package files, need re-download files .","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"plan-installation-up-front","dir":"Reference","previous_headings":"","what":"Plan installation up front","title":"A list of the most important pak features — Great pak features","text":"pak creates installation plan downloading packages. plan unsuccessful, fails without downloading packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"auto-install-missing-dependencies","dir":"Reference","previous_headings":"","what":"Auto-install missing dependencies","title":"A list of the most important pak features — Great pak features","text":"requesting installation package, pak makes sure dependencies also installed.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"keeping-binary-packages-up-to-date","dir":"Reference","previous_headings":"","what":"Keeping binary packages up-to-date","title":"A list of the most important pak features — Great pak features","text":"pak automatically discards binary packages cache, new build version available CRAN.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"correct-cran-metadata-errors","dir":"Reference","previous_headings":"","what":"Correct CRAN metadata errors","title":"A list of the most important pak features — Great pak features","text":"pak can correct CRAN's metadata issues, e.g.: New version package released since obtained metadata. macOS binary package available https://mac.r-project.org/ synchronization issue.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"graceful-handling-of-locked-package-dlls-on-windows","dir":"Reference","previous_headings":"","what":"Graceful handling of locked package DLLs on Windows","title":"A list of the most important pak features — Great pak features","text":"pak handles situation locked package DLLs, well possible. detects process locked , offers choice terminating processes. also unloads packages current R session needed.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"pak-keeps-its-own-dependencies-isolated","dir":"Reference","previous_headings":"","what":"pak keeps its own dependencies isolated","title":"A list of the most important pak features — Great pak features","text":"pak keeps dependencies private package library never loads packages. (background processes).","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"pak-comes-as-a-self-contained-binary-package","dir":"Reference","previous_headings":"","what":"pak comes as a self-contained binary package","title":"A list of the most important pak features — Great pak features","text":"common platforms. dependencies, system dependencies, compiler needed. (See also installation manual.)","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"install-packages-from-multiple-sources","dir":"Reference","previous_headings":"","what":"Install packages from multiple sources","title":"A list of the most important pak features — Great pak features","text":"CRAN, Bioconductor GitHub URLs Local files directories.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"ignore-certain-optional-dependencies","dir":"Reference","previous_headings":"","what":"Ignore certain optional dependencies","title":"A list of the most important pak features — Great pak features","text":"pak can ignore certain optional dependencies requested.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"cran-package-file-sizes","dir":"Reference","previous_headings":"","what":"CRAN package file sizes","title":"A list of the most important pak features — Great pak features","text":"pak knows sizes CRAN package files, can estimate much data need download, installation.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"bioconductor-version-detection","dir":"Reference","previous_headings":"","what":"Bioconductor version detection","title":"A list of the most important pak features — Great pak features","text":"pak automatically selects Bioconductor version appropriate R version. need set repositories.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"time-travel-with-mran-or-rspm","dir":"Reference","previous_headings":"","what":"Time travel with MRAN or RSPM","title":"A list of the most important pak features — Great pak features","text":"pak can use MRAN (Microsoft R Application Network, https://mran.microsoft.com/) RSPM (RStudio Public Package Manager, https://packagemanager.rstudio.com/client/#/) install snapshots CRAN.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"pak-can-install-dependencies-of-local-packages","dir":"Reference","previous_headings":"","what":"pak can install dependencies of local packages","title":"A list of the most important pak features — Great pak features","text":"handy package development!","code":""},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":null,"dir":"Reference","previous_headings":"","what":"Simplified manual. Start here! — Get started with pak","title":"Simplified manual. Start here! — Get started with pak","text":"need read long manual pages simple task. manual page collects common pak use cases.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-a-package-from-cran-or-bioconductor","dir":"Reference","previous_headings":"","what":"Install a package from CRAN or Bioconductor","title":"Simplified manual. Start here! — Get started with pak","text":"pak automatically sets CRAN repository Bioconductor repositories correspons current R version.","code":"pak::pkg_install(\"tibble\")"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-a-package-from-github","dir":"Reference","previous_headings":"","what":"Install a package from GitHub","title":"Simplified manual. Start here! — Get started with pak","text":"Use user/repo form. can specify branch tag: user/repo@branch user/repo@tag.","code":"pak::pkg_install(\"tidyverse/tibble\") #> #> → Will update 2 packages. #> → All 2 packages (0 B) are cached. #> + tibble 3.1.8 → 3.1.8.9002 👷🏻🔧 (GitHub: 37ec86a) #> + vctrs 0.5.1 → 0.5.1.9000 👷🏾‍♀️🔧 (GitHub: 2d7de76) #> ℹ No downloads are needed, 2 pkgs are cached #> ℹ Packaging vctrs 0.5.1.9000 #> ✔ Packaged vctrs 0.5.1.9000 (1.4s) #> ℹ Building vctrs 0.5.1.9000 #> ✔ Built vctrs 0.5.1.9000 (11.2s) #> ✔ Installed vctrs 0.5.1.9000 (github::r-lib/vctrs@2d7de76) (34ms) #> ℹ Packaging tibble 3.1.8.9002 #> ✔ Packaged tibble 3.1.8.9002 (502ms) #> ℹ Building tibble 3.1.8.9002 #> ✔ Built tibble 3.1.8.9002 (2.7s) #> ✔ Installed tibble 3.1.8.9002 (github::tidyverse/tibble@37ec86a) (28ms) #> ✔ 1 pkg + 10 deps: kept 9, upd 2 [17.5s]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-a-package-from-a-url","dir":"Reference","previous_headings":"","what":"Install a package from a URL","title":"Simplified manual. Start here! — Get started with pak","text":"URL may point R package file, made R CMD build, .tar.gz .zip archive package tree.","code":"pak::pkg_install( \"url::https://cran.r-project.org/src/contrib/Archive/tibble/tibble_3.1.7.tar.gz\" ) #> #> → Will install 1 package. #> → Will update 1 package. #> → All 2 packages (38.65 kB) are cached. #> + ellipsis 0.3.2 #> + tibble 3.1.8.9002 → 3.1.7 👷🏻‍♀️🔧 #> ℹ No downloads are needed, 2 pkgs (38.65 kB) are cached #> ✔ Installed ellipsis 0.3.2 (18ms) #> ℹ Building tibble 3.1.7 #> ✔ Built tibble 3.1.7 (2.5s) #> ✔ Installed tibble 3.1.7 (31ms) #> ✔ 1 pkg + 11 deps: kept 10, upd 1, added 1 [3.3s]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"update-a-package","dir":"Reference","previous_headings":"","what":"Update a package","title":"Simplified manual. Start here! — Get started with pak","text":"pak::pkg_install() automatically updates package.","code":"pak::pkg_install(\"tibble\") #> #> → Will update 1 package. #> → The package (724.32 kB) is cached. #> + tibble 3.1.7 → 3.1.8 #> ℹ No downloads are needed, 1 pkg (724.32 kB) is cached #> ✔ Installed tibble 3.1.8 (36ms) #> ✔ 1 pkg + 10 deps: kept 10, upd 1 [368ms]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"update-all-dependencies-of-a-package","dir":"Reference","previous_headings":"","what":"Update all dependencies of a package","title":"Simplified manual. Start here! — Get started with pak","text":"upgrade = TRUE updates package dependencies, necessary.","code":"pak::pkg_install(\"tibble\", upgrade = TRUE) #> #> ℹ No downloads are needed #> ✔ 1 pkg + 10 deps: kept 11 [278ms]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"reinstall-a-package","dir":"Reference","previous_headings":"","what":"Reinstall a package","title":"Simplified manual. Start here! — Get started with pak","text":"Add ?reinstall package name package reference general:","code":"pak::pkg_install(\"tibble?reinstall\") #> #> → Will install 1 package. #> → The package (724.32 kB) is cached. #> + tibble 3.1.8 #> ℹ No downloads are needed, 1 pkg (724.32 kB) is cached #> ✔ Installed tibble 3.1.8 (60ms) #> ✔ 1 pkg + 10 deps: kept 10, added 1 [340ms]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"dependencies-of-a-cran-or-bioconductor-package","dir":"Reference","previous_headings":"","what":"Dependencies of a CRAN or Bioconductor package","title":"Simplified manual. Start here! — Get started with pak","text":"results returned data frame.","code":"pak::pkg_deps(\"tibble\") #> # A data frame: 11 × 32 #> ref type direct direc…¹ status package version license needs…² #> #> 1 cli stan… FALSE FALSE OK cli 3.4.1 MIT + … FALSE #> 2 fansi stan… FALSE FALSE OK fansi 1.0.3 GPL-2 … FALSE #> 3 glue stan… FALSE FALSE OK glue 1.6.2 MIT + … FALSE #> 4 lifecycle stan… FALSE FALSE OK lifecy… 1.0.3 MIT + … FALSE #> 5 magrittr stan… FALSE FALSE OK magrit… 2.0.3 MIT + … FALSE #> 6 pillar stan… FALSE FALSE OK pillar 1.8.1 MIT + … FALSE #> 7 pkgconfig stan… FALSE FALSE OK pkgcon… 2.0.3 MIT + … FALSE #> 8 rlang stan… FALSE FALSE OK rlang 1.0.6 MIT + … FALSE #> 9 tibble stan… TRUE TRUE OK tibble 3.1.8 MIT + … FALSE #> 10 utf8 stan… FALSE FALSE OK utf8 1.2.2 Apache… FALSE #> 11 vctrs stan… FALSE FALSE OK vctrs 0.5.1 MIT + … FALSE #> # … with 23 more variables: priority , md5sum , sha256 , #> # filesize , built , platform , rversion , #> # repotype , repodir , target , deps , #> # mirror , sources , remote , error , #> # metadata , dep_types , params , sysreqs , #> # cache_status , lib_status , old_version , #> # new_version , and abbreviated variable names ¹​directpkg, …"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"dependency-tree-of-a-cran-bioconductor-package","dir":"Reference","previous_headings":"","what":"Dependency tree of a CRAN / Bioconductor package","title":"Simplified manual. Start here! — Get started with pak","text":"results also silently returned data frame.","code":"pak::pkg_deps_tree(\"tibble\") #> tibble 3.1.8 ✨ #> ├─fansi 1.0.3 ✨ #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli 3.4.1 ✨ #> │ ├─glue 1.6.2 ✨ #> │ └─rlang 1.0.6 ✨ #> ├─magrittr 2.0.3 ✨ #> ├─pillar 1.8.1 ✨ #> │ ├─cli #> │ ├─fansi #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─utf8 1.2.2 ✨ #> │ └─vctrs 0.5.1 ✨ #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ └─rlang #> ├─pkgconfig 2.0.3 ✨ #> ├─rlang #> └─vctrs #> #> Key: ✨ new"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"dependency-tree-of-a-package-on-github","dir":"Reference","previous_headings":"","what":"Dependency tree of a package on GitHub","title":"Simplified manual. Start here! — Get started with pak","text":"Use user/repo form. usual, can also select branch, tag, sha, user/repo@branch, user/repo@tag user/repo@sha forms.","code":"pak::pkg_deps_tree(\"tidyverse/tibble\") #> tidyverse/tibble 3.1.8.9002 ✨👷🏼🔧 #> ├─fansi 1.0.3 ✨ #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli 3.4.1 ✨ #> │ ├─glue 1.6.2 ✨ #> │ └─rlang 1.0.6 ✨ #> ├─magrittr 2.0.3 ✨ #> ├─pillar 1.8.1 ✨ #> │ ├─cli #> │ ├─fansi #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─utf8 1.2.2 ✨ #> │ └─r-lib/vctrs 0.5.1.9000 ✨👷🏼🔧 #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ └─rlang #> ├─pkgconfig 2.0.3 ✨ #> ├─rlang #> └─r-lib/vctrs #> #> Key: ✨ new | 👷🏼 build | 🔧 compile"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"dependency-tree-of-the-package-in-the-current-directory","dir":"Reference","previous_headings":"","what":"Dependency tree of the package in the current directory","title":"Simplified manual. Start here! — Get started with pak","text":"Assuming package directory tibble.","code":"pak::local_deps_tree(\"tibble\") #> local::tibble 3.1.8 ✨👷🏻‍♀️🔧 #> ├─fansi 1.0.3 ✨ #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli 3.4.1 ✨ #> │ ├─glue 1.6.2 ✨ #> │ └─rlang 1.0.6 ✨ #> ├─magrittr 2.0.3 ✨ #> ├─pillar 1.8.1 ✨ #> │ ├─cli #> │ ├─fansi #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─utf8 1.2.2 ✨ #> │ └─vctrs 0.5.1 ✨ #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ └─rlang #> ├─pkgconfig 2.0.3 ✨ #> ├─rlang #> └─vctrs #> #> Key: ✨ new | 👷🏻‍♀️ build | 🔧 compile"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"explain-a-recursive-dependency","dir":"Reference","previous_headings":"","what":"Explain a recursive dependency","title":"Simplified manual. Start here! — Get started with pak","text":"tibble depend rlang? Use can also use user/repo form packages GitHub, url::... packages URLs, etc.","code":"pak::pkg_deps_explain(\"tibble\", \"rlang\") #> tibble -> lifecycle -> rlang #> tibble -> pillar -> lifecycle -> rlang #> tibble -> pillar -> rlang #> tibble -> pillar -> vctrs -> lifecycle -> rlang #> tibble -> pillar -> vctrs -> rlang #> tibble -> rlang #> tibble -> vctrs -> lifecycle -> rlang #> tibble -> vctrs -> rlang"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-dependencies-of-local-package","dir":"Reference","previous_headings":"","what":"Install dependencies of local package","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::local_install_deps() #> ✔ Loading metadata database ... done #> #> → The package (0 B) is cached. #> ℹ No downloads are needed #> ✔ 10 deps: kept 10 [3.2s]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-local-package","dir":"Reference","previous_headings":"","what":"Install local package","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::local_install() #> #> → Will update 1 package. #> → The package (0 B) is cached. #> + tibble 3.1.8 → 3.1.8 👷🏻‍♂️🔧 #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got tibble 3.1.8 (source) (96 B) #> ℹ Packaging tibble 3.1.8 #> ✔ Packaged tibble 3.1.8 (864ms) #> ℹ Building tibble 3.1.8 #> ✔ Built tibble 3.1.8 (2.4s) #> ✔ Installed tibble 3.1.8 (local) (38ms) #> ✔ 1 pkg + 10 deps: kept 10, upd 1, dld 1 (NA B) [4.2s]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-all-dependencies-of-local-package","dir":"Reference","previous_headings":"","what":"Install all dependencies of local package","title":"Simplified manual. Start here! — Get started with pak","text":"Installs development optional dependencies well.","code":"pak::local_install_dev_deps() #> #> → Will install 86 packages. #> → Will update 2 packages. #> → All 89 packages (100.53 MB) are cached. #> + askpass 1.1 #> + base64enc 0.1-3 #> + bench 1.1.2 #> + bit 4.0.5 #> + bit64 4.0.5 #> + blob 1.2.3 #> + brio 1.1.3 #> + bslib 0.4.1 #> + cachem 1.0.6 #> + callr 3.7.3 #> + clipr 0.8.0 #> + colorspace 2.0-3 #> + covr 3.6.1 #> + crayon 1.5.2 #> + curl 4.3.3 #> + desc 1.4.2 #> + DiagrammeR 1.0.9 #> + diffobj 0.3.5 #> + digest 0.6.31 #> + downloader 0.4 #> + dplyr 1.0.10 #> + evaluate 0.19 👷🏿‍♂️ #> + farver 2.1.1 #> + fastmap 1.1.0 #> + formattable 0.2.1 #> + fs 1.5.2 #> + generics 0.1.3 #> + ggplot2 3.4.0 #> + gridExtra 2.3 #> + gtable 0.3.1 #> + highr 0.9 #> + hms 1.1.2 #> + htmltools 0.5.4 #> + htmlwidgets 1.6.0 👷🏾‍♂️ #> + httr 1.4.4 #> + igraph 1.3.5 #> + influenceR 0.1.0.1 #> + isoband 0.2.6 #> + jquerylib 0.1.4 #> + jsonlite 1.8.4 #> + knitr 1.41 #> + labeling 0.4.2 #> + lazyeval 0.2.2 #> + lubridate 1.9.0 #> + Matrix 1.5-1 → 1.5-3 #> + memoise 2.0.1 #> + mime 0.12 #> + mockr 0.2.0 #> + munsell 0.5.0 #> + nlme 3.1-160 → 3.1-161 👷‍♂️🔧 #> + nycflights13 1.0.2 #> + openssl 2.0.5 #> + pkgbuild 1.4.0 #> + pkgload 1.3.2 #> + praise 1.0.0 #> + prettyunits 1.1.1 #> + processx 3.8.0 #> + profmem 0.6.0 #> + ps 1.7.2 #> + purrr 0.3.5 #> + R6 2.5.1 #> + rappdirs 0.3.3 #> + RColorBrewer 1.1-3 #> + readr 2.1.3 #> + rematch2 2.1.2 #> + rex 1.2.1 #> + rmarkdown 2.19 👷‍♂️ #> + rprojroot 2.0.3 #> + rstudioapi 0.14 #> + sass 0.4.4 #> + scales 1.2.1 #> + stringi 1.7.8 #> + stringr 1.5.0 #> + sys 3.4.1 #> + testthat 3.1.6 #> + tidyr 1.2.1 #> + tidyselect 1.2.0 #> + timechange 0.1.1 #> + tinytex 0.43 👷🏻‍♂️ #> + tzdb 0.3.0 #> + viridis 0.6.2 #> + viridisLite 0.4.1 #> + visNetwork 2.1.2 #> + vroom 1.6.0 #> + waldo 0.4.0 #> + withr 2.5.0 #> + xfun 0.35 #> + yaml 2.3.6 #> ℹ No downloads are needed, 88 pkgs (100.53 MB) are cached #> ℹ Packaging tibble 3.1.8 #> ℹ Building evaluate 0.19 #> ℹ Building nlme 3.1-161 #> ✔ Installed R6 2.5.1 (31ms) #> ✔ Installed DiagrammeR 1.0.9 (76ms) #> ✔ Installed RColorBrewer 1.1-3 (72ms) #> ✔ Installed askpass 1.1 (79ms) #> ✔ Installed Matrix 1.5-3 (137ms) #> ✔ Installed base64enc 0.1-3 (125ms) #> ✔ Installed bench 1.1.2 (90ms) #> ✔ Installed bit64 4.0.5 (44ms) #> ✔ Installed bit 4.0.5 (43ms) #> ✔ Installed blob 1.2.3 (41ms) #> ✔ Installed brio 1.1.3 (40ms) #> ✔ Installed cachem 1.0.6 (31ms) #> ✔ Installed callr 3.7.3 (53ms) #> ✔ Installed clipr 0.8.0 (89ms) #> ✔ Installed colorspace 2.0-3 (99ms) #> ✔ Installed covr 3.6.1 (58ms) #> ✔ Installed crayon 1.5.2 (75ms) #> ✔ Installed curl 4.3.3 (83ms) #> ✔ Packaged tibble 3.1.8 (684ms) #> ✔ Installed bslib 0.4.1 (315ms) #> ✔ Installed desc 1.4.2 (77ms) #> ✔ Installed diffobj 0.3.5 (68ms) #> ✔ Installed digest 0.6.31 (60ms) #> ✔ Installed downloader 0.4 (39ms) #> ✔ Installed dplyr 1.0.10 (39ms) #> ✔ Installed farver 2.1.1 (41ms) #> ✔ Installed fastmap 1.1.0 (38ms) #> ✔ Installed formattable 0.2.1 (43ms) #> ✔ Built evaluate 0.19 (903ms) #> ✔ Installed fs 1.5.2 (49ms) #> ✔ Installed generics 0.1.3 (46ms) #> ✔ Installed ggplot2 3.4.0 (65ms) #> ✔ Installed gridExtra 2.3 (43ms) #> ✔ Installed gtable 0.3.1 (38ms) #> ✔ Installed highr 0.9 (37ms) #> ✔ Installed hms 1.1.2 (39ms) #> ✔ Installed htmltools 0.5.4 (40ms) #> ✔ Installed httr 1.4.4 (40ms) #> ✔ Installed influenceR 0.1.0.1 (17ms) #> ✔ Installed igraph 1.3.5 (96ms) #> ✔ Installed isoband 0.2.6 (68ms) #> ✔ Installed jquerylib 0.1.4 (38ms) #> ✔ Installed jsonlite 1.8.4 (37ms) #> ✔ Installed labeling 0.4.2 (14ms) #> ✔ Installed knitr 1.41 (73ms) #> ✔ Installed lazyeval 0.2.2 (43ms) #> ✔ Installed lubridate 1.9.0 (38ms) #> ✔ Installed memoise 2.0.1 (39ms) #> ✔ Installed mime 0.12 (58ms) #> ✔ Installed mockr 0.2.0 (38ms) #> ✔ Installed munsell 0.5.0 (36ms) #> ✔ Installed nycflights13 1.0.2 (37ms) #> ✔ Installed openssl 2.0.5 (41ms) #> ✔ Installed pkgbuild 1.4.0 (39ms) #> ✔ Installed pkgload 1.3.2 (37ms) #> ✔ Installed praise 1.0.0 (35ms) #> ✔ Installed prettyunits 1.1.1 (56ms) #> ✔ Installed processx 3.8.0 (37ms) #> ✔ Installed profmem 0.6.0 (37ms) #> ✔ Installed ps 1.7.2 (37ms) #> ✔ Installed purrr 0.3.5 (38ms) #> ✔ Installed rappdirs 0.3.3 (37ms) #> ✔ Installed readr 2.1.3 (42ms) #> ✔ Installed rematch2 2.1.2 (41ms) #> ✔ Installed rex 1.2.1 (58ms) #> ✔ Installed rprojroot 2.0.3 (58ms) #> ✔ Installed rstudioapi 0.14 (40ms) #> ✔ Installed sass 0.4.4 (42ms) #> ✔ Installed scales 1.2.1 (39ms) #> ✔ Installed stringr 1.5.0 (33ms) #> ✔ Installed sys 3.4.1 (49ms) #> ✔ Installed testthat 3.1.6 (88ms) #> ✔ Installed tidyr 1.2.1 (77ms) #> ✔ Installed stringi 1.7.8 (195ms) #> ✔ Installed tidyselect 1.2.0 (113ms) #> ✔ Installed timechange 0.1.1 (55ms) #> ✔ Installed tzdb 0.3.0 (40ms) #> ✔ Installed viridisLite 0.4.1 (39ms) #> ✔ Installed viridis 0.6.2 (39ms) #> ✔ Installed visNetwork 2.1.2 (77ms) #> ✔ Installed vroom 1.6.0 (77ms) #> ✔ Installed waldo 0.4.0 (62ms) #> ✔ Installed withr 2.5.0 (40ms) #> ✔ Installed xfun 0.35 (39ms) #> ℹ Building tinytex 0.43 #> ✔ Installed yaml 2.3.6 (43ms) #> ✔ Installed evaluate 0.19 (15ms) #> ✔ Built tinytex 0.43 (1.1s) #> ✔ Installed tinytex 0.43 (15ms) #> ℹ Building rmarkdown 2.19 #> ✔ Built rmarkdown 2.19 (3.9s) #> ✔ Installed rmarkdown 2.19 (85ms) #> ℹ Building htmlwidgets 1.6.0 #> ✔ Built nlme 3.1-161 (8s) #> ✔ Installed nlme 3.1-161 (33ms) #> ✔ Built htmlwidgets 1.6.0 (1.1s) #> ✔ Installed htmlwidgets 1.6.0 (22ms) #> ✔ 103 deps: kept 15, upd 2, added 86 [10.2s]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"list-current-repositories","dir":"Reference","previous_headings":"","what":"List current repositories","title":"Simplified manual. Start here! — Get started with pak","text":"set CRAN Bioconductor repository, pak automatically.","code":"pak::repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"add-custom-repository","dir":"Reference","previous_headings":"","what":"Add custom repository","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::repo_add(rhub = 'https://r-hub.r-universe.dev') pak::repo_get() #> # A data frame: 6 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 rhub https://r-hub.r-universe.dev cran… * NA #> 3 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 6 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"remove-custom-repositories","dir":"Reference","previous_headings":"","what":"Remove custom repositories","title":"Simplified manual. Start here! — Get started with pak","text":"set repos option CRAN repo , unset completely, pak keeps CRAN (default) Bioconductor.","code":"options(repos = getOption(\"repos\")[\"CRAN\"]) pak::repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"time-travel-using-rspm","dir":"Reference","previous_headings":"","what":"Time travel using RSPM","title":"Simplified manual. Start here! — Get started with pak","text":"Sets repository equivalent CRAN's state closest specified date. Name repository CRAN, otherwise pak also add default CRAN repository.","code":"pak::repo_add(CRAN = \"RSPM@2022-06-30\") pak::repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://packagemanager.posit.co/c… cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"time-travel-using-mran","dir":"Reference","previous_headings":"","what":"Time travel using MRAN","title":"Simplified manual. Start here! — Get started with pak","text":"Sets repository equivalent CRAN's state specified date. Name repository CRAN, otherwise pak also add default CRAN repository.","code":"pak::repo_add(CRAN = \"MRAN@2022-06-30\") pak::repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cran.microsoft.com/snapsh… cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"caches","dir":"Reference","previous_headings":"","what":"Caches","title":"Simplified manual. Start here! — Get started with pak","text":"default pak caches metadata downloaded packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"inspect-metadata-cache","dir":"Reference","previous_headings":"","what":"Inspect metadata cache","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::meta_list() #> ✔ Updated metadata database: 4.55 MB in 4 files. #> ✔ Updating metadata database ... done #> # A data frame: 43,718 × 32 #> package version depends sugge…¹ license imports linki…² archs enhan…³ #> #> 1 A3 1.0.0 R (>= … random… GPL (>… NA NA NA NA #> 2 AATtoo… 0.0.1 R (>= … NA GPL-3 magrit… NA NA NA #> 3 ABACUS 1.0.0 R (>= … rmarkd… GPL-3 ggplot… NA NA NA #> 4 ABC.RAP 0.9.0 R (>= … knitr,… GPL-3 graphi… NA NA NA #> 5 ABCana… 1.2.1 R (>= … NA GPL-3 plotrix NA NA NA #> 6 ABCopt… 0.15.0 NA testth… MIT + … Rcpp, … Rcpp ABCo… NA #> 7 ABCp2 1.2 MASS NA GPL-2 NA NA NA NA #> 8 ABHgen… 1.0.1 NA knitr,… GPL-3 ggplot… NA NA NA #> 9 ABPS 0.3 NA testth… GPL (>… kernlab NA NA NA #> 10 ACA 1.1 R (>= … NA GPL graphi… NA NA NA #> # … with 43,708 more rows, 23 more variables: os_type , #> # priority , license_is_foss , license_restricts_use , #> # repodir , rversion , platform , #> # needscompilation , ref , type , direct , #> # status , target , mirror , sources , #> # filesize , sha256 , sysreqs , built , #> # published , deps , md5sum , path , and …"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"update-metadata-cache","dir":"Reference","previous_headings":"","what":"Update metadata cache","title":"Simplified manual. Start here! — Get started with pak","text":"default pkg_install() similar functions automatically update metadata currently set repositories older 24 hours. can also force update manually:","code":"pak::meta_update() #> ✔ Updating metadata database ... done"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"clean-metadata-cache","dir":"Reference","previous_headings":"","what":"Clean metadata cache","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::meta_clean(force = TRUE) pak::meta_summary() #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metad #> ata\" #> #> $current_db #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metad #> ata/pkgs-d1c324e625.rds\" #> #> $raw_files #> character(0) #> #> $db_files #> character(0) #> #> $size #> [1] 0 #>"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"inspect-package-cache","dir":"Reference","previous_headings":"","what":"Inspect package cache","title":"Simplified manual. Start here! — Get started with pak","text":"Downloaded packages also cached.","code":"pak::cache_list() #> # A data frame: 480 × 11 #> fullpath path package url etag sha256 version platf…¹ built #> #> 1 /Users/gaborc… arch… NA http… \"\\\"1… 0c8f0… NA NA NA #> 2 /Users/gaborc… bin/… evalua… http… \"\\\"1… 08a39… 0.17 aarch6… NA #> 3 /Users/gaborc… bin/… crayon http… \"\\\"2… 1e6d5… 1.5.2 aarch6… NA #> 4 /Users/gaborc… bin/… common… http… \"\\\"4… 47b4a… 1.8.1 aarch6… NA #> 5 /Users/gaborc… bin/… curl http… \"\\\"b… 7b8ba… 4.3.3 aarch6… NA #> 6 /Users/gaborc… bin/… tinytex http… \"\\\"2… 7e9ba… 0.42 aarch6… NA #> 7 /Users/gaborc… bin/… jsonli… http… \"\\\"1… 68e59… 1.8.2 aarch6… NA #> 8 /Users/gaborc… bin/… lifecy… http… \"\\\"1… 7ce27… 1.0.3 aarch6… NA #> 9 /Users/gaborc… bin/… vctrs http… \"\\\"1… c3a69… 0.4.2 aarch6… NA #> 10 /Users/gaborc… src/… pkgcac… NA NA 9b70a… NA NA 0 #> # … with 470 more rows, 2 more variables: vignettes , #> # rversion , and abbreviated variable name ¹​platform"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"view-a-package-cache-summary","dir":"Reference","previous_headings":"","what":"View a package cache summary","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::cache_summary() #> $cachepath #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/pkg\" #> #> $files #> [1] 480 #> #> $size #> [1] 653325143 #>"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"clean-package-cache","dir":"Reference","previous_headings":"","what":"Clean package cache","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::cache_clean()"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"list-packages-in-a-library","dir":"Reference","previous_headings":"","what":"List packages in a library","title":"Simplified manual. Start here! — Get started with pak","text":"Pass directory library argument.","code":"pak::lib_status(Sys.getenv(\"R_LIBS_USER\")) #> # A data frame: 701 × 39 #> library package title version depends repos…¹ license needs…² built #> #> 1 /Users/g… abc \"Too… 2.2.1 R (>= … CRAN GPL (>… FALSE R 4.… #> 2 /Users/g… abc.da… \"Dat… 1.0 R (>= … CRAN GPL (>… FALSE R 4.… #> 3 /Users/g… abind \"Com… 1.4-5 R (>= … CRAN LGPL (… FALSE R 4.… #> 4 /Users/g… ade4 \"Ana… 1.7-19 R (>= … CRAN GPL (>… TRUE R 4.… #> 5 /Users/g… ape \"Ana… 5.6-2 R (>= … CRAN GPL-2 … TRUE R 4.… #> 6 /Users/g… aplot \"Dec… 0.1.7 NA CRAN Artist… FALSE R 4.… #> 7 /Users/g… archive \"Mul… 1.1.5 R (>= … CRAN MIT + … TRUE R 4.… #> 8 /Users/g… arrayh… \"Con… 1.1-0 NA CRAN GPL FALSE R 4.… #> 9 /Users/g… arrow \"Int… 9.0.0 R (>= … CRAN Apache… TRUE R 4.… #> 10 /Users/g… arules \"Min… 1.7-5 R (>= … CRAN GPL-3 TRUE R 4.… #> # … with 691 more rows, 30 more variables: remotetype , #> # remotepkgref , remoteref , remoterepos , #> # remotepkgplatform , remotesha , imports , #> # suggests , linkingto , remotes , remotehost , #> # remoterepo , remoteusername , enhances , #> # biocviews , remoteurl , remotesubdir , #> # priority , remoteetag , remotepackaged , …"},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":null,"dir":"Reference","previous_headings":"","what":"Install missing packages on the fly — handle_package_not_found","title":"Install missing packages on the fly — handle_package_not_found","text":"Use function set global error handler, called R fails load package. handler offer choice installing missing package (dependencies), cases can also remedy error restart code.","code":""},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install missing packages on the fly — handle_package_not_found","text":"","code":"handle_package_not_found(err)"},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install missing packages on the fly — handle_package_not_found","text":"err error object, class packageNotFoundError.","code":""},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install missing packages on the fly — handle_package_not_found","text":"Nothing.","code":""},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install missing packages on the fly — handle_package_not_found","text":"supposed call function directly. Instead, set global error handler, possibly .Rprofile file: Global error handlers supported R 4.0.0 later. Currently handle_package_not_found() anything non-interactive mode (including knitr, testthat RStudio notebooks), might change future. cases possible remedy original computation tried load missing package, pak offer successful installation. Currently, R 4.0.4, possible continue failed library() call.","code":"if (interactive() && getRversion() >= \"4.0.0\") { globalCallingHandlers( packageNotFoundError = function(err) { try(pak::handle_package_not_found(err)) } ) }"},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":null,"dir":"Reference","previous_headings":"","what":"All about installing pak. — Installing pak","title":"All about installing pak. — Installing pak","text":"Read default installation methods work want release candidate development version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"pre-built-binaries","dir":"Reference","previous_headings":"","what":"Pre-built binaries","title":"All about installing pak. — Installing pak","text":"pre-built binaries advantage completely self-containted dependency free. additional R packages, system libraries tools (e.g. compilers) needed . Install pre-built binary build pak repository GitHub: supported following systems:","code":"install.packages(\"pak\", repos = sprintf( \"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch ))"},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"notes","dir":"Reference","previous_headings":"","what":"Notes","title":"All about installing pak. — Installing pak","text":"macOS support official CRAN R build. builds, e.g. Homebrew R, supported. support R builds R shared library. CRAN's Windows macOS installers , R builds common Linux distributions. might issue build R without --enable-R-shlib option.","code":""},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"install-from-cran","dir":"Reference","previous_headings":"","what":"Install from CRAN","title":"All about installing pak. — Installing pak","text":"Install released version package CRAN usual: potentially needs C compiler platforms CRAN binaries packages .","code":"install.packages(\"pak\")"},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"nightly-builds","dir":"Reference","previous_headings":"","what":"Nightly builds","title":"All about installing pak. — Installing pak","text":"nightly binary builds, systems table :","code":"install.packages(\"pak\", repos = sprintf( \"https://r-lib.github.io/p/pak/devel/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch ))"},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"stable-rc-and-devel-streams","dir":"Reference","previous_headings":"","what":"stable, rc and devel streams","title":"All about installing pak. — Installing pak","text":"three types binaries available: stable corresponds latest CRAN release CRAN. rc release candidate build, available 1-2 weeks release. Otherwise stable build. devel builds development tree. release might rc build. streams available different repository URLs:","code":"stream <- \"rc\" install.packages(\"pak\", repos = sprintf( \"https://r-lib.github.io/p/pak/%s/%s/%s/%s\", stream, .Platform$pkgType, R.Version()$os, R.Version()$arch ))"},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Status of packages in a library — lib_status","title":"Status of packages in a library — lib_status","text":"Status packages library","code":""},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Status of packages in a library — lib_status","text":"","code":"lib_status(lib = .libPaths()[1]) pkg_list(lib = .libPaths()[1])"},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Status of packages in a library — lib_status","text":"lib Path library.","code":""},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Status of packages in a library — lib_status","text":"Data frame contains data packages installed library. always columns: biocviews: corresponding field DESCRIPTION, must present Bioconductor packages, packages typically . built: Built field DESCRIPTION. depends, suggests, Imports, linkingto, enhances: corresponding fields DESCRIPTION files. deps: list data frames, dependencies package. columns: ref, type (dependency type lowercase), package (dependent package, R), op version, last two version requirement. op can >=, >, == <=, although first one common practice. library: path package library containing package. license: DESCRIPTION. md5sum: DESCTIPTION, typically NA, except Windows. needscompilation: DESCRIPTION, column logical. package: package name. platform: Built field DESCRIPTION, current platform missing DESCRIPTION. priority: DESCRIPTION, usually base, recommended, missing. ref: corresponding installed::* package reference. repository: DESCRIPTION. packages CRAN repository CRAN, repositories, e.g. R-universe adds repository URL . repotype: cran, bioc missing. rversion: Built field. field, current R version. sysreqs: SystemRequirements field DESCRIPTION. title: package title. type: always installed. version: package version (string).","code":""},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"notes-","dir":"Reference","previous_headings":"","what":"Notes:","title":"Status of packages in a library — lib_status","text":"addition, also remote* config/needs/* entries DESCRIPTION files. (Case insensitive.) columns type character, except needscompilation, logical deps, list columns. entry missing package, set NA. Note column names lowercase, even corresponding entries DESCRIPTION. order columns deterministic, assume order. Additional columns might present, internal pak used user code.","code":""},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Status of packages in a library — lib_status","text":"","code":"lib_status(.Library) #> # A data frame: 31 × 31 #> library package version prior…¹ title license sugge…² built depends #> #> 1 /Library… base 4.2.2 base \"The… Part o… methods R 4.… NA #> 2 /Library… boot 1.3-28 recomm… \"Boo… Unlimi… MASS, … R 4.… R (>= … #> 3 /Library… class 7.3-20 recomm… \"Fun… GPL-2 … NA R 4.… R (>= … #> 4 /Library… cluster 2.1.4 recomm… \"\\\"F… GPL (>… MASS, … R 4.… R (>= … #> 5 /Library… codeto… 0.2-18 recomm… \"Cod… GPL NA R 4.… R (>= … #> 6 /Library… compil… 4.2.2 base \"The… Part o… NA R 4.… NA #> 7 /Library… datase… 4.2.2 base \"The… Part o… NA R 4.… NA #> 8 /Library… filelo… 1.0.2 NA \"Por… MIT + … callr … R 4.… NA #> 9 /Library… foreign 0.8-83 recomm… \"Rea… GPL (>… NA R 4.… R (>= … #> 10 /Library… graphi… 4.2.2 base \"The… Part o… NA R 4.… NA #> # … with 21 more rows, 22 more variables: needscompilation , #> # repository , imports , remotetype , #> # remotepkgref , remoteref , remoterepos , #> # remotepkgplatform , remotesha , enhances , #> # linkingto , md5sum , platform , biocviews , #> # sysreqs , ref , type , status , rversion , #> # sources , repotype , deps , and abbreviated …"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Dependencies of a package tree — local_deps","title":"Dependencies of a package tree — local_deps","text":"Dependencies package tree","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dependencies of a package tree — local_deps","text":"","code":"local_deps(root = \".\", upgrade = TRUE, dependencies = NA) local_deps_tree(root = \".\", upgrade = TRUE, dependencies = NA) local_dev_deps(root = \".\", upgrade = TRUE, dependencies = TRUE) local_dev_deps_tree(root = \".\", upgrade = TRUE, dependencies = TRUE)"},{"path":"https://pak.r-lib.org/dev/reference/local_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dependencies of a package tree — local_deps","text":"root Path package tree. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dependencies of a package tree — local_deps","text":"functions return dependencies data frame. local_deps_tree() local_dev_deps_tree() also print dependency tree.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_deps_explain.html","id":null,"dir":"Reference","previous_headings":"","what":"Explain dependencies of a package tree — local_deps_explain","title":"Explain dependencies of a package tree — local_deps_explain","text":"functions similar pkg_deps_explain(), work local package tree. local_dev_deps_explain() also includes development dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_deps_explain.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Explain dependencies of a package tree — local_deps_explain","text":"","code":"local_deps_explain(deps, root = \".\", upgrade = TRUE, dependencies = NA) local_dev_deps_explain(deps, root = \".\", upgrade = TRUE, dependencies = TRUE)"},{"path":"https://pak.r-lib.org/dev/reference/local_deps_explain.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Explain dependencies of a package tree — local_deps_explain","text":"deps Package names dependencies explain. root Path package tree. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Install a package tree — local_install","title":"Install a package tree — local_install","text":"Installs package tree (source package file), together dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install a package tree — local_install","text":"","code":"local_install( root = \".\", lib = .libPaths()[1], upgrade = TRUE, ask = interactive(), dependencies = NA )"},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install a package tree — local_install","text":"root Path package tree. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. ask Whether ask confirmation installing different version package already installed. Installations add new packages never require confirmation. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install a package tree — local_install","text":"Data frame, information installed package(s).","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install a package tree — local_install","text":"local_install() equivalent pkg_install(\"local::.\").","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Install the dependencies of a package tree — local_install_deps","title":"Install the dependencies of a package tree — local_install_deps","text":"Installs hard dependencies package tree (source package file), without installing package tree .","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install the dependencies of a package tree — local_install_deps","text":"","code":"local_install_deps( root = \".\", lib = .libPaths()[1], upgrade = TRUE, ask = interactive(), dependencies = NA )"},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install the dependencies of a package tree — local_install_deps","text":"root Path package tree. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. ask Whether ask confirmation installing different version package already installed. Installations add new packages never require confirmation. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install the dependencies of a package tree — local_install_deps","text":"Data frame, information installed package(s).","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install the dependencies of a package tree — local_install_deps","text":"Note development (optional) dependencies, Suggests DESCRIPTION, installed. want install well, use local_install_dev_deps().","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_install_dev_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Install all (development) dependencies of a package tree — local_install_dev_deps","title":"Install all (development) dependencies of a package tree — local_install_dev_deps","text":"Installs dependencies package tree (source package file), without installing package tree . installs development dependencies well, specified Suggests field DESCRIPTION.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install_dev_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install all (development) dependencies of a package tree — local_install_dev_deps","text":"","code":"local_install_dev_deps( root = \".\", lib = .libPaths()[1], upgrade = TRUE, ask = interactive(), dependencies = TRUE )"},{"path":"https://pak.r-lib.org/dev/reference/local_install_dev_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install all (development) dependencies of a package tree — local_install_dev_deps","text":"root Path package tree. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. ask Whether ask confirmation installing different version package already installed. Installations add new packages never require confirmation. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_package_trees.html","id":null,"dir":"Reference","previous_headings":"","what":"About local package trees — local_package_trees","title":"About local package trees — local_package_trees","text":"pak can install packages local package trees. convenient package development. See following functions: local_install() installs package package tree dependencies. local_install_deps() installs hard dependencies package. local_install_dev_deps() installs hard soft dependencies package. function intended package development.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_package_trees.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"About local package trees — local_package_trees","text":"Note last two functions install package specified package tree , dependencies. convenient package loaded via means, e.g. devtools::load_all(), development.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":null,"dir":"Reference","previous_headings":"","what":"Query system requirements — local_system_requirements","title":"Query system requirements — local_system_requirements","text":"Returns character vector commands run install system requirements queried operating system. local_system_requirements() queries system requirements dev package (dependencies) given root path. pkg_system_requirements() queries system requirements existing packages (dependencies).","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query system requirements — local_system_requirements","text":"","code":"local_system_requirements( os = NULL, os_release = NULL, root = \".\", execute = FALSE, sudo = execute, echo = FALSE ) pkg_system_requirements( package, os = NULL, os_release = NULL, execute = FALSE, sudo = execute, echo = FALSE )"},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query system requirements — local_system_requirements","text":"os, os_release operating system operating system release version, e.g. \"ubuntu\", \"debian\", \"centos\", \"redhat\". See https://github.com/rstudio/r-system-requirements#operating-systems full list supported operating systems. NULL, default, looked using distro::distro(). root Path package tree. execute, sudo execute TRUE, pak execute system commands (). sudo TRUE, pak prepend commands sudo. echo echo TRUE execute TRUE, echo command output. package Package names lookup system requirements .","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query system requirements — local_system_requirements","text":"character vector commands needed install system requirements package.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query system requirements — local_system_requirements","text":"","code":"if (FALSE) { local_system_requirements(\"ubuntu\", \"20.04\") } if (FALSE) { pkg_system_requirements(\"pak\", \"ubuntu\", \"20.04\") pkg_system_requirements(\"pak\", \"redhat\", \"7\") pkg_system_requirements(\"config\", \"ubuntu\", \"20.04\") # no sys reqs pkg_system_requirements(\"curl\", \"ubuntu\", \"20.04\") pkg_system_requirements(\"git2r\", \"ubuntu\", \"20.04\") pkg_system_requirements(c(\"config\", \"git2r\", \"curl\"), \"ubuntu\", \"20.04\") # queried packages must exist pkg_system_requirements(\"iDontExist\", \"ubuntu\", \"20.04\") pkg_system_requirements(c(\"curl\", \"iDontExist\"), \"ubuntu\", \"20.04\") }"},{"path":"https://pak.r-lib.org/dev/reference/lockfile_create.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a lock file — lockfile_create","title":"Create a lock file — lockfile_create","text":"lock file can used later, possibly new R session, carry installation dependencies, lockfile_install().","code":""},{"path":"https://pak.r-lib.org/dev/reference/lockfile_create.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a lock file — lockfile_create","text":"","code":"lockfile_create( pkg = \"deps::.\", lockfile = \"pkg.lock\", lib = NULL, upgrade = FALSE, dependencies = NA )"},{"path":"https://pak.r-lib.org/dev/reference/lockfile_create.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a lock file — lockfile_create","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. lockfile Path lock file. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/lockfile_create.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a lock file — lockfile_create","text":"Note, since URLs CRAN CRAN-like repositories change time, practice use lock file much later. example, binary packages older package version might deleted repository, breaking URLs lock file. Currently intended use case lock files CI systems, facilitate caching. (hash ) lock file provides good key caching systems.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/lockfile_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Install packages based on a lock file — lockfile_install","title":"Install packages based on a lock file — lockfile_install","text":"Install lock file created lockfile_create().","code":""},{"path":"https://pak.r-lib.org/dev/reference/lockfile_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install packages based on a lock file — lockfile_install","text":"","code":"lockfile_install(lockfile = \"pkg.lock\", lib = .libPaths()[1], update = TRUE)"},{"path":"https://pak.r-lib.org/dev/reference/lockfile_install.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install packages based on a lock file — lockfile_install","text":"lockfile Path lock file. lib Library carry installation . update Whether online install packages either installed lib, different version installed .","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata cache utilities — meta_summary","title":"Metadata cache utilities — meta_summary","text":"Various utilities inspect, update clean metadata cache. See pkgcache package need control metadata cache.","code":""},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata cache utilities — meta_summary","text":"","code":"meta_summary() meta_list(pkg = NULL) meta_update() meta_clean(force = FALSE)"},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata cache utilities — meta_summary","text":"pkg Package names, specified entries pkg returned. force FALSE, pak ask confirmation.","code":""},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata cache utilities — meta_summary","text":"meta_summary() returns list entries: cachepath: absolute path metadata cache. current_db: file contains current metadata database. currently RDS file, might change future. raw_files: files downloaded PACKAGES* files. db_files: metadata database files. size: total size metadata cache. meta_list() returns data frame available packages configured repositories. meta_update() returns nothing. meta_clean() returns nothing","code":""},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Metadata cache utilities — meta_summary","text":"meta_summary() returns summary metadata cache. meta_list() lists () packages metadata database. meta_update() updates metadata database. normally need call function manually, pak functions (e.g. pkg_install(), pkg_download(), etc.) call automatically, make sure use latest available metadata. meta_clean() deletes whole metadata DB.","code":""},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata cache utilities — meta_summary","text":"Metadata cache summary: current metadata DB: Selected packages : Update metadata DB Delete metadata DB","code":"meta_summary() #> $cachepath #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata\" #> #> $current_db #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/pkgs-34444e3072.rds\" #> #> $raw_files #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCann-59693086a0/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [2] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCann-59693086a0/src/contrib/PACKAGES.gz\" #> [3] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCexp-90d4a3978b/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [4] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCexp-90d4a3978b/src/contrib/PACKAGES.gz\" #> [5] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCsoft-2a43920999/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [6] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCsoft-2a43920999/src/contrib/PACKAGES.gz\" #> [7] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCworkflows-26330ba3ca/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [8] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCworkflows-26330ba3ca/src/contrib/PACKAGES.gz\" #> [9] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/CRAN-075c426938/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [10] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/CRAN-075c426938/src/contrib/PACKAGES.gz\" #> #> $db_files #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/pkgs-34444e3072.rds\" #> [2] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/pkgs-ccacf1b389.rds\" #> #> $size #> [1] 174848200 meta_list() #> ✔ Loading metadata database ... done #> # A data frame: 45,279 × 32 #> package version depends sugge…¹ license imports linki…² archs enhan…³ #> #> 1 A3 1.0.0 R (>= … random… GPL (>… NA NA NA NA #> 2 AATtoo… 0.0.2 R (>= … NA GPL-3 magrit… NA NA NA #> 3 ABACUS 1.0.0 R (>= … rmarkd… GPL-3 ggplot… NA NA NA #> 4 ABC.RAP 0.9.0 R (>= … knitr,… GPL-3 graphi… NA NA NA #> 5 ABCana… 1.2.1 R (>= … NA GPL-3 plotrix NA NA NA #> 6 ABCopt… 0.15.0 NA testth… MIT + … Rcpp, … Rcpp ABCo… NA #> 7 ABCp2 1.2 MASS NA GPL-2 NA NA NA NA #> 8 ABHgen… 1.0.1 NA knitr,… GPL-3 ggplot… NA NA NA #> 9 ABPS 0.3 NA testth… GPL (>… kernlab NA NA NA #> 10 ACA 1.1 R (>= … NA GPL graphi… NA NA NA #> # … with 45,269 more rows, 23 more variables: #> # license_restricts_use , os_type , priority , #> # license_is_foss , repodir , rversion , #> # platform , needscompilation , ref , type , #> # direct , status , target , mirror , #> # sources , filesize , sha256 , sysreqs , #> # built , published , deps , md5sum , … meta_list(pkg = c(\"shiny\", \"htmlwidgets\")) #> package version depends sugge…¹ license imports linki…² archs enhan…³ #> * #> 1 htmlwid… 1.5.4 NA \"knitr… MIT + … \"grDev… NA NA shiny … #> 2 shiny 1.7.3 R (>= … \"datas… GPL-3 … \"utils… NA NA NA #> 3 htmlwid… 1.6.0 NA \"testt… MIT + … \"grDev… NA NA shiny … #> 4 shiny 1.7.4 R (>= … \"datas… GPL-3 … \"utils… NA NA NA #> # … with 23 more variables: license_restricts_use , os_type , #> # priority , license_is_foss , repodir , #> # rversion , platform , needscompilation , ref , #> # type , direct , status , target , mirror , #> # sources , filesize , sha256 , sysreqs , #> # built , published , deps , md5sum , #> # path , and abbreviated variable names ¹​suggests, ²​linkingto, #> … meta_update() #> ✔ Updated metadata database: 1.23 MB in 1 file. #> ✔ Updating metadata database ... done meta_clean() #> ℹ Cleaning up cache directory /Users/gaborcsardi/Library/Caches/org.R-pr #> oject.R/R/pkgcache/_metadata."},{"path":"https://pak.r-lib.org/dev/reference/package-dependency-types.html","id":null,"dir":"Reference","previous_headings":"","what":"Various types of R package dependencies — Package dependency types","title":"Various types of R package dependencies — Package dependency types","text":"Various types R package dependencies","code":""},{"path":"https://pak.r-lib.org/dev/reference/package-dependency-types.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Various types of R package dependencies — Package dependency types","text":"R packages may various types dependencies, see Writing R Extensions.pak groups dependencies three groups: hard dependencies: \"Depends\", \"Imports\", \"LinkingTo\", soft dependencies: \"Suggests\" \"Enhances\", extra dependencies, see . NA \"hard\" install package required dependencies, TRUE install required dependencies, plus optional development dependencies. TRUE: means hard dependencies plus Suggests direct installations, hard dependencies dependent packages. FALSE: dependencies installed . NA (atomic type, NA_character_, etc. well): hard dependencies installed. list two entries named direct indirect, taken requested dependency types, direct installations dependent packages. character vector, taken dependency types direct installations, hard dependencies used dependent packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/package-dependency-types.html","id":"extra-dependencies","dir":"Reference","previous_headings":"","what":"Extra dependencies","title":"Various types of R package dependencies — Package dependency types","text":"pak supports extra dependency types direct installations CRAN-like repositories. specified Config/Needs/ prefix DESCRIPTION can contain package references, separated commas. example can specify packages needed pkgdown website package:   use dependency types, need specify dependencies argument pak functions. Note Config/Needs/* fields currently used CRAN packages, packages CRAN-like repositories general. Usually specify Config/Needs/* dependency type installed together \"hard\" \"\", install hard soft dependencies well.","code":"Config/Needs/website: r-lib/pkgdown"},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":null,"dir":"Reference","previous_headings":"","what":"Environment variables and options that modify the default behavior — pak configuration","title":"Environment variables and options that modify the default behavior — pak configuration","text":"pak behavior can finetuned environment variables options (base::options()).","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"ncpus","dir":"Reference","previous_headings":"","what":"Ncpus","title":"Environment variables and options that modify the default behavior — pak configuration","text":"Set desired number worker processes package installation. set, pak use number logical processors machine.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"repos","dir":"Reference","previous_headings":"","what":"repos","title":"Environment variables and options that modify the default behavior — pak configuration","text":"CRAN-like repositories use. See base::options() details.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"pak-configuration","dir":"Reference","previous_headings":"","what":"pak configuration","title":"Environment variables and options that modify the default behavior — pak configuration","text":"Configuration entries (unless noted otherwise manual page) corresponding environment variable, corresponding option. environment variable always uppercase uses underscores word separator. always PKG_ prefix. option typically lowercase, use uses underscores word separator, always pkg. prefix (notice dot!). examples:","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"pak-configuration-entries","dir":"Reference","previous_headings":"","what":"pak configuration entries","title":"Environment variables and options that modify the default behavior — pak configuration","text":"‘cache_dir’: (Env var: PKG_CACHE_DIR, option: pkg.cache_dir.) Directory download packages . Defaults temporary directory within R session temporary directory, see base::tempdir(). ‘cran_mirror’: (Env var: PKG_CRAN_MIRROR, option: pkg.cran_mirror.) CRAN mirror use. Defaults repos option (see base::options()), set https://cran.rstudio.com. See also pak::repo_add() pak::repo_get() ‘include_linkingto’: (Env var: PKG_INCLUDE_LINKINGTO, option: pkg.include_linkingto.) Whether always include LinkingTo dependencies solution installation, even needed packages installed binaries. sometimes useful, see e.g. https://github.com/r-lib/pak/issues/485 example use case. ‘library’: (Env var: PKG_LIBRARY, option: pkg.library.) Package library install packages . also used already installed packages considering dependencies. ‘metadata_cache_dir’: (Env var: PKG_METADATA_CACHE_DIR, option: pkg.metadata_cache_dir.) Location metadata replica pkgcache::cranlike_metadata_cache. Defaults temporary directory within R session temporary directory, see base::tempdir(). ‘metadata_update_after’: (Env var: PKG_METADATA_UPDATE_AFTER, option: pkg.metadata_update_after.) time interval difftime object. pak update metadata cache older . default one day. PKG_METADATA_UPDATE_AFTER environment variable may set seconds (s suffix), minutes (m suffix), hours (h suffix), days (d suffix). E.g: 1d means one day. ‘package_cache_dir’: (Env var: PKG_PACKAGE_CACHE_DIR, option: pkg.package_cache_dir.) Location package cache disk. See pak::cache_summary(). Default selected pkgcache. ‘platforms’: (Env var: PKG_PLATFORMS, option: pkg.platforms.) Character vector platforms download install packages . See pkgdepends::default_platforms() possible platform names. Defaults platform current R session, plus \"source\". ‘r_versions’: (Env var: PKG_R_VERSIONS, option: pkg.r_versions.) Character vector, R versions download install packages . defaults current R version. ‘sysreqs’: (Env var: PKG_SYSREQS, option: pkg.sysreqs.) Whether automatically look install system requirements. TRUE, pkgdepends try install required system packages. FALSE, system requirements still printed (including OS packages supported platforms), installed. default TRUE supported platforms, current user root user password-less sudo configured current user. ‘sysreqs_db_update’: (Env var: PKG_SYSREQS_DB_UPDATE, option: pkg.sysreqs_db_update.) Whether try update system requirements database GitHub. update fails, cached build-database used. Defaults TRUE. ‘sysreqs_db_update_timeout’: (Env var: PKG_SYSREQS_DB_UPDATE_TIMEOUT, option: pkg.sysreqs_db_update_timeout.) Timeout system requirements database update. Defaults five seconds. ‘sysreqs_dry_run’: (Env var: PKG_SYSREQS_DRY_RUN, option: pkg.sysreqs_dry_run.) TRUE, pak prints system commands install system requirements, execute . ‘sysreqs_platform’: (Env var: PKG_SYSREQS_PLATFORM, option: pkg.sysreqs_platform.) platform use system requirements lookup. Linux, system requirements currently supported, must string containing distribution name release, separated dash. E.g.: \"ubuntu-22.04\", \"rhel-9\". ‘sysreqs_rspm_repo_id’: (Env var: PKG_SYSREQS_RSPM_REPO_ID, option: pkg.sysreqs_rspm_repo_id.) Posit Package Manager (formerly RStudio Package Manager) repository id use CRAN system requirements lookup. Defaults RSPM_REPO_ID environment variable, set. set, defaults 1. ‘sysreqs_rspm_url’: (Env var: PKG_SYSREQS_RSPM_URL, option: pkg.sysreqs_rspm_url.) Root URL Posit Package Manager (formerly RStudio Package Manager) system requirements lookup. default RSPM_ROOT environment variable used, set. set, defaults https://packagemanager.posit.co. ‘sysreqs_sudo’: (Env var: PKG_SYSREQS_SUDO, option: pkg.sysreqs_sudo.) Whether use sudo install system requirements, Unix. default TRUE Linux effective user id current process root user. ‘sysreqs_update’: (Env var: PKG_SYSREQS_UPDATE, option: pkg.sysreqs_update.) Whether try update system packages already installed. defaults TRUE CI systems: CI environment variable set true. ‘sysreqs_verbose’: (Env var: PKG_SYSREQS_VERBOSE, option: pkg.sysreqs_verbose.) Whether echo output system requirements installation. Defaults TRUE CI environment variable set. ‘use_bioconductor’: (Env var: PKG_USE_BIOCONDUCTOR, option: pkg.use_bioconductor.) Whether automatically use Bioconductor repositories. Defaults TRUE. ‘windows_archs’: (Env var: PKG_WINDOWS_ARCHS, option: pkg.windows_archs.) Character scalar specifying architectures download/install Windows. possible values : \"prefer-x64\": Generally prefer x64 binaries. current R session x64, download/install x64 packages. (packages might still multi-architecture binaries!) current R session i386, download/install packages architectures. might mean compiling packages source binary packages x64 , like CRAN Windows binaries R 4.2.x currently. \"prefer-x64\" default R 4.2.0 later. \"\": Always download/install packages i386 x64 architectures. might need compilation source available binaries x64 , like CRAN Windows binaries R 4.2.x currently. \"\" default R 4.2.0 earlier.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"notes","dir":"Reference","previous_headings":"","what":"Notes","title":"Environment variables and options that modify the default behavior — pak configuration","text":"version 0.4.0 pak copies PKG_* environment variables pkg.* options pak subprocess, actually used, need restart R reaload pak configuration change.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak.html","id":null,"dir":"Reference","previous_headings":"","what":"Install specified required packages — pak","title":"Install specified required packages — pak","text":"Install specified packages, ones required package project current working directory.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install specified required packages — pak","text":"","code":"pak(pkg = NULL, ...)"},{"path":"https://pak.r-lib.org/dev/reference/pak.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install specified required packages — pak","text":"pkg Package names remote package specifications install. See pak package sources details. NULL, install development dependencies current package. ... Extra arguments passed pkg_install() local_install_dev_deps().","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install specified required packages — pak","text":"convenience function: want install packages, easier type pkg_install(). want install packages needed development package project, easier type local_install_dev_deps(). need remember two functions install packages, just one.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_cleanup.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up pak caches — pak_cleanup","title":"Clean up pak caches — pak_cleanup","text":"Clean pak caches","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_cleanup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up pak caches — pak_cleanup","text":"","code":"pak_cleanup( package_cache = TRUE, metadata_cache = TRUE, pak_lib = TRUE, force = FALSE )"},{"path":"https://pak.r-lib.org/dev/reference/pak_cleanup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up pak caches — pak_cleanup","text":"package_cache Whether clean cache package files. metadata_cache Whether clean cache package meta data. pak_lib argument now deprecated nothing. force ask confirmation. Note use function non-interactive mode, specify force = TRUE.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_install_extra.html","id":null,"dir":"Reference","previous_headings":"","what":"Install all optional dependencies of pak — pak_install_extra","title":"Install all optional dependencies of pak — pak_install_extra","text":"packages required pak functionality. recommended functions return values best used packages. E.g. many functions return data frames, print nicer pillar package available.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_install_extra.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install all optional dependencies of pak — pak_install_extra","text":"","code":"pak_install_extra(upgrade = FALSE)"},{"path":"https://pak.r-lib.org/dev/reference/pak_install_extra.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install all optional dependencies of pak — pak_install_extra","text":"upgrade Whether install upgrade latest versions optional packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_install_extra.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install all optional dependencies of pak — pak_install_extra","text":"Currently one package optional: pillar.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":null,"dir":"Reference","previous_headings":"","what":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Install packages CRAN, Bioconductor, GitHub, URLs, etc. Learn tell pak packages install, packages can found. want quick overview package sources, see \"Get started pak\".","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"package-references","dir":"Reference","previous_headings":"","what":"Package references","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Many pkgdepends pak functions take package names arguments. E.g. pak::pkg_install() takes names packages install, pak::pkg_deps_tree() takes names packages draw dependency trees . function can also take generic package reference instead package name. package reference also tells pak find package, package source. specify package source, use name prefix, :: separator. E.g. cran::mypkg means mypkg package CRAN. package name special package reference, implicitly specifies configured CRAN(-like) repositories package source. (call standard package source.) mypkg equivalent standard::mypkg pak look mypkg configured CRAN-like repositories. explicitly specify CRAN-like repositories (e.g. options(\"repos\")), pak uses CRAN Bioconductor repositories default. list currently supported package sources. discuss detail . cran: CRAN package. bioc: Bioconductor package. standard: package configured CRAN-like repository. github: package GitHub. gitlab: package GitLab. git: package git repository. local: local package file directory. url: URL points package archive. installed installed package. deps dependencies local package file directory. special reference type accepts package source. See . param special reference change references downloaded installed. See \"Parameters\" .","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"shorthands","dir":"Reference","previous_headings":"","what":"Shorthands","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"save typing, always need fully specify package source package reference. seen package name implicitly standard package source. complete rules shorthands, order applied: ref valid package name, package name @ version specification, standard package source used. E.g. pkg equivalent standard::pkg pkg@1.0 equivalent standard::pkg@1.0. ref valid github ref type without github:: prefix, github used. E.g. user/repo equivalent github::user/repo user/repo@tag equivalent github::user/repo@tag, etc. ref GitHub URL (see ) without github:: prefix, github used. ref path starts . / \\ ~ local used. (pak check path exists.) package reference form =?, special param type. See \"Parameters\" . package reference explicit package source, package source determined rules, pak throws error.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"package-names","dir":"Reference","previous_headings":"","what":"Package names","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"pak looking dependencies package, needs able determine name dependency package reference. sometimes easy dependencies Remotes (similar) fields. github:: gitlab:: dependencies pak assumes package name name repository. hold, need specify package name explicitly, using = prefix. E.g. pins=rstudio/pins-r. specify package source type package name, package name comes first: pins=github::rstudio/pins-r. git:: dependencies, pak assumes package name last component repository. hold, need specify package name explicitly, using = prefix. E.g. pins=git::https://github.com/rstudio/pins-r. local:: dependencies, always need specify package name explicitly. E.g. pins=local::~/works/pins. url:: dependencies, always need specify package name explicitly. E.g. ggplot2=url::https://cloud.r-project.org/src/contrib/....","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"parameters","dir":"Reference","previous_headings":"","what":"Parameters","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Package references may optional parameters, added question mark. Different parameters separated ampersand (&) character. (similar HTTP URLs take query parameters.) Parameters may flags turn behavior, can string value, assigned equal sign (=). value assigned, assume true value. example two package refs equivalent:  ","code":"cran::testthat?source&nocache cran::testthat?source=true&nocache=true"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"parameters-for-downstream-packages","dir":"Reference","previous_headings":"","what":"Parameters for downstream packages","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"pak allows specifying parameters downstream packages, using =? special package reference, package name package, parameters, . useful want add parameter downstream dependency. example, install ggplot2, always reinstall cli package dependency use ggplot2 cli=?reinstall package references. latter tells pak always reinstall cli, even already installed.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"currently-supported-parameters","dir":"Reference","previous_headings":"","what":"Currently supported parameters","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"ignore flag parameter. specified, package ignored. usually makes sense packagename=?ignore form, ignore downstream soft dependency. versions hard dependency ignored lead solution error. ignore--r version number parameter. package ignored R versions older specified one. E.g. Matrix=?ignore--r=4.1.2 ignore Matrix package R versions older 4.1.2. parameter really makes sense packgename=?ignore form. source flag parameter. specified, source R package requested CRAN-like repository. package installations source always triggers re-install. words, source implies reinstall parameter. parameter supported bioc::, cran:: standard:: remote types, ignored others. reinstall requests re-install package installations. supported bioc::, cran::, git::, github::, gitlab::, local::, standard::, url:: remote types. nocache ignore package cache. always download package file, add downloaded (built) package(s) package cache. supported bioc::, cran::, git::, github::, gitlab::, standard:: url:: remote types.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"cran-packages-cran-","dir":"Reference","previous_headings":"","what":"CRAN packages (cran::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"package CRAN. Full syntax:   valid package name. version version requirement. Examples:   Note: pak currently parses version specification part (everything @), use .","code":"[cran::][@[>=] | @current | @last] forecast forecast@8.8 forecast@>=8.8 cran::forecast forecast@last forecast@current"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"bioconductor-packages-bioc-","dir":"Reference","previous_headings":"","what":"Bioconductor packages (bioc::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"package Bioconductor. syntax CRAN packages, except prefix.  ","code":"[bioc::][@[>=] | @current | @last]"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"standard-packages-standard-","dir":"Reference","previous_headings":"","what":"Standard packages (standard::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"packages either CRAN Bioconductor, full syntax CRAN packages, except prefix:  ","code":"[standard::][@[>=] | current | last]"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"github-packages-github-","dir":"Reference","previous_headings":"","what":"GitHub packages (github::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Packages GitHub repository. Full syntax:   name package. missing, name repository used. GitHub username organization name. name repository. optional subdirectory, package within subdirectory repository. specifies certain version package, see . may specify: git branch, tag (prefix ) commit hash: @; pull request: #; latest release: @*release. missing, latest commit default branch used. Examples:   convenience GitHub HTTP URLs can also used specify package GitHub. Examples:   GitHub remote string can also used instead URL, example: git@github.com:r-lib/pak.git","code":"[=][github::]/[/][] r-lib/crayon github::r-lib/crayon r-lib/crayon@84be6207 r-lib/crayon@branch r-lib/crayon#41 r-lib/crayon@release https://github.com/r-lib/withr # A branch: https://github.com/r-lib/withr/tree/ghactions # A tag: https://github.com/r-lib/withr/tree/v2.1.1 # A commit: https://github.com/r-lib/withr/commit/8fbcb548e316 # A pull request: https://github.com/r-lib/withr/pull/76 # A release: https://github.com/r-lib/withr/releases/tag/v2.1.0"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"gitlab-packages-gitlab-","dir":"Reference","previous_headings":"","what":"GitLab packages (gitlab::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Packages GitLab repository. Full syntax:   name package. missing, name repository used. GitLab username group name. name repository. optional subdirectory, package within subdirectory repository. may specify git branch, tag (prefix ) commit hash. missing, latest commit default branch used. Examples:  ","code":"[=][github::]/[/][] gitlab::gaborcsardi/cli gitlab::r-hub/filelock@main"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"packages-in-git-repositories-git-","dir":"Reference","previous_headings":"","what":"Packages in git repositories (git::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Full syntax:   name package. missing, last component used. host name path git repository. git repositories need .git suffix , others forgiving. specifies certain version package: git branch, tag (prefix ) commit hash: @. missing, latest commit default branch used. Examples:   Note pak built-git client, require system git installation. system git installed, pak use credentials stored configured git credential store, automatically, via gitcreds package.","code":"[=]git::https?://[] git::https://github.com/r-lib/crayon git::https://github.com/r-lib/crayon.git git::https://github.com/r-lib/crayon.git@84be6207 git::https://github.com/r-lib/crayon.git@branch git::https://gitlab.com/gaborcsardi/cli.git"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"local-packages-local-","dir":"Reference","previous_headings":"","what":"Local packages (local::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"path refers package file built R CMD build, directory contains package. Full syntax:   brevity, can omit local:: prefix, specify absolute path, path user's home directory, starting ~, relative path starting ./ .\\\\. single dot (\".\") considered local package current working directory. Examples:   specify local package dependency (.e. DESCRIPTION), also need specify name package, see \"Package names\" .","code":"local:: local::/foo/bar/package_1.0.0.tar.gz local::/foo/bar/pkg local::. /absolute/path/package_1.0.0.tar.gz ~/path/from/home ./relative/path ."},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"urls-url-","dir":"Reference","previous_headings":"","what":"URLs (url::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"can use url:: refer URLs hold R package archives (.e. properly built R CMD build), compressed directories package trees (.e. built R CMD build). pak figure needs run R CMD build package first. remote type supports .tar.gz .zip files. Note URLs ideal remote types, pak needs download package file resolve dependencies. happens, puts package file cache, downloads needed installing package later. Examples:   specify package URL dependency (.e. DESCRIPTION), also need specify name package, see \"Package names\" .","code":"url::https://cloud.r-project.org/src/contrib/Archive/cli/cli_1.0.0.tar.gz url::https://github.com/tidyverse/stringr/archive/HEAD.zip"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"installed-packages-installed-","dir":"Reference","previous_headings":"","what":"Installed packages (installed::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"usually used internally, can also used directly. Full syntax:   library package installed . package name. Example:  ","code":"installed::/ installed::~/R/3.6/crayon"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"package-dependencies-deps-","dir":"Reference","previous_headings":"","what":"Package dependencies (deps::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Usually used internally, specifies dependencies local package. can used download install dependencies package, without downloading installing package . Full syntax:   Examples:  ","code":"deps:: deps::/foo/bar/package_1.0.0.tar.gz deps::/foo/bar/pkg deps::."},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"any-packages","dir":"Reference","previous_headings":"","what":"any:: packages","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Sometimes need install additional packages, mind installed . example. want install cli GitHub, r-lib/cli. also want install glue, mind version glue installed, long compatible requested cli version. cli specifies development version glue, fine. cli fine CRAN version glue, OK, . future version cli depend glue, still want glue installed, CRAN. :: reference type exactly . example might write   first, fail rlib/cli requests (say) tidyverse/glue, pkg_install() \"glue\" interpreted \"standard::glue\", creating conflict tidyverse/glue. hand   works, independently glue version requested cli.","code":"pak::pkg_install(c(\"glue\", \"r-lib/cli\")) pak::pkg_install(c(\"any::glue\", \"r-lib/cli\"))"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"parameter-refs-param-","dir":"Reference","previous_headings":"","what":"Parameter refs (param::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"See \"Parameters\" .","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"the-remotes-field","dir":"Reference","previous_headings":"","what":"The Remotes field","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"DESCRIPTION file R package can mark regular dependency defined Depends, Imports, Suggests Enhances fields installed non-standard package source adding package reference Remotes entry. pak download install package specified location, instead CRAN-like repository. remote dependencies specified Remotes comma separated list package sources:   Note still need add package one regular dependency fields, .e. Imports, Suggests, etc. concrete example specifies r-lib/glue package:   CRAN Bioconductor repositories support Remotes field, need remove field, submitting package either .","code":"Remotes: , , [ ... ] Imports: glue Remotes: r-lib/glue, r-lib/httr@v0.4, klutometis/roxygen#142, r-lib/testthat@c67018fa4970"},{"path":"https://pak.r-lib.org/dev/reference/pak_setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up private pak library (deprecated) — pak_setup","title":"Set up private pak library (deprecated) — pak_setup","text":"function deprecated nothing. Recent versions pak need pak_setup() call.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up private pak library (deprecated) — pak_setup","text":"","code":"pak_setup(mode = c(\"auto\", \"download\", \"copy\"), quiet = FALSE)"},{"path":"https://pak.r-lib.org/dev/reference/pak_setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up private pak library (deprecated) — pak_setup","text":"mode get packages . \"download\" try download CRAN. \"copy\" try copy current \"regular\" package library. \"auto\" try copy first, fails, tries download. quiet Whether omit messages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up private pak library (deprecated) — pak_setup","text":"path private library, invisibly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_sitrep.html","id":null,"dir":"Reference","previous_headings":"","what":"pak SITuation REPort — pak_sitrep","title":"pak SITuation REPort — pak_sitrep","text":"prints pak version, current library path, location private library, whether pak private library exists, whether pak private library functional.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_sitrep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"pak SITuation REPort — pak_sitrep","text":"","code":"pak_sitrep()"},{"path":"https://pak.r-lib.org/dev/reference/pak_sitrep.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"pak SITuation REPort — pak_sitrep","text":"","code":"pak_sitrep() #> compatible) #> - pak repository: - (local install?) #> * Optional packages installed: #> - pillar #> * Library path: #> - /private/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T/RtmpcpVAdU/fi #> led8ef3d7a46fc #> - /private/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T/RtmpcpVAdU/fi #> led8ef2562d6ef #> - /Users/gaborcsardi/Library/R/arm64/4.2/library #> - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library #> * Private library location: #> - /Users/gaborcsardi/Library/Caches/org.R-project.R/R/pak/lib/4.2/aarch6 #> 4 #> * Private library exists. #> * Private library is functional"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_solver.html","id":null,"dir":"Reference","previous_headings":"","what":"Find the ideal set of packages and versions to install — The dependency solver","title":"Find the ideal set of packages and versions to install — The dependency solver","text":"pak contains package dependency solver, makes sure package source version requirements packages satisfied, starting installation. CRAN BioC packages usually automatic, repositories generally consistent state. packages depend package sources, however, case.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_solver.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Find the ideal set of packages and versions to install — The dependency solver","text":"example conflict detected: r-lib/pkgcache@conflict depends main branch r-lib/cli, whereas, explicitly requested message branch. Since install versions single library, pak quits. pak considers package installation, package given name , (e.g. dependency another package), package may package source. necessary, one R package library may contain one version package given name. pak's behavior best explained via example. Assume installing local package (see ), e.g. local::., local package depends pkgA user/pkgB, latter package GitHub (see ), pkgA also depends pkgB. Now pak must install pkgB user/pkgB. case pak interprets pkgB package package source, instead standard package, installing user/pkgB satisfies requirements. Note cran::pkgB user/pkgB requirements result conflict pak resolve. first one must CRAN package, second one must GitHub package, two different packages installed R package library.","code":"> pak::pkg_install(c(\"r-lib/pkgcache@conflict\", \"r-lib/cli@message\")) Error: Cannot install packages: * Cannot install `r-lib/pkgcache@conflict`. - Cannot install dependency r-lib/cli@main * Cannot install `r-lib/cli@main`. - Conflicts r-lib/cli@message"},{"path":"https://pak.r-lib.org/dev/reference/pak_update.html","id":null,"dir":"Reference","previous_headings":"","what":"Update pak itself — pak_update","title":"Update pak itself — pak_update","text":"Use function update released development version pak.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_update.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update pak itself — pak_update","text":"","code":"pak_update(force = FALSE, stream = c(\"auto\", \"stable\", \"rc\", \"devel\"))"},{"path":"https://pak.r-lib.org/dev/reference/pak_update.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update pak itself — pak_update","text":"force Whether force update, even newer version available. stream Whether update \"stable\", \"rc\" (release candidate) \"devel\" (development) version. \"auto\" updates stream current one. Often release candidate version, \"rc\" also installs stable version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_update.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update pak itself — pak_update","text":"Nothing.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Look up the dependencies of a package — pkg_deps","title":"Look up the dependencies of a package — pkg_deps","text":"Look dependencies package","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Look up the dependencies of a package — pkg_deps","text":"","code":"pkg_deps(pkg, upgrade = TRUE, dependencies = NA)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Look up the dependencies of a package — pkg_deps","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Look up the dependencies of a package — pkg_deps","text":"data frame dependency data, includes pkg well. following columns. built: Built field DESCRIPTION file binary packages, information available. cache_status: whether package file package cache. NA installed:: package refs. dep_types: character vector dependency types considered package. (list column.) deps: dependencies package, data frame. See \"Package dependency tables\" . direct: whether package (ref, really) directly specified, added dependency. error: list column contains error objects refs pkgdepends failed resolve. filesize: file size bytes, NA information available. license: license package, NA available. md5sum: MD5 checksum package file, available, NA . metadata: named character vector. fields () added installed DESCRIPTION file package. mirror: URL CRAN(-like) mirror site metadata obtained . NA non-CRAN-like sources, e.g. local files, installed packages, GitHub, etc. needscompilation: whether package needs compilation. package: package name. priority: \"base\" base packages, \"recommended\" recommended packages, NA otherwise. ref: package reference. remote: parsed remote_ref objects, see parse_pkg_refs(). list column. repodir: directory package CRAN-like repository. sha256: SHA256 hash package file, available, otherwise NA. sources: URLs package can downloaded . necessarily URL can download HTTP client. E.g. local:: refs path, git:: refs URL git. zero length vector installed:: refs. status: status dependency resolution, \"OK\" \"FAILED\". target: path package saved CRAN-repository. type: ref type. version: package version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"package-dependency-tables","dir":"Reference","previous_headings":"","what":"Package dependency tables","title":"Look up the dependencies of a package — pkg_deps","text":"package dependency tables deps list column five columns currently: ref: package ref dependency. type: dependency type, lowercase. .e. imports, suggests, etc. package: package name dependency. op: operator version requirements, e.g. >=. version: version number, version requirements.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Look up the dependencies of a package — pkg_deps","text":"package GitHub:","code":"pkg_deps(\"dplyr\") #> # A data frame: 16 × 32 #> ref type direct direc…¹ status package version license needs…² #> #> 1 R6 stan… FALSE FALSE OK R6 2.5.1 MIT + … FALSE #> 2 cli stan… FALSE FALSE OK cli 3.4.1 MIT + … FALSE #> 3 dplyr stan… TRUE TRUE OK dplyr 1.0.10 MIT + … FALSE #> 4 fansi stan… FALSE FALSE OK fansi 1.0.3 GPL-2 … FALSE #> 5 generics stan… FALSE FALSE OK generi… 0.1.3 MIT + … FALSE #> 6 glue stan… FALSE FALSE OK glue 1.6.2 MIT + … FALSE #> 7 lifecycle stan… FALSE FALSE OK lifecy… 1.0.3 MIT + … FALSE #> 8 magrittr stan… FALSE FALSE OK magrit… 2.0.3 MIT + … FALSE #> 9 pillar stan… FALSE FALSE OK pillar 1.8.1 MIT + … FALSE #> 10 pkgconfig stan… FALSE FALSE OK pkgcon… 2.0.3 MIT + … FALSE #> 11 rlang stan… FALSE FALSE OK rlang 1.0.6 MIT + … FALSE #> 12 tibble stan… FALSE FALSE OK tibble 3.1.8 MIT + … FALSE #> 13 tidysele… stan… FALSE FALSE OK tidyse… 1.2.0 MIT + … FALSE #> 14 utf8 stan… FALSE FALSE OK utf8 1.2.2 Apache… FALSE #> 15 vctrs stan… FALSE FALSE OK vctrs 0.5.1 MIT + … FALSE #> 16 withr stan… FALSE FALSE OK withr 2.5.0 MIT + … FALSE #> # … with 23 more variables: priority , md5sum , sha256 , #> # filesize , built , platform , rversion , #> # repotype , repodir , target , deps , #> # mirror , sources , remote , error , #> # metadata , dep_types , params , sysreqs , #> # cache_status , lib_status , old_version , #> # new_version , and abbreviated variable names ¹​directpkg, … pkg_deps(\"r-lib/callr\") #> # A data frame: 4 × 32 #> ref type direct direc…¹ status package version license needs…² #> #> 1 r-lib/cal… gith… TRUE TRUE OK callr 3.7.3.… MIT + … TRUE #> 2 R6 stan… FALSE FALSE OK R6 2.5.1 MIT + … FALSE #> 3 processx stan… FALSE FALSE OK proces… 3.8.0 MIT + … FALSE #> 4 ps stan… FALSE FALSE OK ps 1.7.2 MIT + … FALSE #> # … with 23 more variables: priority , md5sum , sha256 , #> # filesize , built , platform , rversion , #> # repotype , repodir , target , deps , #> # mirror , sources , remote , error , #> # metadata , dep_types , params , sysreqs , #> # cache_status , lib_status , old_version , #> # new_version , and abbreviated variable names ¹​directpkg, …"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":null,"dir":"Reference","previous_headings":"","what":"Explain how a package depends on other packages — pkg_deps_explain","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"Extract dependency chains pkg deps.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"","code":"pkg_deps_explain(pkg, deps, upgrade = TRUE, dependencies = NA)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. deps Package names dependencies explain. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"named list print method. First entries function arguments: pkg, deps, dependencies, last one paths contains results named list, names package names deps.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"function similar pkg_deps_tree(), output easier read interested certain packages (deps).","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"dplyr depend rlang? GH version usethis depend cli ps?","code":"pkg_deps_explain(\"dplyr\", \"rlang\") #> ✔ Updated metadata database: 5.09 MB in 12 files. #> ✔ Updating metadata database ... done #> dplyr -> lifecycle -> rlang #> dplyr -> rlang #> dplyr -> tibble -> lifecycle -> rlang #> dplyr -> tibble -> pillar -> lifecycle -> rlang #> dplyr -> tibble -> pillar -> rlang #> dplyr -> tibble -> pillar -> vctrs -> lifecycle -> rlang #> dplyr -> tibble -> pillar -> vctrs -> rlang #> dplyr -> tibble -> rlang #> dplyr -> tibble -> vctrs -> lifecycle -> rlang #> dplyr -> tibble -> vctrs -> rlang #> dplyr -> tidyselect -> lifecycle -> rlang #> dplyr -> tidyselect -> rlang #> dplyr -> tidyselect -> vctrs -> lifecycle -> rlang #> dplyr -> tidyselect -> vctrs -> rlang #> dplyr -> vctrs -> lifecycle -> rlang #> dplyr -> vctrs -> rlang #> dplyr -> pillar -> lifecycle -> rlang #> dplyr -> pillar -> rlang #> dplyr -> pillar -> vctrs -> lifecycle -> rlang #> dplyr -> pillar -> vctrs -> rlang pkg_deps_explain(\"r-lib/usethis\", c(\"cli\", \"ps\")) #> usethis -> cli #> usethis -> desc -> cli #> usethis -> gh -> cli #> usethis -> lifecycle -> cli #> #> x ps"},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw the dependency tree of a package — pkg_deps_tree","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"Draw dependency tree package","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"","code":"pkg_deps_tree(pkg, upgrade = TRUE, dependencies = NA)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"data frame pkg_deps(), invisibly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"","code":"pkg_deps_tree(\"dplyr\") #> dplyr 1.0.10 ✨ #> ├─generics 0.1.3 ✨ #> ├─glue 1.6.2 ✨ #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli 3.4.1 ✨ #> │ ├─glue #> │ └─rlang 1.0.6 ✨ #> ├─magrittr 2.0.3 ✨ #> ├─R6 2.5.1 ✨ #> ├─rlang #> ├─tibble 3.1.8 ✨ #> │ ├─fansi 1.0.3 ✨ #> │ ├─lifecycle #> │ ├─magrittr #> │ ├─pillar 1.8.1 ✨ #> │ │ ├─cli #> │ │ ├─fansi #> │ │ ├─glue #> │ │ ├─lifecycle #> │ │ ├─rlang #> │ │ ├─utf8 1.2.2 ✨ #> │ │ └─vctrs 0.5.1 ✨ #> │ │ ├─cli #> │ │ ├─glue #> │ │ ├─lifecycle #> │ │ └─rlang #> │ ├─pkgconfig 2.0.3 ✨ #> │ ├─rlang #> │ └─vctrs #> ├─tidyselect 1.2.0 ✨ #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─vctrs #> │ └─withr 2.5.0 ✨ #> ├─vctrs #> └─pillar #> #> Key: ✨ new pkg_deps_tree(\"r-lib/usethis\") #> r-lib/usethis 2.1.6.9000 ✨👷🏼🔧 #> ├─cli 3.4.1 ✨ #> ├─clipr 0.8.0 ✨ #> ├─crayon 1.5.2 ✨ #> ├─curl 4.3.3 ✨ #> ├─desc 1.4.2 ✨ #> │ ├─cli #> │ ├─R6 2.5.1 ✨ #> │ └─rprojroot 2.0.3 ✨ #> ├─fs 1.5.2 ✨ #> ├─gert 1.9.2 ✨ ⬇ (1.91 MB) #> │ ├─askpass 1.1 ✨ #> │ │ └─sys 3.4.1 ✨ #> │ ├─credentials 1.3.2 ✨ ⬇ (170.15 kB) #> │ │ ├─openssl 2.0.5 ✨ #> │ │ │ └─askpass #> │ │ ├─sys #> │ │ ├─curl #> │ │ ├─jsonlite 1.8.4 ✨ #> │ │ └─askpass #> │ ├─openssl #> │ ├─rstudioapi 0.14 ✨ #> │ ├─sys #> │ └─zip 2.2.2 ✨ #> ├─gh 1.3.1 ✨ ⬇ (95.20 kB) #> │ ├─cli #> │ ├─gitcreds 0.1.2 ✨ ⬇ (95.59 kB) #> │ ├─httr 1.4.4 ✨ #> │ │ ├─curl #> │ │ ├─jsonlite #> │ │ ├─mime 0.12 ✨ #> │ │ ├─openssl #> │ │ └─R6 #> │ ├─ini 0.3.1 ✨ ⬇ (13.13 kB) #> │ └─jsonlite #> ├─glue 1.6.2 ✨ #> ├─jsonlite #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli #> │ ├─glue #> │ └─rlang 1.0.6 ✨ #> ├─purrr 0.3.5 ✨ #> │ ├─magrittr 2.0.3 ✨ #> │ └─rlang #> ├─rappdirs 0.3.3 ✨ #> ├─rlang #> ├─rprojroot #> ├─rstudioapi #> ├─whisker 0.4.1 ✨ ⬇ (65.36 kB) #> ├─withr 2.5.0 ✨ #> └─yaml 2.3.6 ✨ #> #> Key: ✨ new | ⬇ download | 👷🏼 build | 🔧 compile"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":null,"dir":"Reference","previous_headings":"","what":"Download a package and its dependencies — pkg_download","title":"Download a package and its dependencies — pkg_download","text":"TODO: explain result","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download a package and its dependencies — pkg_download","text":"","code":"pkg_download( pkg, dest_dir = \".\", dependencies = FALSE, platforms = NULL, r_versions = NULL )"},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download a package and its dependencies — pkg_download","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. dest_dir Destination directory packages. exist, created. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies. platforms Types binary source packages download. default value pkgdepends::default_platforms(). r_versions R version(s) download packages . (matter source packages, binaries.) defaults current R version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download a package and its dependencies — pkg_download","text":"Data frame information downloaded packages, invisibly. Columns: built: Built field DESCRIPTION file binary packages, information available. cache_status: whether package file package cache. NA installed:: package refs. dep_types: character vector dependency types considered package. (list column.) deps: dependencies package, data frame. See \"Package dependency tables\" . direct: whether package (ref, really) directly specified, added dependency. error: list column contains error objects refs pkgdepends failed resolve. filesize: file size bytes, NA information available. license: license package, NA available. md5sum: MD5 checksum package file, available, NA . metadata: named character vector. fields () added installed DESCRIPTION file package. mirror: URL CRAN(-like) mirror site metadata obtained . NA non-CRAN-like sources, e.g. local files, installed packages, GitHub, etc. needscompilation: whether package needs compilation. package: package name. priority: \"base\" base packages, \"recommended\" recommended packages, NA otherwise. ref: package reference. remote: parsed remote_ref objects, see parse_pkg_refs(). list column. repodir: directory package CRAN-like repository. sha256: SHA256 hash package file, available, otherwise NA. sources: URLs package can downloaded . necessarily URL can download HTTP client. E.g. local:: refs path, git:: refs URL git. zero length vector installed:: refs. status: status dependency resolution, \"OK\" \"FAILED\". target: path package saved CRAN-repository. type: ref type. version: package version. fulltarget: absolute path downloaded file. one fulltarget fulltarget_tree must exist disk. fulltarget_tree: absolute path package tree directory. one fulltarget fulltarget_tree must exist disk. download_status: \"\" \"Got\", depending whether file obtained cache. download_error: error object failed downloads. file_size: Size file, NA. installed:: refs, NA, also NA refs created fulltarget_tree instead fulltarget.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"package-dependency-tables","dir":"Reference","previous_headings":"","what":"Package dependency tables","title":"Download a package and its dependencies — pkg_download","text":"package dependency tables deps list column five columns currently: ref: package ref dependency. type: dependency type, lowercase. .e. imports, suggests, etc. package: package name dependency. op: operator version requirements, e.g. >=. version: version number, version requirements.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download a package and its dependencies — pkg_download","text":"","code":"dl <- pkg_download(\"forcats\") #> ℹ No downloads are needed, 2 pkgs (641.53 kB) are cached dl #> # A data frame: 2 × 35 #> ref type direct direc…¹ status package version license needs…² #> #> 1 forcats standard TRUE TRUE OK forcats 0.5.2 MIT + … FALSE #> 2 forcats standard TRUE TRUE OK forcats 0.5.2 MIT + … FALSE #> # … with 26 more variables: priority , md5sum , sha256 , #> # filesize , built , platform , rversion , #> # repotype , repodir , target , deps , #> # mirror , sources , remote , error , #> # metadata , extra , dep_types , params , #> # sysreqs , cache_status , fulltarget , #> # fulltarget_tree , download_status , … dl$fulltarget #> [1] \"./bin/macosx/big-sur-arm64/contrib/4.2/forcats_0.5.2.tgz\" #> [2] \"./src/contrib/forcats_0.5.2.tar.gz\" pkg_download(\"r-lib/pak\", platforms = \"source\") #> ℹ No downloads are needed, 1 pkg is cached"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":null,"dir":"Reference","previous_headings":"","what":"Query the history of a CRAN package — pkg_history","title":"Query the history of a CRAN package — pkg_history","text":"Query history CRAN package","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query the history of a CRAN package — pkg_history","text":"","code":"pkg_history(pkg)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query the history of a CRAN package — pkg_history","text":"pkg Package name.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query the history of a CRAN package — pkg_history","text":"data frame, one row per package version. columns entries DESCRIPTION files released package versions.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query the history of a CRAN package — pkg_history","text":"","code":"pkg_history(\"ggplot2\") #> # A data frame: 44 × 30 #> Package Type Title Version Date Author Maint…¹ Descr…² License #> * #> 1 ggplot2 Package An impl… 0.5 2007… Hadle… Hadley… \"An im… GPL #> 2 ggplot2 Package An impl… 0.5.1 2007… Hadle… Hadley… \"An im… GPL #> 3 ggplot2 Package An impl… 0.5.2 2007… Hadle… Hadley… \"An im… GPL #> 4 ggplot2 Package An impl… 0.5.4 2007… Hadle… Hadley… \"An im… GPL #> 5 ggplot2 Package An impl… 0.5.5 2007… Hadle… Hadley… \"An im… GPL #> 6 ggplot2 Package An impl… 0.5.6 2007… Hadle… Hadley… \"An im… GPL #> 7 ggplot2 Package An impl… 0.5.7 2007… Hadle… Hadley… \"An im… GPL #> 8 ggplot2 Package An impl… 0.6 2008… Hadle… Hadley… \"An im… GPL #> 9 ggplot2 Package An impl… 0.7 2008… Hadle… Hadley… \"An im… GPL #> 10 ggplot2 Package An impl… 0.8 2008… Hadle… Hadley… \"An im… GPL #> # … with 34 more rows, 21 more variables: SaveImage , #> # LazyData , Packaged , crandb_file_date , date , #> # dependencies , URL , LazyLoad , Extends , #> # Collate , Repository , `Date/Publication` , #> # NeedsCompilation , VignetteBuilder , BugReports , #> # `Authors@R` , RoxygenNote , Encoding , MD5sum , #> # `Config/Needs/website` , `Config/testthat/edition` , …"},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Install packages — pkg_install","title":"Install packages — pkg_install","text":"Install one packages dependencies single package library.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install packages — pkg_install","text":"","code":"pkg_install( pkg, lib = .libPaths()[[1L]], upgrade = FALSE, ask = interactive(), dependencies = NA )"},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install packages — pkg_install","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. ask Whether ask confirmation installing different version package already installed. Installations add new packages never require confirmation. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install packages — pkg_install","text":"(Invisibly) data frame information installed package(s).","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Install packages — pkg_install","text":"Upgrade dplyr dependencies: Install development version dplyr: Switch back CRAN version. fast pak cached prior install.","code":"pkg_install(\"dplyr\") #> #> → Will install 5 packages. #> → All 5 packages (2.14 MB) are cached. #> + dplyr 1.0.9 #> + generics 0.1.2 #> + purrr 0.3.4 #> + R6 2.5.1 #> + tidyselect 1.1.2 #> ℹ No downloads are needed, 5 pkgs (2.14 MB) are cached #> ✔ Got R6 2.5.1 (aarch64-apple-darwin20) (82.52 kB) #> ✔ Installed R6 2.5.1 (43ms) #> ✔ Installed generics 0.1.2 (62ms) #> ✔ Installed dplyr 1.0.9 (88ms) #> ✔ Installed purrr 0.3.4 (88ms) #> ✔ Installed tidyselect 1.1.2 (94ms) #> ✔ 1 pkg + 17 deps: kept 12, added 5, dld 1 (82.52 kB) [1.2s] pkg_install(\"dplyr\", upgrade = TRUE) #> #> → Will update 1 package. #> → The package (742.51 kB) is cached. #> + rlang 1.0.2 → 1.0.3 👷🏿‍♀️🔧 #> ℹ No downloads are needed, 1 pkg (742.51 kB) is cached #> ℹ Building rlang 1.0.3 #> ✔ Built rlang 1.0.3 (5.8s) #> ✔ Installed rlang 1.0.3 (32ms) #> ✔ 1 pkg + 17 deps: kept 17, upd 1 [6.3s] pkg_install(\"tidyverse/dplyr\") #> ✔ Loading metadata database ... done #> #> → Will install 16 packages. #> → All 16 packages (8.09 MB) are cached. #> + cli 3.4.1 #> + dplyr 1.0.99.9000 👷🏾‍♂️🔧 (GitHub: e6252f8) #> + fansi 1.0.3 #> + generics 0.1.3 #> + glue 1.6.2 #> + lifecycle 1.0.3 #> + magrittr 2.0.3 #> + pillar 1.8.1 #> + pkgconfig 2.0.3 #> + R6 2.5.1 #> + rlang 1.0.6 #> + tibble 3.1.8 #> + tidyselect 1.2.0 #> + utf8 1.2.2 #> + vctrs 0.5.1 #> + withr 2.5.0 #> ℹ No downloads are needed, 16 pkgs (8.09 MB) are cached #> ✔ Installed R6 2.5.1 (58ms) #> ✔ Installed cli 3.4.1 (69ms) #> ✔ Installed fansi 1.0.3 (92ms) #> ✔ Installed generics 0.1.3 (99ms) #> ✔ Installed glue 1.6.2 (108ms) #> ✔ Installed lifecycle 1.0.3 (144ms) #> ✔ Installed magrittr 2.0.3 (152ms) #> ✔ Installed pillar 1.8.1 (160ms) #> ✔ Installed pkgconfig 2.0.3 (63ms) #> ✔ Installed rlang 1.0.6 (37ms) #> ✔ Installed tibble 3.1.8 (41ms) #> ✔ Installed tidyselect 1.2.0 (38ms) #> ✔ Installed utf8 1.2.2 (36ms) #> ✔ Installed vctrs 0.5.1 (39ms) #> ✔ Installed withr 2.5.0 (30ms) #> ℹ Packaging dplyr 1.0.99.9000 #> ✔ Packaged dplyr 1.0.99.9000 (8.3s) #> ℹ Building dplyr 1.0.99.9000 #> ✔ Built dplyr 1.0.99.9000 (5.2s) #> ✔ Installed dplyr 1.0.99.9000 (github::tidyverse/dplyr@e6252f8) (24ms) #> ✔ 1 pkg + 15 deps: added 16 [18.9s] pkg_install(\"dplyr\") #> ✔ Updated metadata database: 2.43 MB in 6 files. #> ✔ Updating metadata database ... done #> #> → Will install 16 packages. #> → All 16 packages (9.42 MB) are cached. #> + cli 3.4.1 #> + dplyr 1.0.10 #> + fansi 1.0.3 #> + generics 0.1.3 #> + glue 1.6.2 #> + lifecycle 1.0.3 #> + magrittr 2.0.3 #> + pillar 1.8.1 #> + pkgconfig 2.0.3 #> + R6 2.5.1 #> + rlang 1.0.6 #> + tibble 3.1.8 #> + tidyselect 1.2.0 #> + utf8 1.2.2 #> + vctrs 0.5.1 #> + withr 2.5.0 #> ℹ No downloads are needed, 16 pkgs (9.42 MB) are cached #> ✔ Installed R6 2.5.1 (66ms) #> ✔ Installed cli 3.4.1 (76ms) #> ✔ Installed dplyr 1.0.10 (111ms) #> ✔ Installed fansi 1.0.3 (119ms) #> ✔ Installed generics 0.1.3 (125ms) #> ✔ Installed glue 1.6.2 (132ms) #> ✔ Installed lifecycle 1.0.3 (149ms) #> ✔ Installed magrittr 2.0.3 (162ms) #> ✔ Installed pillar 1.8.1 (56ms) #> ✔ Installed pkgconfig 2.0.3 (35ms) #> ✔ Installed rlang 1.0.6 (57ms) #> ✔ Installed tibble 3.1.8 (41ms) #> ✔ Installed tidyselect 1.2.0 (40ms) #> ✔ Installed utf8 1.2.2 (37ms) #> ✔ Installed vctrs 0.5.1 (39ms) #> ✔ Installed withr 2.5.0 (31ms) #> ✔ 1 pkg + 15 deps: added 16 [7.2s]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if an R package name is available — pkg_name_check","title":"Check if an R package name is available — pkg_name_check","text":"Additionally, look candidate name number dictionaries, make sure negative meaning.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if an R package name is available — pkg_name_check","text":"","code":"pkg_name_check(name, dictionaries = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if an R package name is available — pkg_name_check","text":"name Package name candidate. dictionaries Character vector, dictionaries query. Available dictionaries: * wikipedia * wiktionary, * sentiment (https://github.com/fnielsen/afinn), * urban (Urban Dictionary). NULL (default), Urban Dictionary omitted, often offensive.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if an R package name is available — pkg_name_check","text":"pkg_name_check object custom print method.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"valid-package-name-check","dir":"Reference","previous_headings":"","what":"Valid package name check","title":"Check if an R package name is available — pkg_name_check","text":"Check validity name package name. See 'Writing R Extensions' allowed package names. Also checked list names known cause problems.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"cran-checks","dir":"Reference","previous_headings":"","what":"CRAN checks","title":"Check if an R package name is available — pkg_name_check","text":"Check name names past current packages CRAN, including base recommended packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"bioconductor-checks","dir":"Reference","previous_headings":"","what":"Bioconductor checks","title":"Check if an R package name is available — pkg_name_check","text":"Check name past current Bioconductor packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"profanity-check","dir":"Reference","previous_headings":"","what":"Profanity check","title":"Check if an R package name is available — pkg_name_check","text":"Check name https://www.purgomalum.com/service/containsprofanity make sure profanity.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"dictionaries","dir":"Reference","previous_headings":"","what":"Dictionaries","title":"Check if an R package name is available — pkg_name_check","text":"See dictionaries argument.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if an R package name is available — pkg_name_check","text":"","code":"pkg_name_check(\"sicily\") #> ╔══════════════════════════════════════════════════════════════════════╗ #> ║ –*– sicily –*– ║ #> ╚══════════════════════════════════════════════════════════════════════╝ #> ┌──────────────────────────────────────────────────────────────────────┐ #> │ ✔ valid name ✔ CRAN ✔ Bioconductor │ #> │ ✔ not a profanity │ #> └──────────────────────────────────────────────────────────────────────┘ #> ┌ Wikipedia ───────────────────────────────────────────────────────────┐ #> │ Sicily Sicily (Italian: Sicilia [siˈtʃiːlja], Sicilian │ #> │ pronunciation: [sɪˈʃiːlja]) is the largest island in the │ #> │ Mediterranean Sea and one of the 20 regions of Italy. The Strait of │ #> │ Messina divides it from the region of Calabria in Southern Italy. │ #> │ It is one of the five Italian autonomous regions and is officially │ #> │ referred to as Regione Siciliana. The region has 5 million │ #> │ … │ #> └──────────────────────────────── https://en.wikipedia.org/wiki/Sicily ┘ #> ┌ Wiktionary ──────────────────────────────────────────────────────────┐ #> │ sicily No English definition found │ #> └──────────────────────────────────────────────────────────────────── ┘ #> ┌──────────────────────────────────────────────────────────────────────┐ #> │ Sentiment: 😐 (0) │ #> └──────────────────────────────────────────────────────────────────────┘"},{"path":"https://pak.r-lib.org/dev/reference/pkg_remove.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove installed packages — pkg_remove","title":"Remove installed packages — pkg_remove","text":"Remove installed packages","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_remove.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove installed packages — pkg_remove","text":"","code":"pkg_remove(pkg, lib = .libPaths()[[1L]])"},{"path":"https://pak.r-lib.org/dev/reference/pkg_remove.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove installed packages — pkg_remove","text":"pkg character vector packages remove. lib library remove packages .","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_remove.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove installed packages — pkg_remove","text":"Nothing.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Search CRAN packages — pkg_search","title":"Search CRAN packages — pkg_search","text":"Search indexed database current CRAN packages. uses pkgsearch package. See package details also pkgsearch::pkg_search() pagination, advanced searching, etc.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search CRAN packages — pkg_search","text":"","code":"pkg_search(query, ...)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search CRAN packages — pkg_search","text":"query Search query string. ... Additional arguments passed pkgsearch::pkg_search()","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search CRAN packages — pkg_search","text":"data frame, also pak_search_result object custom print method. see underlying table, can use [] drop extra classes. See examples .","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search CRAN packages — pkg_search","text":"Simple search See underlying data frame","code":"pkg_search(\"survival\") #> #> 1 survival 3.4.0 -- by Terry M Therneau, 4 months ago #> Survival Analysis #> #> 2 survminer 0.4.9 -- by Alboukadel Kassambara, 2 years ago #> Drawing Survival Curves using 'ggplot2' #> #> 3 flexsurv 2.2 -- by Christopher Jackson, 6 months ago #> Flexible Parametric Survival and Multi-State Models #> #> 4 muhaz 1.2.6.4 -- by David Winsemius, 2 years ago #> Hazard Function Estimation in Survival Analysis #> #> 5 pec 2022.5.4 -- by Thomas A. Gerds, 8 months ago #> Prediction Error Curves for Risk Prediction Models in Survival Analysi #> s #> #> 6 randomForestSRC 3.1.1 -- by Udaya B. Kogalur, 5 months ago #> Fast Unified Random Forests for Survival, Regression, and Classificati #> on (RF-SRC) #> #> 7 relsurv 2.2.8 -- by Damjan Manevski, 4 months ago #> Relative Survival #> #> 8 survRM2 1.0.4 -- by Hajime Uno, 6 months ago #> Comparing Restricted Mean Survival Time #> #> 9 titanic 0.1.0 -- by Paul Hendricks, 7 years ago #> Titanic Passenger Survival Data Set #> #> 10 KMsurv 0.1.5 -- by Jun Yan, 10 years ago #> Data sets from Klein and Moeschberger (1997), Survival Analysis psro <- pkg_search(\"ropensci\") psro[] #> # A data frame: 10 × 15 #> score package version title descr…¹ date maint…² #> #> 1 538. webmockr 0.8.2 Stub… \"Stubb… 2022-08-28 19:20:02 Scott … #> 2 520. RSelenium 1.7.9 R Bi… \"Provi… 2022-09-02 07:10:11 Ju Yeo… #> 3 416. tracerer 2.2.2 Trac… \"'BEAS… 2021-05-30 08:40:03 Richèl… #> 4 376. rfisheries 0.2 'Pro… \"A pro… 2016-02-19 08:50:03 Karthi… #> 5 367. mcbette 1.15 Mode… \"'BEAS… 2022-08-27 12:30:02 Richèl… #> 6 359. taxize 0.9.100 Taxo… \"Inter… 2022-04-22 07:30:02 Zachar… #> 7 350. beastier 2.4.11 Call… \"'BEAS… 2022-08-11 13:40:04 Richèl… #> 8 347. spocc 1.2.0 Inte… \"A pro… 2021-01-05 19:50:03 Scott … #> 9 316. chromer 0.3 Inte… \"A pro… 2022-10-27 22:45:36 Karl W… #> 10 315. visdat 0.5.3 Prel… \"Creat… 2019-02-15 14:30:03 Nichol… #> # … with 8 more variables: maintainer_email , revdeps , #> # downloads_last_month , license , url , #> # bugreports , package_data >, ago , and #> # abbreviated variable names ¹​description, ²​maintainer_name"},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Display installed locations of a package — pkg_status","title":"Display installed locations of a package — pkg_status","text":"Display installed locations package","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Display installed locations of a package — pkg_status","text":"","code":"pkg_status(pkg, lib = .libPaths())"},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Display installed locations of a package — pkg_status","text":"pkg Name one installed packages display status . lib One library paths lookup packages status . default libraries used.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Display installed locations of a package — pkg_status","text":"Data frame data installations pkg. always columns: biocviews: corresponding field DESCRIPTION, must present Bioconductor packages, packages typically . built: Built field DESCRIPTION. depends, suggests, Imports, linkingto, enhances: corresponding fields DESCRIPTION files. deps: list data frames, dependencies package. columns: ref, type (dependency type lowercase), package (dependent package, R), op version, last two version requirement. op can >=, >, == <=, although first one common practice. library: path package library containing package. license: DESCRIPTION. md5sum: DESCTIPTION, typically NA, except Windows. needscompilation: DESCRIPTION, column logical. package: package name. platform: Built field DESCRIPTION, current platform missing DESCRIPTION. priority: DESCRIPTION, usually base, recommended, missing. ref: corresponding installed::* package reference. repository: DESCRIPTION. packages CRAN repository CRAN, repositories, e.g. R-universe adds repository URL . repotype: cran, bioc missing. rversion: Built field. field, current R version. sysreqs: SystemRequirements field DESCRIPTION. title: package title. type: always installed. version: package version (string).","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"notes-","dir":"Reference","previous_headings":"","what":"Notes:","title":"Display installed locations of a package — pkg_status","text":"addition, also remote* config/needs/* entries DESCRIPTION files. (Case insensitive.) columns type character, except needscompilation, logical deps, list columns. entry missing package, set NA. Note column names lowercase, even corresponding entries DESCRIPTION. order columns deterministic, assume order. Additional columns might present, internal pak used user code.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Display installed locations of a package — pkg_status","text":"","code":"pkg_status(\"MASS\") #> # A data frame: 2 × 39 #> library package title version depends repos…¹ license needs…² built #> * #> 1 /Users/ga… MASS Supp… 7.3-58… R (>= … CRAN GPL-2 … TRUE R 4.… #> 2 /Library/… MASS Supp… 7.3-58… R (>= … CRAN GPL-2 … TRUE R 4.… #> # … with 30 more variables: remotetype , remotepkgref , #> # remoteref , remoterepos , remotepkgplatform , #> # remotesha , imports , suggests , linkingto , #> # remotes , remotehost , remoterepo , #> # remoteusername , enhances , biocviews , #> # remoteurl , remotesubdir , priority , #> # remoteetag , remotepackaged , md5sum , …"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_sysreqs.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate system requirements of one of more packages — pkg_sysreqs","title":"Calculate system requirements of one of more packages — pkg_sysreqs","text":"Calculate system requirements one packages","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_sysreqs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate system requirements of one of more packages — pkg_sysreqs","text":"","code":"pkg_sysreqs(pkg, upgrade = TRUE, dependencies = NA, sysreqs_platform = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_sysreqs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate system requirements of one of more packages — pkg_sysreqs","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies. sysreqs_platform System requirements platform. NULL, sysreqs_platform configuration option used, defaults current platform. Set option pak detect platform correctly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_sysreqs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate system requirements of one of more packages — pkg_sysreqs","text":"List entries: os: character string. Operating system. distribution: character string. Linux distribution, NA OS Linux. version: character string. Distribution version, NA OS Linux. pre_install: character vector. Commands run installation system packages. install_scripts: character vector. Commands run install system packages. post_install: character vector. Commands run installation system packages. packages: data frame. Information system packages needed. columns: sysreq: string, cross-platform name system requirement. packages: list column character vectors. names R packages system requirement. pre_install: list column character vectors. Commands run package installation system requirement. system_packages: list column character vectors. Names system packages install. post_install: list column character vectors. Commands run package installation system requirement.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_has_binaries.html","id":null,"dir":"Reference","previous_headings":"","what":"Does PPM build binary packages for the current platform? — ppm_has_binaries","title":"Does PPM build binary packages for the current platform? — ppm_has_binaries","text":"PPM build binary packages current platform?","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_has_binaries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Does PPM build binary packages for the current platform? — ppm_has_binaries","text":"","code":"ppm_has_binaries()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_has_binaries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Does PPM build binary packages for the current platform? — ppm_has_binaries","text":"TRUE FALSE.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_has_binaries.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Does PPM build binary packages for the current platform? — ppm_has_binaries","text":"","code":"if (FALSE) { system_r_platform() ppm_has_binaries() }"},{"path":"https://pak.r-lib.org/dev/reference/ppm_platforms.html","id":null,"dir":"Reference","previous_headings":"","what":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","title":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","text":"List platforms supported Posit Package Manager (PPM)","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_platforms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","text":"","code":"ppm_platforms()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_platforms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","text":"Data frame columns: name: platform name, essentially identifier, os: operating system, linux, windows macOS currently, binary_url: URL segment binary repository URL platform, see ppm_snapshots(). distribution: Linux platforms name distribution, release: Linux platforms, name release, binaries: whether PPM builds binaries platform.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_platforms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","text":"","code":"if (FALSE) { ppm_platforms() }"},{"path":"https://pak.r-lib.org/dev/reference/ppm_r_versions.html","id":null,"dir":"Reference","previous_headings":"","what":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","title":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","text":"List R versions supported Posit Package Manager (PPM)","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_r_versions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","text":"","code":"ppm_r_versions()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_r_versions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","text":"Data frame columns: r_version: minor R versions, .e. version numbers containing first two components R versions supported PPM instance.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_r_versions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","text":"","code":"if (FALSE) { ppm_r_versions() }"},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"Returns current Posit Package Manager (PPM) repository URL","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"","code":"ppm_repo_url()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"String scalar, repository URL configured PPM instance. PPM instance configured, URL Posit Public Package Manager instance. includes repository name, e.g. https://packagemanager.posit.co/.","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"URL form {base}/{repo}, e.g. https://packagemanager.posit.co/. configure hosted PPM instance, set PKGCACHE_PPM_URL environment variable base URL (e.g. https://packagemanager.posit.co). use repo_add() PPM snapshots, may also set PKGCACHE_PPM_REPO environment variable name default repository. Linux, instead setting environment variables, can also add PPM repository repos option, see base::options(). environment variables set, ppm_repo_url() try extract PPM base URL repository name option. PKGCACHE_PPM_URL environment variable set, repos option contain PPM URL (Linux), pak uses public PPM instance https://packagemanager.posit.co, cran repository.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"","code":"if (FALSE) { ppm_repo_url() }"},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":null,"dir":"Reference","previous_headings":"","what":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"List available Posit Package Manager (PPM) snapshots","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"","code":"ppm_snapshots()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"Data frame two columns: date: time snapshot taken, POSIXct vector, id: integer id snapshot, can used repository URL.","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"repository URL snapshot following form Windows: {base} base URL PPM (see ppm_repo_url()) {id} either date id snapshot, latest latest snapshot. E.g. equivalent: Linux distribution PPM support, repository URL contains binary packages looks like : {id} , {binary_url} code name release supported Linux distribution. See binary_url column result ppm_platforms() code names.","code":"{base}/{repo}/{id} https://packagemanager.posit.co/cran/5 https://packagemanager.posit.co/cran/2017-10-10 {base}/{repo}/__linux__/{binary_url}/{id}"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"","code":"if (FALSE) { ppm_snapshots() }"},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a new CRAN-like repository — repo_add","title":"Add a new CRAN-like repository — repo_add","text":"Add new repository list repositories pak uses look packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a new CRAN-like repository — repo_add","text":"","code":"repo_add(..., .list = NULL) repo_resolve(spec)"},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a new CRAN-like repository — repo_add","text":"... Repository specifications, possibly named character vectors. See details . .list List character vector repository specifications. argument easier use programmatically .... See details . spec Repository specification, possibly named character scalar.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a new CRAN-like repository — repo_add","text":"repo_resolve() returns named character scalar, URL repository.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add a new CRAN-like repository — repo_add","text":"repo_add() adds new repositories. resolves specified repositories using repo_resolve() modifies repos global option. repo_add() effect current R session. want keep configuration R sessions, set repos option desired value user project .Rprofile file.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"repository-specifications","dir":"Reference","previous_headings":"","what":"Repository specifications","title":"Add a new CRAN-like repository — repo_add","text":"format repository specification named unnamed character scalar. name missing, pak adds name automatically. repository named CRAN main CRAN repository, otherwise names informational. Currently supported repository specifications: URL pointing root CRAN-like repository. Example: RSPM@, RSPM (RStudio Package Manager) snapshot, specified date. RSPM@- RSPM snapshot, day release . RSPM@R- RSPM snapshot, day R released. MRAN@, MRAN (Microsoft R Application Network) snapshot, specified date. MRAN@- MRAN snapshot, day release . MRAN@R- MRAN snapshot, day R released. Notes: See RSPM https://packagemanager.rstudio.com/client/#/. See MRAN snapshots https://mran.microsoft.com/timemachine. dates (times) can specified ISO 8601 format. RSPM snapshot available date, next available date used. Dates first, last RSPM snapshot trigger error. Dates first, last MRAN snapshot trigger error. Unknown R package versions trigger error.","code":"https://cloud.r-project.org"},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"exaples","dir":"Reference","previous_headings":"","what":"Exaples","title":"Add a new CRAN-like repository — repo_add","text":"","code":"repo_add(RSPMdplyr100 = \"RSPM@dplyr-1.0.0\") repo_get() #> # A data frame: 6 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 RSPMdplyr100 https://packagemanager.posit.co/c… cran… * NA #> 3 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 6 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version repo_resolve(\"MRAN@2020-01-21\") #> CRAN #> \"https://cran.microsoft.com/snapshot/2020-01-21\" repo_resolve(\"RSPM@2020-01-21\") #> CRAN #> \"https://packagemanager.posit.co/cran/245\" repo_resolve(\"MRAN@dplyr-1.0.0\") #> CRAN #> \"https://cran.microsoft.com/snapshot/2020-05-30\" repo_resolve(\"RSPM@dplyr-1.0.0\") #> CRAN #> \"https://packagemanager.posit.co/cran/289\" repo_resolve(\"MRAN@R-4.0.0\") #> CRAN #> \"https://cran.microsoft.com/snapshot/2020-04-25\" repo_resolve(\"RSPM@R-4.0.0\") #> CRAN #> \"https://packagemanager.posit.co/cran/276\""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":null,"dir":"Reference","previous_headings":"","what":"Query the currently configured CRAN-like repositories — repo_get","title":"Query the currently configured CRAN-like repositories — repo_get","text":"pak uses repos option, see options(). also automatically adds CRAN mirror none set , correct version Bioconductor repositories. See cran_mirror bioc arguments.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query the currently configured CRAN-like repositories — repo_get","text":"","code":"repo_get(r_version = getRversion(), bioc = TRUE, cran_mirror = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query the currently configured CRAN-like repositories — repo_get","text":"r_version R version use determine correct Bioconductor version, bioc = TRUE. bioc Whether automatically add Bioconductor repositories result. cran_mirror CRAN mirror use. Leave NULL use mirror getOption(\"repos\") automatically selected one.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Query the currently configured CRAN-like repositories — repo_get","text":"repo_get() returns table currently configured repositories.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query the currently configured CRAN-like repositories — repo_get","text":"","code":"repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Show the status of CRAN-like repositories — repo_status","title":"Show the status of CRAN-like repositories — repo_status","text":"checks status configured supplied repositories.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show the status of CRAN-like repositories — repo_status","text":"","code":"repo_status( platforms = NULL, r_version = getRversion(), bioc = TRUE, cran_mirror = NULL ) repo_ping( platforms = NULL, r_version = getRversion(), bioc = TRUE, cran_mirror = NULL )"},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show the status of CRAN-like repositories — repo_status","text":"platforms Platforms use, default current platform, plus source packages. r_version R version(s) use, default current R version, via getRversion(). bioc Whether add Bioconductor repositories. already configured via options(repos), can set FALSE. cran_mirror CRAN mirror use.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show the status of CRAN-like repositories — repo_status","text":"data frame row every repository, every queried platform R version. columns: name: name repository. comes names configured repositories options(\"repos\"), added pkgcache. typically CRAN CRAN, current Bioconductor repositories BioCsoft, BioCann, BioCexp, BioCworkflows. url: base URL repository. bioc_version: Bioconductor version, NA non-Bioconductor repositories. platform: platform, possible values source, macos windows currently. path: path packages within base URL, given platform R version. r_version: R version, one specified R versions. ok: Logical flag, whether repository contains metadata file given platform R version. ping: HTTP response time repository seconds. ok column FALSE, columns NA. error: error object HTTP query failed repository, platform R version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Show the status of CRAN-like repositories — repo_status","text":"repo_ping() similar repo_status() also prints short summary data, returns result invisibly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show the status of CRAN-like repositories — repo_status","text":"","code":"repo_status() #> # A data frame: 10 × 10 #> name url type bioc_…¹ platf…² path r_ver…³ ok ping error #> #> 1 CRAN http… cran NA source src/… 4.2 TRUE 0.269 #> 2 CRAN http… cran NA aarch6… bin/… 4.2 TRUE 0.265 #> 3 BioCsoft http… bioc 3.16 source src/… 4.2 TRUE 0.264 #> 4 BioCsoft http… bioc 3.16 aarch6… bin/… 4.2 TRUE 0.271 #> 5 BioCann http… bioc 3.16 source src/… 4.2 TRUE 0.383 #> 6 BioCann http… bioc 3.16 aarch6… bin/… 4.2 TRUE 0.392 #> 7 BioCexp http… bioc 3.16 source src/… 4.2 TRUE 0.507 #> 8 BioCexp http… bioc 3.16 aarch6… bin/… 4.2 TRUE 0.739 #> 9 BioCwor… http… bioc 3.16 source src/… 4.2 TRUE 0.505 #> 10 BioCwor… http… bioc 3.16 aarch6… bin/… 4.2 TRUE 0.766 #> # … with abbreviated variable names ¹​bioc_version, ²​platform, #> # ³​r_version repo_status( platforms = c(\"windows\", \"macos\"), r_version = c(\"4.0\", \"4.1\") ) #> # A data frame: 15 × 10 #> name url type bioc_…¹ platf…² r_ver…³ path ok ping #> #> 1 CRAN https… cran NA i386+x… 4.0 bin/… TRUE 0.198 #> 2 CRAN https… cran NA i386+x… 4.1 bin/… TRUE 0.197 #> 3 CRAN https… cran NA aarch6… 4.1 bin/… TRUE 0.197 #> 4 BioCsoft https… bioc 3.12 i386+x… 4.0 bin/… TRUE 0.988 #> 5 BioCann https… bioc 3.12 i386+x… 4.0 bin/… TRUE 1.03 #> 6 BioCexp https… bioc 3.12 i386+x… 4.0 bin/… TRUE 1.25 #> 7 BioCworkflows https… bioc 3.12 i386+x… 4.0 bin/… TRUE 1.47 #> 8 BioCsoft https… bioc 3.14 i386+x… 4.1 bin/… TRUE 1.48 #> 9 BioCsoft https… bioc 3.14 aarch6… 4.1 bin/… FALSE NA #> 10 BioCann https… bioc 3.14 i386+x… 4.1 bin/… TRUE 1.45 #> 11 BioCann https… bioc 3.14 aarch6… 4.1 bin/… FALSE NA #> 12 BioCexp https… bioc 3.14 i386+x… 4.1 bin/… TRUE 1.72 #> 13 BioCexp https… bioc 3.14 aarch6… 4.1 bin/… FALSE NA #> 14 BioCworkflows https… bioc 3.14 i386+x… 4.1 bin/… TRUE 1.71 #> 15 BioCworkflows https… bioc 3.14 aarch6… 4.1 bin/… FALSE NA #> # … with 1 more variable: error , and abbreviated variable names #> # ¹​bioc_version, ²​platform, ³​r_version repo_ping() #> Repository summary: source aarch64-apple-darwin20 #> CRAN @ cloud.r-project.org ✔ ✔ (194ms) #> BioCsoft @ bioconductor.org ✔ ✔ (352ms) #> BioCann @ bioconductor.org ✔ ✔ (511ms) #> BioCexp @ bioconductor.org ✔ ✔ (675ms) #> BioCworkflows @ bioconductor.org ✔ ✔ (698ms)"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":null,"dir":"Reference","previous_headings":"","what":"System requirements — System requirements","title":"System requirements — System requirements","text":"pak takes care system requirements.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"introduction","dir":"Reference","previous_headings":"","what":"Introduction","title":"System requirements — System requirements","text":"Many R packages need external software present machine, otherwise work, even load. example RPostgres R package uses PostgreSQL client library, default dynamically links Linux systems. means (administrators system) need install library, typically form system package: libpq-dev Ubuntu Debian systems, postgresql-server-devel postgresql-devel RedHat, Fedora, etc. systems. good news pak helps : - looks required system packages installing R packages, - checks required system packages installed, - installs automatically, superuser, can use password-less sudo start superuser shell. addition, pak also functions query system requirements system packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"requirements-supported-platforms","dir":"Reference","previous_headings":"","what":"Requirements, supported platforms","title":"System requirements — System requirements","text":"Call pak::sysreqs_platforms() list platforms support system requirements: Call pak::sysreqs_is_supported() see system supported: vignette built Ubuntu 22.04.2 LTS, platform pak support. following see output code.","code":"pak::sysreqs_platforms() ## # A data frame: 10 × 7 ## name os distribution version update_command install_command ## ## 1 Ubuntu Lin… linux ubuntu * apt-get -y up… apt-get -y ins… ## 2 Debian Lin… linux debian * apt-get -y up… apt-get -y ins… ## 3 CentOS Lin… linux centos * NA yum install -y ## 4 Rocky Linux linux rockylinux * NA dnf install -y ## 5 Red Hat En… linux redhat 6 NA yum install -y ## 6 Red Hat En… linux redhat 7 NA yum install -y ## 7 Red Hat En… linux redhat * NA dnf install -y ## 8 Fedora Lin… linux fedora * NA dnf install -y ## 9 openSUSE L… linux opensuse * NA zypper --non-i… ## 10 SUSE Linux… linux sle * NA zypper --non-i… ## # ℹ 1 more variable: query_command pak::sysreqs_is_supported() ## [1] TRUE"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"r-package-installation","dir":"Reference","previous_headings":"","what":"R package installation","title":"System requirements — System requirements","text":"using pak superuser, supported platform, pak look system requirements, install missing ones. example:","code":"pak::pkg_install(\"RPostgres\") ## ✔ Loading metadata database ... done ## ## → Will install 17 packages. ## → All 17 packages (0 B) are cached. ## + DBI 1.1.3 ## + RPostgres 1.4.5 + ✖ libpq-dev ## + Rcpp 1.0.10 ## + bit 4.0.5 ## + bit64 4.0.5 ## + blob 1.2.4 ## + cli 3.6.1 ## + generics 0.1.3 ## + glue 1.6.2 ## + hms 1.1.3 ## + lifecycle 1.0.3 ## + lubridate 1.9.2 ## + pkgconfig 2.0.3 ## + rlang 1.1.1 ## + timechange 0.2.0 ## + vctrs 0.6.2 ## + withr 2.5.0 ## → Will install 1 system package: ## + libpq-dev - RPostgres ## ℹ No downloads are needed, 17 pkgs are cached ## ℹ Installing system requirements ## ℹ Executing `sh -c apt-get -y update` ## ℹ Executing `sh -c apt-get -y install libpq-dev` ## ✔ Installed DBI 1.1.3 (1.1s) ## ✔ Installed RPostgres 1.4.5 (1.2s) ## ✔ Installed Rcpp 1.0.10 (1.2s) ## ✔ Installed bit 4.0.5 (1.2s) ## ✔ Installed bit64 4.0.5 (148ms) ## ✔ Installed blob 1.2.4 (63ms) ## ✔ Installed cli 3.6.1 (88ms) ## ✔ Installed generics 0.1.3 (61ms) ## ✔ Installed glue 1.6.2 (63ms) ## ✔ Installed hms 1.1.3 (62ms) ## ✔ Installed lifecycle 1.0.3 (61ms) ## ✔ Installed lubridate 1.9.2 (87ms) ## ✔ Installed pkgconfig 2.0.3 (62ms) ## ✔ Installed rlang 1.1.1 (1.1s) ## ✔ Installed timechange 0.2.0 (1.1s) ## ✔ Installed vctrs 0.6.2 (1.1s) ## ✔ Installed withr 2.5.0 (1.1s) ## ✔ 1 pkg + 16 deps: added 17 [17.5s]"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"running-r-as-a-regular-user","dir":"Reference","previous_headings":"","what":"Running R as a regular user","title":"System requirements — System requirements","text":"don’t want use R superuser, can set sudo without password, works well. pak automatically detect password-less sudo capability, use install system packages, needed. run R regular (root) user, password-less sudo available, pak print system requirements, try install update . installing source packages need link system libraries, installation probably fail, install system packages. installing binary R packages, installation typically succeeds, won’t able load packages R, install required system packages. example, system required system package installed RPostgres. installing source R package, installation already fails: hand, installing binary packages, e.g. Posit Package Manager, installation typically succeeds, loading package fails:","code":"pak::pkg_install(\"RPostgres?source\") ## + plogr 0.2.0 ## ✖ Missing 1 system package. You'll probably need to install it ## manually: ## + libpq-dev - RPostgres ## ℹ No downloads are needed, 2 pkgs (1.47 MB) are cached ## ✔ Installed plogr 0.2.0 (1.1s) ## ℹ Building RPostgres 1.4.5 ## ✖ Failed to build RPostgres 1.4.5 ## Registered S3 methods overwritten by 'callr': ## method from ## format.callr_status_error ## print.callr_status_error ## Error: ## ! error in pak subprocess ## Caused by error in `stop_task_build(state, worker)`: ## ! Failed to build source package 'RPostgres' ## Full installation output: ## * installing *source* package ‘RPostgres’ ... ## ** package ‘RPostgres’ successfully unpacked and MD5 sums checked ## staged installation is only possible with locking ## ** using non-staged installation ## Using PKG_CFLAGS= ## Using PKG_LIBS=-lpq ## Using PKG_PLOGR= ## ------------------------- ANTICONF ERROR --------------------------- ## Configuration failed because libpq was not found. Try installing: ## * deb: libpq-dev libssl-dev (Debian, Ubuntu, etc) ## * rpm: postgresql-devel (Fedora, EPEL) ## * rpm: postgreql8-devel, psstgresql92-devel, postgresql93-devel, or pos ## tgresql94-devel (Amazon Linux) ## * csw: postgresql_dev (Solaris) ## * brew: libpq (OSX) ## If libpq is already installed, check that either: ## (i) 'pkg-config' is in your PATH AND PKG_CONFIG_PATH contains ## a libpq.pc file; or ## (ii) 'pg_config' is in your PATH. ## If neither can detect , you can set INCLUDE_DIR ## and LIB_DIR manually via: ## R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' ## --------------------------[ ERROR MESSAGE ]---------------------------- ## :1:10: fatal error: libpq-fe.h: No such file or directory ## compilation terminated. ## ----------------------------------------------------------------------- ## ERROR: configuration failed for package ‘RPostgres’ ## * removing ‘/tmp/RtmpsOXbPZ/pkg-lib4a492949a49e/RPostgres’ ## --- ## Backtrace: ## 1. pak::pkg_install(\"RPostgres?source\") ## 2. pak:::remote(function(...) get(\"pkg_install_do_plan\", asNamespace(\"pa ## k\")… at package.R:84:3 ## 3. err$throw(res$error) at subprocess.R:115:5 ## --- ## Subprocess backtrace: ## 1. base::withCallingHandlers(cli_message = function(msg) { … ## 2. get(\"pkg_install_do_plan\", asNamespace(\"pak\"))(...) ## 3. proposal$install() ## 4. pkgdepends::install_package_plan(plan, lib = private$library, num_wo ## rkers = nw… ## 5. base::withCallingHandlers({ … ## 6. pkgdepends:::handle_events(state, events) ## 7. pkgdepends:::handle_event(state, i) ## 8. pkgdepends:::stop_task(state, worker) ## 9. pkgdepends:::stop_task_build(state, worker) ## 10. base::throw(new_pkg_build_error(\"Failed to build source package {pkg ## }\", … ## 11. | base::signalCondition(cond) ## 12. global (function (e) … ## Execution halted pak::pkg_install(\"RPostgres\") library(RPostgres) ## → Will install 17 packages. ## → All 17 packages (0 B) are cached. ## + DBI 1.1.3 ## + RPostgres 1.4.5 + ✖ libpq-dev ## + Rcpp 1.0.10 ## + bit 4.0.5 ## + bit64 4.0.5 ## + blob 1.2.4 ## + cli 3.6.1 ## + generics 0.1.3 ## + glue 1.6.2 ## + hms 1.1.3 ## + lifecycle 1.0.3 ## + lubridate 1.9.2 ## + pkgconfig 2.0.3 ## + rlang 1.1.1 ## + timechange 0.2.0 ## + vctrs 0.6.2 ## + withr 2.5.0 ## ✖ Missing 1 system package. You'll probably need to install it ## manually: ## + libpq-dev - RPostgres ## ℹ No downloads are needed, 17 pkgs are cached ## ✔ Installed DBI 1.1.3 (1.1s) ## ✔ Installed RPostgres 1.4.5 (1.1s) ## ✔ Installed Rcpp 1.0.10 (1.2s) ## ✔ Installed bit 4.0.5 (1.2s) ## ✔ Installed bit64 4.0.5 (144ms) ## ✔ Installed blob 1.2.4 (1.1s) ## ✔ Installed cli 3.6.1 (1.1s) ## ✔ Installed generics 0.1.3 (90ms) ## ✔ Installed glue 1.6.2 (87ms) ## ✔ Installed hms 1.1.3 (1.1s) ## ✔ Installed lifecycle 1.0.3 (1.1s) ## ✔ Installed lubridate 1.9.2 (1.1s) ## ✔ Installed pkgconfig 2.0.3 (1.1s) ## ✔ Installed rlang 1.1.1 (1.1s) ## ✔ Installed timechange 0.2.0 (1.1s) ## ✔ Installed vctrs 0.6.2 (1.1s) ## ✔ Installed withr 2.5.0 (1.1s) ## ✔ 1 pkg + 16 deps: added 17 [11.6s] ## Error: package or namespace load failed for ‘RPostgres’ in dyn.load(file ## , DLLpath = DLLpath, ...): ## unable to load shared object '/tmp/RtmpWqZycA/lib/RPostgres/libs/RPostg ## res.so': ## libpq.so.5: cannot open shared object file: No such file or directory ## Execution halted"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"other-queries","dir":"Reference","previous_headings":"","what":"Other queries","title":"System requirements — System requirements","text":"addition automatic system package lookup installation, pak also functions help system dependencies. sysreqs_db_list() function lists system requirements pak knows . sysreqs_db_match() manually matches SystemREquirements fields againts system requirements: can also use query system requirements platfosm: sysreqs_list_system_packages() cross-platform way listing installed system packages capabilities: sysreqs_check_installed() handy function checks system requirements installed R packages installed library: sysreqs_fix_installed() goes one step also tries install missing system requirements.","code":"pak::sysreqs_db_list() ## # A data frame: 106 × 5 ## name patterns packages pre_install post_install ## ## 1 QuantLib ## 2 apparmor ## 3 atk ## 4 automake ## 5 berkeleydb ## 6 blender ## 7 bowtie2 ## 8 bwidget ## 9 cairo ## 10 chrome ## # ℹ 96 more rows sq <- pak::sysreqs_db_match(\"Needs libcurl and also Java.\") sq ## [[1]] ## # A data frame: 2 × 5 ## spec sysreq packages pre_install post_install ## ## 1 Needs libcurl and also Java. java ## 2 Needs libcurl and also Java. libcurl ## sq[[1]]$packages ## [[1]] ## [1] \"default-jdk\" ## ## [[2]] ## [1] \"libcurl4-openssl-dev\" ## sqrhel9 <- pak::sysreqs_db_match(\"Needs libcurl and also Java.\", \"redhat-9\") sqrhel9 ## [[1]] ## # A data frame: 2 × 5 ## spec sysreq packages pre_install post_install ## ## 1 Needs libcurl and also Java. java ## 2 Needs libcurl and also Java. libcurl ## sqrhel9[[1]]$packages ## [[1]] ## [1] \"java-11-openjdk-devel\" ## ## [[2]] ## [1] \"libcurl-devel\" ## pak::sysreqs_list_system_packages() ## # A data frame: 433 × 4 ## status package version provides ## ## 1 ii adduser 3.118ubuntu5 ## 2 ii apt 2.4.8 ## 3 ii autoconf 2.71-2 ## 4 ii automake 1:1.16.5-1.3 ## 5 ii autotools-dev 20220109.1 ## 6 ii base-files 12ubuntu4.3 ## 7 ii base-passwd 3.5.52build1 ## 8 ii bash 5.1-6ubuntu1 ## 9 ii binutils 2.38-4ubuntu2.1 ## 10 ii binutils-common 2.38-4ubuntu2.1 ## # ℹ 423 more rows pak::sysreqs_check_installed() ## system package installed required by ## -------------- -- ----------- ## git ✔ gitcreds ## gsfonts ✔ magick ## imagemagick ✔ magick ## libarchive-dev ✔ archive ## libcurl4-openssl-dev ✔ curl ## libfontconfig1-dev ✔ systemfonts ## libfreetype6-dev ✔ ragg, systemfonts, textshaping ## libfribidi-dev ✔ textshaping ## libharfbuzz-dev ✔ textshaping ## libicu-dev ✔ stringi ## libjpeg-dev ✔ ragg ## libmagick++-dev ✔ magick ## libnode-dev ✔ V8 ## libpng-dev ✔ ragg ## libpq-dev ✖ RPostgres ## libssl-dev ✔ curl, openssl ## libtiff-dev ✔ ragg ## libxml2-dev ✔ xml2 ## make ✔ fs, sass ## pandoc ✔ knitr, rmarkdown ## zlib1g-dev ✔ data.table"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"build-time-and-run-time-dependencies","dir":"Reference","previous_headings":"","what":"Build-time and run-time dependencies","title":"System requirements — System requirements","text":"system requirements database pak uses currently differentiate build-time run-time dependencies. build-time dependency system package need installing R package source. run-time dependency system package need using R package. Linux distribution create (least) two packages software library: runtime package development package. R package uses software library, runtime package run-time dependency development package build-time dependency. However, pak currently know difference build-time run-time dependencies, install types dependencies, always. means pak usually installs system packages strictly necessary. typically development packages libraries, .e. header files, typically cause issues. short disk space, can try removing .","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"how-it-works","dir":"Reference","previous_headings":"","what":"How it works","title":"System requirements — System requirements","text":"pak uses database system requirements https://github.com/rstudio/r-system-requirements. copy database embedded package, also tries download updated versions database GitHub, current copy older one day. can explicitly update database GitHub using sysreqs_db_update() function. CRAN packages, downloads SystemRequierements fields https://cran2.r-pkg.org/metadata/, database updated daily. planning moving database GitHub, creating similar database Bioconductor. packages sources require pak obtain package DESCRIPTION file (e.g. github::, git::, etc.), pak obtrains SystemRequirements directly DESCRIPTION file. SystemRequirements fields, pak matches database, obtain cacnonized list system requirements. pak queries local platform, see exact system packages needed. also queries installed system packages, avoid trying install system packages already installed.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"configuration","dir":"Reference","previous_headings":"","what":"Configuration","title":"System requirements — System requirements","text":"several pak configuration options can use adjust system requirements handled. list , please see options sysreqs prefix ?pak-config manual page complete current list. sysreqs: whether install system requirements. default TRUE platform supported user can install system packages, either superuser, via sudo. FALSE (user install system packages), platform supported, system requirements printed, installed. sysreqs_db_update: whether try update system requirements database GitHub. sysreqs_db_update_timeout: timeout system requirements update GitHub. sysreqs_dry_run: TRUE pak prints install commands, actually run . sysreqs_platform: platform name use determining system requirements. Defaults current platform. using Linux distribution compatible distribution pak supports, can set option manually. E.g. Ubuntu-based distros can set ubuntu-22.04, appropriate Ubuntu version. sysreqs_sudo: whether use sudo install system packages. set, pak tries auto-detect sudo needed . sysreqs_update: whether try update system packages already installed. pak know version system package required, try update system packages default. think need newer system packages, can set option TRUE. sysreqs_verbose: whether print output system package installation commands. Useful debugging, TRUE default CI environment.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"windows","dir":"Reference","previous_headings":"","what":"Windows","title":"System requirements — System requirements","text":"system requirements database information system dependencies Windows, pak use information try install system software Windows. CRAN, PPM Bioconductor Windows binary packages available majority R packages serve, packages practically always link system libraries statically, don’t need external software. wish compile Windows packages source, need install appropriate version Rtools, possibly extra packages using pacman tool Rtools4x. Rtools42 newer Rtools versions bundle lots libraries, likely extra pacman packages needed. Rtools40 leaner default installation, ’ll probably need install packages manually: https://github.com/r-windows/docs/blob/master/rtools40.md#readme planning adding better Windows system software support pak future.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"macos","dir":"Reference","previous_headings":"","what":"macOS","title":"System requirements — System requirements","text":"pak currently system requirement information macOS. macOS similar Windows, repositories serve statically linked macOS binary packages need system software. need compile packages source, possibly need install sytem libraries, either via Homebrew, downloading CRAN’s static library builds https://mac.r-project.org/bin/ planning adding better macOS system software support pak future.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if installed packages have all their system requirements — sysreqs_check_installed","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"sysreqs_check_installed() checks system requirements packages (subset packages) installed. sysreqs_fix_installed() installs missing system packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"","code":"sysreqs_check_installed(packages = NULL, library = .libPaths()[1]) sysreqs_fix_installed(packages = NULL, library = .libPaths()[1])"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"packages NULL, packages checked. package packages installed, pak throws warning. library Library libraries check.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"Data frame custom print format method, pkg_sysreqs_check_result class. columns : system_package: string, name required system package. installed: logical, whether system package correctly installed. packages: list column character vectors. names installed R packages need system package. pre_install: list column character vectors. Commands run installation system package. post_install: list column character vectors. Commands run installation system package. data frame also two attributes additional data: sysreqs_records: raw system requirements records, system_packages: list installed system packages. sysreqs_fix_packages() returns value, invisibly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"functions use sysreqs_platform configuration option, see Configuration . Set pak detect platform correctly.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"","code":"# This only works on supported platforms sysreqs_check_installed() #> system package installed required by #> -------------- -- -----------"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List contents of the system requirements DB, for a platform — sysreqs_db_list","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"also tries update system dependency database, outdated. (.e. older allowed metadata_update_after configuration option .","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"","code":"sysreqs_db_list(sysreqs_platform = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"sysreqs_platform System requirements platform. NULL, sysreqs_platform configuration option used, defaults current platform. Set option pak detect platform correctly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"Data frame columns: name: cross platform system dependency name database. patterns: one regular expressions match SystemRequirements fields. packages: one system package names install. pre_install: command(s) run installing packages. post_install:: command(s) run installing packages.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"","code":"sysreqs_db_list(sysreqs_platform = \"ubuntu-22.04\") #> # A data frame: 109 × 5 #> name patterns packages pre_install post_install #> #> 1 QuantLib #> 2 apparmor #> 3 atk #> 4 automake #> 5 berkeleydb #> 6 blender #> 7 boost #> 8 bowtie2 #> 9 bwidget #> 10 cairo #> # ℹ 99 more rows"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":null,"dir":"Reference","previous_headings":"","what":"Match system requirement descriptions to the database — sysreqs_db_match","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"usual workflow pak matches SystemRequirements fields DESCRIPTION files database.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"","code":"sysreqs_db_match(specs, sysreqs_platform = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"specs Character vector system requirements descriptions. sysreqs_platform System requirements platform. NULL, sysreqs_platform configuration option used, defaults current platform. Set option pak detect platform correctly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"Data frame columns: spec: input specs. sysreq: name system library tool. packages: system packages, list column character vectors. Rarely can empty string, e.g. pre_install script performs installation. pre_install: list column character vectors. Shell script(s) run installation. post_install: list column character vectors. Shell script(s) run installation.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"sysreqs_db_match() function lets match string, mainly useful debugging.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"","code":"sysreqs_db_match( c(\"Needs libcurl\", \"Java, libssl\"), sysreqs_platform = \"ubuntu-22.04\" ) #> [[1]] #> # A data frame: 1 × 5 #> spec sysreq packages pre_install post_install #> #> 1 Needs libcurl libcurl #> #> [[2]] #> # A data frame: 1 × 5 #> spec sysreq packages pre_install post_install #> #> 1 Java, libssl java #>"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_update.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the cached copy of the system requirements database — sysreqs_db_update","title":"Update the cached copy of the system requirements database — sysreqs_db_update","text":"Update cached copy system requirements database","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_update.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the cached copy of the system requirements database — sysreqs_db_update","text":"","code":"sysreqs_db_update()"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_update.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update the cached copy of the system requirements database — sysreqs_db_update","text":"cached copy recent, update attempted. See metadata_update_after configuration option .","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if a platform has system requirements support — sysreqs_is_supported","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"Check platform system requirements support","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"","code":"sysreqs_is_supported(sysreqs_platform = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"sysreqs_platform System requirements platform. NULL, sysreqs_platform configuration option used, defaults current platform. Set option pak detect platform correctly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"Logical scalar.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"","code":"sysreqs_is_supported() #> [1] TRUE"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":null,"dir":"Reference","previous_headings":"","what":"List installed system packages — sysreqs_list_system_packages","title":"List installed system packages — sysreqs_list_system_packages","text":"List installed system packages","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List installed system packages — sysreqs_list_system_packages","text":"","code":"sysreqs_list_system_packages()"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List installed system packages — sysreqs_list_system_packages","text":"Data frame columns: status. two three characters, notation dpkg Debian based systems. \"ii\" means package correctly installed. RPM based systems always \"ii\" currently. package: name system package. version: installed version system package. capabilities: list column character vectors, capabilities provided package.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"List installed system packages — sysreqs_list_system_packages","text":"function uses sysreqs_platform configuration option, see Configuration . Set pak detect platform correctly.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List installed system packages — sysreqs_list_system_packages","text":"","code":"sysreqs_list_system_packages()[1:10,] #> # A data frame: 10 × 4 #> status package version provides #> * #> 1 ii acl 2.3.1-1 #> 2 ii adduser 3.118ubuntu5 #> 3 ii adoptium-ca-certificates 1.0.2-1 #> 4 ii adwaita-icon-theme 41.0-1ubuntu1 #> 5 ii alsa-topology-conf 1.2.5.1-2 #> 6 ii alsa-ucm-conf 1.2.6.3-1ubuntu1.6 #> 7 ii ant 1.10.12-1 #> 8 ii ant-optional 1.10.12-1 #> 9 ii apache2 2.4.52-1ubuntu4.5 #> 10 ii apache2-bin 2.4.52-1ubuntu4.5 "},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_platforms.html","id":null,"dir":"Reference","previous_headings":"","what":"List platforms with system requirements support — sysreqs_platforms","title":"List platforms with system requirements support — sysreqs_platforms","text":"List platforms system requirements support","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_platforms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List platforms with system requirements support — sysreqs_platforms","text":"","code":"sysreqs_platforms()"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_platforms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List platforms with system requirements support — sysreqs_platforms","text":"Data frame columns: name: human readable OS name. os: OS name, e.g. linux. distribution: OS id, e.g. ubuntu redhat. version: distribution version. star means versions supported, also supported vendor. update_command: command run update system package metadata. install_command: command run install packages. query_command: name tool use query system package information.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_platforms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List platforms with system requirements support — sysreqs_platforms","text":"","code":"sysreqs_platforms() #> # A data frame: 10 × 7 #> name os distribution version update_command install_command #> #> 1 Ubuntu Linux linux ubuntu * apt-get -y up… apt-get -y ins… #> 2 Debian Linux linux debian * apt-get -y up… apt-get -y ins… #> 3 CentOS Linux linux centos * NA yum install -y #> 4 Rocky Linux linux rockylinux * NA dnf install -y #> 5 Red Hat Ente… linux redhat 6 NA yum install -y #> 6 Red Hat Ente… linux redhat 7 NA yum install -y #> 7 Red Hat Ente… linux redhat * NA dnf install -y #> 8 Fedora Linux linux fedora * NA dnf install -y #> 9 openSUSE Lin… linux opensuse * NA zypper --non-i… #> 10 SUSE Linux E… linux sle * NA zypper --non-i… #> # ℹ 1 more variable: query_command "},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":null,"dir":"Reference","previous_headings":"","what":"R platforms — system_r_platform","title":"R platforms — system_r_platform","text":"R platforms","code":""},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R platforms — system_r_platform","text":"","code":"system_r_platform() system_r_platform_data()"},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"R platforms — system_r_platform","text":"system_r_platform() returns character scalar. system_r_platform_data() returns data frame character scalar columns: cpu, vendor, os, distribution (Linux), release (Linux), platform: concatenation columns, separated dash.","code":""},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"R platforms — system_r_platform","text":"system_r_platform() detects platform current R version. system_r_platform_data() similar, returns raw data instead character scalar. default pak works source packages binary packages current platform. can change , providing different platform names pkg.platforms option PKG_PLATFORMS environment variable. option may contain following platform names: \"source\" source packages, \"macos\" macOS binaries appropriate R versions pak working . Packages incompatible CPU architectures dropped (defaulting CPU current macOS machine x86_64 non-macOS systems). macOS Darwin version selected based CRAN macOS binaries. E.g. R 3.5.0 macOS binaries built macOS El Capitan. \"windows\" Windows binaries default CRAN architecture. currently Windows Vista supported R versions, might change future. actual binary packages repository might support 32 bit 64 builds, one . practice 32-bit packages rare. CRAN builds including R 4.1 architectures, R 4.2 64 bit . \"windows\" alias i386+x86_64-w64-mingw32 currently. platform string like R.version$platform, Linux name version distribution also included. Examples: x86_64-apple-darwin17.0: macOS High Sierra. aarch64-apple-darwin20: macOS Big Sur arm64. x86_64-w64-mingw32: 64 bit Windows. i386-w64-mingw32: 32 bit Windows. i386+x86_64-w64-mingw32: 64 bit + 32 bit Windows. i386-pc-solaris2.10: 32 bit Solaris. (broken 64 Solaris builds might platform string, unfortunately.) x86_64-pc-linux-gnu-debian-10: Debian Linux 10 x86_64. x86_64-pc-linux-musl-alpine-3.14.1: Alpine Linux. x86_64-pc-linux-gnu-unknown: Unknown Linux Distribution x86_64. s390x-ibm-linux-gnu-ubuntu-20.04: Ubuntu Linux 20.04 S390x. amd64-portbld-freebsd12.1: FreeBSD 12.1 x86_64.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R platforms — system_r_platform","text":"","code":"if (FALSE) { system_r_platform() system_r_platform_data() }"},{"path":[]},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-051","dir":"Changelog","previous_headings":"","what":"pak 0.5.1","title":"pak 0.5.1","text":"CRAN release: 2023-04-27 user visible changes.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-050","dir":"Changelog","previous_headings":"","what":"pak 0.5.0","title":"pak 0.5.0","text":"CRAN release: 2023-04-20 meta_*() functions now consider platforms, cran_mirror r_versions config entries, see ?\"pak-config\". Better Posit Package Manager (PPM) support. New +ppm_has_binaries(), ppm_r_versions(), ppm_repo_url(), ppm_snapshots() ppm_platforms() functions help interacting PPM. See new ‘pkgcache Posit Package Manager Linux’ article https://r-lib.github.io/pkgcache. (r-lib/pkgcache#47 r-lib/pkgdepends#186). New system_r_platform() system_r_platform_data() functions query current platform. pak now support git repositories package references. E.g. git::https://github.com/r-lib/pak.git. pak now supports versioned CRAN packages, e.g. dplyr@1.1.1 always install dplyr 1.1.1. Note CRAN packages supported, Bioconductor packages (yet). pak now alternative system requirements lookup implementation. supports Fedora Debian systems well, addition Debian, Ubuntu, SUSE RedHat derivatives. can switch implementation setting R_PKG_SYSREQS2 environment variable true. pak now better job looking dependencies hand-selected dependency types. E.g. dependencies = \"LinkingTo\". pak now removes ?ignore-d packages dependencies, uses correct version comparison ?ignore-.r (https://github.com/r-lib/actions/issues/708). pak now fail circular soft dependencies (#306). pak now reports dependency solver failures better cases (#305, https://github.com/r-lib/pak/issues/474). pak now uses locally built CRAN binaries cache. Use ?nocache parameter opt , cache_delete(package = ...) remove package cache.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-040","dir":"Changelog","previous_headings":"","what":"pak 0.4.0","title":"pak 0.4.0","text":"CRAN release: 2023-01-15 pak much improved informative error messages now. work yet finished, find unclear error message, please open issue. Thank ! solver now robust non-canonical input (e.g. DESCRIPTION files) (https://github.com/r-lib/pak/issues/423). Better installation output. Standard output error now collected together (https://github.com/r-lib/pkgdepends/commit/0669f0f8c). solver now better job multiple versions package present repository (https://github.com/r-lib/actions/issues/559). pkg_name_check() now works , needed fix changes https://crandb.r-pkg.org. Explicit package names local URL package sources, package=local::... package=url::... now parsed correctly dependencies. pak now robust Archs fields missing CRAN metadata packages compiled code (https://github.com/r-lib/pak/issues/448). url:: packages now always work correctly, even digest package installed (https://github.com/r-lib/pak/issues/433). pak now robust installing packages subdirectories GitHub repositories (https://github.com/r-lib/pak/issues/431, @paleolimbot). Parameters ?reinstall, ?source ?ignore now work correctly specified package=?parameter format (#294). ?ignore parameter works correctly now. Dependency resolution now fail package found. pak can now install url:: remotes GitHub. pak now fail package .tar.gz GitHub snapshot subdirectory, subdirectory subdirectory. pak now errors early deduce name package Remotes Config/Needs/* entry. Solver failures now include details cases previously . pak can now update packages Docker containers old version installed different Docker later (https://github.com/r-lib/pak/issues/251) Update R version -> Bioconductor version mapping. R 4.2.x now maps Bioconductor 3.16.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-031","dir":"Changelog","previous_headings":"","what":"pak 0.3.1","title":"pak 0.3.1","text":"CRAN release: 2022-09-08 ?ignore parameter works correctly now. Dependency resolution now fail package found. pak can now install url:: remotes GitHub. pak now fail package .tar.gz GitHub snapshot subdirectory, subdirectory subdirectory. pak now errors early deduce name package Remotes Config/Needs/* entry. Solver failures now include details cases previously . pak can now update packages Docker containers old version installed different Docker later (#251) pak errors now user friendlier better formatted. pak now load tibble dependencies pak subprocess, dlls locked pak subprocess Windows. pak now fail installing package uses non-UTF-8 encoding R 4.3.x later (#404).","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-030","dir":"Changelog","previous_headings":"","what":"pak 0.3.0","title":"pak 0.3.0","text":"CRAN release: 2022-04-11 pak functions used return tibbles return data frames now. data frames tibbles similar, completely compatible. convert outputs pak functions tibbles call tibble::as_tibble() function . pillar package loaded, improves printing returned data frames. Relatedly, pak::pak_install_extra() installs pillar now, instead tibble. pak now supports file:// repositories. pak now uses HTTP 1.1 download packages Linux, addition macOS. fixes HTTP issues servers (#358). New ?ignore--r parameter ignore optional dependencies need newer R version (https://github.com/r-lib/pkgdepends/issues/243). New ?ignore parameter ignore optional dependency. Allow specifying downstream package parameters package=?param syntax. lockfile_install() now works better :: refs, pak always install version planned . System requirement installation now robust works Unix shell expressions (#347). CRAN-like resolution robust now repository missing usual metadata. lock file pretty JSON now. pak now handles version requirement types properly: ‘<’, ‘<=’, ==, >=, >. dependency solver now uses better heuristics (effectively) freeze multiple repositories multiple versions packages (e.g. RSPM CRAN) (https://github.com/r-lib/pkgdepends/pull/277)","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-021","dir":"Changelog","previous_headings":"","what":"pak 0.2.1","title":"pak 0.2.1","text":"CRAN release: 2021-12-20 user visible changes.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-020","dir":"Changelog","previous_headings":"","what":"pak 0.2.0","title":"pak 0.2.0","text":"CRAN release: 2021-12-01 Lots news, much list. completely new package now.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-012","dir":"Changelog","previous_headings":"","what":"pak 0.1.2","title":"pak 0.1.2","text":"CRAN release: 2019-02-19 First version CRAN.","code":""}] +[{"path":"https://pak.r-lib.org/dev/articles/internals.html","id":"the-embedded-library","dir":"Articles","previous_headings":"","what":"The embedded library","title":"pak internals","text":"pak bundles dependencies installed package, user’s cache directory. can happen several ways: running inside R CMD check, R CMD INSTALL installs dependencies installing package data, /library within installed package. Downloading installing (currently) 37 dependencies takes 1-1.5 minutes platforms binaries, 4 minutes platforms compile everything source (measured Linux). goal create self-contained binaries CRAN. main advantage data step can show progress /messages user. bundling fails, pak errors. avoid creating non-functional binary package. Hopefully CRAN just try creating binary , later. also works well platforms (yet) binaries, e.g. M1 macs, Linux new experimental Windows platform. running inside R CMD check, pak bundle dependencies, make checks faster. Unlike traditional R CMD check setup, CRAN install package check. Instead, pre-install , refer install log check. set env vars pre-install, pak still bundle dependencies case. pak installed GitHub, using remotes::install_github() similar, dependency bundling happens. nice platforms build self-contained binary. see also next item. DESCRIPTION Remotes field, pak bundle dependencies, emits message suggests using create_dev_lib(). can’t easily install GitHub using base R functions . running R CMD check, pak uses testthat.R bundle dependencies temporary installation used check. However, pak copies dependencies case, make check faster. copying dependencies fails, pak skips test suite. reason copying testthat.R instead install time way avoid check warning large /library directory. pak installation currently tested bundled dependencies, setup.R bundles , user’s cache directory. make sure can still use devtools::test() alike development. developing pak interactively, e.g. using load_all(), use create_dev_lib() copy dependencies user’s cache directory. summary, various bundling modes: install.packages() binary pkg CRAN → pak ready use install.packages() source pkg CRAN → install /library R CMD INSTALL CRAN (build binaries) → install /library R CMD INSTALL (CRAN) R CMD check → bundle R CMD check → copy /library, ignore errors remotes::install_github() without Remotes → install /library remotes::install_github() Remotes → bundle devtools::test() similar → copy user’s cache directory","code":""},{"path":"https://pak.r-lib.org/dev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Gábor Csárdi. Author, maintainer. Jim Hester. Author. . Copyright holder, funder.","code":""},{"path":"https://pak.r-lib.org/dev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Csárdi G, Hester J (2023). pak: Another Approach Package Installation. R package version 0.5.1.9000, https://pak.r-lib.org/.","code":"@Manual{, title = {pak: Another Approach to Package Installation}, author = {Gábor Csárdi and Jim Hester}, year = {2023}, note = {R package version 0.5.1.9000}, url = {https://pak.r-lib.org/}, }"},{"path":"https://pak.r-lib.org/dev/index.html","id":"pak","dir":"","previous_headings":"","what":"Another Approach to Package Installation","title":"Another Approach to Package Installation","text":"Fresh Approach R Package Installation pak installs R packages CRAN, Bioconductor, GitHub, URLs, git repositories, local files directories. alternative install.packages() devtools::install_github(). pak fast, safe convenient. 🚀 Short tour 🔗 Quick links (start doubt!) ✨ Features ⬇️ Installation 📘 License","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/index.html","id":"install-or-update-packages-from-cran-or-bioconductor","dir":"","previous_headings":"🚀 Short tour","what":"Install or update packages from CRAN or Bioconductor","title":"Another Approach to Package Installation","text":"","code":"pak::pkg_install(\"tibble\") #> ✔ Updated metadata database: 2.53 MB in 3 files. #> ✔ Updating metadata database ... done #> #> → Will install 11 packages. #> → Will download 11 CRAN packages (4.52 MB). #> + cli 3.6.1 [bld][cmp][dl] (567.29 kB) #> + fansi 1.0.4 [bld][cmp][dl] (482.06 kB) #> + glue 1.6.2 [bld][cmp][dl] (106.51 kB) #> + lifecycle 1.0.3 [bld][dl] (106.85 kB) #> + magrittr 2.0.3 [bld][cmp][dl] (267.07 kB) #> + pillar 1.9.0 [bld][dl] (444.53 kB) #> + pkgconfig 2.0.3 [bld][dl] (6.08 kB) #> + rlang 1.1.1 [bld][cmp][dl] (762.53 kB) #> + tibble 3.2.1 [bld][cmp][dl] (565.98 kB) #> + utf8 1.2.3 [bld][cmp][dl] (241.41 kB) #> + vctrs 0.6.3 [bld][cmp][dl] (967.34 kB) #> #> ℹ Getting 11 pkgs (4.52 MB) #> ✔ Got pkgconfig 2.0.3 (source) (6.08 kB) #> ✔ Got glue 1.6.2 (source) (106.51 kB) #> ✔ Got lifecycle 1.0.3 (source) (106.85 kB) #> ✔ Got fansi 1.0.4 (source) (482.06 kB) #> ✔ Got cli 3.6.1 (source) (567.29 kB) #> ✔ Got magrittr 2.0.3 (source) (267.07 kB) #> ✔ Got tibble 3.2.1 (source) (565.98 kB) #> ✔ Got pillar 1.9.0 (source) (444.53 kB) #> ✔ Got utf8 1.2.3 (source) (241.41 kB) #> ✔ Got vctrs 0.6.3 (source) (967.34 kB) #> ✔ Got rlang 1.1.1 (source) (762.53 kB) #> ℹ Building cli 3.6.1 #> ℹ Building fansi 1.0.4 #> ✔ Built fansi 1.0.4 (4.5s) #> ℹ Building glue 1.6.2 #> ✔ Built glue 1.6.2 (1.7s) #> ℹ Building magrittr 2.0.3 #> ✔ Built magrittr 2.0.3 (1.4s) #> ℹ Building pkgconfig 2.0.3 #> ✔ Built pkgconfig 2.0.3 (910ms) #> ℹ Building rlang 1.1.1 #> ✔ Built cli 3.6.1 (10s) #> ℹ Building utf8 1.2.3 #> ✔ Built rlang 1.1.1 (12.5s) #> ✔ Installed cli 3.6.1 (39ms) #> ✔ Installed fansi 1.0.4 (1s) #> ✔ Installed glue 1.6.2 (26ms) #> ✔ Installed magrittr 2.0.3 (28ms) #> ✔ Installed pkgconfig 2.0.3 (27ms) #> ✔ Installed rlang 1.1.1 (54ms) #> ℹ Building lifecycle 1.0.3 #> ✔ Built utf8 1.2.3 (13.4s) #> ✔ Installed utf8 1.2.3 (28ms) #> ✔ Built lifecycle 1.0.3 (1.4s) #> ✔ Installed lifecycle 1.0.3 (23ms) #> ℹ Building vctrs 0.6.3 #> ✔ Built vctrs 0.6.3 (19.7s) #> ✔ Installed vctrs 0.6.3 (60ms) #> ℹ Building pillar 1.9.0 #> ✔ Built pillar 1.9.0 (3.5s) #> ✔ Installed pillar 1.9.0 (34ms) #> ℹ Building tibble 3.2.1 #> ✔ Built tibble 3.2.1 (3.3s) #> ✔ Installed tibble 3.2.1 (36ms) #> ✔ 1 pkg + 10 deps: added 11, dld 11 (4.52 MB) [59.7s]"},{"path":"https://pak.r-lib.org/dev/index.html","id":"install-packages-from-github","dir":"","previous_headings":"🚀 Short tour","what":"Install packages from GitHub","title":"Another Approach to Package Installation","text":"","code":"pak::pkg_install(\"tidyverse/tibble\") #> #> → Will update 1 package. #> → The package (0 B) is cached. #> + tibble 3.2.1 → 3.2.1.9005 [bld][cmp] (GitHub: 4de5c15) #> #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got tibble 3.2.1.9005 (source) (1.32 MB) #> ℹ Packaging tibble 3.2.1.9005 #> ✔ Packaged tibble 3.2.1.9005 (471ms) #> ℹ Building tibble 3.2.1.9005 #> ✔ Built tibble 3.2.1.9005 (3.1s) #> ✔ Installed tibble 3.2.1.9005 (github::tidyverse/tibble@4de5c15) (27ms) #> ✔ 1 pkg + 10 deps: kept 10, upd 1, dld 1 (NA B) [6.3s]"},{"path":"https://pak.r-lib.org/dev/index.html","id":"look-up-dependencies","dir":"","previous_headings":"🚀 Short tour","what":"Look up dependencies","title":"Another Approach to Package Installation","text":"","code":"pak::pkg_deps_tree(\"tibble\") #> tibble 3.2.1 [new][bld][cmp] #> ├─fansi 1.0.4 [new][bld][cmp] #> ├─lifecycle 1.0.3 [new][bld] #> │ ├─cli 3.6.1 [new][bld][cmp] #> │ ├─glue 1.6.2 [new][bld][cmp] #> │ └─rlang 1.1.1 [new][bld][cmp] #> ├─magrittr 2.0.3 [new][bld][cmp] #> ├─pillar 1.9.0 [new][bld] #> │ ├─cli #> │ ├─fansi #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─utf8 1.2.3 [new][bld][cmp] #> │ └─vctrs 0.6.3 [new][bld][cmp] #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ └─rlang #> ├─pkgconfig 2.0.3 [new][bld] #> ├─rlang #> └─vctrs #> #> Key: [new] new | [bld] build | [cmp] compile"},{"path":"https://pak.r-lib.org/dev/index.html","id":"explain-dependencies","dir":"","previous_headings":"🚀 Short tour","what":"Explain dependencies","title":"Another Approach to Package Installation","text":"","code":"pak::pkg_deps_explain(\"tibble\", \"rlang\") #> tibble -> lifecycle -> rlang #> tibble -> pillar -> lifecycle -> rlang #> tibble -> pillar -> rlang #> tibble -> pillar -> vctrs -> lifecycle -> rlang #> tibble -> pillar -> vctrs -> rlang #> tibble -> rlang #> tibble -> vctrs -> lifecycle -> rlang #> tibble -> vctrs -> rlang"},{"path":"https://pak.r-lib.org/dev/index.html","id":"install-a-local-package-and-its-dependencies","dir":"","previous_headings":"🚀 Short tour","what":"Install a local package and its dependencies","title":"Another Approach to Package Installation","text":"","code":"pak::local_install(\"cli\") #> #> → Will update 1 package. #> → The package (0 B) is cached. #> + cli 3.6.1 → 3.6.1 [bld][cmp] #> #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got cli 3.6.1 (source) (567.29 kB) #> ℹ Packaging cli 3.6.1 #> ✔ Packaged cli 3.6.1 (792ms) #> ℹ Building cli 3.6.1 #> ✔ Built cli 3.6.1 (9s) #> ✔ Installed cli 3.6.1 (local) (50ms) #> ✔ 1 pkg: upd 1, dld 1 (567.29 kB) [10.7s]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/index.html","id":"how-do-i--","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"How do I … ?","title":"Another Approach to Package Installation","text":"Start Get Started pak solve specific issues.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"faq","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"FAQ","title":"Another Approach to Package Installation","text":"Check list frequently asked questions.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"reference","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"Reference","title":"Another Approach to Package Installation","text":"complete reference pak functions complete source information pak.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"i-have-another-question","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"I have a(nother) question","title":"Another Approach to Package Installation","text":"Don’t hesitate ask RStudio Community forum. Use pak tag.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"i-would-like-to-report-a-bug","dir":"","previous_headings":"🔗 Quick links (start here if in doubt!)","what":"I would like to report a bug","title":"Another Approach to Package Installation","text":"Head pak issue tracker.","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"sparkles-features","dir":"","previous_headings":"","what":"✨ Features","title":"Another Approach to Package Installation","text":"⚡ Fast - parallel downloads installation, caching, etc. 🦺 Safe - dependency solver, system dependency solver, etc. 🏪 Convenient - packages multiple sources, time travel, etc. See complete list awesome features.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/index.html","id":"pre-built-binaries","dir":"","previous_headings":"⬇️ Installation","what":"Pre-built binaries","title":"Another Approach to Package Installation","text":"Install binary build pak repository GitHub: supported following systems: macOS support official CRAN R build. builds, e.g. Homebrew R, supported.","code":"install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch))"},{"path":"https://pak.r-lib.org/dev/index.html","id":"install-from-cran","dir":"","previous_headings":"⬇️ Installation","what":"Install from CRAN","title":"Another Approach to Package Installation","text":"Install released version package CRAN usual: potentially needs C compiler platforms CRAN binaries packages .","code":"install.packages(\"pak\")"},{"path":"https://pak.r-lib.org/dev/index.html","id":"other-platforms-and-nightly-builds","dir":"","previous_headings":"⬇️ Installation","what":"Other platforms and nightly builds","title":"Another Approach to Package Installation","text":"See installation page!","code":""},{"path":"https://pak.r-lib.org/dev/index.html","id":"blue_book-license","dir":"","previous_headings":"","what":"📘 License","title":"Another Approach to Package Installation","text":"GPL-3 © RStudio","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Package cache utilities — cache_summary","title":"Package cache utilities — cache_summary","text":"Various utilities inspect clean package cache. See pkgcache package need control package cache.","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Package cache utilities — cache_summary","text":"","code":"cache_summary() cache_list(...) cache_delete(...) cache_clean()"},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Package cache utilities — cache_summary","text":"... cache_list() cache_delete(), ... may contain filters, argument name column name. E.g. package, version, etc. Call cache_list() without arguments see available column names. call cache_delete() without arguments, delete cached files.","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Package cache utilities — cache_summary","text":"cache_summary() returns list elements: cachepath: absolute path package cache files: number files (packages) cache size: total size package cache bytes cache_list() returns data frame data cache. cache_delete() returns nothing. cache_clean() returns nothing.","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Package cache utilities — cache_summary","text":"cache_summary() returns summary package cache. cache_list() lists (default), subset packages package cache. cache_delete() deletes files cache. cache_clean() deletes files cache.","code":""},{"path":"https://pak.r-lib.org/dev/reference/cache.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Package cache utilities — cache_summary","text":"","code":"cache_summary() #> $cachepath #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/pkg\" #> #> $files #> [1] 483 #> #> $size #> [1] 654662486 #> cache_list() #> # A data frame: 483 × 11 #> fullpath path package url etag sha256 version platf…¹ built #> #> 1 /Users/gaborc… arch… NA http… \"\\\"1… 0c8f0… NA NA NA #> 2 /Users/gaborc… bin/… evalua… http… \"\\\"1… 08a39… 0.17 aarch6… NA #> 3 /Users/gaborc… bin/… crayon http… \"\\\"2… 1e6d5… 1.5.2 aarch6… NA #> 4 /Users/gaborc… bin/… common… http… \"\\\"4… 47b4a… 1.8.1 aarch6… NA #> 5 /Users/gaborc… bin/… curl http… \"\\\"b… 7b8ba… 4.3.3 aarch6… NA #> 6 /Users/gaborc… bin/… tinytex http… \"\\\"2… 7e9ba… 0.42 aarch6… NA #> 7 /Users/gaborc… bin/… jsonli… http… \"\\\"1… 68e59… 1.8.2 aarch6… NA #> 8 /Users/gaborc… bin/… lifecy… http… \"\\\"1… 7ce27… 1.0.3 aarch6… NA #> 9 /Users/gaborc… bin/… vctrs http… \"\\\"1… c3a69… 0.4.2 aarch6… NA #> 10 /Users/gaborc… src/… pkgcac… NA NA 9b70a… NA NA 0 #> # … with 473 more rows, 2 more variables: vignettes , #> # rversion , and abbreviated variable name ¹​platform cache_list(package = \"recipes\") #> # A data frame: 1 × 11 #> fullp…¹ path package url etag sha256 version platf…² built vigne…³ #> #> 1 /Users… bin/… recipes http… \"\\\"1… e281e… 1.0.2 aarch6… NA NA #> # … with 1 more variable: rversion , and abbreviated variable #> # names ¹​fullpath, ²​platform, ³​vignettes cache_list(platform = \"source\") #> # A data frame: 69 × 11 #> fullpath path package url etag sha256 version platf…¹ built #> #> 1 /Users/gaborc… src/… crayon http… \"\\\"9… 70a9a… 1.5.2 source NA #> 2 /Users/gaborc… src/… zip http… \"\\\"1… 14873… 2.2.1 source NA #> 3 /Users/gaborc… src/… curl http… \"\\\"a… 3567b… 4.3.3 source NA #> 4 /Users/gaborc… src/… rlang http… \"\\\"b… e6973… 1.0.6 source NA #> 5 /Users/gaborc… src/… openssl http… \"\\\"1… 7cde9… 2.0.3 source NA #> 6 /Users/gaborc… src/… tinytex http… \"\\\"8… 205f7… 0.42 source NA #> 7 /Users/gaborc… src/… evalua… http… \"\\\"6… 49c74… 0.17 source NA #> 8 /Users/gaborc… src/… Rcpp http… \"\\\"2… 807ce… 1.0.9 source NA #> 9 /Users/gaborc… src/… knitr http… \"\\\"d… 9b8f9… 1.40 source NA #> 10 /Users/gaborc… src/… lpSolve http… \"\\\"7… f7258… 5.6.17 source NA #> # … with 59 more rows, 2 more variables: vignettes , #> # rversion , and abbreviated variable name ¹​platform cache_delete(package = \"knitr\") cache_delete(platform = \"macos\") cache_clean()"},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":null,"dir":"Reference","previous_headings":"","what":"Frequently Asked Questions — FAQ","title":"Frequently Asked Questions — FAQ","text":"Please take look list asking questions.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-reinstall-a-package-","dir":"Reference","previous_headings":"","what":"How do I reinstall a package?","title":"Frequently Asked Questions — FAQ","text":"pak reinstall package, version already installed. Sometimes still want reinstall, e.g. fix broken installation. case can delete package install , use ?reinstall parameter:","code":"pak::pkg_install(\"tibble\") #> #> → Will install 13 packages. #> → All 13 packages (7.68 MB) are cached. #> + cli 3.3.0 #> + crayon 1.5.1 #> + ellipsis 0.3.2 #> + fansi 1.0.3 #> + glue 1.6.2 #> + lifecycle 1.0.1 #> + magrittr 2.0.3 #> + pillar 1.7.0 #> + pkgconfig 2.0.3 #> + rlang 1.0.2 #> + tibble 3.1.7 #> + utf8 1.2.2 #> + vctrs 0.4.1 #> ℹ No downloads are needed, 13 pkgs (7.68 MB) are cached #> ✔ Got utf8 1.2.2 (aarch64-apple-darwin20) (209.24 kB) #> ✔ Installed cli 3.3.0 (76ms) #> ✔ Installed crayon 1.5.1 (87ms) #> ✔ Installed ellipsis 0.3.2 (97ms) #> ✔ Installed fansi 1.0.3 (103ms) #> ✔ Installed glue 1.6.2 (111ms) #> ✔ Installed lifecycle 1.0.1 (153ms) #> ✔ Installed magrittr 2.0.3 (158ms) #> ✔ Installed pillar 1.7.0 (162ms) #> ✔ Installed pkgconfig 2.0.3 (87ms) #> ✔ Installed rlang 1.0.2 (39ms) #> ✔ Installed tibble 3.1.7 (41ms) #> ✔ Installed utf8 1.2.2 (39ms) #> ✔ Installed vctrs 0.4.1 (32ms) #> ✔ 1 pkg + 12 deps: added 13, dld 1 (209.24 kB) [1.8s] pak::pkg_install(\"tibble?reinstall\") #> #> → Will install 1 package. #> → The package (724.32 kB) is cached. #> + tibble 3.1.7 #> ℹ No downloads are needed, 1 pkg (724.32 kB) is cached #> ✔ Installed tibble 3.1.7 (42ms) #> ✔ 1 pkg + 12 deps: kept 11, added 1 [343ms]"},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-install-a-dependency-from-a-binary-package","dir":"Reference","previous_headings":"","what":"How do I install a dependency from a binary package","title":"Frequently Asked Questions — FAQ","text":"Sometimes suffifient install binary package older version dependency, instead newer source package potentially needs compilers, system tools libraries. pkg_install() lockfile_create() default upgrade = FALSE, always chooses binaries source packages, use pkg_install() need anything extra. local_install_* functions default upgrade = TRUE, pak() pkf = NULL, need explicitly use upgrade = FALSE.","code":""},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-install-a-package-from-source-","dir":"Reference","previous_headings":"","what":"How do I install a package from source?","title":"Frequently Asked Questions — FAQ","text":"force installation source package (instead binary package), use ?source parameter:","code":"pak::pkg_install(\"tibble?source\") #> #> → Will install 1 package. #> → The package (672.34 kB) is cached. #> + tibble 3.1.7 👷🏼‍♀️🔧 #> ℹ No downloads are needed, 1 pkg (672.34 kB) is cached #> ℹ Building tibble 3.1.7 #> ✔ Built tibble 3.1.7 (3.1s) #> ✔ Installed tibble 3.1.7 (35ms) #> ✔ 1 pkg + 12 deps: kept 11, added 1 [4.1s]"},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-install-the-latest-version-of-a-dependency-","dir":"Reference","previous_headings":"","what":"How do I install the latest version of a dependency?","title":"Frequently Asked Questions — FAQ","text":"want always install dependency source, want latest version reason, can use source parameter = form: =?source. example install tibble, cli dependency installed source write:","code":"pak::pkg_install(c(\"tibble\", \"cli=?source\")) #> #> → Will install 1 package. #> → The package (540.04 kB) is cached. #> + cli 3.3.0 👷🏽🔧 #> ℹ No downloads are needed, 1 pkg (540.04 kB) is cached #> ℹ Building cli 3.3.0 #> ✔ Built cli 3.3.0 (4.5s) #> ✔ Installed cli 3.3.0 (68ms) #> ✔ 1 pkg + 12 deps: kept 11, added 1 [4.9s]"},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-do-i-ignore-an-optional-dependency-","dir":"Reference","previous_headings":"","what":"How do I ignore an optional dependency?","title":"Frequently Asked Questions — FAQ","text":"syntax Note can ignore optional dependencies, .e. packages Suggests Enhances.","code":"pak::pkg_install( c(\"tibble\", \"DiagrammeR=?ignore\", \"formattable=?ignore\"), dependencies = TRUE ) #> #> ℹ No downloads are needed #> ✔ 1 pkg + 12 deps: kept 12 [583ms] =?ignore"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/faq.html","id":"how-can-i-use-pak-with-renv-","dir":"Reference","previous_headings":"","what":"How can I use pak with renv?","title":"Frequently Asked Questions — FAQ","text":"currently, keep eye issue: https://github.com/r-lib/pak/issues/343","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":null,"dir":"Reference","previous_headings":"","what":"A list of the most important pak features — Great pak features","title":"A list of the most important pak features — Great pak features","text":"list important pak features.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"parallel-http","dir":"Reference","previous_headings":"","what":"Parallel HTTP","title":"A list of the most important pak features — Great pak features","text":"pak performs HTTP queries concurrently. true downloads package metadata package repositories, resolves packages CRAN, GitHub, URLs, etc, downloads actual package files, etc.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"parallel-installation","dir":"Reference","previous_headings":"","what":"Parallel installation","title":"A list of the most important pak features — Great pak features","text":"pak installs packages concurrently, much dependency graph allows .","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"caching","dir":"Reference","previous_headings":"","what":"Caching","title":"A list of the most important pak features — Great pak features","text":"pak caches metadata package files, need re-download files .","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"plan-installation-up-front","dir":"Reference","previous_headings":"","what":"Plan installation up front","title":"A list of the most important pak features — Great pak features","text":"pak creates installation plan downloading packages. plan unsuccessful, fails without downloading packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"auto-install-missing-dependencies","dir":"Reference","previous_headings":"","what":"Auto-install missing dependencies","title":"A list of the most important pak features — Great pak features","text":"requesting installation package, pak makes sure dependencies also installed.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"keeping-binary-packages-up-to-date","dir":"Reference","previous_headings":"","what":"Keeping binary packages up-to-date","title":"A list of the most important pak features — Great pak features","text":"pak automatically discards binary packages cache, new build version available CRAN.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"correct-cran-metadata-errors","dir":"Reference","previous_headings":"","what":"Correct CRAN metadata errors","title":"A list of the most important pak features — Great pak features","text":"pak can correct CRAN's metadata issues, e.g.: New version package released since obtained metadata. macOS binary package available https://mac.r-project.org/ synchronization issue.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"graceful-handling-of-locked-package-dlls-on-windows","dir":"Reference","previous_headings":"","what":"Graceful handling of locked package DLLs on Windows","title":"A list of the most important pak features — Great pak features","text":"pak handles situation locked package DLLs, well possible. detects process locked , offers choice terminating processes. also unloads packages current R session needed.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"pak-keeps-its-own-dependencies-isolated","dir":"Reference","previous_headings":"","what":"pak keeps its own dependencies isolated","title":"A list of the most important pak features — Great pak features","text":"pak keeps dependencies private package library never loads packages. (background processes).","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"pak-comes-as-a-self-contained-binary-package","dir":"Reference","previous_headings":"","what":"pak comes as a self-contained binary package","title":"A list of the most important pak features — Great pak features","text":"common platforms. dependencies, system dependencies, compiler needed. (See also installation manual.)","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"install-packages-from-multiple-sources","dir":"Reference","previous_headings":"","what":"Install packages from multiple sources","title":"A list of the most important pak features — Great pak features","text":"CRAN, Bioconductor GitHub URLs Local files directories.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"ignore-certain-optional-dependencies","dir":"Reference","previous_headings":"","what":"Ignore certain optional dependencies","title":"A list of the most important pak features — Great pak features","text":"pak can ignore certain optional dependencies requested.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"cran-package-file-sizes","dir":"Reference","previous_headings":"","what":"CRAN package file sizes","title":"A list of the most important pak features — Great pak features","text":"pak knows sizes CRAN package files, can estimate much data need download, installation.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"bioconductor-version-detection","dir":"Reference","previous_headings":"","what":"Bioconductor version detection","title":"A list of the most important pak features — Great pak features","text":"pak automatically selects Bioconductor version appropriate R version. need set repositories.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"time-travel-with-mran-or-rspm","dir":"Reference","previous_headings":"","what":"Time travel with MRAN or RSPM","title":"A list of the most important pak features — Great pak features","text":"pak can use MRAN (Microsoft R Application Network, https://mran.microsoft.com/) RSPM (RStudio Public Package Manager, https://packagemanager.rstudio.com/client/#/) install snapshots CRAN.","code":""},{"path":"https://pak.r-lib.org/dev/reference/features.html","id":"pak-can-install-dependencies-of-local-packages","dir":"Reference","previous_headings":"","what":"pak can install dependencies of local packages","title":"A list of the most important pak features — Great pak features","text":"handy package development!","code":""},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":null,"dir":"Reference","previous_headings":"","what":"Simplified manual. Start here! — Get started with pak","title":"Simplified manual. Start here! — Get started with pak","text":"need read long manual pages simple task. manual page collects common pak use cases.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-a-package-from-cran-or-bioconductor","dir":"Reference","previous_headings":"","what":"Install a package from CRAN or Bioconductor","title":"Simplified manual. Start here! — Get started with pak","text":"pak automatically sets CRAN repository Bioconductor repositories correspons current R version.","code":"pak::pkg_install(\"tibble\")"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-a-package-from-github","dir":"Reference","previous_headings":"","what":"Install a package from GitHub","title":"Simplified manual. Start here! — Get started with pak","text":"Use user/repo form. can specify branch tag: user/repo@branch user/repo@tag.","code":"pak::pkg_install(\"tidyverse/tibble\") #> #> → Will update 2 packages. #> → All 2 packages (0 B) are cached. #> + tibble 3.1.8 → 3.1.8.9002 👷🏻🔧 (GitHub: 37ec86a) #> + vctrs 0.5.1 → 0.5.1.9000 👷🏾‍♀️🔧 (GitHub: 2d7de76) #> ℹ No downloads are needed, 2 pkgs are cached #> ℹ Packaging vctrs 0.5.1.9000 #> ✔ Packaged vctrs 0.5.1.9000 (1.4s) #> ℹ Building vctrs 0.5.1.9000 #> ✔ Built vctrs 0.5.1.9000 (11.2s) #> ✔ Installed vctrs 0.5.1.9000 (github::r-lib/vctrs@2d7de76) (34ms) #> ℹ Packaging tibble 3.1.8.9002 #> ✔ Packaged tibble 3.1.8.9002 (502ms) #> ℹ Building tibble 3.1.8.9002 #> ✔ Built tibble 3.1.8.9002 (2.7s) #> ✔ Installed tibble 3.1.8.9002 (github::tidyverse/tibble@37ec86a) (28ms) #> ✔ 1 pkg + 10 deps: kept 9, upd 2 [17.5s]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-a-package-from-a-url","dir":"Reference","previous_headings":"","what":"Install a package from a URL","title":"Simplified manual. Start here! — Get started with pak","text":"URL may point R package file, made R CMD build, .tar.gz .zip archive package tree.","code":"pak::pkg_install( \"url::https://cran.r-project.org/src/contrib/Archive/tibble/tibble_3.1.7.tar.gz\" ) #> #> → Will install 1 package. #> → Will update 1 package. #> → All 2 packages (38.65 kB) are cached. #> + ellipsis 0.3.2 #> + tibble 3.1.8.9002 → 3.1.7 👷🏻‍♀️🔧 #> ℹ No downloads are needed, 2 pkgs (38.65 kB) are cached #> ✔ Installed ellipsis 0.3.2 (18ms) #> ℹ Building tibble 3.1.7 #> ✔ Built tibble 3.1.7 (2.5s) #> ✔ Installed tibble 3.1.7 (31ms) #> ✔ 1 pkg + 11 deps: kept 10, upd 1, added 1 [3.3s]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"update-a-package","dir":"Reference","previous_headings":"","what":"Update a package","title":"Simplified manual. Start here! — Get started with pak","text":"pak::pkg_install() automatically updates package.","code":"pak::pkg_install(\"tibble\") #> #> → Will update 1 package. #> → The package (724.32 kB) is cached. #> + tibble 3.1.7 → 3.1.8 #> ℹ No downloads are needed, 1 pkg (724.32 kB) is cached #> ✔ Installed tibble 3.1.8 (36ms) #> ✔ 1 pkg + 10 deps: kept 10, upd 1 [368ms]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"update-all-dependencies-of-a-package","dir":"Reference","previous_headings":"","what":"Update all dependencies of a package","title":"Simplified manual. Start here! — Get started with pak","text":"upgrade = TRUE updates package dependencies, necessary.","code":"pak::pkg_install(\"tibble\", upgrade = TRUE) #> #> ℹ No downloads are needed #> ✔ 1 pkg + 10 deps: kept 11 [278ms]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"reinstall-a-package","dir":"Reference","previous_headings":"","what":"Reinstall a package","title":"Simplified manual. Start here! — Get started with pak","text":"Add ?reinstall package name package reference general:","code":"pak::pkg_install(\"tibble?reinstall\") #> #> → Will install 1 package. #> → The package (724.32 kB) is cached. #> + tibble 3.1.8 #> ℹ No downloads are needed, 1 pkg (724.32 kB) is cached #> ✔ Installed tibble 3.1.8 (60ms) #> ✔ 1 pkg + 10 deps: kept 10, added 1 [340ms]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"dependencies-of-a-cran-or-bioconductor-package","dir":"Reference","previous_headings":"","what":"Dependencies of a CRAN or Bioconductor package","title":"Simplified manual. Start here! — Get started with pak","text":"results returned data frame.","code":"pak::pkg_deps(\"tibble\") #> # A data frame: 11 × 32 #> ref type direct direc…¹ status package version license needs…² #> #> 1 cli stan… FALSE FALSE OK cli 3.4.1 MIT + … FALSE #> 2 fansi stan… FALSE FALSE OK fansi 1.0.3 GPL-2 … FALSE #> 3 glue stan… FALSE FALSE OK glue 1.6.2 MIT + … FALSE #> 4 lifecycle stan… FALSE FALSE OK lifecy… 1.0.3 MIT + … FALSE #> 5 magrittr stan… FALSE FALSE OK magrit… 2.0.3 MIT + … FALSE #> 6 pillar stan… FALSE FALSE OK pillar 1.8.1 MIT + … FALSE #> 7 pkgconfig stan… FALSE FALSE OK pkgcon… 2.0.3 MIT + … FALSE #> 8 rlang stan… FALSE FALSE OK rlang 1.0.6 MIT + … FALSE #> 9 tibble stan… TRUE TRUE OK tibble 3.1.8 MIT + … FALSE #> 10 utf8 stan… FALSE FALSE OK utf8 1.2.2 Apache… FALSE #> 11 vctrs stan… FALSE FALSE OK vctrs 0.5.1 MIT + … FALSE #> # … with 23 more variables: priority , md5sum , sha256 , #> # filesize , built , platform , rversion , #> # repotype , repodir , target , deps , #> # mirror , sources , remote , error , #> # metadata , dep_types , params , sysreqs , #> # cache_status , lib_status , old_version , #> # new_version , and abbreviated variable names ¹​directpkg, …"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"dependency-tree-of-a-cran-bioconductor-package","dir":"Reference","previous_headings":"","what":"Dependency tree of a CRAN / Bioconductor package","title":"Simplified manual. Start here! — Get started with pak","text":"results also silently returned data frame.","code":"pak::pkg_deps_tree(\"tibble\") #> tibble 3.1.8 ✨ #> ├─fansi 1.0.3 ✨ #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli 3.4.1 ✨ #> │ ├─glue 1.6.2 ✨ #> │ └─rlang 1.0.6 ✨ #> ├─magrittr 2.0.3 ✨ #> ├─pillar 1.8.1 ✨ #> │ ├─cli #> │ ├─fansi #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─utf8 1.2.2 ✨ #> │ └─vctrs 0.5.1 ✨ #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ └─rlang #> ├─pkgconfig 2.0.3 ✨ #> ├─rlang #> └─vctrs #> #> Key: ✨ new"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"dependency-tree-of-a-package-on-github","dir":"Reference","previous_headings":"","what":"Dependency tree of a package on GitHub","title":"Simplified manual. Start here! — Get started with pak","text":"Use user/repo form. usual, can also select branch, tag, sha, user/repo@branch, user/repo@tag user/repo@sha forms.","code":"pak::pkg_deps_tree(\"tidyverse/tibble\") #> tidyverse/tibble 3.1.8.9002 ✨👷🏼🔧 #> ├─fansi 1.0.3 ✨ #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli 3.4.1 ✨ #> │ ├─glue 1.6.2 ✨ #> │ └─rlang 1.0.6 ✨ #> ├─magrittr 2.0.3 ✨ #> ├─pillar 1.8.1 ✨ #> │ ├─cli #> │ ├─fansi #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─utf8 1.2.2 ✨ #> │ └─r-lib/vctrs 0.5.1.9000 ✨👷🏼🔧 #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ └─rlang #> ├─pkgconfig 2.0.3 ✨ #> ├─rlang #> └─r-lib/vctrs #> #> Key: ✨ new | 👷🏼 build | 🔧 compile"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"dependency-tree-of-the-package-in-the-current-directory","dir":"Reference","previous_headings":"","what":"Dependency tree of the package in the current directory","title":"Simplified manual. Start here! — Get started with pak","text":"Assuming package directory tibble.","code":"pak::local_deps_tree(\"tibble\") #> local::tibble 3.1.8 ✨👷🏻‍♀️🔧 #> ├─fansi 1.0.3 ✨ #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli 3.4.1 ✨ #> │ ├─glue 1.6.2 ✨ #> │ └─rlang 1.0.6 ✨ #> ├─magrittr 2.0.3 ✨ #> ├─pillar 1.8.1 ✨ #> │ ├─cli #> │ ├─fansi #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─utf8 1.2.2 ✨ #> │ └─vctrs 0.5.1 ✨ #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ └─rlang #> ├─pkgconfig 2.0.3 ✨ #> ├─rlang #> └─vctrs #> #> Key: ✨ new | 👷🏻‍♀️ build | 🔧 compile"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"explain-a-recursive-dependency","dir":"Reference","previous_headings":"","what":"Explain a recursive dependency","title":"Simplified manual. Start here! — Get started with pak","text":"tibble depend rlang? Use can also use user/repo form packages GitHub, url::... packages URLs, etc.","code":"pak::pkg_deps_explain(\"tibble\", \"rlang\") #> tibble -> lifecycle -> rlang #> tibble -> pillar -> lifecycle -> rlang #> tibble -> pillar -> rlang #> tibble -> pillar -> vctrs -> lifecycle -> rlang #> tibble -> pillar -> vctrs -> rlang #> tibble -> rlang #> tibble -> vctrs -> lifecycle -> rlang #> tibble -> vctrs -> rlang"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-dependencies-of-local-package","dir":"Reference","previous_headings":"","what":"Install dependencies of local package","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::local_install_deps() #> ✔ Loading metadata database ... done #> #> → The package (0 B) is cached. #> ℹ No downloads are needed #> ✔ 10 deps: kept 10 [3.2s]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-local-package","dir":"Reference","previous_headings":"","what":"Install local package","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::local_install() #> #> → Will update 1 package. #> → The package (0 B) is cached. #> + tibble 3.1.8 → 3.1.8 👷🏻‍♂️🔧 #> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got tibble 3.1.8 (source) (96 B) #> ℹ Packaging tibble 3.1.8 #> ✔ Packaged tibble 3.1.8 (864ms) #> ℹ Building tibble 3.1.8 #> ✔ Built tibble 3.1.8 (2.4s) #> ✔ Installed tibble 3.1.8 (local) (38ms) #> ✔ 1 pkg + 10 deps: kept 10, upd 1, dld 1 (NA B) [4.2s]"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"install-all-dependencies-of-local-package","dir":"Reference","previous_headings":"","what":"Install all dependencies of local package","title":"Simplified manual. Start here! — Get started with pak","text":"Installs development optional dependencies well.","code":"pak::local_install_dev_deps() #> #> → Will install 86 packages. #> → Will update 2 packages. #> → All 89 packages (100.53 MB) are cached. #> + askpass 1.1 #> + base64enc 0.1-3 #> + bench 1.1.2 #> + bit 4.0.5 #> + bit64 4.0.5 #> + blob 1.2.3 #> + brio 1.1.3 #> + bslib 0.4.1 #> + cachem 1.0.6 #> + callr 3.7.3 #> + clipr 0.8.0 #> + colorspace 2.0-3 #> + covr 3.6.1 #> + crayon 1.5.2 #> + curl 4.3.3 #> + desc 1.4.2 #> + DiagrammeR 1.0.9 #> + diffobj 0.3.5 #> + digest 0.6.31 #> + downloader 0.4 #> + dplyr 1.0.10 #> + evaluate 0.19 👷🏿‍♂️ #> + farver 2.1.1 #> + fastmap 1.1.0 #> + formattable 0.2.1 #> + fs 1.5.2 #> + generics 0.1.3 #> + ggplot2 3.4.0 #> + gridExtra 2.3 #> + gtable 0.3.1 #> + highr 0.9 #> + hms 1.1.2 #> + htmltools 0.5.4 #> + htmlwidgets 1.6.0 👷🏾‍♂️ #> + httr 1.4.4 #> + igraph 1.3.5 #> + influenceR 0.1.0.1 #> + isoband 0.2.6 #> + jquerylib 0.1.4 #> + jsonlite 1.8.4 #> + knitr 1.41 #> + labeling 0.4.2 #> + lazyeval 0.2.2 #> + lubridate 1.9.0 #> + Matrix 1.5-1 → 1.5-3 #> + memoise 2.0.1 #> + mime 0.12 #> + mockr 0.2.0 #> + munsell 0.5.0 #> + nlme 3.1-160 → 3.1-161 👷‍♂️🔧 #> + nycflights13 1.0.2 #> + openssl 2.0.5 #> + pkgbuild 1.4.0 #> + pkgload 1.3.2 #> + praise 1.0.0 #> + prettyunits 1.1.1 #> + processx 3.8.0 #> + profmem 0.6.0 #> + ps 1.7.2 #> + purrr 0.3.5 #> + R6 2.5.1 #> + rappdirs 0.3.3 #> + RColorBrewer 1.1-3 #> + readr 2.1.3 #> + rematch2 2.1.2 #> + rex 1.2.1 #> + rmarkdown 2.19 👷‍♂️ #> + rprojroot 2.0.3 #> + rstudioapi 0.14 #> + sass 0.4.4 #> + scales 1.2.1 #> + stringi 1.7.8 #> + stringr 1.5.0 #> + sys 3.4.1 #> + testthat 3.1.6 #> + tidyr 1.2.1 #> + tidyselect 1.2.0 #> + timechange 0.1.1 #> + tinytex 0.43 👷🏻‍♂️ #> + tzdb 0.3.0 #> + viridis 0.6.2 #> + viridisLite 0.4.1 #> + visNetwork 2.1.2 #> + vroom 1.6.0 #> + waldo 0.4.0 #> + withr 2.5.0 #> + xfun 0.35 #> + yaml 2.3.6 #> ℹ No downloads are needed, 88 pkgs (100.53 MB) are cached #> ℹ Packaging tibble 3.1.8 #> ℹ Building evaluate 0.19 #> ℹ Building nlme 3.1-161 #> ✔ Installed R6 2.5.1 (31ms) #> ✔ Installed DiagrammeR 1.0.9 (76ms) #> ✔ Installed RColorBrewer 1.1-3 (72ms) #> ✔ Installed askpass 1.1 (79ms) #> ✔ Installed Matrix 1.5-3 (137ms) #> ✔ Installed base64enc 0.1-3 (125ms) #> ✔ Installed bench 1.1.2 (90ms) #> ✔ Installed bit64 4.0.5 (44ms) #> ✔ Installed bit 4.0.5 (43ms) #> ✔ Installed blob 1.2.3 (41ms) #> ✔ Installed brio 1.1.3 (40ms) #> ✔ Installed cachem 1.0.6 (31ms) #> ✔ Installed callr 3.7.3 (53ms) #> ✔ Installed clipr 0.8.0 (89ms) #> ✔ Installed colorspace 2.0-3 (99ms) #> ✔ Installed covr 3.6.1 (58ms) #> ✔ Installed crayon 1.5.2 (75ms) #> ✔ Installed curl 4.3.3 (83ms) #> ✔ Packaged tibble 3.1.8 (684ms) #> ✔ Installed bslib 0.4.1 (315ms) #> ✔ Installed desc 1.4.2 (77ms) #> ✔ Installed diffobj 0.3.5 (68ms) #> ✔ Installed digest 0.6.31 (60ms) #> ✔ Installed downloader 0.4 (39ms) #> ✔ Installed dplyr 1.0.10 (39ms) #> ✔ Installed farver 2.1.1 (41ms) #> ✔ Installed fastmap 1.1.0 (38ms) #> ✔ Installed formattable 0.2.1 (43ms) #> ✔ Built evaluate 0.19 (903ms) #> ✔ Installed fs 1.5.2 (49ms) #> ✔ Installed generics 0.1.3 (46ms) #> ✔ Installed ggplot2 3.4.0 (65ms) #> ✔ Installed gridExtra 2.3 (43ms) #> ✔ Installed gtable 0.3.1 (38ms) #> ✔ Installed highr 0.9 (37ms) #> ✔ Installed hms 1.1.2 (39ms) #> ✔ Installed htmltools 0.5.4 (40ms) #> ✔ Installed httr 1.4.4 (40ms) #> ✔ Installed influenceR 0.1.0.1 (17ms) #> ✔ Installed igraph 1.3.5 (96ms) #> ✔ Installed isoband 0.2.6 (68ms) #> ✔ Installed jquerylib 0.1.4 (38ms) #> ✔ Installed jsonlite 1.8.4 (37ms) #> ✔ Installed labeling 0.4.2 (14ms) #> ✔ Installed knitr 1.41 (73ms) #> ✔ Installed lazyeval 0.2.2 (43ms) #> ✔ Installed lubridate 1.9.0 (38ms) #> ✔ Installed memoise 2.0.1 (39ms) #> ✔ Installed mime 0.12 (58ms) #> ✔ Installed mockr 0.2.0 (38ms) #> ✔ Installed munsell 0.5.0 (36ms) #> ✔ Installed nycflights13 1.0.2 (37ms) #> ✔ Installed openssl 2.0.5 (41ms) #> ✔ Installed pkgbuild 1.4.0 (39ms) #> ✔ Installed pkgload 1.3.2 (37ms) #> ✔ Installed praise 1.0.0 (35ms) #> ✔ Installed prettyunits 1.1.1 (56ms) #> ✔ Installed processx 3.8.0 (37ms) #> ✔ Installed profmem 0.6.0 (37ms) #> ✔ Installed ps 1.7.2 (37ms) #> ✔ Installed purrr 0.3.5 (38ms) #> ✔ Installed rappdirs 0.3.3 (37ms) #> ✔ Installed readr 2.1.3 (42ms) #> ✔ Installed rematch2 2.1.2 (41ms) #> ✔ Installed rex 1.2.1 (58ms) #> ✔ Installed rprojroot 2.0.3 (58ms) #> ✔ Installed rstudioapi 0.14 (40ms) #> ✔ Installed sass 0.4.4 (42ms) #> ✔ Installed scales 1.2.1 (39ms) #> ✔ Installed stringr 1.5.0 (33ms) #> ✔ Installed sys 3.4.1 (49ms) #> ✔ Installed testthat 3.1.6 (88ms) #> ✔ Installed tidyr 1.2.1 (77ms) #> ✔ Installed stringi 1.7.8 (195ms) #> ✔ Installed tidyselect 1.2.0 (113ms) #> ✔ Installed timechange 0.1.1 (55ms) #> ✔ Installed tzdb 0.3.0 (40ms) #> ✔ Installed viridisLite 0.4.1 (39ms) #> ✔ Installed viridis 0.6.2 (39ms) #> ✔ Installed visNetwork 2.1.2 (77ms) #> ✔ Installed vroom 1.6.0 (77ms) #> ✔ Installed waldo 0.4.0 (62ms) #> ✔ Installed withr 2.5.0 (40ms) #> ✔ Installed xfun 0.35 (39ms) #> ℹ Building tinytex 0.43 #> ✔ Installed yaml 2.3.6 (43ms) #> ✔ Installed evaluate 0.19 (15ms) #> ✔ Built tinytex 0.43 (1.1s) #> ✔ Installed tinytex 0.43 (15ms) #> ℹ Building rmarkdown 2.19 #> ✔ Built rmarkdown 2.19 (3.9s) #> ✔ Installed rmarkdown 2.19 (85ms) #> ℹ Building htmlwidgets 1.6.0 #> ✔ Built nlme 3.1-161 (8s) #> ✔ Installed nlme 3.1-161 (33ms) #> ✔ Built htmlwidgets 1.6.0 (1.1s) #> ✔ Installed htmlwidgets 1.6.0 (22ms) #> ✔ 103 deps: kept 15, upd 2, added 86 [10.2s]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"list-current-repositories","dir":"Reference","previous_headings":"","what":"List current repositories","title":"Simplified manual. Start here! — Get started with pak","text":"set CRAN Bioconductor repository, pak automatically.","code":"pak::repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"add-custom-repository","dir":"Reference","previous_headings":"","what":"Add custom repository","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::repo_add(rhub = 'https://r-hub.r-universe.dev') pak::repo_get() #> # A data frame: 6 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 rhub https://r-hub.r-universe.dev cran… * NA #> 3 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 6 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"remove-custom-repositories","dir":"Reference","previous_headings":"","what":"Remove custom repositories","title":"Simplified manual. Start here! — Get started with pak","text":"set repos option CRAN repo , unset completely, pak keeps CRAN (default) Bioconductor.","code":"options(repos = getOption(\"repos\")[\"CRAN\"]) pak::repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"time-travel-using-rspm","dir":"Reference","previous_headings":"","what":"Time travel using RSPM","title":"Simplified manual. Start here! — Get started with pak","text":"Sets repository equivalent CRAN's state closest specified date. Name repository CRAN, otherwise pak also add default CRAN repository.","code":"pak::repo_add(CRAN = \"RSPM@2022-06-30\") pak::repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://packagemanager.posit.co/c… cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"time-travel-using-mran","dir":"Reference","previous_headings":"","what":"Time travel using MRAN","title":"Simplified manual. Start here! — Get started with pak","text":"Sets repository equivalent CRAN's state specified date. Name repository CRAN, otherwise pak also add default CRAN repository.","code":"pak::repo_add(CRAN = \"MRAN@2022-06-30\") pak::repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cran.microsoft.com/snapsh… cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"caches","dir":"Reference","previous_headings":"","what":"Caches","title":"Simplified manual. Start here! — Get started with pak","text":"default pak caches metadata downloaded packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"inspect-metadata-cache","dir":"Reference","previous_headings":"","what":"Inspect metadata cache","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::meta_list() #> ✔ Updated metadata database: 4.55 MB in 4 files. #> ✔ Updating metadata database ... done #> # A data frame: 43,718 × 32 #> package version depends sugge…¹ license imports linki…² archs enhan…³ #> #> 1 A3 1.0.0 R (>= … random… GPL (>… NA NA NA NA #> 2 AATtoo… 0.0.1 R (>= … NA GPL-3 magrit… NA NA NA #> 3 ABACUS 1.0.0 R (>= … rmarkd… GPL-3 ggplot… NA NA NA #> 4 ABC.RAP 0.9.0 R (>= … knitr,… GPL-3 graphi… NA NA NA #> 5 ABCana… 1.2.1 R (>= … NA GPL-3 plotrix NA NA NA #> 6 ABCopt… 0.15.0 NA testth… MIT + … Rcpp, … Rcpp ABCo… NA #> 7 ABCp2 1.2 MASS NA GPL-2 NA NA NA NA #> 8 ABHgen… 1.0.1 NA knitr,… GPL-3 ggplot… NA NA NA #> 9 ABPS 0.3 NA testth… GPL (>… kernlab NA NA NA #> 10 ACA 1.1 R (>= … NA GPL graphi… NA NA NA #> # … with 43,708 more rows, 23 more variables: os_type , #> # priority , license_is_foss , license_restricts_use , #> # repodir , rversion , platform , #> # needscompilation , ref , type , direct , #> # status , target , mirror , sources , #> # filesize , sha256 , sysreqs , built , #> # published , deps , md5sum , path , and …"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"update-metadata-cache","dir":"Reference","previous_headings":"","what":"Update metadata cache","title":"Simplified manual. Start here! — Get started with pak","text":"default pkg_install() similar functions automatically update metadata currently set repositories older 24 hours. can also force update manually:","code":"pak::meta_update() #> ✔ Updating metadata database ... done"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"clean-metadata-cache","dir":"Reference","previous_headings":"","what":"Clean metadata cache","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::meta_clean(force = TRUE) pak::meta_summary() #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metad #> ata\" #> #> $current_db #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metad #> ata/pkgs-d1c324e625.rds\" #> #> $raw_files #> character(0) #> #> $db_files #> character(0) #> #> $size #> [1] 0 #>"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"inspect-package-cache","dir":"Reference","previous_headings":"","what":"Inspect package cache","title":"Simplified manual. Start here! — Get started with pak","text":"Downloaded packages also cached.","code":"pak::cache_list() #> # A data frame: 480 × 11 #> fullpath path package url etag sha256 version platf…¹ built #> #> 1 /Users/gaborc… arch… NA http… \"\\\"1… 0c8f0… NA NA NA #> 2 /Users/gaborc… bin/… evalua… http… \"\\\"1… 08a39… 0.17 aarch6… NA #> 3 /Users/gaborc… bin/… crayon http… \"\\\"2… 1e6d5… 1.5.2 aarch6… NA #> 4 /Users/gaborc… bin/… common… http… \"\\\"4… 47b4a… 1.8.1 aarch6… NA #> 5 /Users/gaborc… bin/… curl http… \"\\\"b… 7b8ba… 4.3.3 aarch6… NA #> 6 /Users/gaborc… bin/… tinytex http… \"\\\"2… 7e9ba… 0.42 aarch6… NA #> 7 /Users/gaborc… bin/… jsonli… http… \"\\\"1… 68e59… 1.8.2 aarch6… NA #> 8 /Users/gaborc… bin/… lifecy… http… \"\\\"1… 7ce27… 1.0.3 aarch6… NA #> 9 /Users/gaborc… bin/… vctrs http… \"\\\"1… c3a69… 0.4.2 aarch6… NA #> 10 /Users/gaborc… src/… pkgcac… NA NA 9b70a… NA NA 0 #> # … with 470 more rows, 2 more variables: vignettes , #> # rversion , and abbreviated variable name ¹​platform"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"view-a-package-cache-summary","dir":"Reference","previous_headings":"","what":"View a package cache summary","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::cache_summary() #> $cachepath #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/pkg\" #> #> $files #> [1] 480 #> #> $size #> [1] 653325143 #>"},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"clean-package-cache","dir":"Reference","previous_headings":"","what":"Clean package cache","title":"Simplified manual. Start here! — Get started with pak","text":"","code":"pak::cache_clean()"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/get-started.html","id":"list-packages-in-a-library","dir":"Reference","previous_headings":"","what":"List packages in a library","title":"Simplified manual. Start here! — Get started with pak","text":"Pass directory library argument.","code":"pak::lib_status(Sys.getenv(\"R_LIBS_USER\")) #> # A data frame: 701 × 39 #> library package title version depends repos…¹ license needs…² built #> #> 1 /Users/g… abc \"Too… 2.2.1 R (>= … CRAN GPL (>… FALSE R 4.… #> 2 /Users/g… abc.da… \"Dat… 1.0 R (>= … CRAN GPL (>… FALSE R 4.… #> 3 /Users/g… abind \"Com… 1.4-5 R (>= … CRAN LGPL (… FALSE R 4.… #> 4 /Users/g… ade4 \"Ana… 1.7-19 R (>= … CRAN GPL (>… TRUE R 4.… #> 5 /Users/g… ape \"Ana… 5.6-2 R (>= … CRAN GPL-2 … TRUE R 4.… #> 6 /Users/g… aplot \"Dec… 0.1.7 NA CRAN Artist… FALSE R 4.… #> 7 /Users/g… archive \"Mul… 1.1.5 R (>= … CRAN MIT + … TRUE R 4.… #> 8 /Users/g… arrayh… \"Con… 1.1-0 NA CRAN GPL FALSE R 4.… #> 9 /Users/g… arrow \"Int… 9.0.0 R (>= … CRAN Apache… TRUE R 4.… #> 10 /Users/g… arules \"Min… 1.7-5 R (>= … CRAN GPL-3 TRUE R 4.… #> # … with 691 more rows, 30 more variables: remotetype , #> # remotepkgref , remoteref , remoterepos , #> # remotepkgplatform , remotesha , imports , #> # suggests , linkingto , remotes , remotehost , #> # remoterepo , remoteusername , enhances , #> # biocviews , remoteurl , remotesubdir , #> # priority , remoteetag , remotepackaged , …"},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":null,"dir":"Reference","previous_headings":"","what":"Install missing packages on the fly — handle_package_not_found","title":"Install missing packages on the fly — handle_package_not_found","text":"Use function set global error handler, called R fails load package. handler offer choice installing missing package (dependencies), cases can also remedy error restart code.","code":""},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install missing packages on the fly — handle_package_not_found","text":"","code":"handle_package_not_found(err)"},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install missing packages on the fly — handle_package_not_found","text":"err error object, class packageNotFoundError.","code":""},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install missing packages on the fly — handle_package_not_found","text":"Nothing.","code":""},{"path":"https://pak.r-lib.org/dev/reference/handle_package_not_found.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install missing packages on the fly — handle_package_not_found","text":"supposed call function directly. Instead, set global error handler, possibly .Rprofile file: Global error handlers supported R 4.0.0 later. Currently handle_package_not_found() anything non-interactive mode (including knitr, testthat RStudio notebooks), might change future. cases possible remedy original computation tried load missing package, pak offer successful installation. Currently, R 4.0.4, possible continue failed library() call.","code":"if (interactive() && getRversion() >= \"4.0.0\") { globalCallingHandlers( packageNotFoundError = function(err) { try(pak::handle_package_not_found(err)) } ) }"},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":null,"dir":"Reference","previous_headings":"","what":"All about installing pak. — Installing pak","title":"All about installing pak. — Installing pak","text":"Read default installation methods work want release candidate development version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"pre-built-binaries","dir":"Reference","previous_headings":"","what":"Pre-built binaries","title":"All about installing pak. — Installing pak","text":"pre-built binaries advantage completely self-containted dependency free. additional R packages, system libraries tools (e.g. compilers) needed . Install pre-built binary build pak repository GitHub: supported following systems:","code":"install.packages(\"pak\", repos = sprintf( \"https://r-lib.github.io/p/pak/stable/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch ))"},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"notes","dir":"Reference","previous_headings":"","what":"Notes","title":"All about installing pak. — Installing pak","text":"macOS support official CRAN R build. builds, e.g. Homebrew R, supported. support R builds R shared library. CRAN's Windows macOS installers , R builds common Linux distributions. might issue build R without --enable-R-shlib option.","code":""},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"install-from-cran","dir":"Reference","previous_headings":"","what":"Install from CRAN","title":"All about installing pak. — Installing pak","text":"Install released version package CRAN usual: potentially needs C compiler platforms CRAN binaries packages .","code":"install.packages(\"pak\")"},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"nightly-builds","dir":"Reference","previous_headings":"","what":"Nightly builds","title":"All about installing pak. — Installing pak","text":"nightly binary builds, systems table :","code":"install.packages(\"pak\", repos = sprintf( \"https://r-lib.github.io/p/pak/devel/%s/%s/%s\", .Platform$pkgType, R.Version()$os, R.Version()$arch ))"},{"path":"https://pak.r-lib.org/dev/reference/install.html","id":"stable-rc-and-devel-streams","dir":"Reference","previous_headings":"","what":"stable, rc and devel streams","title":"All about installing pak. — Installing pak","text":"three types binaries available: stable corresponds latest CRAN release CRAN. rc release candidate build, available 1-2 weeks release. Otherwise stable build. devel builds development tree. release might rc build. streams available different repository URLs:","code":"stream <- \"rc\" install.packages(\"pak\", repos = sprintf( \"https://r-lib.github.io/p/pak/%s/%s/%s/%s\", stream, .Platform$pkgType, R.Version()$os, R.Version()$arch ))"},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Status of packages in a library — lib_status","title":"Status of packages in a library — lib_status","text":"Status packages library","code":""},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Status of packages in a library — lib_status","text":"","code":"lib_status(lib = .libPaths()[1]) pkg_list(lib = .libPaths()[1])"},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Status of packages in a library — lib_status","text":"lib Path library.","code":""},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Status of packages in a library — lib_status","text":"Data frame contains data packages installed library. always columns: biocviews: corresponding field DESCRIPTION, must present Bioconductor packages, packages typically . built: Built field DESCRIPTION. depends, suggests, Imports, linkingto, enhances: corresponding fields DESCRIPTION files. deps: list data frames, dependencies package. columns: ref, type (dependency type lowercase), package (dependent package, R), op version, last two version requirement. op can >=, >, == <=, although first one common practice. library: path package library containing package. license: DESCRIPTION. md5sum: DESCTIPTION, typically NA, except Windows. needscompilation: DESCRIPTION, column logical. package: package name. platform: Built field DESCRIPTION, current platform missing DESCRIPTION. priority: DESCRIPTION, usually base, recommended, missing. ref: corresponding installed::* package reference. repository: DESCRIPTION. packages CRAN repository CRAN, repositories, e.g. R-universe adds repository URL . repotype: cran, bioc missing. rversion: Built field. field, current R version. sysreqs: SystemRequirements field DESCRIPTION. title: package title. type: always installed. version: package version (string).","code":""},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"notes-","dir":"Reference","previous_headings":"","what":"Notes:","title":"Status of packages in a library — lib_status","text":"addition, also remote* config/needs/* entries DESCRIPTION files. (Case insensitive.) columns type character, except needscompilation, logical deps, list columns. entry missing package, set NA. Note column names lowercase, even corresponding entries DESCRIPTION. order columns deterministic, assume order. Additional columns might present, internal pak used user code.","code":""},{"path":"https://pak.r-lib.org/dev/reference/lib_status.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Status of packages in a library — lib_status","text":"","code":"lib_status(.Library) #> # A data frame: 31 × 31 #> library package version prior…¹ title license sugge…² built depends #> #> 1 /Library… base 4.2.2 base \"The… Part o… methods R 4.… NA #> 2 /Library… boot 1.3-28 recomm… \"Boo… Unlimi… MASS, … R 4.… R (>= … #> 3 /Library… class 7.3-20 recomm… \"Fun… GPL-2 … NA R 4.… R (>= … #> 4 /Library… cluster 2.1.4 recomm… \"\\\"F… GPL (>… MASS, … R 4.… R (>= … #> 5 /Library… codeto… 0.2-18 recomm… \"Cod… GPL NA R 4.… R (>= … #> 6 /Library… compil… 4.2.2 base \"The… Part o… NA R 4.… NA #> 7 /Library… datase… 4.2.2 base \"The… Part o… NA R 4.… NA #> 8 /Library… filelo… 1.0.2 NA \"Por… MIT + … callr … R 4.… NA #> 9 /Library… foreign 0.8-83 recomm… \"Rea… GPL (>… NA R 4.… R (>= … #> 10 /Library… graphi… 4.2.2 base \"The… Part o… NA R 4.… NA #> # … with 21 more rows, 22 more variables: needscompilation , #> # repository , imports , remotetype , #> # remotepkgref , remoteref , remoterepos , #> # remotepkgplatform , remotesha , enhances , #> # linkingto , md5sum , platform , biocviews , #> # sysreqs , ref , type , status , rversion , #> # sources , repotype , deps , and abbreviated …"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Dependencies of a package tree — local_deps","title":"Dependencies of a package tree — local_deps","text":"Dependencies package tree","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dependencies of a package tree — local_deps","text":"","code":"local_deps(root = \".\", upgrade = TRUE, dependencies = NA) local_deps_tree(root = \".\", upgrade = TRUE, dependencies = NA) local_dev_deps(root = \".\", upgrade = TRUE, dependencies = TRUE) local_dev_deps_tree(root = \".\", upgrade = TRUE, dependencies = TRUE)"},{"path":"https://pak.r-lib.org/dev/reference/local_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dependencies of a package tree — local_deps","text":"root Path package tree. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dependencies of a package tree — local_deps","text":"functions return dependencies data frame. local_deps_tree() local_dev_deps_tree() also print dependency tree.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_deps_explain.html","id":null,"dir":"Reference","previous_headings":"","what":"Explain dependencies of a package tree — local_deps_explain","title":"Explain dependencies of a package tree — local_deps_explain","text":"functions similar pkg_deps_explain(), work local package tree. local_dev_deps_explain() also includes development dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_deps_explain.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Explain dependencies of a package tree — local_deps_explain","text":"","code":"local_deps_explain(deps, root = \".\", upgrade = TRUE, dependencies = NA) local_dev_deps_explain(deps, root = \".\", upgrade = TRUE, dependencies = TRUE)"},{"path":"https://pak.r-lib.org/dev/reference/local_deps_explain.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Explain dependencies of a package tree — local_deps_explain","text":"deps Package names dependencies explain. root Path package tree. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Install a package tree — local_install","title":"Install a package tree — local_install","text":"Installs package tree (source package file), together dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install a package tree — local_install","text":"","code":"local_install( root = \".\", lib = .libPaths()[1], upgrade = TRUE, ask = interactive(), dependencies = NA )"},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install a package tree — local_install","text":"root Path package tree. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. ask Whether ask confirmation installing different version package already installed. Installations add new packages never require confirmation. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install a package tree — local_install","text":"Data frame, information installed package(s).","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install a package tree — local_install","text":"local_install() equivalent pkg_install(\"local::.\").","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Install the dependencies of a package tree — local_install_deps","title":"Install the dependencies of a package tree — local_install_deps","text":"Installs hard dependencies package tree (source package file), without installing package tree .","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install the dependencies of a package tree — local_install_deps","text":"","code":"local_install_deps( root = \".\", lib = .libPaths()[1], upgrade = TRUE, ask = interactive(), dependencies = NA )"},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install the dependencies of a package tree — local_install_deps","text":"root Path package tree. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. ask Whether ask confirmation installing different version package already installed. Installations add new packages never require confirmation. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install the dependencies of a package tree — local_install_deps","text":"Data frame, information installed package(s).","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install_deps.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install the dependencies of a package tree — local_install_deps","text":"Note development (optional) dependencies, Suggests DESCRIPTION, installed. want install well, use local_install_dev_deps().","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_install_dev_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Install all (development) dependencies of a package tree — local_install_dev_deps","title":"Install all (development) dependencies of a package tree — local_install_dev_deps","text":"Installs dependencies package tree (source package file), without installing package tree . installs development dependencies well, specified Suggests field DESCRIPTION.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_install_dev_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install all (development) dependencies of a package tree — local_install_dev_deps","text":"","code":"local_install_dev_deps( root = \".\", lib = .libPaths()[1], upgrade = TRUE, ask = interactive(), dependencies = TRUE )"},{"path":"https://pak.r-lib.org/dev/reference/local_install_dev_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install all (development) dependencies of a package tree — local_install_dev_deps","text":"root Path package tree. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. ask Whether ask confirmation installing different version package already installed. Installations add new packages never require confirmation. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_package_trees.html","id":null,"dir":"Reference","previous_headings":"","what":"About local package trees — local_package_trees","title":"About local package trees — local_package_trees","text":"pak can install packages local package trees. convenient package development. See following functions: local_install() installs package package tree dependencies. local_install_deps() installs hard dependencies package. local_install_dev_deps() installs hard soft dependencies package. function intended package development.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_package_trees.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"About local package trees — local_package_trees","text":"Note last two functions install package specified package tree , dependencies. convenient package loaded via means, e.g. devtools::load_all(), development.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":null,"dir":"Reference","previous_headings":"","what":"Query system requirements — local_system_requirements","title":"Query system requirements — local_system_requirements","text":"Returns character vector commands run install system requirements queried operating system. local_system_requirements() queries system requirements dev package (dependencies) given root path. pkg_system_requirements() queries system requirements existing packages (dependencies).","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query system requirements — local_system_requirements","text":"","code":"local_system_requirements( os = NULL, os_release = NULL, root = \".\", execute = FALSE, sudo = execute, echo = FALSE ) pkg_system_requirements( package, os = NULL, os_release = NULL, execute = FALSE, sudo = execute, echo = FALSE )"},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query system requirements — local_system_requirements","text":"os, os_release operating system operating system release version, e.g. \"ubuntu\", \"debian\", \"centos\", \"redhat\". See https://github.com/rstudio/r-system-requirements#operating-systems full list supported operating systems. NULL, default, looked using distro::distro(). root Path package tree. execute, sudo execute TRUE, pak execute system commands (). sudo TRUE, pak prepend commands sudo. echo echo TRUE execute TRUE, echo command output. package Package names lookup system requirements .","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query system requirements — local_system_requirements","text":"character vector commands needed install system requirements package.","code":""},{"path":"https://pak.r-lib.org/dev/reference/local_system_requirements.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query system requirements — local_system_requirements","text":"","code":"if (FALSE) { local_system_requirements(\"ubuntu\", \"20.04\") } if (FALSE) { pkg_system_requirements(\"pak\", \"ubuntu\", \"20.04\") pkg_system_requirements(\"pak\", \"redhat\", \"7\") pkg_system_requirements(\"config\", \"ubuntu\", \"20.04\") # no sys reqs pkg_system_requirements(\"curl\", \"ubuntu\", \"20.04\") pkg_system_requirements(\"git2r\", \"ubuntu\", \"20.04\") pkg_system_requirements(c(\"config\", \"git2r\", \"curl\"), \"ubuntu\", \"20.04\") # queried packages must exist pkg_system_requirements(\"iDontExist\", \"ubuntu\", \"20.04\") pkg_system_requirements(c(\"curl\", \"iDontExist\"), \"ubuntu\", \"20.04\") }"},{"path":"https://pak.r-lib.org/dev/reference/lockfile_create.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a lock file — lockfile_create","title":"Create a lock file — lockfile_create","text":"lock file can used later, possibly new R session, carry installation dependencies, lockfile_install().","code":""},{"path":"https://pak.r-lib.org/dev/reference/lockfile_create.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a lock file — lockfile_create","text":"","code":"lockfile_create( pkg = \"deps::.\", lockfile = \"pkg.lock\", lib = NULL, upgrade = FALSE, dependencies = NA )"},{"path":"https://pak.r-lib.org/dev/reference/lockfile_create.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a lock file — lockfile_create","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. lockfile Path lock file. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/lockfile_create.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a lock file — lockfile_create","text":"Note, since URLs CRAN CRAN-like repositories change time, practice use lock file much later. example, binary packages older package version might deleted repository, breaking URLs lock file. Currently intended use case lock files CI systems, facilitate caching. (hash ) lock file provides good key caching systems.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/lockfile_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Install packages based on a lock file — lockfile_install","title":"Install packages based on a lock file — lockfile_install","text":"Install lock file created lockfile_create().","code":""},{"path":"https://pak.r-lib.org/dev/reference/lockfile_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install packages based on a lock file — lockfile_install","text":"","code":"lockfile_install(lockfile = \"pkg.lock\", lib = .libPaths()[1], update = TRUE)"},{"path":"https://pak.r-lib.org/dev/reference/lockfile_install.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install packages based on a lock file — lockfile_install","text":"lockfile Path lock file. lib Library carry installation . update Whether online install packages either installed lib, different version installed .","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Metadata cache utilities — meta_summary","title":"Metadata cache utilities — meta_summary","text":"Various utilities inspect, update clean metadata cache. See pkgcache package need control metadata cache.","code":""},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metadata cache utilities — meta_summary","text":"","code":"meta_summary() meta_list(pkg = NULL) meta_update() meta_clean(force = FALSE)"},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Metadata cache utilities — meta_summary","text":"pkg Package names, specified entries pkg returned. force FALSE, pak ask confirmation.","code":""},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Metadata cache utilities — meta_summary","text":"meta_summary() returns list entries: cachepath: absolute path metadata cache. current_db: file contains current metadata database. currently RDS file, might change future. raw_files: files downloaded PACKAGES* files. db_files: metadata database files. size: total size metadata cache. meta_list() returns data frame available packages configured repositories. meta_update() returns nothing. meta_clean() returns nothing","code":""},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Metadata cache utilities — meta_summary","text":"meta_summary() returns summary metadata cache. meta_list() lists () packages metadata database. meta_update() updates metadata database. normally need call function manually, pak functions (e.g. pkg_install(), pkg_download(), etc.) call automatically, make sure use latest available metadata. meta_clean() deletes whole metadata DB.","code":""},{"path":"https://pak.r-lib.org/dev/reference/metadata.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metadata cache utilities — meta_summary","text":"Metadata cache summary: current metadata DB: Selected packages : Update metadata DB Delete metadata DB","code":"meta_summary() #> $cachepath #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata\" #> #> $current_db #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/pkgs-34444e3072.rds\" #> #> $raw_files #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCann-59693086a0/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [2] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCann-59693086a0/src/contrib/PACKAGES.gz\" #> [3] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCexp-90d4a3978b/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [4] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCexp-90d4a3978b/src/contrib/PACKAGES.gz\" #> [5] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCsoft-2a43920999/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [6] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCsoft-2a43920999/src/contrib/PACKAGES.gz\" #> [7] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCworkflows-26330ba3ca/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [8] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/BioCworkflows-26330ba3ca/src/contrib/PACKAGES.gz\" #> [9] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/CRAN-075c426938/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES.gz\" #> [10] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/CRAN-075c426938/src/contrib/PACKAGES.gz\" #> #> $db_files #> [1] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/pkgs-34444e3072.rds\" #> [2] \"/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/_metadata/pkgs-ccacf1b389.rds\" #> #> $size #> [1] 174848200 meta_list() #> ✔ Loading metadata database ... done #> # A data frame: 45,279 × 32 #> package version depends sugge…¹ license imports linki…² archs enhan…³ #> #> 1 A3 1.0.0 R (>= … random… GPL (>… NA NA NA NA #> 2 AATtoo… 0.0.2 R (>= … NA GPL-3 magrit… NA NA NA #> 3 ABACUS 1.0.0 R (>= … rmarkd… GPL-3 ggplot… NA NA NA #> 4 ABC.RAP 0.9.0 R (>= … knitr,… GPL-3 graphi… NA NA NA #> 5 ABCana… 1.2.1 R (>= … NA GPL-3 plotrix NA NA NA #> 6 ABCopt… 0.15.0 NA testth… MIT + … Rcpp, … Rcpp ABCo… NA #> 7 ABCp2 1.2 MASS NA GPL-2 NA NA NA NA #> 8 ABHgen… 1.0.1 NA knitr,… GPL-3 ggplot… NA NA NA #> 9 ABPS 0.3 NA testth… GPL (>… kernlab NA NA NA #> 10 ACA 1.1 R (>= … NA GPL graphi… NA NA NA #> # … with 45,269 more rows, 23 more variables: #> # license_restricts_use , os_type , priority , #> # license_is_foss , repodir , rversion , #> # platform , needscompilation , ref , type , #> # direct , status , target , mirror , #> # sources , filesize , sha256 , sysreqs , #> # built , published , deps , md5sum , … meta_list(pkg = c(\"shiny\", \"htmlwidgets\")) #> package version depends sugge…¹ license imports linki…² archs enhan…³ #> * #> 1 htmlwid… 1.5.4 NA \"knitr… MIT + … \"grDev… NA NA shiny … #> 2 shiny 1.7.3 R (>= … \"datas… GPL-3 … \"utils… NA NA NA #> 3 htmlwid… 1.6.0 NA \"testt… MIT + … \"grDev… NA NA shiny … #> 4 shiny 1.7.4 R (>= … \"datas… GPL-3 … \"utils… NA NA NA #> # … with 23 more variables: license_restricts_use , os_type , #> # priority , license_is_foss , repodir , #> # rversion , platform , needscompilation , ref , #> # type , direct , status , target , mirror , #> # sources , filesize , sha256 , sysreqs , #> # built , published , deps , md5sum , #> # path , and abbreviated variable names ¹​suggests, ²​linkingto, #> … meta_update() #> ✔ Updated metadata database: 1.23 MB in 1 file. #> ✔ Updating metadata database ... done meta_clean() #> ℹ Cleaning up cache directory /Users/gaborcsardi/Library/Caches/org.R-pr #> oject.R/R/pkgcache/_metadata."},{"path":"https://pak.r-lib.org/dev/reference/package-dependency-types.html","id":null,"dir":"Reference","previous_headings":"","what":"Various types of R package dependencies — Package dependency types","title":"Various types of R package dependencies — Package dependency types","text":"Various types R package dependencies","code":""},{"path":"https://pak.r-lib.org/dev/reference/package-dependency-types.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Various types of R package dependencies — Package dependency types","text":"R packages may various types dependencies, see Writing R Extensions.pak groups dependencies three groups: hard dependencies: \"Depends\", \"Imports\", \"LinkingTo\", soft dependencies: \"Suggests\" \"Enhances\", extra dependencies, see . NA \"hard\" install package required dependencies, TRUE install required dependencies, plus optional development dependencies. TRUE: means hard dependencies plus Suggests direct installations, hard dependencies dependent packages. FALSE: dependencies installed . NA (atomic type, NA_character_, etc. well): hard dependencies installed. list two entries named direct indirect, taken requested dependency types, direct installations dependent packages. character vector, taken dependency types direct installations, hard dependencies used dependent packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/package-dependency-types.html","id":"extra-dependencies","dir":"Reference","previous_headings":"","what":"Extra dependencies","title":"Various types of R package dependencies — Package dependency types","text":"pak supports extra dependency types direct installations CRAN-like repositories. specified Config/Needs/ prefix DESCRIPTION can contain package references, separated commas. example can specify packages needed pkgdown website package:   use dependency types, need specify dependencies argument pak functions. Note Config/Needs/* fields currently used CRAN packages, packages CRAN-like repositories general. Usually specify Config/Needs/* dependency type installed together \"hard\" \"\", install hard soft dependencies well.","code":"Config/Needs/website: r-lib/pkgdown"},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":null,"dir":"Reference","previous_headings":"","what":"Environment variables and options that modify the default behavior — pak configuration","title":"Environment variables and options that modify the default behavior — pak configuration","text":"pak behavior can finetuned environment variables options (base::options()).","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"ncpus","dir":"Reference","previous_headings":"","what":"Ncpus","title":"Environment variables and options that modify the default behavior — pak configuration","text":"Set desired number worker processes package installation. set, pak use number logical processors machine.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"repos","dir":"Reference","previous_headings":"","what":"repos","title":"Environment variables and options that modify the default behavior — pak configuration","text":"CRAN-like repositories use. See base::options() details.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"pak-configuration","dir":"Reference","previous_headings":"","what":"pak configuration","title":"Environment variables and options that modify the default behavior — pak configuration","text":"Configuration entries (unless noted otherwise manual page) corresponding environment variable, corresponding option. environment variable always uppercase uses underscores word separator. always PKG_ prefix. option typically lowercase, use uses underscores word separator, always pkg. prefix (notice dot!). examples:","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"pak-configuration-entries","dir":"Reference","previous_headings":"","what":"pak configuration entries","title":"Environment variables and options that modify the default behavior — pak configuration","text":"‘cache_dir’: (Env var: PKG_CACHE_DIR, option: pkg.cache_dir.) Directory download packages . Defaults temporary directory within R session temporary directory, see base::tempdir(). ‘cran_mirror’: (Env var: PKG_CRAN_MIRROR, option: pkg.cran_mirror.) CRAN mirror use. Defaults repos option (see base::options()), set https://cran.rstudio.com. See also pak::repo_add() pak::repo_get() ‘include_linkingto’: (Env var: PKG_INCLUDE_LINKINGTO, option: pkg.include_linkingto.) Whether always include LinkingTo dependencies solution installation, even needed packages installed binaries. sometimes useful, see e.g. https://github.com/r-lib/pak/issues/485 example use case. ‘library’: (Env var: PKG_LIBRARY, option: pkg.library.) Package library install packages . also used already installed packages considering dependencies. ‘metadata_cache_dir’: (Env var: PKG_METADATA_CACHE_DIR, option: pkg.metadata_cache_dir.) Location metadata replica pkgcache::cranlike_metadata_cache. Defaults temporary directory within R session temporary directory, see base::tempdir(). ‘metadata_update_after’: (Env var: PKG_METADATA_UPDATE_AFTER, option: pkg.metadata_update_after.) time interval difftime object. pak update metadata cache older . default one day. PKG_METADATA_UPDATE_AFTER environment variable may set seconds (s suffix), minutes (m suffix), hours (h suffix), days (d suffix). E.g: 1d means one day. ‘package_cache_dir’: (Env var: PKG_PACKAGE_CACHE_DIR, option: pkg.package_cache_dir.) Location package cache disk. See pak::cache_summary(). Default selected pkgcache. ‘platforms’: (Env var: PKG_PLATFORMS, option: pkg.platforms.) Character vector platforms download install packages . See pkgdepends::default_platforms() possible platform names. Defaults platform current R session, plus \"source\". ‘r_versions’: (Env var: PKG_R_VERSIONS, option: pkg.r_versions.) Character vector, R versions download install packages . defaults current R version. ‘sysreqs’: (Env var: PKG_SYSREQS, option: pkg.sysreqs.) Whether automatically look install system requirements. TRUE, pkgdepends try install required system packages. FALSE, system requirements still printed (including OS packages supported platforms), installed. default TRUE supported platforms, current user root user password-less sudo configured current user. ‘sysreqs_db_update’: (Env var: PKG_SYSREQS_DB_UPDATE, option: pkg.sysreqs_db_update.) Whether try update system requirements database GitHub. update fails, cached build-database used. Defaults TRUE. ‘sysreqs_db_update_timeout’: (Env var: PKG_SYSREQS_DB_UPDATE_TIMEOUT, option: pkg.sysreqs_db_update_timeout.) Timeout system requirements database update. Defaults five seconds. ‘sysreqs_dry_run’: (Env var: PKG_SYSREQS_DRY_RUN, option: pkg.sysreqs_dry_run.) TRUE, pak prints system commands install system requirements, execute . ‘sysreqs_platform’: (Env var: PKG_SYSREQS_PLATFORM, option: pkg.sysreqs_platform.) platform use system requirements lookup. Linux, system requirements currently supported, must string containing distribution name release, separated dash. E.g.: \"ubuntu-22.04\", \"rhel-9\". ‘sysreqs_rspm_repo_id’: (Env var: PKG_SYSREQS_RSPM_REPO_ID, option: pkg.sysreqs_rspm_repo_id.) Posit Package Manager (formerly RStudio Package Manager) repository id use CRAN system requirements lookup. Defaults RSPM_REPO_ID environment variable, set. set, defaults 1. ‘sysreqs_rspm_url’: (Env var: PKG_SYSREQS_RSPM_URL, option: pkg.sysreqs_rspm_url.) Root URL Posit Package Manager (formerly RStudio Package Manager) system requirements lookup. default RSPM_ROOT environment variable used, set. set, defaults https://packagemanager.posit.co. ‘sysreqs_sudo’: (Env var: PKG_SYSREQS_SUDO, option: pkg.sysreqs_sudo.) Whether use sudo install system requirements, Unix. default TRUE Linux effective user id current process root user. ‘sysreqs_update’: (Env var: PKG_SYSREQS_UPDATE, option: pkg.sysreqs_update.) Whether try update system packages already installed. defaults TRUE CI systems: CI environment variable set true. ‘sysreqs_verbose’: (Env var: PKG_SYSREQS_VERBOSE, option: pkg.sysreqs_verbose.) Whether echo output system requirements installation. Defaults TRUE CI environment variable set. ‘use_bioconductor’: (Env var: PKG_USE_BIOCONDUCTOR, option: pkg.use_bioconductor.) Whether automatically use Bioconductor repositories. Defaults TRUE. ‘windows_archs’: (Env var: PKG_WINDOWS_ARCHS, option: pkg.windows_archs.) Character scalar specifying architectures download/install Windows. possible values : \"prefer-x64\": Generally prefer x64 binaries. current R session x64, download/install x64 packages. (packages might still multi-architecture binaries!) current R session i386, download/install packages architectures. might mean compiling packages source binary packages x64 , like CRAN Windows binaries R 4.2.x currently. \"prefer-x64\" default R 4.2.0 later. \"\": Always download/install packages i386 x64 architectures. might need compilation source available binaries x64 , like CRAN Windows binaries R 4.2.x currently. \"\" default R 4.2.0 earlier.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak-config.html","id":"notes","dir":"Reference","previous_headings":"","what":"Notes","title":"Environment variables and options that modify the default behavior — pak configuration","text":"version 0.4.0 pak copies PKG_* environment variables pkg.* options pak subprocess, actually used, need restart R reaload pak configuration change.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak.html","id":null,"dir":"Reference","previous_headings":"","what":"Install specified required packages — pak","title":"Install specified required packages — pak","text":"Install specified packages, ones required package project current working directory.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install specified required packages — pak","text":"","code":"pak(pkg = NULL, ...)"},{"path":"https://pak.r-lib.org/dev/reference/pak.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install specified required packages — pak","text":"pkg Package names remote package specifications install. See pak package sources details. NULL, install development dependencies current package. ... Extra arguments passed pkg_install() local_install_dev_deps().","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install specified required packages — pak","text":"convenience function: want install packages, easier type pkg_install(). want install packages needed development package project, easier type local_install_dev_deps(). need remember two functions install packages, just one.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_cleanup.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean up pak caches — pak_cleanup","title":"Clean up pak caches — pak_cleanup","text":"Clean pak caches","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_cleanup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean up pak caches — pak_cleanup","text":"","code":"pak_cleanup( package_cache = TRUE, metadata_cache = TRUE, pak_lib = TRUE, force = FALSE )"},{"path":"https://pak.r-lib.org/dev/reference/pak_cleanup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean up pak caches — pak_cleanup","text":"package_cache Whether clean cache package files. metadata_cache Whether clean cache package meta data. pak_lib argument now deprecated nothing. force ask confirmation. Note use function non-interactive mode, specify force = TRUE.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_install_extra.html","id":null,"dir":"Reference","previous_headings":"","what":"Install all optional dependencies of pak — pak_install_extra","title":"Install all optional dependencies of pak — pak_install_extra","text":"packages required pak functionality. recommended functions return values best used packages. E.g. many functions return data frames, print nicer pillar package available.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_install_extra.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install all optional dependencies of pak — pak_install_extra","text":"","code":"pak_install_extra(upgrade = FALSE)"},{"path":"https://pak.r-lib.org/dev/reference/pak_install_extra.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install all optional dependencies of pak — pak_install_extra","text":"upgrade Whether install upgrade latest versions optional packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_install_extra.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install all optional dependencies of pak — pak_install_extra","text":"Currently one package optional: pillar.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":null,"dir":"Reference","previous_headings":"","what":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Install packages CRAN, Bioconductor, GitHub, URLs, etc. Learn tell pak packages install, packages can found. want quick overview package sources, see \"Get started pak\".","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"package-references","dir":"Reference","previous_headings":"","what":"Package references","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Many pkgdepends pak functions take package names arguments. E.g. pak::pkg_install() takes names packages install, pak::pkg_deps_tree() takes names packages draw dependency trees . function can also take generic package reference instead package name. package reference also tells pak find package, package source. specify package source, use name prefix, :: separator. E.g. cran::mypkg means mypkg package CRAN. package name special package reference, implicitly specifies configured CRAN(-like) repositories package source. (call standard package source.) mypkg equivalent standard::mypkg pak look mypkg configured CRAN-like repositories. explicitly specify CRAN-like repositories (e.g. options(\"repos\")), pak uses CRAN Bioconductor repositories default. list currently supported package sources. discuss detail . cran: CRAN package. bioc: Bioconductor package. standard: package configured CRAN-like repository. github: package GitHub. gitlab: package GitLab. git: package git repository. local: local package file directory. url: URL points package archive. installed installed package. deps dependencies local package file directory. special reference type accepts package source. See . param special reference change references downloaded installed. See \"Parameters\" .","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"shorthands","dir":"Reference","previous_headings":"","what":"Shorthands","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"save typing, always need fully specify package source package reference. seen package name implicitly standard package source. complete rules shorthands, order applied: ref valid package name, package name @ version specification, standard package source used. E.g. pkg equivalent standard::pkg pkg@1.0 equivalent standard::pkg@1.0. ref valid github ref type without github:: prefix, github used. E.g. user/repo equivalent github::user/repo user/repo@tag equivalent github::user/repo@tag, etc. ref GitHub URL (see ) without github:: prefix, github used. ref path starts . / \\ ~ local used. (pak check path exists.) package reference form =?, special param type. See \"Parameters\" . package reference explicit package source, package source determined rules, pak throws error.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"package-names","dir":"Reference","previous_headings":"","what":"Package names","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"pak looking dependencies package, needs able determine name dependency package reference. sometimes easy dependencies Remotes (similar) fields. github:: gitlab:: dependencies pak assumes package name name repository. hold, need specify package name explicitly, using = prefix. E.g. pins=rstudio/pins-r. specify package source type package name, package name comes first: pins=github::rstudio/pins-r. git:: dependencies, pak assumes package name last component repository. hold, need specify package name explicitly, using = prefix. E.g. pins=git::https://github.com/rstudio/pins-r. local:: dependencies, always need specify package name explicitly. E.g. pins=local::~/works/pins. url:: dependencies, always need specify package name explicitly. E.g. ggplot2=url::https://cloud.r-project.org/src/contrib/....","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"parameters","dir":"Reference","previous_headings":"","what":"Parameters","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Package references may optional parameters, added question mark. Different parameters separated ampersand (&) character. (similar HTTP URLs take query parameters.) Parameters may flags turn behavior, can string value, assigned equal sign (=). value assigned, assume true value. example two package refs equivalent:  ","code":"cran::testthat?source&nocache cran::testthat?source=true&nocache=true"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"parameters-for-downstream-packages","dir":"Reference","previous_headings":"","what":"Parameters for downstream packages","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"pak allows specifying parameters downstream packages, using =? special package reference, package name package, parameters, . useful want add parameter downstream dependency. example, install ggplot2, always reinstall cli package dependency use ggplot2 cli=?reinstall package references. latter tells pak always reinstall cli, even already installed.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"currently-supported-parameters","dir":"Reference","previous_headings":"","what":"Currently supported parameters","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"ignore flag parameter. specified, package ignored. usually makes sense packagename=?ignore form, ignore downstream soft dependency. versions hard dependency ignored lead solution error. ignore--r version number parameter. package ignored R versions older specified one. E.g. Matrix=?ignore--r=4.1.2 ignore Matrix package R versions older 4.1.2. parameter really makes sense packgename=?ignore form. source flag parameter. specified, source R package requested CRAN-like repository. package installations source always triggers re-install. words, source implies reinstall parameter. parameter supported bioc::, cran:: standard:: remote types, ignored others. reinstall requests re-install package installations. supported bioc::, cran::, git::, github::, gitlab::, local::, standard::, url:: remote types. nocache ignore package cache. always download package file, add downloaded (built) package(s) package cache. supported bioc::, cran::, git::, github::, gitlab::, standard:: url:: remote types.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"cran-packages-cran-","dir":"Reference","previous_headings":"","what":"CRAN packages (cran::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"package CRAN. Full syntax:   valid package name. version version requirement. Examples:   Note: pak currently parses version specification part (everything @), use .","code":"[cran::][@[>=] | @current | @last] forecast forecast@8.8 forecast@>=8.8 cran::forecast forecast@last forecast@current"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"bioconductor-packages-bioc-","dir":"Reference","previous_headings":"","what":"Bioconductor packages (bioc::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"package Bioconductor. syntax CRAN packages, except prefix.  ","code":"[bioc::][@[>=] | @current | @last]"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"standard-packages-standard-","dir":"Reference","previous_headings":"","what":"Standard packages (standard::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"packages either CRAN Bioconductor, full syntax CRAN packages, except prefix:  ","code":"[standard::][@[>=] | current | last]"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"github-packages-github-","dir":"Reference","previous_headings":"","what":"GitHub packages (github::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Packages GitHub repository. Full syntax:   name package. missing, name repository used. GitHub username organization name. name repository. optional subdirectory, package within subdirectory repository. specifies certain version package, see . may specify: git branch, tag (prefix ) commit hash: @; pull request: #; latest release: @*release. missing, latest commit default branch used. Examples:   convenience GitHub HTTP URLs can also used specify package GitHub. Examples:   GitHub remote string can also used instead URL, example: git@github.com:r-lib/pak.git","code":"[=][github::]/[/][] r-lib/crayon github::r-lib/crayon r-lib/crayon@84be6207 r-lib/crayon@branch r-lib/crayon#41 r-lib/crayon@release https://github.com/r-lib/withr # A branch: https://github.com/r-lib/withr/tree/ghactions # A tag: https://github.com/r-lib/withr/tree/v2.1.1 # A commit: https://github.com/r-lib/withr/commit/8fbcb548e316 # A pull request: https://github.com/r-lib/withr/pull/76 # A release: https://github.com/r-lib/withr/releases/tag/v2.1.0"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"gitlab-packages-gitlab-","dir":"Reference","previous_headings":"","what":"GitLab packages (gitlab::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Packages GitLab repository. Full syntax:   name package. missing, name repository used. GitLab username group name. name repository. optional subdirectory, package within subdirectory repository. may specify git branch, tag (prefix ) commit hash. missing, latest commit default branch used. Examples:  ","code":"[=][github::]/[/][] gitlab::gaborcsardi/cli gitlab::r-hub/filelock@main"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"packages-in-git-repositories-git-","dir":"Reference","previous_headings":"","what":"Packages in git repositories (git::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Full syntax:   name package. missing, last component used. host name path git repository. git repositories need .git suffix , others forgiving. specifies certain version package: git branch, tag (prefix ) commit hash: @. missing, latest commit default branch used. Examples:   Note pak built-git client, require system git installation. system git installed, pak use credentials stored configured git credential store, automatically, via gitcreds package.","code":"[=]git::https?://[] git::https://github.com/r-lib/crayon git::https://github.com/r-lib/crayon.git git::https://github.com/r-lib/crayon.git@84be6207 git::https://github.com/r-lib/crayon.git@branch git::https://gitlab.com/gaborcsardi/cli.git"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"local-packages-local-","dir":"Reference","previous_headings":"","what":"Local packages (local::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"path refers package file built R CMD build, directory contains package. Full syntax:   brevity, can omit local:: prefix, specify absolute path, path user's home directory, starting ~, relative path starting ./ .\\\\. single dot (\".\") considered local package current working directory. Examples:   specify local package dependency (.e. DESCRIPTION), also need specify name package, see \"Package names\" .","code":"local:: local::/foo/bar/package_1.0.0.tar.gz local::/foo/bar/pkg local::. /absolute/path/package_1.0.0.tar.gz ~/path/from/home ./relative/path ."},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"urls-url-","dir":"Reference","previous_headings":"","what":"URLs (url::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"can use url:: refer URLs hold R package archives (.e. properly built R CMD build), compressed directories package trees (.e. built R CMD build). pak figure needs run R CMD build package first. remote type supports .tar.gz .zip files. Note URLs ideal remote types, pak needs download package file resolve dependencies. happens, puts package file cache, downloads needed installing package later. Examples:   specify package URL dependency (.e. DESCRIPTION), also need specify name package, see \"Package names\" .","code":"url::https://cloud.r-project.org/src/contrib/Archive/cli/cli_1.0.0.tar.gz url::https://github.com/tidyverse/stringr/archive/HEAD.zip"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"installed-packages-installed-","dir":"Reference","previous_headings":"","what":"Installed packages (installed::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"usually used internally, can also used directly. Full syntax:   library package installed . package name. Example:  ","code":"installed::/ installed::~/R/3.6/crayon"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"package-dependencies-deps-","dir":"Reference","previous_headings":"","what":"Package dependencies (deps::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Usually used internally, specifies dependencies local package. can used download install dependencies package, without downloading installing package . Full syntax:   Examples:  ","code":"deps:: deps::/foo/bar/package_1.0.0.tar.gz deps::/foo/bar/pkg deps::."},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"any-packages","dir":"Reference","previous_headings":"","what":"any:: packages","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"Sometimes need install additional packages, mind installed . example. want install cli GitHub, r-lib/cli. also want install glue, mind version glue installed, long compatible requested cli version. cli specifies development version glue, fine. cli fine CRAN version glue, OK, . future version cli depend glue, still want glue installed, CRAN. :: reference type exactly . example might write   first, fail rlib/cli requests (say) tidyverse/glue, pkg_install() \"glue\" interpreted \"standard::glue\", creating conflict tidyverse/glue. hand   works, independently glue version requested cli.","code":"pak::pkg_install(c(\"glue\", \"r-lib/cli\")) pak::pkg_install(c(\"any::glue\", \"r-lib/cli\"))"},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"parameter-refs-param-","dir":"Reference","previous_headings":"","what":"Parameter refs (param::)","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"See \"Parameters\" .","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_package_sources.html","id":"the-remotes-field","dir":"Reference","previous_headings":"","what":"The Remotes field","title":"Install packages from CRAN, Bioconductor, GitHub, URLs, etc. — Package sources","text":"DESCRIPTION file R package can mark regular dependency defined Depends, Imports, Suggests Enhances fields installed non-standard package source adding package reference Remotes entry. pak download install package specified location, instead CRAN-like repository. remote dependencies specified Remotes comma separated list package sources:   Note still need add package one regular dependency fields, .e. Imports, Suggests, etc. concrete example specifies r-lib/glue package:   CRAN Bioconductor repositories support Remotes field, need remove field, submitting package either .","code":"Remotes: , , [ ... ] Imports: glue Remotes: r-lib/glue, r-lib/httr@v0.4, klutometis/roxygen#142, r-lib/testthat@c67018fa4970"},{"path":"https://pak.r-lib.org/dev/reference/pak_setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up private pak library (deprecated) — pak_setup","title":"Set up private pak library (deprecated) — pak_setup","text":"function deprecated nothing. Recent versions pak need pak_setup() call.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up private pak library (deprecated) — pak_setup","text":"","code":"pak_setup(mode = c(\"auto\", \"download\", \"copy\"), quiet = FALSE)"},{"path":"https://pak.r-lib.org/dev/reference/pak_setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up private pak library (deprecated) — pak_setup","text":"mode get packages . \"download\" try download CRAN. \"copy\" try copy current \"regular\" package library. \"auto\" try copy first, fails, tries download. quiet Whether omit messages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up private pak library (deprecated) — pak_setup","text":"path private library, invisibly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_sitrep.html","id":null,"dir":"Reference","previous_headings":"","what":"pak SITuation REPort — pak_sitrep","title":"pak SITuation REPort — pak_sitrep","text":"prints pak version, current library path, location private library, whether pak private library exists, whether pak private library functional.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_sitrep.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"pak SITuation REPort — pak_sitrep","text":"","code":"pak_sitrep()"},{"path":"https://pak.r-lib.org/dev/reference/pak_sitrep.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"pak SITuation REPort — pak_sitrep","text":"","code":"pak_sitrep() #> compatible) #> - pak repository: - (local install?) #> * Optional packages installed: #> - pillar #> * Library path: #> - /private/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T/RtmpcpVAdU/fi #> led8ef3d7a46fc #> - /private/var/folders/ph/fpcmzfd16rgbbk8mxvy9m2_h0000gn/T/RtmpcpVAdU/fi #> led8ef2562d6ef #> - /Users/gaborcsardi/Library/R/arm64/4.2/library #> - /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library #> * Private library location: #> - /Users/gaborcsardi/Library/Caches/org.R-project.R/R/pak/lib/4.2/aarch6 #> 4 #> * Private library exists. #> * Private library is functional"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pak_solver.html","id":null,"dir":"Reference","previous_headings":"","what":"Find the ideal set of packages and versions to install — The dependency solver","title":"Find the ideal set of packages and versions to install — The dependency solver","text":"pak contains package dependency solver, makes sure package source version requirements packages satisfied, starting installation. CRAN BioC packages usually automatic, repositories generally consistent state. packages depend package sources, however, case.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_solver.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Find the ideal set of packages and versions to install — The dependency solver","text":"example conflict detected: r-lib/pkgcache@conflict depends main branch r-lib/cli, whereas, explicitly requested message branch. Since install versions single library, pak quits. pak considers package installation, package given name , (e.g. dependency another package), package may package source. necessary, one R package library may contain one version package given name. pak's behavior best explained via example. Assume installing local package (see ), e.g. local::., local package depends pkgA user/pkgB, latter package GitHub (see ), pkgA also depends pkgB. Now pak must install pkgB user/pkgB. case pak interprets pkgB package package source, instead standard package, installing user/pkgB satisfies requirements. Note cran::pkgB user/pkgB requirements result conflict pak resolve. first one must CRAN package, second one must GitHub package, two different packages installed R package library.","code":"> pak::pkg_install(c(\"r-lib/pkgcache@conflict\", \"r-lib/cli@message\")) Error: Cannot install packages: * Cannot install `r-lib/pkgcache@conflict`. - Cannot install dependency r-lib/cli@main * Cannot install `r-lib/cli@main`. - Conflicts r-lib/cli@message"},{"path":"https://pak.r-lib.org/dev/reference/pak_update.html","id":null,"dir":"Reference","previous_headings":"","what":"Update pak itself — pak_update","title":"Update pak itself — pak_update","text":"Use function update released development version pak.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_update.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update pak itself — pak_update","text":"","code":"pak_update(force = FALSE, stream = c(\"auto\", \"stable\", \"rc\", \"devel\"))"},{"path":"https://pak.r-lib.org/dev/reference/pak_update.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update pak itself — pak_update","text":"force Whether force update, even newer version available. stream Whether update \"stable\", \"rc\" (release candidate) \"devel\" (development) version. \"auto\" updates stream current one. Often release candidate version, \"rc\" also installs stable version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pak_update.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update pak itself — pak_update","text":"Nothing.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":null,"dir":"Reference","previous_headings":"","what":"Look up the dependencies of a package — pkg_deps","title":"Look up the dependencies of a package — pkg_deps","text":"Look dependencies package","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Look up the dependencies of a package — pkg_deps","text":"","code":"pkg_deps(pkg, upgrade = TRUE, dependencies = NA)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Look up the dependencies of a package — pkg_deps","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Look up the dependencies of a package — pkg_deps","text":"data frame dependency data, includes pkg well. following columns. built: Built field DESCRIPTION file binary packages, information available. cache_status: whether package file package cache. NA installed:: package refs. dep_types: character vector dependency types considered package. (list column.) deps: dependencies package, data frame. See \"Package dependency tables\" . direct: whether package (ref, really) directly specified, added dependency. error: list column contains error objects refs pkgdepends failed resolve. filesize: file size bytes, NA information available. license: license package, NA available. md5sum: MD5 checksum package file, available, NA . metadata: named character vector. fields () added installed DESCRIPTION file package. mirror: URL CRAN(-like) mirror site metadata obtained . NA non-CRAN-like sources, e.g. local files, installed packages, GitHub, etc. needscompilation: whether package needs compilation. package: package name. priority: \"base\" base packages, \"recommended\" recommended packages, NA otherwise. ref: package reference. remote: parsed remote_ref objects, see parse_pkg_refs(). list column. repodir: directory package CRAN-like repository. sha256: SHA256 hash package file, available, otherwise NA. sources: URLs package can downloaded . necessarily URL can download HTTP client. E.g. local:: refs path, git:: refs URL git. zero length vector installed:: refs. status: status dependency resolution, \"OK\" \"FAILED\". target: path package saved CRAN-repository. type: ref type. version: package version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"package-dependency-tables","dir":"Reference","previous_headings":"","what":"Package dependency tables","title":"Look up the dependencies of a package — pkg_deps","text":"package dependency tables deps list column five columns currently: ref: package ref dependency. type: dependency type, lowercase. .e. imports, suggests, etc. package: package name dependency. op: operator version requirements, e.g. >=. version: version number, version requirements.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Look up the dependencies of a package — pkg_deps","text":"package GitHub:","code":"pkg_deps(\"dplyr\") #> # A data frame: 16 × 32 #> ref type direct direc…¹ status package version license needs…² #> #> 1 R6 stan… FALSE FALSE OK R6 2.5.1 MIT + … FALSE #> 2 cli stan… FALSE FALSE OK cli 3.4.1 MIT + … FALSE #> 3 dplyr stan… TRUE TRUE OK dplyr 1.0.10 MIT + … FALSE #> 4 fansi stan… FALSE FALSE OK fansi 1.0.3 GPL-2 … FALSE #> 5 generics stan… FALSE FALSE OK generi… 0.1.3 MIT + … FALSE #> 6 glue stan… FALSE FALSE OK glue 1.6.2 MIT + … FALSE #> 7 lifecycle stan… FALSE FALSE OK lifecy… 1.0.3 MIT + … FALSE #> 8 magrittr stan… FALSE FALSE OK magrit… 2.0.3 MIT + … FALSE #> 9 pillar stan… FALSE FALSE OK pillar 1.8.1 MIT + … FALSE #> 10 pkgconfig stan… FALSE FALSE OK pkgcon… 2.0.3 MIT + … FALSE #> 11 rlang stan… FALSE FALSE OK rlang 1.0.6 MIT + … FALSE #> 12 tibble stan… FALSE FALSE OK tibble 3.1.8 MIT + … FALSE #> 13 tidysele… stan… FALSE FALSE OK tidyse… 1.2.0 MIT + … FALSE #> 14 utf8 stan… FALSE FALSE OK utf8 1.2.2 Apache… FALSE #> 15 vctrs stan… FALSE FALSE OK vctrs 0.5.1 MIT + … FALSE #> 16 withr stan… FALSE FALSE OK withr 2.5.0 MIT + … FALSE #> # … with 23 more variables: priority , md5sum , sha256 , #> # filesize , built , platform , rversion , #> # repotype , repodir , target , deps , #> # mirror , sources , remote , error , #> # metadata , dep_types , params , sysreqs , #> # cache_status , lib_status , old_version , #> # new_version , and abbreviated variable names ¹​directpkg, … pkg_deps(\"r-lib/callr\") #> # A data frame: 4 × 32 #> ref type direct direc…¹ status package version license needs…² #> #> 1 r-lib/cal… gith… TRUE TRUE OK callr 3.7.3.… MIT + … TRUE #> 2 R6 stan… FALSE FALSE OK R6 2.5.1 MIT + … FALSE #> 3 processx stan… FALSE FALSE OK proces… 3.8.0 MIT + … FALSE #> 4 ps stan… FALSE FALSE OK ps 1.7.2 MIT + … FALSE #> # … with 23 more variables: priority , md5sum , sha256 , #> # filesize , built , platform , rversion , #> # repotype , repodir , target , deps , #> # mirror , sources , remote , error , #> # metadata , dep_types , params , sysreqs , #> # cache_status , lib_status , old_version , #> # new_version , and abbreviated variable names ¹​directpkg, …"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":null,"dir":"Reference","previous_headings":"","what":"Explain how a package depends on other packages — pkg_deps_explain","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"Extract dependency chains pkg deps.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"","code":"pkg_deps_explain(pkg, deps, upgrade = TRUE, dependencies = NA)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. deps Package names dependencies explain. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"named list print method. First entries function arguments: pkg, deps, dependencies, last one paths contains results named list, names package names deps.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"function similar pkg_deps_tree(), output easier read interested certain packages (deps).","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_explain.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Explain how a package depends on other packages — pkg_deps_explain","text":"dplyr depend rlang? GH version usethis depend cli ps?","code":"pkg_deps_explain(\"dplyr\", \"rlang\") #> ✔ Updated metadata database: 5.09 MB in 12 files. #> ✔ Updating metadata database ... done #> dplyr -> lifecycle -> rlang #> dplyr -> rlang #> dplyr -> tibble -> lifecycle -> rlang #> dplyr -> tibble -> pillar -> lifecycle -> rlang #> dplyr -> tibble -> pillar -> rlang #> dplyr -> tibble -> pillar -> vctrs -> lifecycle -> rlang #> dplyr -> tibble -> pillar -> vctrs -> rlang #> dplyr -> tibble -> rlang #> dplyr -> tibble -> vctrs -> lifecycle -> rlang #> dplyr -> tibble -> vctrs -> rlang #> dplyr -> tidyselect -> lifecycle -> rlang #> dplyr -> tidyselect -> rlang #> dplyr -> tidyselect -> vctrs -> lifecycle -> rlang #> dplyr -> tidyselect -> vctrs -> rlang #> dplyr -> vctrs -> lifecycle -> rlang #> dplyr -> vctrs -> rlang #> dplyr -> pillar -> lifecycle -> rlang #> dplyr -> pillar -> rlang #> dplyr -> pillar -> vctrs -> lifecycle -> rlang #> dplyr -> pillar -> vctrs -> rlang pkg_deps_explain(\"r-lib/usethis\", c(\"cli\", \"ps\")) #> usethis -> cli #> usethis -> desc -> cli #> usethis -> gh -> cli #> usethis -> lifecycle -> cli #> #> x ps"},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw the dependency tree of a package — pkg_deps_tree","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"Draw dependency tree package","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"","code":"pkg_deps_tree(pkg, upgrade = TRUE, dependencies = NA)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. upgrade Whether use recent available package versions. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"data frame pkg_deps(), invisibly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_deps_tree.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Draw the dependency tree of a package — pkg_deps_tree","text":"","code":"pkg_deps_tree(\"dplyr\") #> dplyr 1.0.10 ✨ #> ├─generics 0.1.3 ✨ #> ├─glue 1.6.2 ✨ #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli 3.4.1 ✨ #> │ ├─glue #> │ └─rlang 1.0.6 ✨ #> ├─magrittr 2.0.3 ✨ #> ├─R6 2.5.1 ✨ #> ├─rlang #> ├─tibble 3.1.8 ✨ #> │ ├─fansi 1.0.3 ✨ #> │ ├─lifecycle #> │ ├─magrittr #> │ ├─pillar 1.8.1 ✨ #> │ │ ├─cli #> │ │ ├─fansi #> │ │ ├─glue #> │ │ ├─lifecycle #> │ │ ├─rlang #> │ │ ├─utf8 1.2.2 ✨ #> │ │ └─vctrs 0.5.1 ✨ #> │ │ ├─cli #> │ │ ├─glue #> │ │ ├─lifecycle #> │ │ └─rlang #> │ ├─pkgconfig 2.0.3 ✨ #> │ ├─rlang #> │ └─vctrs #> ├─tidyselect 1.2.0 ✨ #> │ ├─cli #> │ ├─glue #> │ ├─lifecycle #> │ ├─rlang #> │ ├─vctrs #> │ └─withr 2.5.0 ✨ #> ├─vctrs #> └─pillar #> #> Key: ✨ new pkg_deps_tree(\"r-lib/usethis\") #> r-lib/usethis 2.1.6.9000 ✨👷🏼🔧 #> ├─cli 3.4.1 ✨ #> ├─clipr 0.8.0 ✨ #> ├─crayon 1.5.2 ✨ #> ├─curl 4.3.3 ✨ #> ├─desc 1.4.2 ✨ #> │ ├─cli #> │ ├─R6 2.5.1 ✨ #> │ └─rprojroot 2.0.3 ✨ #> ├─fs 1.5.2 ✨ #> ├─gert 1.9.2 ✨ ⬇ (1.91 MB) #> │ ├─askpass 1.1 ✨ #> │ │ └─sys 3.4.1 ✨ #> │ ├─credentials 1.3.2 ✨ ⬇ (170.15 kB) #> │ │ ├─openssl 2.0.5 ✨ #> │ │ │ └─askpass #> │ │ ├─sys #> │ │ ├─curl #> │ │ ├─jsonlite 1.8.4 ✨ #> │ │ └─askpass #> │ ├─openssl #> │ ├─rstudioapi 0.14 ✨ #> │ ├─sys #> │ └─zip 2.2.2 ✨ #> ├─gh 1.3.1 ✨ ⬇ (95.20 kB) #> │ ├─cli #> │ ├─gitcreds 0.1.2 ✨ ⬇ (95.59 kB) #> │ ├─httr 1.4.4 ✨ #> │ │ ├─curl #> │ │ ├─jsonlite #> │ │ ├─mime 0.12 ✨ #> │ │ ├─openssl #> │ │ └─R6 #> │ ├─ini 0.3.1 ✨ ⬇ (13.13 kB) #> │ └─jsonlite #> ├─glue 1.6.2 ✨ #> ├─jsonlite #> ├─lifecycle 1.0.3 ✨ #> │ ├─cli #> │ ├─glue #> │ └─rlang 1.0.6 ✨ #> ├─purrr 0.3.5 ✨ #> │ ├─magrittr 2.0.3 ✨ #> │ └─rlang #> ├─rappdirs 0.3.3 ✨ #> ├─rlang #> ├─rprojroot #> ├─rstudioapi #> ├─whisker 0.4.1 ✨ ⬇ (65.36 kB) #> ├─withr 2.5.0 ✨ #> └─yaml 2.3.6 ✨ #> #> Key: ✨ new | ⬇ download | 👷🏼 build | 🔧 compile"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":null,"dir":"Reference","previous_headings":"","what":"Download a package and its dependencies — pkg_download","title":"Download a package and its dependencies — pkg_download","text":"TODO: explain result","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download a package and its dependencies — pkg_download","text":"","code":"pkg_download( pkg, dest_dir = \".\", dependencies = FALSE, platforms = NULL, r_versions = NULL )"},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download a package and its dependencies — pkg_download","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. dest_dir Destination directory packages. exist, created. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies. platforms Types binary source packages download. default value pkgdepends::default_platforms(). r_versions R version(s) download packages . (matter source packages, binaries.) defaults current R version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download a package and its dependencies — pkg_download","text":"Data frame information downloaded packages, invisibly. Columns: built: Built field DESCRIPTION file binary packages, information available. cache_status: whether package file package cache. NA installed:: package refs. dep_types: character vector dependency types considered package. (list column.) deps: dependencies package, data frame. See \"Package dependency tables\" . direct: whether package (ref, really) directly specified, added dependency. error: list column contains error objects refs pkgdepends failed resolve. filesize: file size bytes, NA information available. license: license package, NA available. md5sum: MD5 checksum package file, available, NA . metadata: named character vector. fields () added installed DESCRIPTION file package. mirror: URL CRAN(-like) mirror site metadata obtained . NA non-CRAN-like sources, e.g. local files, installed packages, GitHub, etc. needscompilation: whether package needs compilation. package: package name. priority: \"base\" base packages, \"recommended\" recommended packages, NA otherwise. ref: package reference. remote: parsed remote_ref objects, see parse_pkg_refs(). list column. repodir: directory package CRAN-like repository. sha256: SHA256 hash package file, available, otherwise NA. sources: URLs package can downloaded . necessarily URL can download HTTP client. E.g. local:: refs path, git:: refs URL git. zero length vector installed:: refs. status: status dependency resolution, \"OK\" \"FAILED\". target: path package saved CRAN-repository. type: ref type. version: package version. fulltarget: absolute path downloaded file. one fulltarget fulltarget_tree must exist disk. fulltarget_tree: absolute path package tree directory. one fulltarget fulltarget_tree must exist disk. download_status: \"\" \"Got\", depending whether file obtained cache. download_error: error object failed downloads. file_size: Size file, NA. installed:: refs, NA, also NA refs created fulltarget_tree instead fulltarget.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"package-dependency-tables","dir":"Reference","previous_headings":"","what":"Package dependency tables","title":"Download a package and its dependencies — pkg_download","text":"package dependency tables deps list column five columns currently: ref: package ref dependency. type: dependency type, lowercase. .e. imports, suggests, etc. package: package name dependency. op: operator version requirements, e.g. >=. version: version number, version requirements.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_download.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download a package and its dependencies — pkg_download","text":"","code":"dl <- pkg_download(\"forcats\") #> ℹ No downloads are needed, 2 pkgs (641.53 kB) are cached dl #> # A data frame: 2 × 35 #> ref type direct direc…¹ status package version license needs…² #> #> 1 forcats standard TRUE TRUE OK forcats 0.5.2 MIT + … FALSE #> 2 forcats standard TRUE TRUE OK forcats 0.5.2 MIT + … FALSE #> # … with 26 more variables: priority , md5sum , sha256 , #> # filesize , built , platform , rversion , #> # repotype , repodir , target , deps , #> # mirror , sources , remote , error , #> # metadata , extra , dep_types , params , #> # sysreqs , cache_status , fulltarget , #> # fulltarget_tree , download_status , … dl$fulltarget #> [1] \"./bin/macosx/big-sur-arm64/contrib/4.2/forcats_0.5.2.tgz\" #> [2] \"./src/contrib/forcats_0.5.2.tar.gz\" pkg_download(\"r-lib/pak\", platforms = \"source\") #> ℹ No downloads are needed, 1 pkg is cached"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":null,"dir":"Reference","previous_headings":"","what":"Query the history of a CRAN package — pkg_history","title":"Query the history of a CRAN package — pkg_history","text":"Query history CRAN package","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query the history of a CRAN package — pkg_history","text":"","code":"pkg_history(pkg)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query the history of a CRAN package — pkg_history","text":"pkg Package name.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Query the history of a CRAN package — pkg_history","text":"data frame, one row per package version. columns entries DESCRIPTION files released package versions.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_history.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query the history of a CRAN package — pkg_history","text":"","code":"pkg_history(\"ggplot2\") #> # A data frame: 44 × 30 #> Package Type Title Version Date Author Maint…¹ Descr…² License #> * #> 1 ggplot2 Package An impl… 0.5 2007… Hadle… Hadley… \"An im… GPL #> 2 ggplot2 Package An impl… 0.5.1 2007… Hadle… Hadley… \"An im… GPL #> 3 ggplot2 Package An impl… 0.5.2 2007… Hadle… Hadley… \"An im… GPL #> 4 ggplot2 Package An impl… 0.5.4 2007… Hadle… Hadley… \"An im… GPL #> 5 ggplot2 Package An impl… 0.5.5 2007… Hadle… Hadley… \"An im… GPL #> 6 ggplot2 Package An impl… 0.5.6 2007… Hadle… Hadley… \"An im… GPL #> 7 ggplot2 Package An impl… 0.5.7 2007… Hadle… Hadley… \"An im… GPL #> 8 ggplot2 Package An impl… 0.6 2008… Hadle… Hadley… \"An im… GPL #> 9 ggplot2 Package An impl… 0.7 2008… Hadle… Hadley… \"An im… GPL #> 10 ggplot2 Package An impl… 0.8 2008… Hadle… Hadley… \"An im… GPL #> # … with 34 more rows, 21 more variables: SaveImage , #> # LazyData , Packaged , crandb_file_date , date , #> # dependencies , URL , LazyLoad , Extends , #> # Collate , Repository , `Date/Publication` , #> # NeedsCompilation , VignetteBuilder , BugReports , #> # `Authors@R` , RoxygenNote , Encoding , MD5sum , #> # `Config/Needs/website` , `Config/testthat/edition` , …"},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Install packages — pkg_install","title":"Install packages — pkg_install","text":"Install one packages dependencies single package library.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install packages — pkg_install","text":"","code":"pkg_install( pkg, lib = .libPaths()[[1L]], upgrade = FALSE, ask = interactive(), dependencies = NA )"},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install packages — pkg_install","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. lib Package library install packages . Note dependent packages installed , even already installed another library. exceptions base recommended packages installed .Library. duplicated lib, unless newer version recommemded package needed. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. ask Whether ask confirmation installing different version package already installed. Installations add new packages never require confirmation. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install packages — pkg_install","text":"(Invisibly) data frame information installed package(s).","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_install.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Install packages — pkg_install","text":"Upgrade dplyr dependencies: Install development version dplyr: Switch back CRAN version. fast pak cached prior install.","code":"pkg_install(\"dplyr\") #> #> → Will install 5 packages. #> → All 5 packages (2.14 MB) are cached. #> + dplyr 1.0.9 #> + generics 0.1.2 #> + purrr 0.3.4 #> + R6 2.5.1 #> + tidyselect 1.1.2 #> ℹ No downloads are needed, 5 pkgs (2.14 MB) are cached #> ✔ Got R6 2.5.1 (aarch64-apple-darwin20) (82.52 kB) #> ✔ Installed R6 2.5.1 (43ms) #> ✔ Installed generics 0.1.2 (62ms) #> ✔ Installed dplyr 1.0.9 (88ms) #> ✔ Installed purrr 0.3.4 (88ms) #> ✔ Installed tidyselect 1.1.2 (94ms) #> ✔ 1 pkg + 17 deps: kept 12, added 5, dld 1 (82.52 kB) [1.2s] pkg_install(\"dplyr\", upgrade = TRUE) #> #> → Will update 1 package. #> → The package (742.51 kB) is cached. #> + rlang 1.0.2 → 1.0.3 👷🏿‍♀️🔧 #> ℹ No downloads are needed, 1 pkg (742.51 kB) is cached #> ℹ Building rlang 1.0.3 #> ✔ Built rlang 1.0.3 (5.8s) #> ✔ Installed rlang 1.0.3 (32ms) #> ✔ 1 pkg + 17 deps: kept 17, upd 1 [6.3s] pkg_install(\"tidyverse/dplyr\") #> ✔ Loading metadata database ... done #> #> → Will install 16 packages. #> → All 16 packages (8.09 MB) are cached. #> + cli 3.4.1 #> + dplyr 1.0.99.9000 👷🏾‍♂️🔧 (GitHub: e6252f8) #> + fansi 1.0.3 #> + generics 0.1.3 #> + glue 1.6.2 #> + lifecycle 1.0.3 #> + magrittr 2.0.3 #> + pillar 1.8.1 #> + pkgconfig 2.0.3 #> + R6 2.5.1 #> + rlang 1.0.6 #> + tibble 3.1.8 #> + tidyselect 1.2.0 #> + utf8 1.2.2 #> + vctrs 0.5.1 #> + withr 2.5.0 #> ℹ No downloads are needed, 16 pkgs (8.09 MB) are cached #> ✔ Installed R6 2.5.1 (58ms) #> ✔ Installed cli 3.4.1 (69ms) #> ✔ Installed fansi 1.0.3 (92ms) #> ✔ Installed generics 0.1.3 (99ms) #> ✔ Installed glue 1.6.2 (108ms) #> ✔ Installed lifecycle 1.0.3 (144ms) #> ✔ Installed magrittr 2.0.3 (152ms) #> ✔ Installed pillar 1.8.1 (160ms) #> ✔ Installed pkgconfig 2.0.3 (63ms) #> ✔ Installed rlang 1.0.6 (37ms) #> ✔ Installed tibble 3.1.8 (41ms) #> ✔ Installed tidyselect 1.2.0 (38ms) #> ✔ Installed utf8 1.2.2 (36ms) #> ✔ Installed vctrs 0.5.1 (39ms) #> ✔ Installed withr 2.5.0 (30ms) #> ℹ Packaging dplyr 1.0.99.9000 #> ✔ Packaged dplyr 1.0.99.9000 (8.3s) #> ℹ Building dplyr 1.0.99.9000 #> ✔ Built dplyr 1.0.99.9000 (5.2s) #> ✔ Installed dplyr 1.0.99.9000 (github::tidyverse/dplyr@e6252f8) (24ms) #> ✔ 1 pkg + 15 deps: added 16 [18.9s] pkg_install(\"dplyr\") #> ✔ Updated metadata database: 2.43 MB in 6 files. #> ✔ Updating metadata database ... done #> #> → Will install 16 packages. #> → All 16 packages (9.42 MB) are cached. #> + cli 3.4.1 #> + dplyr 1.0.10 #> + fansi 1.0.3 #> + generics 0.1.3 #> + glue 1.6.2 #> + lifecycle 1.0.3 #> + magrittr 2.0.3 #> + pillar 1.8.1 #> + pkgconfig 2.0.3 #> + R6 2.5.1 #> + rlang 1.0.6 #> + tibble 3.1.8 #> + tidyselect 1.2.0 #> + utf8 1.2.2 #> + vctrs 0.5.1 #> + withr 2.5.0 #> ℹ No downloads are needed, 16 pkgs (9.42 MB) are cached #> ✔ Installed R6 2.5.1 (66ms) #> ✔ Installed cli 3.4.1 (76ms) #> ✔ Installed dplyr 1.0.10 (111ms) #> ✔ Installed fansi 1.0.3 (119ms) #> ✔ Installed generics 0.1.3 (125ms) #> ✔ Installed glue 1.6.2 (132ms) #> ✔ Installed lifecycle 1.0.3 (149ms) #> ✔ Installed magrittr 2.0.3 (162ms) #> ✔ Installed pillar 1.8.1 (56ms) #> ✔ Installed pkgconfig 2.0.3 (35ms) #> ✔ Installed rlang 1.0.6 (57ms) #> ✔ Installed tibble 3.1.8 (41ms) #> ✔ Installed tidyselect 1.2.0 (40ms) #> ✔ Installed utf8 1.2.2 (37ms) #> ✔ Installed vctrs 0.5.1 (39ms) #> ✔ Installed withr 2.5.0 (31ms) #> ✔ 1 pkg + 15 deps: added 16 [7.2s]"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if an R package name is available — pkg_name_check","title":"Check if an R package name is available — pkg_name_check","text":"Additionally, look candidate name number dictionaries, make sure negative meaning.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if an R package name is available — pkg_name_check","text":"","code":"pkg_name_check(name, dictionaries = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if an R package name is available — pkg_name_check","text":"name Package name candidate. dictionaries Character vector, dictionaries query. Available dictionaries: * wikipedia * wiktionary, * sentiment (https://github.com/fnielsen/afinn), * urban (Urban Dictionary). NULL (default), Urban Dictionary omitted, often offensive.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if an R package name is available — pkg_name_check","text":"pkg_name_check object custom print method.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"valid-package-name-check","dir":"Reference","previous_headings":"","what":"Valid package name check","title":"Check if an R package name is available — pkg_name_check","text":"Check validity name package name. See 'Writing R Extensions' allowed package names. Also checked list names known cause problems.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"cran-checks","dir":"Reference","previous_headings":"","what":"CRAN checks","title":"Check if an R package name is available — pkg_name_check","text":"Check name names past current packages CRAN, including base recommended packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"bioconductor-checks","dir":"Reference","previous_headings":"","what":"Bioconductor checks","title":"Check if an R package name is available — pkg_name_check","text":"Check name past current Bioconductor packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"profanity-check","dir":"Reference","previous_headings":"","what":"Profanity check","title":"Check if an R package name is available — pkg_name_check","text":"Check name https://www.purgomalum.com/service/containsprofanity make sure profanity.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"dictionaries","dir":"Reference","previous_headings":"","what":"Dictionaries","title":"Check if an R package name is available — pkg_name_check","text":"See dictionaries argument.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_name_check.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if an R package name is available — pkg_name_check","text":"","code":"pkg_name_check(\"sicily\") #> ╔══════════════════════════════════════════════════════════════════════╗ #> ║ –*– sicily –*– ║ #> ╚══════════════════════════════════════════════════════════════════════╝ #> ┌──────────────────────────────────────────────────────────────────────┐ #> │ ✔ valid name ✔ CRAN ✔ Bioconductor │ #> │ ✔ not a profanity │ #> └──────────────────────────────────────────────────────────────────────┘ #> ┌ Wikipedia ───────────────────────────────────────────────────────────┐ #> │ Sicily Sicily (Italian: Sicilia [siˈtʃiːlja], Sicilian │ #> │ pronunciation: [sɪˈʃiːlja]) is the largest island in the │ #> │ Mediterranean Sea and one of the 20 regions of Italy. The Strait of │ #> │ Messina divides it from the region of Calabria in Southern Italy. │ #> │ It is one of the five Italian autonomous regions and is officially │ #> │ referred to as Regione Siciliana. The region has 5 million │ #> │ … │ #> └──────────────────────────────── https://en.wikipedia.org/wiki/Sicily ┘ #> ┌ Wiktionary ──────────────────────────────────────────────────────────┐ #> │ sicily No English definition found │ #> └──────────────────────────────────────────────────────────────────── ┘ #> ┌──────────────────────────────────────────────────────────────────────┐ #> │ Sentiment: 😐 (0) │ #> └──────────────────────────────────────────────────────────────────────┘"},{"path":"https://pak.r-lib.org/dev/reference/pkg_remove.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove installed packages — pkg_remove","title":"Remove installed packages — pkg_remove","text":"Remove installed packages","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_remove.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove installed packages — pkg_remove","text":"","code":"pkg_remove(pkg, lib = .libPaths()[[1L]])"},{"path":"https://pak.r-lib.org/dev/reference/pkg_remove.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove installed packages — pkg_remove","text":"pkg character vector packages remove. lib library remove packages .","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_remove.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove installed packages — pkg_remove","text":"Nothing.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Search CRAN packages — pkg_search","title":"Search CRAN packages — pkg_search","text":"Search indexed database current CRAN packages. uses pkgsearch package. See package details also pkgsearch::pkg_search() pagination, advanced searching, etc.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search CRAN packages — pkg_search","text":"","code":"pkg_search(query, ...)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search CRAN packages — pkg_search","text":"query Search query string. ... Additional arguments passed pkgsearch::pkg_search()","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search CRAN packages — pkg_search","text":"data frame, also pak_search_result object custom print method. see underlying table, can use [] drop extra classes. See examples .","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_search.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search CRAN packages — pkg_search","text":"Simple search See underlying data frame","code":"pkg_search(\"survival\") #> #> 1 survival 3.4.0 -- by Terry M Therneau, 4 months ago #> Survival Analysis #> #> 2 survminer 0.4.9 -- by Alboukadel Kassambara, 2 years ago #> Drawing Survival Curves using 'ggplot2' #> #> 3 flexsurv 2.2 -- by Christopher Jackson, 6 months ago #> Flexible Parametric Survival and Multi-State Models #> #> 4 muhaz 1.2.6.4 -- by David Winsemius, 2 years ago #> Hazard Function Estimation in Survival Analysis #> #> 5 pec 2022.5.4 -- by Thomas A. Gerds, 8 months ago #> Prediction Error Curves for Risk Prediction Models in Survival Analysi #> s #> #> 6 randomForestSRC 3.1.1 -- by Udaya B. Kogalur, 5 months ago #> Fast Unified Random Forests for Survival, Regression, and Classificati #> on (RF-SRC) #> #> 7 relsurv 2.2.8 -- by Damjan Manevski, 4 months ago #> Relative Survival #> #> 8 survRM2 1.0.4 -- by Hajime Uno, 6 months ago #> Comparing Restricted Mean Survival Time #> #> 9 titanic 0.1.0 -- by Paul Hendricks, 7 years ago #> Titanic Passenger Survival Data Set #> #> 10 KMsurv 0.1.5 -- by Jun Yan, 10 years ago #> Data sets from Klein and Moeschberger (1997), Survival Analysis psro <- pkg_search(\"ropensci\") psro[] #> # A data frame: 10 × 15 #> score package version title descr…¹ date maint…² #> #> 1 538. webmockr 0.8.2 Stub… \"Stubb… 2022-08-28 19:20:02 Scott … #> 2 520. RSelenium 1.7.9 R Bi… \"Provi… 2022-09-02 07:10:11 Ju Yeo… #> 3 416. tracerer 2.2.2 Trac… \"'BEAS… 2021-05-30 08:40:03 Richèl… #> 4 376. rfisheries 0.2 'Pro… \"A pro… 2016-02-19 08:50:03 Karthi… #> 5 367. mcbette 1.15 Mode… \"'BEAS… 2022-08-27 12:30:02 Richèl… #> 6 359. taxize 0.9.100 Taxo… \"Inter… 2022-04-22 07:30:02 Zachar… #> 7 350. beastier 2.4.11 Call… \"'BEAS… 2022-08-11 13:40:04 Richèl… #> 8 347. spocc 1.2.0 Inte… \"A pro… 2021-01-05 19:50:03 Scott … #> 9 316. chromer 0.3 Inte… \"A pro… 2022-10-27 22:45:36 Karl W… #> 10 315. visdat 0.5.3 Prel… \"Creat… 2019-02-15 14:30:03 Nichol… #> # … with 8 more variables: maintainer_email , revdeps , #> # downloads_last_month , license , url , #> # bugreports , package_data >, ago , and #> # abbreviated variable names ¹​description, ²​maintainer_name"},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Display installed locations of a package — pkg_status","title":"Display installed locations of a package — pkg_status","text":"Display installed locations package","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Display installed locations of a package — pkg_status","text":"","code":"pkg_status(pkg, lib = .libPaths())"},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Display installed locations of a package — pkg_status","text":"pkg Name one installed packages display status . lib One library paths lookup packages status . default libraries used.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Display installed locations of a package — pkg_status","text":"Data frame data installations pkg. always columns: biocviews: corresponding field DESCRIPTION, must present Bioconductor packages, packages typically . built: Built field DESCRIPTION. depends, suggests, Imports, linkingto, enhances: corresponding fields DESCRIPTION files. deps: list data frames, dependencies package. columns: ref, type (dependency type lowercase), package (dependent package, R), op version, last two version requirement. op can >=, >, == <=, although first one common practice. library: path package library containing package. license: DESCRIPTION. md5sum: DESCTIPTION, typically NA, except Windows. needscompilation: DESCRIPTION, column logical. package: package name. platform: Built field DESCRIPTION, current platform missing DESCRIPTION. priority: DESCRIPTION, usually base, recommended, missing. ref: corresponding installed::* package reference. repository: DESCRIPTION. packages CRAN repository CRAN, repositories, e.g. R-universe adds repository URL . repotype: cran, bioc missing. rversion: Built field. field, current R version. sysreqs: SystemRequirements field DESCRIPTION. title: package title. type: always installed. version: package version (string).","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"notes-","dir":"Reference","previous_headings":"","what":"Notes:","title":"Display installed locations of a package — pkg_status","text":"addition, also remote* config/needs/* entries DESCRIPTION files. (Case insensitive.) columns type character, except needscompilation, logical deps, list columns. entry missing package, set NA. Note column names lowercase, even corresponding entries DESCRIPTION. order columns deterministic, assume order. Additional columns might present, internal pak used user code.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_status.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Display installed locations of a package — pkg_status","text":"","code":"pkg_status(\"MASS\") #> # A data frame: 2 × 39 #> library package title version depends repos…¹ license needs…² built #> * #> 1 /Users/ga… MASS Supp… 7.3-58… R (>= … CRAN GPL-2 … TRUE R 4.… #> 2 /Library/… MASS Supp… 7.3-58… R (>= … CRAN GPL-2 … TRUE R 4.… #> # … with 30 more variables: remotetype , remotepkgref , #> # remoteref , remoterepos , remotepkgplatform , #> # remotesha , imports , suggests , linkingto , #> # remotes , remotehost , remoterepo , #> # remoteusername , enhances , biocviews , #> # remoteurl , remotesubdir , priority , #> # remoteetag , remotepackaged , md5sum , …"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/pkg_sysreqs.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate system requirements of one of more packages — pkg_sysreqs","title":"Calculate system requirements of one of more packages — pkg_sysreqs","text":"Calculate system requirements one packages","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_sysreqs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate system requirements of one of more packages — pkg_sysreqs","text":"","code":"pkg_sysreqs(pkg, upgrade = TRUE, dependencies = NA, sysreqs_platform = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/pkg_sysreqs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate system requirements of one of more packages — pkg_sysreqs","text":"pkg Package names package references. E.g. ggplot2: package CRAN, Bioconductor CRAN-like repository general, tidyverse/ggplot2: package GitHub, tidyverse/ggplot2@v3.4.0: package GitHub tag branch, https://examples.com/.../ggplot2_3.3.6.tar.gz: package URL, .: package current working directory. See \"Package sources\" details. upgrade FALSE, default, pak minimum amount work give latest version(s) pkg. upgrade dependent packages pkg, one dependencies explicitly require higher version currently . also prefer binary package source package, even binary package older. upgrade = TRUE, pak ensure latest version(s) pkg dependencies. dependencies kinds dependencies install. commonly one following values: NA: required (hard) dependencies, TRUE: required dependencies plus optional development dependencies, FALSE: install dependencies. (might end non-working package, /installation might fail.) See Package dependency types possible values information package dependencies. sysreqs_platform System requirements platform. NULL, sysreqs_platform configuration option used, defaults current platform. Set option pak detect platform correctly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/pkg_sysreqs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate system requirements of one of more packages — pkg_sysreqs","text":"List entries: os: character string. Operating system. distribution: character string. Linux distribution, NA OS Linux. version: character string. Distribution version, NA OS Linux. pre_install: character vector. Commands run installation system packages. install_scripts: character vector. Commands run install system packages. post_install: character vector. Commands run installation system packages. packages: data frame. Information system packages needed. columns: sysreq: string, cross-platform name system requirement. packages: list column character vectors. names R packages system requirement. pre_install: list column character vectors. Commands run package installation system requirement. system_packages: list column character vectors. Names system packages install. post_install: list column character vectors. Commands run package installation system requirement.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_has_binaries.html","id":null,"dir":"Reference","previous_headings":"","what":"Does PPM build binary packages for the current platform? — ppm_has_binaries","title":"Does PPM build binary packages for the current platform? — ppm_has_binaries","text":"PPM build binary packages current platform?","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_has_binaries.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Does PPM build binary packages for the current platform? — ppm_has_binaries","text":"","code":"ppm_has_binaries()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_has_binaries.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Does PPM build binary packages for the current platform? — ppm_has_binaries","text":"TRUE FALSE.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_has_binaries.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Does PPM build binary packages for the current platform? — ppm_has_binaries","text":"","code":"if (FALSE) { system_r_platform() ppm_has_binaries() }"},{"path":"https://pak.r-lib.org/dev/reference/ppm_platforms.html","id":null,"dir":"Reference","previous_headings":"","what":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","title":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","text":"List platforms supported Posit Package Manager (PPM)","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_platforms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","text":"","code":"ppm_platforms()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_platforms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","text":"Data frame columns: name: platform name, essentially identifier, os: operating system, linux, windows macOS currently, binary_url: URL segment binary repository URL platform, see ppm_snapshots(). distribution: Linux platforms name distribution, release: Linux platforms, name release, binaries: whether PPM builds binaries platform.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_platforms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all platforms supported by Posit Package Manager (PPM) — ppm_platforms","text":"","code":"if (FALSE) { ppm_platforms() }"},{"path":"https://pak.r-lib.org/dev/reference/ppm_r_versions.html","id":null,"dir":"Reference","previous_headings":"","what":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","title":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","text":"List R versions supported Posit Package Manager (PPM)","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_r_versions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","text":"","code":"ppm_r_versions()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_r_versions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","text":"Data frame columns: r_version: minor R versions, .e. version numbers containing first two components R versions supported PPM instance.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_r_versions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all R versions supported by Posit Package Manager (PPM) — ppm_r_versions","text":"","code":"if (FALSE) { ppm_r_versions() }"},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"Returns current Posit Package Manager (PPM) repository URL","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"","code":"ppm_repo_url()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"String scalar, repository URL configured PPM instance. PPM instance configured, URL Posit Public Package Manager instance. includes repository name, e.g. https://packagemanager.posit.co/.","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"URL form {base}/{repo}, e.g. https://packagemanager.posit.co/. configure hosted PPM instance, set PKGCACHE_PPM_URL environment variable base URL (e.g. https://packagemanager.posit.co). use repo_add() PPM snapshots, may also set PKGCACHE_PPM_REPO environment variable name default repository. Linux, instead setting environment variables, can also add PPM repository repos option, see base::options(). environment variables set, ppm_repo_url() try extract PPM base URL repository name option. PKGCACHE_PPM_URL environment variable set, repos option contain PPM URL (Linux), pak uses public PPM instance https://packagemanager.posit.co, cran repository.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_repo_url.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Returns the current Posit Package Manager (PPM) repository URL — ppm_repo_url","text":"","code":"if (FALSE) { ppm_repo_url() }"},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":null,"dir":"Reference","previous_headings":"","what":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"List available Posit Package Manager (PPM) snapshots","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"","code":"ppm_snapshots()"},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"Data frame two columns: date: time snapshot taken, POSIXct vector, id: integer id snapshot, can used repository URL.","code":""},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"repository URL snapshot following form Windows: {base} base URL PPM (see ppm_repo_url()) {id} either date id snapshot, latest latest snapshot. E.g. equivalent: Linux distribution PPM support, repository URL contains binary packages looks like : {id} , {binary_url} code name release supported Linux distribution. See binary_url column result ppm_platforms() code names.","code":"{base}/{repo}/{id} https://packagemanager.posit.co/cran/5 https://packagemanager.posit.co/cran/2017-10-10 {base}/{repo}/__linux__/{binary_url}/{id}"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/ppm_snapshots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List all available Posit Package Manager (PPM) snapshots — ppm_snapshots","text":"","code":"if (FALSE) { ppm_snapshots() }"},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a new CRAN-like repository — repo_add","title":"Add a new CRAN-like repository — repo_add","text":"Add new repository list repositories pak uses look packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a new CRAN-like repository — repo_add","text":"","code":"repo_add(..., .list = NULL) repo_resolve(spec)"},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a new CRAN-like repository — repo_add","text":"... Repository specifications, possibly named character vectors. See details . .list List character vector repository specifications. argument easier use programmatically .... See details . spec Repository specification, possibly named character scalar.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a new CRAN-like repository — repo_add","text":"repo_resolve() returns named character scalar, URL repository.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add a new CRAN-like repository — repo_add","text":"repo_add() adds new repositories. resolves specified repositories using repo_resolve() modifies repos global option. repo_add() effect current R session. want keep configuration R sessions, set repos option desired value user project .Rprofile file.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"repository-specifications","dir":"Reference","previous_headings":"","what":"Repository specifications","title":"Add a new CRAN-like repository — repo_add","text":"format repository specification named unnamed character scalar. name missing, pak adds name automatically. repository named CRAN main CRAN repository, otherwise names informational. Currently supported repository specifications: URL pointing root CRAN-like repository. Example: RSPM@, RSPM (RStudio Package Manager) snapshot, specified date. RSPM@- RSPM snapshot, day release . RSPM@R- RSPM snapshot, day R released. MRAN@, MRAN (Microsoft R Application Network) snapshot, specified date. MRAN@- MRAN snapshot, day release . MRAN@R- MRAN snapshot, day R released. Notes: See RSPM https://packagemanager.rstudio.com/client/#/. See MRAN snapshots https://mran.microsoft.com/timemachine. dates (times) can specified ISO 8601 format. RSPM snapshot available date, next available date used. Dates first, last RSPM snapshot trigger error. Dates first, last MRAN snapshot trigger error. Unknown R package versions trigger error.","code":"https://cloud.r-project.org"},{"path":"https://pak.r-lib.org/dev/reference/repo_add.html","id":"exaples","dir":"Reference","previous_headings":"","what":"Exaples","title":"Add a new CRAN-like repository — repo_add","text":"","code":"repo_add(RSPMdplyr100 = \"RSPM@dplyr-1.0.0\") repo_get() #> # A data frame: 6 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 RSPMdplyr100 https://packagemanager.posit.co/c… cran… * NA #> 3 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 6 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version repo_resolve(\"MRAN@2020-01-21\") #> CRAN #> \"https://cran.microsoft.com/snapshot/2020-01-21\" repo_resolve(\"RSPM@2020-01-21\") #> CRAN #> \"https://packagemanager.posit.co/cran/245\" repo_resolve(\"MRAN@dplyr-1.0.0\") #> CRAN #> \"https://cran.microsoft.com/snapshot/2020-05-30\" repo_resolve(\"RSPM@dplyr-1.0.0\") #> CRAN #> \"https://packagemanager.posit.co/cran/289\" repo_resolve(\"MRAN@R-4.0.0\") #> CRAN #> \"https://cran.microsoft.com/snapshot/2020-04-25\" repo_resolve(\"RSPM@R-4.0.0\") #> CRAN #> \"https://packagemanager.posit.co/cran/276\""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":null,"dir":"Reference","previous_headings":"","what":"Query the currently configured CRAN-like repositories — repo_get","title":"Query the currently configured CRAN-like repositories — repo_get","text":"pak uses repos option, see options(). also automatically adds CRAN mirror none set , correct version Bioconductor repositories. See cran_mirror bioc arguments.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Query the currently configured CRAN-like repositories — repo_get","text":"","code":"repo_get(r_version = getRversion(), bioc = TRUE, cran_mirror = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Query the currently configured CRAN-like repositories — repo_get","text":"r_version R version use determine correct Bioconductor version, bioc = TRUE. bioc Whether automatically add Bioconductor repositories result. cran_mirror CRAN mirror use. Leave NULL use mirror getOption(\"repos\") automatically selected one.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Query the currently configured CRAN-like repositories — repo_get","text":"repo_get() returns table currently configured repositories.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_get.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Query the currently configured CRAN-like repositories — repo_get","text":"","code":"repo_get() #> # A data frame: 5 × 5 #> name url type r_ver…¹ bioc_…² #> * #> 1 CRAN https://cloud.r-project.org cran * NA #> 2 BioCsoft https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 3 BioCann https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 4 BioCexp https://bioconductor.org/packages… bioc 4.2.2 3.16 #> 5 BioCworkflows https://bioconductor.org/packages… bioc 4.2.2 3.16 #> # … with abbreviated variable names ¹​r_version, ²​bioc_version"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Show the status of CRAN-like repositories — repo_status","title":"Show the status of CRAN-like repositories — repo_status","text":"checks status configured supplied repositories.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show the status of CRAN-like repositories — repo_status","text":"","code":"repo_status( platforms = NULL, r_version = getRversion(), bioc = TRUE, cran_mirror = NULL ) repo_ping( platforms = NULL, r_version = getRversion(), bioc = TRUE, cran_mirror = NULL )"},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show the status of CRAN-like repositories — repo_status","text":"platforms Platforms use, default current platform, plus source packages. r_version R version(s) use, default current R version, via getRversion(). bioc Whether add Bioconductor repositories. already configured via options(repos), can set FALSE. cran_mirror CRAN mirror use.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show the status of CRAN-like repositories — repo_status","text":"data frame row every repository, every queried platform R version. columns: name: name repository. comes names configured repositories options(\"repos\"), added pkgcache. typically CRAN CRAN, current Bioconductor repositories BioCsoft, BioCann, BioCexp, BioCworkflows. url: base URL repository. bioc_version: Bioconductor version, NA non-Bioconductor repositories. platform: platform, possible values source, macos windows currently. path: path packages within base URL, given platform R version. r_version: R version, one specified R versions. ok: Logical flag, whether repository contains metadata file given platform R version. ping: HTTP response time repository seconds. ok column FALSE, columns NA. error: error object HTTP query failed repository, platform R version.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Show the status of CRAN-like repositories — repo_status","text":"repo_ping() similar repo_status() also prints short summary data, returns result invisibly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/repo_status.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show the status of CRAN-like repositories — repo_status","text":"","code":"repo_status() #> # A data frame: 10 × 10 #> name url type bioc_…¹ platf…² path r_ver…³ ok ping error #> #> 1 CRAN http… cran NA source src/… 4.2 TRUE 0.269 #> 2 CRAN http… cran NA aarch6… bin/… 4.2 TRUE 0.265 #> 3 BioCsoft http… bioc 3.16 source src/… 4.2 TRUE 0.264 #> 4 BioCsoft http… bioc 3.16 aarch6… bin/… 4.2 TRUE 0.271 #> 5 BioCann http… bioc 3.16 source src/… 4.2 TRUE 0.383 #> 6 BioCann http… bioc 3.16 aarch6… bin/… 4.2 TRUE 0.392 #> 7 BioCexp http… bioc 3.16 source src/… 4.2 TRUE 0.507 #> 8 BioCexp http… bioc 3.16 aarch6… bin/… 4.2 TRUE 0.739 #> 9 BioCwor… http… bioc 3.16 source src/… 4.2 TRUE 0.505 #> 10 BioCwor… http… bioc 3.16 aarch6… bin/… 4.2 TRUE 0.766 #> # … with abbreviated variable names ¹​bioc_version, ²​platform, #> # ³​r_version repo_status( platforms = c(\"windows\", \"macos\"), r_version = c(\"4.0\", \"4.1\") ) #> # A data frame: 15 × 10 #> name url type bioc_…¹ platf…² r_ver…³ path ok ping #> #> 1 CRAN https… cran NA i386+x… 4.0 bin/… TRUE 0.198 #> 2 CRAN https… cran NA i386+x… 4.1 bin/… TRUE 0.197 #> 3 CRAN https… cran NA aarch6… 4.1 bin/… TRUE 0.197 #> 4 BioCsoft https… bioc 3.12 i386+x… 4.0 bin/… TRUE 0.988 #> 5 BioCann https… bioc 3.12 i386+x… 4.0 bin/… TRUE 1.03 #> 6 BioCexp https… bioc 3.12 i386+x… 4.0 bin/… TRUE 1.25 #> 7 BioCworkflows https… bioc 3.12 i386+x… 4.0 bin/… TRUE 1.47 #> 8 BioCsoft https… bioc 3.14 i386+x… 4.1 bin/… TRUE 1.48 #> 9 BioCsoft https… bioc 3.14 aarch6… 4.1 bin/… FALSE NA #> 10 BioCann https… bioc 3.14 i386+x… 4.1 bin/… TRUE 1.45 #> 11 BioCann https… bioc 3.14 aarch6… 4.1 bin/… FALSE NA #> 12 BioCexp https… bioc 3.14 i386+x… 4.1 bin/… TRUE 1.72 #> 13 BioCexp https… bioc 3.14 aarch6… 4.1 bin/… FALSE NA #> 14 BioCworkflows https… bioc 3.14 i386+x… 4.1 bin/… TRUE 1.71 #> 15 BioCworkflows https… bioc 3.14 aarch6… 4.1 bin/… FALSE NA #> # … with 1 more variable: error , and abbreviated variable names #> # ¹​bioc_version, ²​platform, ³​r_version repo_ping() #> Repository summary: source aarch64-apple-darwin20 #> CRAN @ cloud.r-project.org ✔ ✔ (194ms) #> BioCsoft @ bioconductor.org ✔ ✔ (352ms) #> BioCann @ bioconductor.org ✔ ✔ (511ms) #> BioCexp @ bioconductor.org ✔ ✔ (675ms) #> BioCworkflows @ bioconductor.org ✔ ✔ (698ms)"},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":null,"dir":"Reference","previous_headings":"","what":"System requirements — System requirements","title":"System requirements — System requirements","text":"pak takes care system requirements.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"introduction","dir":"Reference","previous_headings":"","what":"Introduction","title":"System requirements — System requirements","text":"Many R packages need external software present machine, otherwise work, even load. example RPostgres R package uses PostgreSQL client library, default dynamically links Linux systems. means (administrators system) need install library, typically form system package: libpq-dev Ubuntu Debian systems, postgresql-server-devel postgresql-devel RedHat, Fedora, etc. systems. good news pak helps : - looks required system packages installing R packages, - checks required system packages installed, - installs automatically, superuser, can use password-less sudo start superuser shell. addition, pak also functions query system requirements system packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"requirements-supported-platforms","dir":"Reference","previous_headings":"","what":"Requirements, supported platforms","title":"System requirements — System requirements","text":"Call pak::sysreqs_platforms() list platforms support system requirements: Call pak::sysreqs_is_supported() see system supported: vignette built Ubuntu 22.04.2 LTS, platform pak support. following see output code.","code":"pak::sysreqs_platforms() ## # A data frame: 10 × 7 ## name os distribution version update_command install_command ## ## 1 Ubuntu Lin… linux ubuntu * apt-get -y up… apt-get -y ins… ## 2 Debian Lin… linux debian * apt-get -y up… apt-get -y ins… ## 3 CentOS Lin… linux centos * NA yum install -y ## 4 Rocky Linux linux rockylinux * NA dnf install -y ## 5 Red Hat En… linux redhat 6 NA yum install -y ## 6 Red Hat En… linux redhat 7 NA yum install -y ## 7 Red Hat En… linux redhat * NA dnf install -y ## 8 Fedora Lin… linux fedora * NA dnf install -y ## 9 openSUSE L… linux opensuse * NA zypper --non-i… ## 10 SUSE Linux… linux sle * NA zypper --non-i… ## # ℹ 1 more variable: query_command pak::sysreqs_is_supported() ## [1] TRUE"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"r-package-installation","dir":"Reference","previous_headings":"","what":"R package installation","title":"System requirements — System requirements","text":"using pak superuser, supported platform, pak look system requirements, install missing ones. example:","code":"pak::pkg_install(\"RPostgres\") ## ✔ Loading metadata database ... done ## ## → Will install 17 packages. ## → All 17 packages (0 B) are cached. ## + DBI 1.1.3 ## + RPostgres 1.4.5 + ✖ libpq-dev ## + Rcpp 1.0.10 ## + bit 4.0.5 ## + bit64 4.0.5 ## + blob 1.2.4 ## + cli 3.6.1 ## + generics 0.1.3 ## + glue 1.6.2 ## + hms 1.1.3 ## + lifecycle 1.0.3 ## + lubridate 1.9.2 ## + pkgconfig 2.0.3 ## + rlang 1.1.1 ## + timechange 0.2.0 ## + vctrs 0.6.2 ## + withr 2.5.0 ## → Will install 1 system package: ## + libpq-dev - RPostgres ## ℹ No downloads are needed, 17 pkgs are cached ## ℹ Installing system requirements ## ℹ Executing `sh -c apt-get -y update` ## ℹ Executing `sh -c apt-get -y install libpq-dev` ## ✔ Installed DBI 1.1.3 (1.1s) ## ✔ Installed RPostgres 1.4.5 (1.2s) ## ✔ Installed Rcpp 1.0.10 (1.2s) ## ✔ Installed bit 4.0.5 (1.2s) ## ✔ Installed bit64 4.0.5 (148ms) ## ✔ Installed blob 1.2.4 (63ms) ## ✔ Installed cli 3.6.1 (88ms) ## ✔ Installed generics 0.1.3 (61ms) ## ✔ Installed glue 1.6.2 (63ms) ## ✔ Installed hms 1.1.3 (62ms) ## ✔ Installed lifecycle 1.0.3 (61ms) ## ✔ Installed lubridate 1.9.2 (87ms) ## ✔ Installed pkgconfig 2.0.3 (62ms) ## ✔ Installed rlang 1.1.1 (1.1s) ## ✔ Installed timechange 0.2.0 (1.1s) ## ✔ Installed vctrs 0.6.2 (1.1s) ## ✔ Installed withr 2.5.0 (1.1s) ## ✔ 1 pkg + 16 deps: added 17 [17.5s]"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"running-r-as-a-regular-user","dir":"Reference","previous_headings":"","what":"Running R as a regular user","title":"System requirements — System requirements","text":"don’t want use R superuser, can set sudo without password, works well. pak automatically detect password-less sudo capability, use install system packages, needed. run R regular (root) user, password-less sudo available, pak print system requirements, try install update . installing source packages need link system libraries, installation probably fail, install system packages. installing binary R packages, installation typically succeeds, won’t able load packages R, install required system packages. example, system required system package installed RPostgres. installing source R package, installation already fails: hand, installing binary packages, e.g. Posit Package Manager, installation typically succeeds, loading package fails:","code":"pak::pkg_install(\"RPostgres?source\") ## + plogr 0.2.0 ## ✖ Missing 1 system package. You'll probably need to install it ## manually: ## + libpq-dev - RPostgres ## ℹ No downloads are needed, 2 pkgs (1.47 MB) are cached ## ✔ Installed plogr 0.2.0 (1.1s) ## ℹ Building RPostgres 1.4.5 ## ✖ Failed to build RPostgres 1.4.5 ## Registered S3 methods overwritten by 'callr': ## method from ## format.callr_status_error ## print.callr_status_error ## Error: ## ! error in pak subprocess ## Caused by error in `stop_task_build(state, worker)`: ## ! Failed to build source package 'RPostgres' ## Full installation output: ## * installing *source* package ‘RPostgres’ ... ## ** package ‘RPostgres’ successfully unpacked and MD5 sums checked ## staged installation is only possible with locking ## ** using non-staged installation ## Using PKG_CFLAGS= ## Using PKG_LIBS=-lpq ## Using PKG_PLOGR= ## ------------------------- ANTICONF ERROR --------------------------- ## Configuration failed because libpq was not found. Try installing: ## * deb: libpq-dev libssl-dev (Debian, Ubuntu, etc) ## * rpm: postgresql-devel (Fedora, EPEL) ## * rpm: postgreql8-devel, psstgresql92-devel, postgresql93-devel, or pos ## tgresql94-devel (Amazon Linux) ## * csw: postgresql_dev (Solaris) ## * brew: libpq (OSX) ## If libpq is already installed, check that either: ## (i) 'pkg-config' is in your PATH AND PKG_CONFIG_PATH contains ## a libpq.pc file; or ## (ii) 'pg_config' is in your PATH. ## If neither can detect , you can set INCLUDE_DIR ## and LIB_DIR manually via: ## R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' ## --------------------------[ ERROR MESSAGE ]---------------------------- ## :1:10: fatal error: libpq-fe.h: No such file or directory ## compilation terminated. ## ----------------------------------------------------------------------- ## ERROR: configuration failed for package ‘RPostgres’ ## * removing ‘/tmp/RtmpsOXbPZ/pkg-lib4a492949a49e/RPostgres’ ## --- ## Backtrace: ## 1. pak::pkg_install(\"RPostgres?source\") ## 2. pak:::remote(function(...) get(\"pkg_install_do_plan\", asNamespace(\"pa ## k\")… at package.R:84:3 ## 3. err$throw(res$error) at subprocess.R:115:5 ## --- ## Subprocess backtrace: ## 1. base::withCallingHandlers(cli_message = function(msg) { … ## 2. get(\"pkg_install_do_plan\", asNamespace(\"pak\"))(...) ## 3. proposal$install() ## 4. pkgdepends::install_package_plan(plan, lib = private$library, num_wo ## rkers = nw… ## 5. base::withCallingHandlers({ … ## 6. pkgdepends:::handle_events(state, events) ## 7. pkgdepends:::handle_event(state, i) ## 8. pkgdepends:::stop_task(state, worker) ## 9. pkgdepends:::stop_task_build(state, worker) ## 10. base::throw(new_pkg_build_error(\"Failed to build source package {pkg ## }\", … ## 11. | base::signalCondition(cond) ## 12. global (function (e) … ## Execution halted pak::pkg_install(\"RPostgres\") library(RPostgres) ## → Will install 17 packages. ## → All 17 packages (0 B) are cached. ## + DBI 1.1.3 ## + RPostgres 1.4.5 + ✖ libpq-dev ## + Rcpp 1.0.10 ## + bit 4.0.5 ## + bit64 4.0.5 ## + blob 1.2.4 ## + cli 3.6.1 ## + generics 0.1.3 ## + glue 1.6.2 ## + hms 1.1.3 ## + lifecycle 1.0.3 ## + lubridate 1.9.2 ## + pkgconfig 2.0.3 ## + rlang 1.1.1 ## + timechange 0.2.0 ## + vctrs 0.6.2 ## + withr 2.5.0 ## ✖ Missing 1 system package. You'll probably need to install it ## manually: ## + libpq-dev - RPostgres ## ℹ No downloads are needed, 17 pkgs are cached ## ✔ Installed DBI 1.1.3 (1.1s) ## ✔ Installed RPostgres 1.4.5 (1.1s) ## ✔ Installed Rcpp 1.0.10 (1.2s) ## ✔ Installed bit 4.0.5 (1.2s) ## ✔ Installed bit64 4.0.5 (144ms) ## ✔ Installed blob 1.2.4 (1.1s) ## ✔ Installed cli 3.6.1 (1.1s) ## ✔ Installed generics 0.1.3 (90ms) ## ✔ Installed glue 1.6.2 (87ms) ## ✔ Installed hms 1.1.3 (1.1s) ## ✔ Installed lifecycle 1.0.3 (1.1s) ## ✔ Installed lubridate 1.9.2 (1.1s) ## ✔ Installed pkgconfig 2.0.3 (1.1s) ## ✔ Installed rlang 1.1.1 (1.1s) ## ✔ Installed timechange 0.2.0 (1.1s) ## ✔ Installed vctrs 0.6.2 (1.1s) ## ✔ Installed withr 2.5.0 (1.1s) ## ✔ 1 pkg + 16 deps: added 17 [11.6s] ## Error: package or namespace load failed for ‘RPostgres’ in dyn.load(file ## , DLLpath = DLLpath, ...): ## unable to load shared object '/tmp/RtmpWqZycA/lib/RPostgres/libs/RPostg ## res.so': ## libpq.so.5: cannot open shared object file: No such file or directory ## Execution halted"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"other-queries","dir":"Reference","previous_headings":"","what":"Other queries","title":"System requirements — System requirements","text":"addition automatic system package lookup installation, pak also functions help system dependencies. sysreqs_db_list() function lists system requirements pak knows . sysreqs_db_match() manually matches SystemREquirements fields againts system requirements: can also use query system requirements platfosm: sysreqs_list_system_packages() cross-platform way listing installed system packages capabilities: sysreqs_check_installed() handy function checks system requirements installed R packages installed library: sysreqs_fix_installed() goes one step also tries install missing system requirements.","code":"pak::sysreqs_db_list() ## # A data frame: 106 × 5 ## name patterns packages pre_install post_install ## ## 1 QuantLib ## 2 apparmor ## 3 atk ## 4 automake ## 5 berkeleydb ## 6 blender ## 7 bowtie2 ## 8 bwidget ## 9 cairo ## 10 chrome ## # ℹ 96 more rows sq <- pak::sysreqs_db_match(\"Needs libcurl and also Java.\") sq ## [[1]] ## # A data frame: 2 × 5 ## spec sysreq packages pre_install post_install ## ## 1 Needs libcurl and also Java. java ## 2 Needs libcurl and also Java. libcurl ## sq[[1]]$packages ## [[1]] ## [1] \"default-jdk\" ## ## [[2]] ## [1] \"libcurl4-openssl-dev\" ## sqrhel9 <- pak::sysreqs_db_match(\"Needs libcurl and also Java.\", \"redhat-9\") sqrhel9 ## [[1]] ## # A data frame: 2 × 5 ## spec sysreq packages pre_install post_install ## ## 1 Needs libcurl and also Java. java ## 2 Needs libcurl and also Java. libcurl ## sqrhel9[[1]]$packages ## [[1]] ## [1] \"java-11-openjdk-devel\" ## ## [[2]] ## [1] \"libcurl-devel\" ## pak::sysreqs_list_system_packages() ## # A data frame: 433 × 4 ## status package version provides ## ## 1 ii adduser 3.118ubuntu5 ## 2 ii apt 2.4.8 ## 3 ii autoconf 2.71-2 ## 4 ii automake 1:1.16.5-1.3 ## 5 ii autotools-dev 20220109.1 ## 6 ii base-files 12ubuntu4.3 ## 7 ii base-passwd 3.5.52build1 ## 8 ii bash 5.1-6ubuntu1 ## 9 ii binutils 2.38-4ubuntu2.1 ## 10 ii binutils-common 2.38-4ubuntu2.1 ## # ℹ 423 more rows pak::sysreqs_check_installed() ## system package installed required by ## -------------- -- ----------- ## git ✔ gitcreds ## gsfonts ✔ magick ## imagemagick ✔ magick ## libarchive-dev ✔ archive ## libcurl4-openssl-dev ✔ curl ## libfontconfig1-dev ✔ systemfonts ## libfreetype6-dev ✔ ragg, systemfonts, textshaping ## libfribidi-dev ✔ textshaping ## libharfbuzz-dev ✔ textshaping ## libicu-dev ✔ stringi ## libjpeg-dev ✔ ragg ## libmagick++-dev ✔ magick ## libnode-dev ✔ V8 ## libpng-dev ✔ ragg ## libpq-dev ✖ RPostgres ## libssl-dev ✔ curl, openssl ## libtiff-dev ✔ ragg ## libxml2-dev ✔ xml2 ## make ✔ fs, sass ## pandoc ✔ knitr, rmarkdown ## zlib1g-dev ✔ data.table"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"build-time-and-run-time-dependencies","dir":"Reference","previous_headings":"","what":"Build-time and run-time dependencies","title":"System requirements — System requirements","text":"system requirements database pak uses currently differentiate build-time run-time dependencies. build-time dependency system package need installing R package source. run-time dependency system package need using R package. Linux distribution create (least) two packages software library: runtime package development package. R package uses software library, runtime package run-time dependency development package build-time dependency. However, pak currently know difference build-time run-time dependencies, install types dependencies, always. means pak usually installs system packages strictly necessary. typically development packages libraries, .e. header files, typically cause issues. short disk space, can try removing .","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"how-it-works","dir":"Reference","previous_headings":"","what":"How it works","title":"System requirements — System requirements","text":"pak uses database system requirements https://github.com/rstudio/r-system-requirements. copy database embedded package, also tries download updated versions database GitHub, current copy older one day. can explicitly update database GitHub using sysreqs_db_update() function. CRAN packages, downloads SystemRequierements fields https://cran2.r-pkg.org/metadata/, database updated daily. planning moving database GitHub, creating similar database Bioconductor. packages sources require pak obtain package DESCRIPTION file (e.g. github::, git::, etc.), pak obtrains SystemRequirements directly DESCRIPTION file. SystemRequirements fields, pak matches database, obtain cacnonized list system requirements. pak queries local platform, see exact system packages needed. also queries installed system packages, avoid trying install system packages already installed.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"configuration","dir":"Reference","previous_headings":"","what":"Configuration","title":"System requirements — System requirements","text":"several pak configuration options can use adjust system requirements handled. list , please see options sysreqs prefix ?pak-config manual page complete current list. sysreqs: whether install system requirements. default TRUE platform supported user can install system packages, either superuser, via sudo. FALSE (user install system packages), platform supported, system requirements printed, installed. sysreqs_db_update: whether try update system requirements database GitHub. sysreqs_db_update_timeout: timeout system requirements update GitHub. sysreqs_dry_run: TRUE pak prints install commands, actually run . sysreqs_platform: platform name use determining system requirements. Defaults current platform. using Linux distribution compatible distribution pak supports, can set option manually. E.g. Ubuntu-based distros can set ubuntu-22.04, appropriate Ubuntu version. sysreqs_sudo: whether use sudo install system packages. set, pak tries auto-detect sudo needed . sysreqs_update: whether try update system packages already installed. pak know version system package required, try update system packages default. think need newer system packages, can set option TRUE. sysreqs_verbose: whether print output system package installation commands. Useful debugging, TRUE default CI environment.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"windows","dir":"Reference","previous_headings":"","what":"Windows","title":"System requirements — System requirements","text":"system requirements database information system dependencies Windows, pak use information try install system software Windows. CRAN, PPM Bioconductor Windows binary packages available majority R packages serve, packages practically always link system libraries statically, don’t need external software. wish compile Windows packages source, need install appropriate version Rtools, possibly extra packages using pacman tool Rtools4x. Rtools42 newer Rtools versions bundle lots libraries, likely extra pacman packages needed. Rtools40 leaner default installation, ’ll probably need install packages manually: https://github.com/r-windows/docs/blob/master/rtools40.md#readme planning adding better Windows system software support pak future.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs.html","id":"macos","dir":"Reference","previous_headings":"","what":"macOS","title":"System requirements — System requirements","text":"pak currently system requirement information macOS. macOS similar Windows, repositories serve statically linked macOS binary packages need system software. need compile packages source, possibly need install sytem libraries, either via Homebrew, downloading CRAN’s static library builds https://mac.r-project.org/bin/ planning adding better macOS system software support pak future.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if installed packages have all their system requirements — sysreqs_check_installed","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"sysreqs_check_installed() checks system requirements packages (subset packages) installed. sysreqs_fix_installed() installs missing system packages.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"","code":"sysreqs_check_installed(packages = NULL, library = .libPaths()[1]) sysreqs_fix_installed(packages = NULL, library = .libPaths()[1])"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"packages NULL, packages checked. package packages installed, pak throws warning. library Library libraries check.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"Data frame custom print format method, pkg_sysreqs_check_result class. columns : system_package: string, name required system package. installed: logical, whether system package correctly installed. packages: list column character vectors. names installed R packages need system package. pre_install: list column character vectors. Commands run installation system package. post_install: list column character vectors. Commands run installation system package. data frame also two attributes additional data: sysreqs_records: raw system requirements records, system_packages: list installed system packages. sysreqs_fix_packages() returns value, invisibly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"functions use sysreqs_platform configuration option, see Configuration . Set pak detect platform correctly.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_check_installed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if installed packages have all their system requirements — sysreqs_check_installed","text":"","code":"# This only works on supported platforms sysreqs_check_installed() #> system package installed required by #> -------------- -- -----------"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List contents of the system requirements DB, for a platform — sysreqs_db_list","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"also tries update system dependency database, outdated. (.e. older allowed metadata_update_after configuration option .","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"","code":"sysreqs_db_list(sysreqs_platform = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"sysreqs_platform System requirements platform. NULL, sysreqs_platform configuration option used, defaults current platform. Set option pak detect platform correctly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"Data frame columns: name: cross platform system dependency name database. patterns: one regular expressions match SystemRequirements fields. packages: one system package names install. pre_install: command(s) run installing packages. post_install:: command(s) run installing packages.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List contents of the system requirements DB, for a platform — sysreqs_db_list","text":"","code":"sysreqs_db_list(sysreqs_platform = \"ubuntu-22.04\") #> # A data frame: 109 × 5 #> name patterns packages pre_install post_install #> #> 1 QuantLib #> 2 apparmor #> 3 atk #> 4 automake #> 5 berkeleydb #> 6 blender #> 7 boost #> 8 bowtie2 #> 9 bwidget #> 10 cairo #> # ℹ 99 more rows"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":null,"dir":"Reference","previous_headings":"","what":"Match system requirement descriptions to the database — sysreqs_db_match","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"usual workflow pak matches SystemRequirements fields DESCRIPTION files database.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"","code":"sysreqs_db_match(specs, sysreqs_platform = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"specs Character vector system requirements descriptions. sysreqs_platform System requirements platform. NULL, sysreqs_platform configuration option used, defaults current platform. Set option pak detect platform correctly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"Data frame columns: spec: input specs. sysreq: name system library tool. packages: system packages, list column character vectors. Rarely can empty string, e.g. pre_install script performs installation. pre_install: list column character vectors. Shell script(s) run installation. post_install: list column character vectors. Shell script(s) run installation.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"sysreqs_db_match() function lets match string, mainly useful debugging.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_match.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Match system requirement descriptions to the database — sysreqs_db_match","text":"","code":"sysreqs_db_match( c(\"Needs libcurl\", \"Java, libssl\"), sysreqs_platform = \"ubuntu-22.04\" ) #> [[1]] #> # A data frame: 1 × 5 #> spec sysreq packages pre_install post_install #> #> 1 Needs libcurl libcurl #> #> [[2]] #> # A data frame: 1 × 5 #> spec sysreq packages pre_install post_install #> #> 1 Java, libssl java #>"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_update.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the cached copy of the system requirements database — sysreqs_db_update","title":"Update the cached copy of the system requirements database — sysreqs_db_update","text":"Update cached copy system requirements database","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_update.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the cached copy of the system requirements database — sysreqs_db_update","text":"","code":"sysreqs_db_update()"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_db_update.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update the cached copy of the system requirements database — sysreqs_db_update","text":"cached copy recent, update attempted. See metadata_update_after configuration option .","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if a platform has system requirements support — sysreqs_is_supported","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"Check platform system requirements support","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"","code":"sysreqs_is_supported(sysreqs_platform = NULL)"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"sysreqs_platform System requirements platform. NULL, sysreqs_platform configuration option used, defaults current platform. Set option pak detect platform correctly.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"Logical scalar.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_is_supported.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if a platform has system requirements support — sysreqs_is_supported","text":"","code":"sysreqs_is_supported() #> [1] TRUE"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":null,"dir":"Reference","previous_headings":"","what":"List installed system packages — sysreqs_list_system_packages","title":"List installed system packages — sysreqs_list_system_packages","text":"List installed system packages","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List installed system packages — sysreqs_list_system_packages","text":"","code":"sysreqs_list_system_packages()"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List installed system packages — sysreqs_list_system_packages","text":"Data frame columns: status. two three characters, notation dpkg Debian based systems. \"ii\" means package correctly installed. RPM based systems always \"ii\" currently. package: name system package. version: installed version system package. capabilities: list column character vectors, capabilities provided package.","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"List installed system packages — sysreqs_list_system_packages","text":"function uses sysreqs_platform configuration option, see Configuration . Set pak detect platform correctly.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_list_system_packages.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List installed system packages — sysreqs_list_system_packages","text":"","code":"sysreqs_list_system_packages()[1:10,] #> # A data frame: 10 × 4 #> status package version provides #> * #> 1 ii acl 2.3.1-1 #> 2 ii adduser 3.118ubuntu5 #> 3 ii adoptium-ca-certificates 1.0.2-1 #> 4 ii adwaita-icon-theme 41.0-1ubuntu1 #> 5 ii alsa-topology-conf 1.2.5.1-2 #> 6 ii alsa-ucm-conf 1.2.6.3-1ubuntu1.6 #> 7 ii ant 1.10.12-1 #> 8 ii ant-optional 1.10.12-1 #> 9 ii apache2 2.4.52-1ubuntu4.5 #> 10 ii apache2-bin 2.4.52-1ubuntu4.5 "},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_platforms.html","id":null,"dir":"Reference","previous_headings":"","what":"List platforms with system requirements support — sysreqs_platforms","title":"List platforms with system requirements support — sysreqs_platforms","text":"List platforms system requirements support","code":""},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_platforms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List platforms with system requirements support — sysreqs_platforms","text":"","code":"sysreqs_platforms()"},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_platforms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List platforms with system requirements support — sysreqs_platforms","text":"Data frame columns: name: human readable OS name. os: OS name, e.g. linux. distribution: OS id, e.g. ubuntu redhat. version: distribution version. star means versions supported, also supported vendor. update_command: command run update system package metadata. install_command: command run install packages. query_command: name tool use query system package information.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/sysreqs_platforms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List platforms with system requirements support — sysreqs_platforms","text":"","code":"sysreqs_platforms() #> # A data frame: 10 × 7 #> name os distribution version update_command install_command #> #> 1 Ubuntu Linux linux ubuntu * apt-get -y up… apt-get -y ins… #> 2 Debian Linux linux debian * apt-get -y up… apt-get -y ins… #> 3 CentOS Linux linux centos * NA yum install -y #> 4 Rocky Linux linux rockylinux * NA dnf install -y #> 5 Red Hat Ente… linux redhat 6 NA yum install -y #> 6 Red Hat Ente… linux redhat 7 NA yum install -y #> 7 Red Hat Ente… linux redhat * NA dnf install -y #> 8 Fedora Linux linux fedora * NA dnf install -y #> 9 openSUSE Lin… linux opensuse * NA zypper --non-i… #> 10 SUSE Linux E… linux sle * NA zypper --non-i… #> # ℹ 1 more variable: query_command "},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":null,"dir":"Reference","previous_headings":"","what":"R platforms — system_r_platform","title":"R platforms — system_r_platform","text":"R platforms","code":""},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R platforms — system_r_platform","text":"","code":"system_r_platform() system_r_platform_data()"},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"R platforms — system_r_platform","text":"system_r_platform() returns character scalar. system_r_platform_data() returns data frame character scalar columns: cpu, vendor, os, distribution (Linux), release (Linux), platform: concatenation columns, separated dash.","code":""},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"R platforms — system_r_platform","text":"system_r_platform() detects platform current R version. system_r_platform_data() similar, returns raw data instead character scalar. default pak works source packages binary packages current platform. can change , providing different platform names pkg.platforms option PKG_PLATFORMS environment variable. option may contain following platform names: \"source\" source packages, \"macos\" macOS binaries appropriate R versions pak working . Packages incompatible CPU architectures dropped (defaulting CPU current macOS machine x86_64 non-macOS systems). macOS Darwin version selected based CRAN macOS binaries. E.g. R 3.5.0 macOS binaries built macOS El Capitan. \"windows\" Windows binaries default CRAN architecture. currently Windows Vista supported R versions, might change future. actual binary packages repository might support 32 bit 64 builds, one . practice 32-bit packages rare. CRAN builds including R 4.1 architectures, R 4.2 64 bit . \"windows\" alias i386+x86_64-w64-mingw32 currently. platform string like R.version$platform, Linux name version distribution also included. Examples: x86_64-apple-darwin17.0: macOS High Sierra. aarch64-apple-darwin20: macOS Big Sur arm64. x86_64-w64-mingw32: 64 bit Windows. i386-w64-mingw32: 32 bit Windows. i386+x86_64-w64-mingw32: 64 bit + 32 bit Windows. i386-pc-solaris2.10: 32 bit Solaris. (broken 64 Solaris builds might platform string, unfortunately.) x86_64-pc-linux-gnu-debian-10: Debian Linux 10 x86_64. x86_64-pc-linux-musl-alpine-3.14.1: Alpine Linux. x86_64-pc-linux-gnu-unknown: Unknown Linux Distribution x86_64. s390x-ibm-linux-gnu-ubuntu-20.04: Ubuntu Linux 20.04 S390x. amd64-portbld-freebsd12.1: FreeBSD 12.1 x86_64.","code":""},{"path":[]},{"path":"https://pak.r-lib.org/dev/reference/system_r_platform.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R platforms — system_r_platform","text":"","code":"if (FALSE) { system_r_platform() system_r_platform_data() }"},{"path":[]},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-051","dir":"Changelog","previous_headings":"","what":"pak 0.5.1","title":"pak 0.5.1","text":"CRAN release: 2023-04-27 user visible changes.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-050","dir":"Changelog","previous_headings":"","what":"pak 0.5.0","title":"pak 0.5.0","text":"CRAN release: 2023-04-20 meta_*() functions now consider platforms, cran_mirror r_versions config entries, see ?\"pak-config\". Better Posit Package Manager (PPM) support. New +ppm_has_binaries(), ppm_r_versions(), ppm_repo_url(), ppm_snapshots() ppm_platforms() functions help interacting PPM. See new ‘pkgcache Posit Package Manager Linux’ article https://r-lib.github.io/pkgcache. (r-lib/pkgcache#47 r-lib/pkgdepends#186). New system_r_platform() system_r_platform_data() functions query current platform. pak now support git repositories package references. E.g. git::https://github.com/r-lib/pak.git. pak now supports versioned CRAN packages, e.g. dplyr@1.1.1 always install dplyr 1.1.1. Note CRAN packages supported, Bioconductor packages (yet). pak now alternative system requirements lookup implementation. supports Fedora Debian systems well, addition Debian, Ubuntu, SUSE RedHat derivatives. can switch implementation setting R_PKG_SYSREQS2 environment variable true. pak now better job looking dependencies hand-selected dependency types. E.g. dependencies = \"LinkingTo\". pak now removes ?ignore-d packages dependencies, uses correct version comparison ?ignore-.r (https://github.com/r-lib/actions/issues/708). pak now fail circular soft dependencies (#306). pak now reports dependency solver failures better cases (#305, https://github.com/r-lib/pak/issues/474). pak now uses locally built CRAN binaries cache. Use ?nocache parameter opt , cache_delete(package = ...) remove package cache.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-040","dir":"Changelog","previous_headings":"","what":"pak 0.4.0","title":"pak 0.4.0","text":"CRAN release: 2023-01-15 pak much improved informative error messages now. work yet finished, find unclear error message, please open issue. Thank ! solver now robust non-canonical input (e.g. DESCRIPTION files) (https://github.com/r-lib/pak/issues/423). Better installation output. Standard output error now collected together (https://github.com/r-lib/pkgdepends/commit/0669f0f8c). solver now better job multiple versions package present repository (https://github.com/r-lib/actions/issues/559). pkg_name_check() now works , needed fix changes https://crandb.r-pkg.org. Explicit package names local URL package sources, package=local::... package=url::... now parsed correctly dependencies. pak now robust Archs fields missing CRAN metadata packages compiled code (https://github.com/r-lib/pak/issues/448). url:: packages now always work correctly, even digest package installed (https://github.com/r-lib/pak/issues/433). pak now robust installing packages subdirectories GitHub repositories (https://github.com/r-lib/pak/issues/431, @paleolimbot). Parameters ?reinstall, ?source ?ignore now work correctly specified package=?parameter format (#294). ?ignore parameter works correctly now. Dependency resolution now fail package found. pak can now install url:: remotes GitHub. pak now fail package .tar.gz GitHub snapshot subdirectory, subdirectory subdirectory. pak now errors early deduce name package Remotes Config/Needs/* entry. Solver failures now include details cases previously . pak can now update packages Docker containers old version installed different Docker later (https://github.com/r-lib/pak/issues/251) Update R version -> Bioconductor version mapping. R 4.2.x now maps Bioconductor 3.16.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-031","dir":"Changelog","previous_headings":"","what":"pak 0.3.1","title":"pak 0.3.1","text":"CRAN release: 2022-09-08 ?ignore parameter works correctly now. Dependency resolution now fail package found. pak can now install url:: remotes GitHub. pak now fail package .tar.gz GitHub snapshot subdirectory, subdirectory subdirectory. pak now errors early deduce name package Remotes Config/Needs/* entry. Solver failures now include details cases previously . pak can now update packages Docker containers old version installed different Docker later (#251) pak errors now user friendlier better formatted. pak now load tibble dependencies pak subprocess, dlls locked pak subprocess Windows. pak now fail installing package uses non-UTF-8 encoding R 4.3.x later (#404).","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-030","dir":"Changelog","previous_headings":"","what":"pak 0.3.0","title":"pak 0.3.0","text":"CRAN release: 2022-04-11 pak functions used return tibbles return data frames now. data frames tibbles similar, completely compatible. convert outputs pak functions tibbles call tibble::as_tibble() function . pillar package loaded, improves printing returned data frames. Relatedly, pak::pak_install_extra() installs pillar now, instead tibble. pak now supports file:// repositories. pak now uses HTTP 1.1 download packages Linux, addition macOS. fixes HTTP issues servers (#358). New ?ignore--r parameter ignore optional dependencies need newer R version (https://github.com/r-lib/pkgdepends/issues/243). New ?ignore parameter ignore optional dependency. Allow specifying downstream package parameters package=?param syntax. lockfile_install() now works better :: refs, pak always install version planned . System requirement installation now robust works Unix shell expressions (#347). CRAN-like resolution robust now repository missing usual metadata. lock file pretty JSON now. pak now handles version requirement types properly: ‘<’, ‘<=’, ==, >=, >. dependency solver now uses better heuristics (effectively) freeze multiple repositories multiple versions packages (e.g. RSPM CRAN) (https://github.com/r-lib/pkgdepends/pull/277)","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-021","dir":"Changelog","previous_headings":"","what":"pak 0.2.1","title":"pak 0.2.1","text":"CRAN release: 2021-12-20 user visible changes.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-020","dir":"Changelog","previous_headings":"","what":"pak 0.2.0","title":"pak 0.2.0","text":"CRAN release: 2021-12-01 Lots news, much list. completely new package now.","code":""},{"path":"https://pak.r-lib.org/dev/news/index.html","id":"pak-012","dir":"Changelog","previous_headings":"","what":"pak 0.1.2","title":"pak 0.1.2","text":"CRAN release: 2019-02-19 First version CRAN.","code":""}]