diff --git a/.Rbuildignore b/.Rbuildignore index 006c236..e5c5ae1 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -68,3 +68,4 @@ Rplots.pdf$ ^docs ^pkgdown +^CRAN-SUBMISSION$ diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 8127602..07c8c93 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -6,7 +6,7 @@ jobs: R-CMD-check: if: "! contains(github.event.head_commit.message, '[ci skip]')" - timeout-minutes: 45 + timeout-minutes: 30 runs-on: ${{ matrix.config.os }} @@ -18,77 +18,57 @@ jobs: config: - {os: windows-latest, r: 'devel' } - {os: windows-latest, r: 'release' } - - {os: macOS-latest, r: 'devel' } - - {os: macOS-latest, r: 'release' } - - {os: ubuntu-22.04, r: 'devel' } - - {os: ubuntu-22.04, r: 'release' } - - {os: ubuntu-22.04, r: 'oldrel' } - - {os: ubuntu-22.04, r: 'oldrel-1' } - - {os: ubuntu-22.04, r: 'oldrel-2' } - - {os: ubuntu-22.04, r: '3.5' } - - {os: ubuntu-22.04, r: 'release' , language: ko, label: ko } - - {os: ubuntu-22.04, r: 'release' , language: zh_CN, label: zh_CN } - - {os: ubuntu-22.04, r: 'release' , language: zh_TW, label: zh_TW } - +# - {os: macOS-latest, r: 'devel' } +# - {os: macOS-latest, r: 'release' } +# - {os: macOS-latest, r: 'oldrel' } + - {os: ubuntu-latest, r: 'devel' } + - {os: ubuntu-latest, r: 'release' } + - {os: ubuntu-latest, r: 'oldrel' } + - {os: ubuntu-latest, r: 'oldrel-1' } + - {os: ubuntu-latest, r: 'oldrel-2' } + - {os: ubuntu-latest, r: '3.6' } + - {os: ubuntu-latest, r: 'release' , language: ko, label: ko } + - {os: ubuntu-latest, r: 'release' , language: zh_CN, label: zh_CN } + - {os: ubuntu-latest, r: 'release' , language: zh_TW, label: zh_TW } env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest + R_KEEP_PKG_SOURCE: yes R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + ## Test in other locale (optional) + LANGUAGE: ${{ matrix.config.language }} ## R CMD check _R_CHECK_CRAN_INCOMING_: false - _R_CHECK_LENGTH_1_CONDITION_: true - _R_CHECK_LENGTH_1_LOGIC2_: true _R_CHECK_MATRIX_DATA_: true _R_CHECK_SUGGESTS_ONLY_: true _R_CHECK_THINGS_IN_TEMP_DIR_: true - RCMDCHECK_ERROR_ON: note - ## Test in other locale (optional) - LANGUAGE: ${{ matrix.config.language }} - + ## R (>= 4.4.0) Note, no trailing underscore (sic!) + _R_COMPARE_LANG_OBJECTS: eqonly + steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-tinytex@v2 + + - name: Install system dependencies (Linux) + if: runner.os == 'Linux' + run: sudo apt-get install -y tidy + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - name: Query R package dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v3 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + extra-packages: any::rcmdcheck + needs: check - - name: Install R package system dependencies (Linux) - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" - sudo apt install -y libcurl4-openssl-dev - - - name: Install R package dependencies - run: | - remotes::install_deps(dependencies = TRUE) - install.packages(".", repos = NULL, type = "source") ## self vignette engine - shell: Rscript {0} - - - name: Install 'rcmdcheck' + - name: Install itself (to build vignettes) run: | - remotes::install_cran("rcmdcheck") - library(rcmdcheck) ## triggers an error, if installation failed + install.packages(".", repos=NULL, type="source") shell: Rscript {0} - name: Session info @@ -97,15 +77,35 @@ jobs: capabilities() pkgs <- installed.packages()[, "Package"] sessioninfo::session_info(pkgs, include_base = TRUE) + ## Verify LANGUAGE settings by generating a translatable error + cat(sprintf("LANGUAGE=%s\n", sQuote(Sys.getenv("LANGUAGE")))) + cat(sprintf("locales: %s\n", sQuote(Sys.getlocale()))) + tryCatch(log("a"), error = conditionMessage) shell: Rscript {0} - - name: Check - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", if (.Platform$OS.type == "windows" && getRversion() >= "4.2.0") "--no-multiarch"), check_dir = "check") + - name: Check (!Windows) + if: runner.os != 'Windows' + run: | + rcmdcheck::rcmdcheck( + args = "--as-cran", + error_on = "note", + check_dir = "check" + ) + shell: Rscript {0} + + - name: Check (Windows) + if: runner.os == 'Windows' + run: | + rcmdcheck::rcmdcheck( + args = c("--no-manual", "--as-cran"), + error_on = "note", + check_dir = "check" + ) shell: Rscript {0} - name: Upload check results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: ${{ runner.os }}-r${{ matrix.config.r }}-results path: check diff --git a/.github/workflows/covr.yaml b/.github/workflows/covr.yaml deleted file mode 100644 index c8d103a..0000000 --- a/.github/workflows/covr.yaml +++ /dev/null @@ -1,82 +0,0 @@ -on: [push] - -name: covr - -jobs: - covr: - if: "! contains(github.event.head_commit.message, '[ci skip]')" - - timeout-minutes: 30 - - runs-on: ubuntu-22.04 - - name: covr - - strategy: - fail-fast: false - - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - ## R CMD check - _R_CHECK_LENGTH_1_CONDITION_: true - _R_CHECK_LENGTH_1_LOGIC2_: true - _R_CHECK_MATRIX_DATA_: true - _R_CHECK_CRAN_INCOMING_: false - - steps: - - uses: actions/checkout@v3 - - - uses: r-lib/actions/setup-pandoc@v2 - - - uses: r-lib/actions/setup-r@v2 - with: - r-version: release - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - uses: actions/cache@v3 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" - - - name: Install dependencies - run: | - install.packages(c("covr", "sessioninfo")) - remotes::install_deps(dependencies = TRUE) - install.packages(".", repos=NULL, type="source") - shell: Rscript {0} - - - name: Session info - run: | - options(width = 100) - pkgs <- installed.packages()[, "Package"] - sessioninfo::session_info(pkgs, include_base = TRUE) - shell: Rscript {0} - - - name: Test coverage - run: | - ## 1. Get 'Repository Upload Token' from Codecov: - ## https://app.codecov.io/gh///settings - ## 2. Set 'CODECOV_TOKEN' in GitHub Secrets: - ## https://github.com///settings/environments/ - coverage <- covr::package_coverage() - print(coverage) - covr::codecov(coverage = coverage, token="${{secrets.CODECOV_TOKEN}}") - shell: Rscript {0} diff --git a/.github/workflows/revdepcheck-top.yaml b/.github/workflows/revdepcheck-top.yaml index d2b7fbe..b10c775 100644 --- a/.github/workflows/revdepcheck-top.yaml +++ b/.github/workflows/revdepcheck-top.yaml @@ -8,7 +8,7 @@ jobs: timeout-minutes: 30 - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest name: ${{ matrix.config.pkg }} (${{ matrix.config.r }}) @@ -16,14 +16,24 @@ jobs: fail-fast: false matrix: config: - - { r: "release", pkg: "cSEM" } - - { r: "release", pkg: "dipsaus" } - - { r: "release", pkg: "EFAtools" } - - { r: "release", pkg: "fxTWAPLS" } -# - { r: "release", pkg: "gtfs2gps" } + - { r: "release", pkg: "cSEM" } + - { r: "release", pkg: "dipsaus" } + - { r: "release", pkg: "EFAtools" } +# - { r: "release", pkg: "EGAnet" } ## libglpk.so missing +# - { r: "release", pkg: "elevatr" } ## libproj.so missing + - { r: "release", pkg: "fabletools" } + - { r: "release", pkg: "fxTWAPLS" } +# - { r: "release", pkg: "lava" } ## req's Bioc pkgs +# - { r: "release", pkg: "nflfastR" } +# - { r: "release", pkg: "poppr" } ## fails to install +# - { r: "release", pkg: "Seurat" } + - { r: "release", pkg: "SimDesign" } +# - { r: "release", pkg: "tidySEM" } ## fails to install + - { r: "release", pkg: "tsdistributions" } + - { r: "release", pkg: "tsgarch" } + env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest R_REMOTES_NO_ERRORS_FROM_WARNINGS: true ## R CMD check _R_CHECK_LENGTH_1_CONDITION_: true @@ -32,43 +42,35 @@ jobs: _R_CHECK_CRAN_INCOMING_: false steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-tinytex@v2 + + - name: Install system dependencies (Linux) + if: runner.os == 'Linux' + run: sudo apt-get install -y tidy + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + use-public-rspm: true - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v3 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies (Linux) - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" + extra-packages: | + any::rcmdcheck + any::remotes + any::sessioninfo + any::covr + needs: check - name: Install dependencies run: | remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - remotes::install_cran("${{ matrix.config.pkg }}", dependencies=TRUE) + install.packages(".", repos=NULL, type="source") + install.packages("${{ matrix.config.pkg }}", dependencies=TRUE) shell: Rscript {0} - name: Session info @@ -82,6 +84,7 @@ jobs: run: | url=$(Rscript -e "cat(remotes:::download_version_url('${{ matrix.config.pkg }}', version=NULL, repos='https://cloud.r-project.org', type='source'))") wget "$url" + R_PROGRESSR_ENABLE=true R CMD check --no-manual --as-cran "$(basename "$url")" - name: Upload check results @@ -89,4 +92,4 @@ jobs: uses: actions/upload-artifact@v3 with: name: ${{ runner.os }}-r${{ matrix.config.r }}-revdep${{ matrix.config.pkg }}-results - path: check + path: ${{ matrix.config.pkg }}.Rcheck diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml new file mode 100644 index 0000000..74ec7b0 --- /dev/null +++ b/.github/workflows/rhub.yaml @@ -0,0 +1,95 @@ +# R-hub's generic GitHub Actions workflow file. It's canonical location is at +# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml +# You can update this file to a newer version using the rhub2 package: +# +# rhub::rhub_setup() +# +# It is unlikely that you need to modify this file manually. + +name: R-hub +run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}" + +on: + workflow_dispatch: + inputs: + config: + description: 'A comma separated list of R-hub platforms to use.' + type: string + default: 'linux,windows,macos' + name: + description: 'Run name. You can leave this empty now.' + type: string + id: + description: 'Unique ID. You can leave this empty now.' + type: string + +jobs: + + setup: + runs-on: ubuntu-latest + outputs: + containers: ${{ steps.rhub-setup.outputs.containers }} + platforms: ${{ steps.rhub-setup.outputs.platforms }} + + steps: + # NO NEED TO CHECKOUT HERE + - uses: r-hub/actions/setup@v1 + with: + config: ${{ github.event.inputs.config }} + id: rhub-setup + + linux-containers: + needs: setup + if: ${{ needs.setup.outputs.containers != '[]' }} + runs-on: ubuntu-latest + name: ${{ matrix.config.label }} + strategy: + fail-fast: false + matrix: + config: ${{ fromJson(needs.setup.outputs.containers) }} + container: + image: ${{ matrix.config.container }} + + steps: + - uses: r-hub/actions/checkout@v1 + - uses: r-hub/actions/platform-info@v1 + with: + token: ${{ secrets.RHUB_TOKEN }} + job-config: ${{ matrix.config.job-config }} + - uses: r-hub/actions/setup-deps@v1 + with: + token: ${{ secrets.RHUB_TOKEN }} + job-config: ${{ matrix.config.job-config }} + - uses: r-hub/actions/run-check@v1 + with: + token: ${{ secrets.RHUB_TOKEN }} + job-config: ${{ matrix.config.job-config }} + + other-platforms: + needs: setup + if: ${{ needs.setup.outputs.platforms != '[]' }} + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.label }} + strategy: + fail-fast: false + matrix: + config: ${{ fromJson(needs.setup.outputs.platforms) }} + + steps: + - uses: r-hub/actions/checkout@v1 + - uses: r-hub/actions/setup-r@v1 + with: + job-config: ${{ matrix.config.job-config }} + token: ${{ secrets.RHUB_TOKEN }} + - uses: r-hub/actions/platform-info@v1 + with: + token: ${{ secrets.RHUB_TOKEN }} + job-config: ${{ matrix.config.job-config }} + - uses: r-hub/actions/setup-deps@v1 + with: + job-config: ${{ matrix.config.job-config }} + token: ${{ secrets.RHUB_TOKEN }} + - uses: r-hub/actions/run-check@v1 + with: + job-config: ${{ matrix.config.job-config }} + token: ${{ secrets.RHUB_TOKEN }} diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..cd2c74a --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,56 @@ +on: [push] + +name: test-coverage.yaml + +permissions: read-all + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v4 + + - name: Assert CODECOV_TOKEN is set + run: | + if [[ -z "${{secrets.CODECOV_TOKEN}}" ]]; then + >&2 echo "::error::ERROR: 'secrets.CODECOV_TOKEN' not set" + exit 1 + fi + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + print(cov) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b99a84d..71af02b 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,8 +1,8 @@ # Contributing to the 'progressr' package -This Git repository uses the [Git Flow](https://nvie.com/posts/a-successful-git-branching-model/) branching model (the [`git flow`](https://github.com/petervanderdoes/gitflow-avh) extension is useful for this). The [`develop`](https://github.com/HenrikBengtsson/progressr/tree/develop) branch contains the latest contributions and other code that will appear in the next release, and the [`master`](https://github.com/HenrikBengtsson/progressr) branch contains the code of the latest release, which is exactly what is currently on [CRAN](https://cran.r-project.org/package=progressr). +This Git repository uses the [Git Flow](https://nvie.com/posts/a-successful-git-branching-model/) branching model (the [`git flow`](https://github.com/petervanderdoes/gitflow-avh) extension is useful for this). The [`develop`](https://github.com/futureverse/progressr/tree/develop) branch contains the latest contributions and other code that will appear in the next release, and the [`master`](https://github.com/futureverse/progressr) branch contains the code of the latest release, which is exactly what is currently on [CRAN](https://cran.r-project.org/package=progressr). -Contributing to this package is easy. Just send a [pull request](https://help.github.com/articles/using-pull-requests/). When you send your PR, make sure `develop` is the destination branch on the [progressr repository](https://github.com/HenrikBengtsson/progressr). Your PR should pass `R CMD check --as-cran`, which will also be checked by GitHub Actions and when the PR is submitted. +Contributing to this package is easy. Just send a [pull request](https://help.github.com/articles/using-pull-requests/). When you send your PR, make sure `develop` is the destination branch on the [progressr repository](https://github.com/futureverse/progressr). Your PR should pass `R CMD check --as-cran`, which will also be checked by GitHub Actions and when the PR is submitted. We abide to the [Code of Conduct](https://www.contributor-covenant.org/version/2/0/code_of_conduct/) of Contributor Covenant. diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..e977346 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 0.15.0 +Date: 2024-10-29 03:15:56 UTC +SHA: 17f28870f183d82353cd805c54cd23dbc07ad315 diff --git a/DESCRIPTION b/DESCRIPTION index efef441..065ab3b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,11 @@ Package: progressr -Version: 0.14.0 +Version: 0.15.0 Title: An Inclusive, Unifying API for Progress Updates Description: A minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates, e.g. in the terminal using utils::txtProgressBar(), cli::cli_progress_bar(), in a graphical user interface using utils::winProgressBar(), tcltk::tkProgressBar() or shiny::withProgress(), via the speakers using beepr::beep(), or on a file system via the size of a file. Anyone can add additional, customized, progression handlers. The 'progressr' package uses R's condition framework for signaling progress updated. Because of this, progress can be reported from almost anywhere in R, e.g. from classical for and while loops, from map-reduce API:s like the lapply() family of functions, 'purrr', 'plyr', and 'foreach'. It will also work with parallel processing via the 'future' framework, e.g. future.apply::future_lapply(), furrr::future_map(), and 'foreach' with 'doFuture'. The package is compatible with Shiny applications. -Authors@R: c( - person("Henrik", "Bengtsson", role=c("aut", "cre", "cph"), - email = "henrikb@braju.com")) +Authors@R: c(person("Henrik", "Bengtsson", + role = c("aut", "cre", "cph"), + email = "henrikb@braju.com", + comment = c(ORCID = "0000-0002-7579-5165"))) License: GPL (>= 3) Depends: R (>= 3.5.0) @@ -33,7 +34,7 @@ Suggests: base64enc, tools VignetteBuilder: progressr -URL: https://progressr.futureverse.org, https://github.com/HenrikBengtsson/progressr -BugReports: https://github.com/HenrikBengtsson/progressr/issues -RoxygenNote: 7.2.3 +URL: https://progressr.futureverse.org, https://github.com/futureverse/progressr +BugReports: https://github.com/futureverse/progressr/issues +RoxygenNote: 7.3.2 Roxygen: list(markdown = TRUE) diff --git a/NAMESPACE b/NAMESPACE index c859390..96ee9be 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -11,6 +11,7 @@ export(handler_debug) export(handler_filesize) export(handler_newline) export(handler_notifier) +export(handler_ntfy) export(handler_pbcol) export(handler_pbmcapply) export(handler_progress) diff --git a/NEWS.md b/NEWS.md index 134baea..87695d8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,23 @@ +# Version 0.15.0 [2023-10-28] + +## New Features + + * Add `handler_ntfy()` for reporting on progress via the Ntfy.sh + Messaging Service using the **ntfy** package. + + +## Bug Fixes + + * `withProgressShiny()` could produce an `if (config$max_steps == + 0) : ... argument is of length zero` error. + + * `handlers(new_handlers)` would return `NULL`, instead of `list()`, + if there were no prior handlers set. + + * `handler_cli(..., format_done = "...", clear = TRUE)` would not + render the `format_done` message, if set. + + # Version 0.14.0 [2023-08-10] ## New Features @@ -609,7 +629,7 @@ * TESTS: Increased package test coverage of progression handlers by running all code except the last step that calls the backend, which may not be installed or supported on the current platform, - e.g. **tcltk**, **beepr**, notifier. + e.g. **tcltk**, **beepr**, and **notifier**. ## Bug Fixes diff --git a/R/global_progression_handler.R b/R/global_progression_handler.R index 9c5da05..60f6368 100644 --- a/R/global_progression_handler.R +++ b/R/global_progression_handler.R @@ -335,14 +335,24 @@ if (getRversion() < "4.0.0") { } -as_progression_handler <- function(handlers, drop = TRUE) { +as_progression_handler <- function(handlers, drop = TRUE, debug = FALSE) { ## FIXME(?) if (!is.list(handlers)) handlers <- list(handlers) - + + if (debug) { + message("as_progression_handler() ...") + message(sprintf("- Number of progression handlers: %d", length(handlers))) + on.exit({ + message(sprintf("- Number of progression handlers: %d", length(handlers))) + message("as_progression_handler() ... done") + }) + } + for (kk in seq_along(handlers)) { handler <- handlers[[kk]] stop_if_not(is.function(handler)) if (!inherits(handler, "progression_handler")) { + if (debug) message(sprintf("- Handler %d is a function; calling it", kk)) handler <- handler() stop_if_not(is.function(handler), inherits(handler, "progression_handler")) @@ -352,11 +362,17 @@ as_progression_handler <- function(handlers, drop = TRUE) { ## Keep only enabled handlers? if (drop) { + if (debug) message(sprintf("- drop = TRUE => dropping non-enabled handlers")) enabled <- vapply(handlers, FUN = function(h) { env <- environment(h) value <- env$enable isTRUE(value) || is.null(value) }, FUN.VALUE = TRUE) + + if (debug && !all(enabled)) { + message(sprintf("- Detected %d non-enabled handlers: %s", sum(!enabled), vapply(handlers[!enabled], FUN = function(h) class(h)[1], FUN.VALUE = NA_character_))) + } + handlers <- handlers[enabled] } diff --git a/R/handler_cli.R b/R/handler_cli.R index 193ac35..887c430 100644 --- a/R/handler_cli.R +++ b/R/handler_cli.R @@ -172,7 +172,6 @@ handler_cli <- function(show_after = 0.0, intrusiveness = getOption("progressr.i if (ratio >= 1.0) { cli_progress_done(id = pb$id, .envir = pb$envir) - erase_progress_bar(pb) } else { set <- ratio * pb$total stopifnot(length(set) == 1L, is.numeric(set), is.finite(set), @@ -245,7 +244,9 @@ handler_cli <- function(show_after = 0.0, intrusiveness = getOption("progressr.i reporter$update(config = config, state = state, progression = progression, ...) if (config$clear) { pb_update(pb, ratio = 1.0) + erase_progress_bar(pb) } else { + pb_update(pb, ratio = 1.0) cat(file = stderr(), "\n") } diff --git a/R/handler_filesize.R b/R/handler_filesize.R index c5205a2..4732597 100644 --- a/R/handler_filesize.R +++ b/R/handler_filesize.R @@ -27,6 +27,13 @@ handler_filesize <- function(file = "default.progress", intrusiveness = getOption("progressr.intrusiveness.file", 5), target = "file", enable = getOption("progressr.enable", TRUE), ...) { reporter <- local({ set_file_size <- function(config, state, progression, message = state$message) { + ## Troubleshoot https://github.com/futureverse/progressr/issues/168 + stop_if_not( + length(config$max_steps) == 1L, is.numeric(config$max_steps), + !is.na(config$max_steps), is.finite(config$max_steps), + config$max_steps >= 0 + ) + ratio <- if (config$max_steps == 0) 1 else state$step / config$max_steps size <- round(100 * ratio) current_size <- file.size(file) @@ -54,19 +61,23 @@ handler_filesize <- function(file = "default.progress", intrusiveness = getOptio list( initiate = function(config, state, progression, ...) { + if (!state$enabled) return() set_file_size(config = config, state = state, progression = progression) }, interrupt = function(config, state, progression, ...) { + if (!state$enabled) return() msg <- conditionMessage(progression) set_file_size(config = config, state = state, progression = progression, message = msg) }, update = function(config, state, progression, ...) { + if (!state$enabled) return() set_file_size(config = config, state = state, progression = progression) }, finish = function(config, state, progression, ...) { + if (!state$enabled) return() if (config$clear) { if (file_test("-f", file)) file.remove(file) } else { diff --git a/R/handler_notifier.R b/R/handler_notifier.R index 42d3b5f..b858ffb 100644 --- a/R/handler_notifier.R +++ b/R/handler_notifier.R @@ -23,17 +23,12 @@ handler_notifier <- function(intrusiveness = getOption("progressr.intrusiveness. if (!requireNamespace(pkg, quietly = TRUE)) { stop("Package 'notifier' is not available. See ?progressr::handler_notifier() for installation instructions") } - notifier_notify <- get("notify", mode = "function", envir = getNamespace(pkg)) + notifier_ <- get("notify", mode = "function", envir = getNamespace(pkg)) + notifier <- function(title = "R 'progressr' notification", message, ...) { + notifier_(msg = message, title = title) + } } else { - notifier_notify <- function(...) NULL - } - - notify <- function(step, max_steps, message) { - ratio <- if (max_steps == 0) 1 else step / max_steps - ratio <- sprintf("%.0f%%", 100*ratio) - msg <- paste(c("", message), collapse = "") - msg <- sprintf("[%s] %s", ratio, msg) - notifier_notify(msg) + notifier <- function(title = "R 'progressr' notification", message, ...) NULL } reporter <- local({ @@ -46,23 +41,25 @@ handler_notifier <- function(intrusiveness = getOption("progressr.intrusiveness. interrupt = function(config, state, progression, ...) { msg <- conditionMessage(progression) - notify(step = state$step, max_steps = config$max_steps, message = msg) + progress_notify(step = state$step, max_steps = config$max_steps, message = msg, notifier = notifier) }, initiate = function(config, state, progression, ...) { if (!state$enabled || config$times == 1L) return() - notify(step = state$step, max_steps = config$max_steps, message = state$message) + progress_notify(step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) }, update = function(config, state, progression, ...) { if (!state$enabled || progression$amount == 0 || config$times <= 2L) return() - notify(step = state$step, max_steps = config$max_steps, message = state$message) + progress_notify(step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) }, finish = function(config, state, progression, ...) { if (finished) return() if (!state$enabled) return() - if (state$delta > 0) notify(step = state$step, max_steps = config$max_steps, message = state$message) + if (state$delta > 0) { + progress_notify(step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) + } finished <<- TRUE } ) diff --git a/R/handler_ntfy.R b/R/handler_ntfy.R new file mode 100644 index 0000000..77cabec --- /dev/null +++ b/R/handler_ntfy.R @@ -0,0 +1,75 @@ +#' Progression Handler: Progress Reported via the Ntfy.sh Messaging Service +#' +#' A progression handler for `ntfy_send()` of the \pkg{ntfy} package, +#' which sends notifications via the framework. +#' +#' @inheritParams make_progression_handler +#' @inheritParams ntfy::ntfy_send +#' +#' @param \ldots Additional arguments passed to [make_progression_handler()]. +#' +#' @example incl/handler_ntfy.R +#' +#' @section Requirements: +#' This progression handler requires the \pkg{ntfy} package, which is only +#' available from . +#' +#' @keywords internal +#' @export +handler_ntfy <- function(intrusiveness = getOption("progressr.intrusiveness.ntfy", 5), target = "gui", ..., title = "Progress update from R") { + ## Used for package testing purposes only when we want to perform + ## everything except the last part where the backend is called + ntfy_send <- function(...) NULL + if (!is_fake("handler_ntfy")) { + pkg <- "ntfy" + if (!requireNamespace(pkg, quietly = TRUE)) { + stop("Package 'ntfy' is not available. See ?progressr::handler_ntfy() for installation instructions") + } + ntfy_send <- get("ntfy_send", mode = "function", envir = getNamespace(pkg)) + } + + notifier <- function(title, message) { + args <- list( + message = message, + title = title + ) + + do.call(ntfy_send, args = args) + } + + reporter <- local({ + finished <- FALSE + + list( + reset = function(...) { + finished <<- FALSE + }, + + initiate = function(config, state, progression, ...) { + if (!state$enabled || config$times == 1L) return() + progress_notify(title = title, step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) + }, + + interrupt = function(config, state, progression, ...) { + msg <- conditionMessage(progression) + progress_notify(title = title, step = state$step, max_steps = config$max_steps, message = msg, notifier = notifier) + }, + + update = function(config, state, progression, ...) { + if (!state$enabled || progression$amount == 0 || config$times <= 2L) return() + progress_notify(title = title, step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) + }, + + finish = function(config, state, progression, ...) { + if (finished) return() + if (!state$enabled) return() + if (state$delta > 0) progress_notify(title = title, step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) + finished <<- TRUE + } + ) + }) + + make_progression_handler("ntfy", reporter, intrusiveness = intrusiveness, target = target, ...) +} + + diff --git a/R/handler_rpushbullet.R b/R/handler_rpushbullet.R index 5aa90a2..938bf2c 100644 --- a/R/handler_rpushbullet.R +++ b/R/handler_rpushbullet.R @@ -31,26 +31,20 @@ handler_rpushbullet <- function(intrusiveness = getOption("progressr.intrusivene } } - notify <- function(step, max_steps, message) { - ratio <- if (max_steps == 0) 1 else step / max_steps - ratio <- sprintf("%.0f%%", 100*ratio) - msg <- paste(c("", message), collapse = "") + notifier <- function(title, message) { args <- list( - type = "note", + type = "note", title = title, - body = sprintf("[%s] %s", ratio, msg) + body = paste(c("", message), collapse = "") ) + if (!is.null(recipients)) args$recipients <- recipients if (!is.null(email)) args$email <- email if (!is.null(channel)) args$channel <- channel if (!is.null(apikey)) args$apikey <- apikey if (!is.null(device)) args$device <- device - - pbPost( - type = "note", - title = title, - body = sprintf("[%s] %s", ratio, msg) - ) + + do.call(pbPost, args = args) } reporter <- local({ @@ -63,23 +57,23 @@ handler_rpushbullet <- function(intrusiveness = getOption("progressr.intrusivene initiate = function(config, state, progression, ...) { if (!state$enabled || config$times == 1L) return() - notify(step = state$step, max_steps = config$max_steps, message = state$message) + progress_notify(title = title, step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) }, interrupt = function(config, state, progression, ...) { msg <- conditionMessage(progression) - notify(step = state$step, max_steps = config$max_steps, message = msg) + progress_notify(title = title, step = state$step, max_steps = config$max_steps, message = msg, notifier = notifier) }, update = function(config, state, progression, ...) { if (!state$enabled || progression$amount == 0 || config$times <= 2L) return() - notify(step = state$step, max_steps = config$max_steps, message = state$message) + progress_notify(title = title, step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) }, finish = function(config, state, progression, ...) { if (finished) return() if (!state$enabled) return() - if (state$delta > 0) notify(step = state$step, max_steps = config$max_steps, message = state$message) + if (state$delta > 0) progress_notify(title = title, step = state$step, max_steps = config$max_steps, message = state$message, notifier = notifier) finished <<- TRUE } ) diff --git a/R/handler_shiny.R b/R/handler_shiny.R index 2032f09..44d8874 100644 --- a/R/handler_shiny.R +++ b/R/handler_shiny.R @@ -54,6 +54,12 @@ handler_shiny <- function(intrusiveness = getOption("progressr.intrusiveness.gui reporter <- local({ list( interrupt = function(config, state, progression, ...) { + if (!state$enabled) return() + stop_if_not( + length(config$max_steps) == 1L, is.numeric(config$max_steps), + !is.na(config$max_steps), is.finite(config$max_steps), + config$max_steps >= 0 + ) msg <- conditionMessage(progression) amount <- if (config$max_steps == 0) 1 else progression$amount / config$max_steps args <- c( @@ -64,6 +70,12 @@ handler_shiny <- function(intrusiveness = getOption("progressr.intrusiveness.gui }, update = function(config, state, progression, ...) { + if (!state$enabled) return() + stop_if_not( + length(config$max_steps) == 1L, is.numeric(config$max_steps), + !is.na(config$max_steps), is.finite(config$max_steps), + config$max_steps >= 0 + ) amount <- if (config$max_steps == 0) 1 else progression$amount / config$max_steps args <- c( list(amount = amount), diff --git a/R/handlers.R b/R/handlers.R index 96a6087..bb81959 100644 --- a/R/handlers.R +++ b/R/handlers.R @@ -109,6 +109,7 @@ handlers <- function(..., append = FALSE, on_missing = c("error", "warning", "ig } handlers <- list() + names <- names(args) for (kk in seq_along(args)) { handler <- args[[kk]] @@ -164,5 +165,8 @@ handlers <- function(..., append = FALSE, on_missing = c("error", "warning", "ig if (length(current) > 0L) handlers <- c(current, handlers) } - invisible(options(progressr.handlers = handlers)[[1]]) + old_handlers <- options(progressr.handlers = handlers)[[1]] + if (is.null(old_handlers)) old_handlers <- list() + + invisible(old_handlers) } diff --git a/R/notifiers.R b/R/notifiers.R new file mode 100644 index 0000000..16b6af7 --- /dev/null +++ b/R/notifiers.R @@ -0,0 +1,10 @@ +progress_notify <- function(title = "R 'progressr' notification", message, step, max_steps, notifier) { + stop_if_not(is.function(notifier)) + + ratio <- if (max_steps == 0) 1 else step / max_steps + ratio <- sprintf("%.0f%%", 100*ratio) + msg <- paste(c("", message), collapse = "") + body <- sprintf("[%s] %s", ratio, msg) + + notifier(title = title, message = body) +} ## progress_notify() diff --git a/R/progressr-package.R b/R/progressr-package.R index 3d761db..832fadc 100644 --- a/R/progressr-package.R +++ b/R/progressr-package.R @@ -56,11 +56,15 @@ #' In Shiny: #' * [withProgressShiny] #' +#' Via notification systems: +#' * [handler_ntfy] +#' * [handler_notifier] +#' * [handler_rpushbullet] +#' #' @example incl/progressr-package.R #' #' @keywords programming iteration #' -#' @docType package #' @aliases progressr-package #' @name progressr -NULL +"_PACKAGE" diff --git a/R/with_progress.R b/R/with_progress.R index 1b42ab8..168fc77 100644 --- a/R/with_progress.R +++ b/R/with_progress.R @@ -38,6 +38,9 @@ #' @example incl/with_progress.R #' #' @details +#' If you are writing a Shiny app, use the [withProgressShiny()] function +#' instead of this one. +#' #' If the global progression handler is enabled, it is temporarily disabled #' while evaluating the `expr` expression. #' @@ -69,7 +72,8 @@ #' will. #' #' @seealso -#' [base::withCallingHandlers()] +#' For Shiny apps, use [withProgressShiny()] instead of this function. +#' Internally, this function is built around [base::withCallingHandlers()]. #' #' @export with_progress <- function(expr, handlers = progressr::handlers(), cleanup = TRUE, delay_terminal = NULL, delay_stdout = NULL, delay_conditions = NULL, interrupts = getOption("progressr.interrupts", TRUE), interval = NULL, enable = NULL) { @@ -125,7 +129,7 @@ with_progress <- function(expr, handlers = progressr::handlers(), cleanup = TRUE progressr_in_globalenv("allow") on.exit(progressr_in_globalenv("disallow"), add = TRUE) - handlers <- as_progression_handler(handlers) + handlers <- as_progression_handler(handlers, debug = debug) ## Nothing to do? if (length(handlers) == 0L) { diff --git a/README.md b/README.md index a301d86..fc361de 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@
-CRAN check status R CMD check status Top reverse-dependency checks status Coverage Status Life cycle: maturing +CRAN check status R CMD check status Top reverse-dependency checks status Coverage Status Life cycle: maturing
# progressr: An Inclusive, Unifying API for Progress Updates @@ -617,8 +617,35 @@ my_fcn(1:5) ### foreach() with doFuture Here is an example that uses `foreach()` of the **[foreach]** package -to parallelize on the local machine (via **[doFuture]**) while at the -same time signaling progression updates: +together with `%dofuture%` of the **[doFuture]** package to +parallelize while reporting on progress. This example parallelizes on +the local machine, it works alsof for remote machines: + +```r +library(doFuture) ## %dofuture% +plan(multisession) + +library(progressr) +handlers(global = TRUE) +handlers("progress", "beepr") + +my_fcn <- function(xs) { + p <- progressor(along = xs) + foreach(x = xs) %dofuture% { + Sys.sleep(6.0-x) + p(sprintf("x=%g", x)) + sqrt(x) + } +} + +my_fcn(1:5) +# / [================>-----------------------------] 40% x=2 +``` + + +For existing code using the traditional `%dopar%` operators of the +**[foreach]** package, we can register the **[doFuture]** adaptor and +use the same **progressr** as above to progress updates; ```r library(doFuture) @@ -847,7 +874,7 @@ depends on it. The roadmap for developing the API is roughly: additional progression handlers For a more up-to-date view on what features might be added, see -. +. ## Appendix @@ -1027,7 +1054,7 @@ install.packages("progressr") To install the pre-release version that is available in Git branch `develop` on GitHub, use: ```r -remotes::install_github("HenrikBengtsson/progressr", ref="develop") +remotes::install_github("futureverse/progressr", ref="develop") ``` This will install the package from source. diff --git a/cran-comments.md b/cran-comments.md index cc3543f..24f3b92 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,83 +1,3 @@ -# CRAN submission progressr 0.14.0 - -on 2023-08-10 - -I've verified this submission has no negative impact on any of the 82 reverse package dependencies available on CRAN (n = 79) and Bioconductor (n = 3). +I've verified this submission has no negative impact on any of the 110 reverse package dependencies available on CRAN (n = 107) and Bioconductor (n = 3). Thank you - -## Resubmission - -Updated version fixing an R CMD check WARNING reported by R-devel on Debian. - - -## Notes not sent to CRAN - -### R CMD check validation - -The package has been verified using `R CMD check --as-cran` on: - -| R version | GitHub | R-hub | mac/win-builder | -| --------- | ------ | ----- | --------------- | -| 3.5.x | L | | | -| 4.0.x | L | | | -| 4.1.x | L | | | -| 4.2.x | L | | | -| 4.3.x | L M W | L W | M1 W | -| devel | L M W | L | W | - -*Legend: OS: L = Linux, M = macOS, M1 = macOS M1, W = Windows* - - -R-hub checks: - -```r -res <- rhub::check(platforms = c( - "debian-clang-devel", - "debian-gcc-patched", - "fedora-gcc-devel", - "macos-highsierra-release-cran", - "windows-x86_64-release" -)) -print(res) -``` - -gives - -``` -── progressr 0.13.0-9013: OK - - Build ID: progressr_0.13.0-9013.tar.gz-d76d5bc4979b480fa1e4bbe0c5d705a1 - Platform: Debian Linux, R-devel, clang, ISO-8859-15 locale - Submitted: 17m 26.7s ago - Build time: 17m 23.3s - -0 errors ✔ | 0 warnings ✔ | 0 notes ✔ - -── progressr 0.13.0-9013: OK - - Build ID: progressr_0.13.0-9013.tar.gz-bbc8cdfc4d0241ebb3d0129420c7fed4 - Platform: Debian Linux, R-patched, GCC - Submitted: 17m 26.7s ago - Build time: 16m 17.3s - -0 errors ✔ | 0 warnings ✔ | 0 notes ✔ - -── progressr 0.13.0-9013: OK - - Build ID: progressr_0.13.0-9013.tar.gz-71676aa30ce74ff7931c996a95e7b327 - Platform: Fedora Linux, R-devel, GCC - Submitted: 17m 26.7s ago - Build time: 15m 0.3s - -0 errors ✔ | 0 warnings ✔ | 0 notes ✔ - -── progressr 0.13.0-9013: OK - - Build ID: progressr_0.13.0-9013.tar.gz-29b149c623ba4eea91841fd5a9fc6ac7 - Platform: Windows Server 2022, R-release, 32/64 bit - Submitted: 17m 26.7s ago - Build time: 5m 50.8s - -0 errors ✔ | 0 warnings ✔ | 0 notes ✔ -``` diff --git a/incl/OVERVIEW.md b/incl/OVERVIEW.md index 8fea0a0..4ca505a 100644 --- a/incl/OVERVIEW.md +++ b/incl/OVERVIEW.md @@ -609,8 +609,35 @@ my_fcn(1:5) ### foreach() with doFuture Here is an example that uses `foreach()` of the **[foreach]** package -to parallelize on the local machine (via **[doFuture]**) while at the -same time signaling progression updates: +together with `%dofuture%` of the **[doFuture]** package to +parallelize while reporting on progress. This example parallelizes on +the local machine, it works alsof for remote machines: + +```r +library(doFuture) ## %dofuture% +plan(multisession) + +library(progressr) +handlers(global = TRUE) +handlers("progress", "beepr") + +my_fcn <- function(xs) { + p <- progressor(along = xs) + foreach(x = xs) %dofuture% { + Sys.sleep(6.0-x) + p(sprintf("x=%g", x)) + sqrt(x) + } +} + +my_fcn(1:5) +# / [================>-----------------------------] 40% x=2 +``` + + +For existing code using the traditional `%dopar%` operators of the +**[foreach]** package, we can register the **[doFuture]** adaptor and +use the same **progressr** as above to progress updates; ```r library(doFuture) @@ -839,7 +866,7 @@ depends on it. The roadmap for developing the API is roughly: additional progression handlers For a more up-to-date view on what features might be added, see -. +. ## Appendix diff --git a/incl/handler_ntfy.R b/incl/handler_ntfy.R new file mode 100644 index 0000000..5bac29c --- /dev/null +++ b/incl/handler_ntfy.R @@ -0,0 +1,11 @@ +pkg <- "ntfy" +if (requireNamespace(pkg, quietly = TRUE)) { + ## We need to specify a ntfy.sh topic that progress messages + ## should be sent to. See help("ntfy_topic", package = "ntfy") + ## for details + Sys.setenv("NTFY_TOPIC", "R-my-secret-topic") + + handlers("ntfy") + with_progress({ y <- slow_sum(1:10) }) + print(y) +} diff --git a/man/figures/handler_cli-default.svg b/man/figures/handler_cli-default.svg index 654d936..1d6beaa 100644 --- a/man/figures/handler_cli-default.svg +++ b/man/figures/handler_cli-default.svg @@ -1 +1 @@ -■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■100%|P:Adding25ETA:0s■■4%|P:Adding1ETA:3s■■■8%|P:Adding2ETA:4s■■■■■12%|P:Adding3ETA:4s■■■■■■16%|P:Adding4ETA:3s■■■■■■■20%|P:Adding5ETA:3s■■■■■■■■24%|P:Adding6ETA:3s■■■■■■■■■28%|P:Adding7ETA:3s■■■■■■■■■■■32%|P:Adding8ETA:3s■■■■■■■■■■■■36%|P:Adding9ETA:3s■■■■■■■■■■■■■40%|P:Adding10ETA:3s■■■■■■■■■■■■■■44%|P:Adding11ETA:2s■■■■■■■■■■■■■■■48%|P:Adding12ETA:2s■■■■■■■■■■■■■■■■■52%|P:Adding13ETA:2s■■■■■■■■■■■■■■■■■■56%|P:Adding14ETA:2s■■■■■■■■■■■■■■■■■■■60%|P:Adding15ETA:2s■■■■■■■■■■■■■■■■■■■■64%|P:Adding16ETA:2s■■■■■■■■■■■■■■■■■■■■■68%|P:Adding17ETA:1s■■■■■■■■■■■■■■■■■■■■■■■72%|P:Adding18ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■76%|P:Adding19ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■■80%|P:Adding20ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■■■84%|P:Adding21ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■■■■88%|P:Adding22ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■■■■■■92%|P:Adding23ETA:0s■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■96%|P:Adding24ETA:0s \ No newline at end of file +■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■100%|P:Adding25ETA:0s■■4%|P:Adding1ETA:3s■■■8%|P:Adding2ETA:4s■■■■■12%|P:Adding3ETA:4s■■■■■■16%|P:Adding4ETA:3s■■■■■■■20%|P:Adding5ETA:3s■■■■■■■■24%|P:Adding6ETA:3s■■■■■■■■■28%|P:Adding7ETA:3s■■■■■■■■■■■32%|P:Adding8ETA:3s■■■■■■■■■■■■36%|P:Adding9ETA:3s■■■■■■■■■■■■■40%|P:Adding10ETA:2s■■■■■■■■■■■■■■44%|P:Adding11ETA:2s■■■■■■■■■■■■■■■48%|P:Adding12ETA:2s■■■■■■■■■■■■■■■■■52%|P:Adding13ETA:2s■■■■■■■■■■■■■■■■■■56%|P:Adding14ETA:2s■■■■■■■■■■■■■■■■■■■60%|P:Adding15ETA:2s■■■■■■■■■■■■■■■■■■■■64%|P:Adding16ETA:2s■■■■■■■■■■■■■■■■■■■■■68%|P:Adding17ETA:1s■■■■■■■■■■■■■■■■■■■■■■■72%|P:Adding18ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■76%|P:Adding19ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■■80%|P:Adding20ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■■■84%|P:Adding21ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■■■■88%|P:Adding22ETA:1s■■■■■■■■■■■■■■■■■■■■■■■■■■■■■92%|P:Adding23ETA:0s■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■96%|P:Adding24ETA:0s \ No newline at end of file diff --git a/man/figures/handler_cli-format-1.svg b/man/figures/handler_cli-format-1.svg index 5a50896..4834b44 100644 --- a/man/figures/handler_cli-format-1.svg +++ b/man/figures/handler_cli-format-1.svg @@ -1 +1 @@ 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+⠦■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■25/25P:Adding25⠙■■1/25P:Adding1⠹■■■2/25P:Adding2⠸■■■■■3/25P:Adding3⠼■■■■■■4/25P:Adding4⠴■■■■■■■5/25P:Adding5⠦■■■■■■■■6/25P:Adding6⠧■■■■■■■■■7/25P:Adding7⠇■■■■■■■■■■■8/25P:Adding8⠏■■■■■■■■■■■■9/25P:Adding9⠋■■■■■■■■■■■■■10/25P:Adding10⠙■■■■■■■■■■■■■■11/25P:Adding11⠹■■■■■■■■■■■■■■■12/25P:Adding12⠸■■■■■■■■■■■■■■■■■13/25P:Adding13⠼■■■■■■■■■■■■■■■■■■14/25P:Adding14⠴■■■■■■■■■■■■■■■■■■■15/25P:Adding15⠦■■■■■■■■■■■■■■■■■■■■16/25P:Adding16⠧■■■■■■■■■■■■■■■■■■■■■17/25P:Adding17⠇■■■■■■■■■■■■■■■■■■■■■■■18/25P:Adding18⠏■■■■■■■■■■■■■■■■■■■■■■■■19/25P:Adding19⠋■■■■■■■■■■■■■■■■■■■■■■■■■20/25P:Adding20⠙■■■■■■■■■■■■■■■■■■■■■■■■■■21/25P:Adding21⠹■■■■■■■■■■■■■■■■■■■■■■■■■■■22/25P:Adding22⠸■■■■■■■■■■■■■■■■■■■■■■■■■■■■■23/25P:Adding23⠼■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■24/25P:Adding24⠴■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■25/25P:Adding25 \ No newline at end of file diff --git a/man/figures/handler_pbcol-adjust-mid.svg b/man/figures/handler_pbcol-adjust-mid.svg index fd2449b..bd57c87 100644 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-||============================================================|100%||0%|==|4%|=====|8%|=======|12%|==========|16%|============|20%|==============|24%|=================|28%|===================|32%|======================|36%|========================|40%|==========================|44%|=============================|48%|===============================|52%|==================================|56%|====================================|60%|======================================|64%|=========================================|68%|===========================================|72%|==============================================|76%|================================================|80%|==================================================|84%|=====================================================|88%|=======================================================|92%|==========================================================|96% \ No newline at end of file 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-============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== \ No newline at end of file +============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== \ No newline at end of file diff --git a/man/figures/handler_txtprogressbar-style-3.svg 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-||============================================================|100%||0%|==|4%|=====|8%|=======|12%|==========|16%|============|20%|==============|24%|=================|28%|===================|32%|======================|36%|========================|40%|==========================|44%|=============================|48%|===============================|52%|==================================|56%|====================================|60%|======================================|64%|=========================================|68%|===========================================|72%|==============================================|76%|================================================|80%|==================================================|84%|=====================================================|88%|=======================================================|92%|==========================================================|96% \ No newline at end of file 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file mode 100644 index 0000000..c189b27 --- /dev/null +++ b/man/handler_ntfy.Rd @@ -0,0 +1,48 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/handler_ntfy.R +\name{handler_ntfy} +\alias{handler_ntfy} +\title{Progression Handler: Progress Reported via the Ntfy.sh Messaging Service} +\usage{ +handler_ntfy( + intrusiveness = getOption("progressr.intrusiveness.ntfy", 5), + target = "gui", + ..., + title = "Progress update from R" +) +} +\arguments{ +\item{intrusiveness}{(numeric) A non-negative scalar on how intrusive +(disruptive) the reporter to the user.} + +\item{target}{(character vector) Specifies where progression updates are +rendered.} + +\item{title}{title of notification. See \url{https://docs.ntfy.sh/publish/#message-title}} + +\item{\ldots}{Additional arguments passed to \code{\link[=make_progression_handler]{make_progression_handler()}}.} +} +\description{ +A progression handler for \code{ntfy_send()} of the \pkg{ntfy} package, +which sends notifications via the \url{https://ntfy.sh} framework. +} +\section{Requirements}{ + +This progression handler requires the \pkg{ntfy} package, which is only +available from \url{https://github.com/jonocarroll/ntfy}. +} + +\examples{ +pkg <- "ntfy" +if (requireNamespace(pkg, quietly = TRUE)) { + ## We need to specify a ntfy.sh topic that progress messages + ## should be sent to. See help("ntfy_topic", package = "ntfy") + ## for details + Sys.setenv("NTFY_TOPIC", "R-my-secret-topic") + + handlers("ntfy") + with_progress({ y <- slow_sum(1:10) }) + print(y) +} +} +\keyword{internal} diff --git a/man/progressr.Rd b/man/progressr.Rd index 201a7d0..e106604 100644 --- a/man/progressr.Rd +++ b/man/progressr.Rd @@ -73,6 +73,13 @@ In Shiny: \itemize{ \item \link{withProgressShiny} } + +Via notification systems: +\itemize{ +\item \link{handler_ntfy} +\item \link{handler_notifier} +\item \link{handler_rpushbullet} +} } \examples{ @@ -88,6 +95,19 @@ with_progress({ sqrt(x) }) }) +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://progressr.futureverse.org} + \item \url{https://github.com/futureverse/progressr} + \item Report bugs at \url{https://github.com/futureverse/progressr/issues} +} + +} +\author{ +\strong{Maintainer}: Henrik Bengtsson \email{henrikb@braju.com} (\href{https://orcid.org/0000-0002-7579-5165}{ORCID}) [copyright holder] + } \keyword{iteration} \keyword{programming} diff --git a/man/with_progress.Rd b/man/with_progress.Rd index 4ce826f..50eceeb 100644 --- a/man/with_progress.Rd +++ b/man/with_progress.Rd @@ -60,6 +60,9 @@ Returns the value of the expression. Report on Progress while Evaluating an R Expression } \details{ +If you are writing a Shiny app, use the \code{\link[=withProgressShiny]{withProgressShiny()}} function +instead of this one. + If the global progression handler is enabled, it is temporarily disabled while evaluating the \code{expr} expression. @@ -152,5 +155,6 @@ with_progress({ }) } \seealso{ -\code{\link[base:conditions]{base::withCallingHandlers()}} +For Shiny apps, use \code{\link[=withProgressShiny]{withProgressShiny()}} instead of this function. +Internally, this function is built around \code{\link[base:conditions]{base::withCallingHandlers()}}. } diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index f769f48..b27632a 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -3,7 +3,7 @@ url: https://progressr.futureverse.org home: links: - text: Roadmap/Milestones - href: https://github.com/HenrikBengtsson/progressr/milestones + href: https://github.com/futureverse/progressr/milestones - text: The Futureverse Project href: https://www.futureverse.org/ - text: Futureverse User Forum @@ -19,18 +19,20 @@ navbar: pkgs: text: Packages menu: - - text: doFuture + - text: doFuture (map-reduce) href: https://doFuture.futureverse.org - - text: furrr + - text: furrr (map-reduce) href: https://furrr.futureverse.org - text: future href: https://future.futureverse.org - - text: future.apply + - text: future.apply (map-reduce) href: https://future.apply.futureverse.org - - text: future.batchtools + - text: future.batchtools (backend) href: https://future.batchtools.futureverse.org - - text: future.callr + - text: future.callr (backend) href: https://future.callr.futureverse.org + - text: future.mirai (backend) + href: https://future.mirai.futureverse.org - text: future.tests href: https://future.tests.futureverse.org - text: globals @@ -45,8 +47,6 @@ navbar: href: https://BiocParallel.FutureParam.futureverse.org - text: future.tools (experimental) href: https://future.tools.futureverse.org - - text: future.mirai (experimental) - href: https://future.mirai.futureverse.org - text: future.mapreduce (experimental) href: https://future.mapreduce.futureverse.org - text: marshal (experimental) diff --git a/pkgdown/_pkgdown.yml.rsp b/pkgdown/_pkgdown.yml.rsp index 6d931ca..fe85ef5 100644 --- a/pkgdown/_pkgdown.yml.rsp +++ b/pkgdown/_pkgdown.yml.rsp @@ -1,6 +1,8 @@ <% -pkgs <- c("globals", "listenv", "parallelly", "future", "future.apply", "furrr", "future.tests", "future.callr", "future.batchtools", "doFuture", "progressr") -pkgs_extra <- c("BiocParallel.FutureParam", "future.tools", "future.mirai", "future.mapreduce", "marshal") +pkgs_mapreduce <- c("future.apply", "doFuture", "furrr") +pkgs_backend <- c("future.batchtools", "future.callr", "future.mirai") +pkgs <- c("globals", "listenv", "parallelly", "future", "future.tests", "progressr", pkgs_mapreduce, pkgs_backend) +pkgs_extra <- c("BiocParallel.FutureParam", "future.tools", "future.mapreduce", "marshal") pkgs <- c(sort(pkgs), pkgs_extra) urls <- sprintf("https://%s.futureverse.org", pkgs) names(urls) <- pkgs @@ -16,7 +18,7 @@ url: https://<%= pkg %>.futureverse.org home: links: - text: Roadmap/Milestones - href: https://github.com/HenrikBengtsson/<%= pkg %>/milestones + href: https://github.com/<%= gsub("(^.*:|[.]git$)", "", subset(gert::git_remote_list(), name == "origin")$url) %>/milestones - text: The Futureverse Project href: https://www.futureverse.org/ - text: Futureverse User Forum @@ -33,7 +35,7 @@ navbar: text: Packages menu: <% for (name in names(urls)) { %> - - text: <%= name %> <% if (name %in% pkgs_extra) { %>(experimental)<% } %> + - text: <%= name %> <% if (name %in% pkgs_extra) { %>(experimental)<% } else if (name %in% pkgs_backend) { %>(backend)<% } else if (name %in% pkgs_mapreduce) { %>(map-reduce)<% } %> href: <%= urls[name] %> <% } %> cran: diff --git a/revdep/README.md b/revdep/README.md index 6d13e03..8c9c80d 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,111 +1,139 @@ # Platform -|field |value | -|:--------|:---------------------------------------------------------| -|version |R version 4.3.1 (2023-06-16) | -|os |CentOS Linux 7 (Core) | -|system |x86_64, linux-gnu | -|ui |X11 | -|language |en | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |America/Los_Angeles | -|date |2023-08-10 | -|pandoc |3.1.6 @ /software/c4/cbi/software/pandoc-3.1.6/bin/pandoc | +|field |value | +|:--------|:-----------------------------------------------------| +|version |R version 4.4.1 (2024-06-14) | +|os |Rocky Linux 8.10 (Green Obsidian) | +|system |x86_64, linux-gnu | +|ui |X11 | +|language |en | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/Los_Angeles | +|date |2024-10-28 | +|pandoc |3.5 @ /software/c4/cbi/software/pandoc-3.5/bin/pandoc | # Dependencies |package |old |new |Δ | |:---------|:------|:-----------|:--| -|progressr |0.13.0 |0.13.0-9013 |* | -|digest |0.6.33 |0.6.33 | | +|progressr |0.14.0 |0.14.0-9011 |* | +|digest |0.6.37 |0.6.37 | | # Revdeps -## All (82) +## All (110) |package |version |error |warning |note | |:------------------|:----------|:-----|:-------|:----| +|adestr |1.0.0 | | | | |[AIPW](problems.md#aipw)|0.6.3.2 | | |1 | -|[AlpsNMR](problems.md#alpsnmr)|4.2.0 |1 | | | -|antaresEditObject |0.5.1 | | | | -|baseballr |1.5.0 | | | | -|bayesmove |0.2.1 | | | | -|bbotk |0.7.2 | | | | -|beer |1.4.0 | | | | +|ale |0.3.0 | | | | +|[AlpsNMR](problems.md#alpsnmr)|4.6.0 |1 | | | +|antaresEditObject |0.7.1 | | | | +|ao |1.1.0 | | | | +|baseballr |1.6.0 | | | | +|[baskexact](problems.md#baskexact)|1.0.1 | | |1 | +|basksim |1.0.0 | | | | +|[bayesmove](problems.md#bayesmove)|0.2.1 | | |1 | +|bbotk |1.2.0 | | | | +|beer |1.8.0 | | | | |bolasso |0.2.0 | | | | -|campsis |1.4.1 | | | | +|calmr |0.6.1 | | | | +|campsis |1.5.4 | | | | |canaper |1.0.1 | | | | -|cfbfastR |1.9.0 | | | | -|[cSEM](problems.md#csem)|0.5.0 | | |1 | -|cyclestreets |0.6.0 | | | | -|[dipsaus](problems.md#dipsaus)|0.2.8 | | |1 | -|easyalluvial |0.3.1 | | | | +|cccrm |3.0.3 | | | | +|[crumble](problems.md#crumble)|0.1.0 |1 | | | +|[cSEM](problems.md#csem)|0.5.0 | | |2 | +|cyclestreets |1.0.2 | | | | +|dapper |1.0.0 | | | | +|[deseats](problems.md#deseats)|1.1.0 | | |1 | +|[dipsaus](problems.md#dipsaus)|0.2.9 | | |1 | +|drugdevelopR |1.0.1 | | | | +|easyalluvial |0.3.2 | | | | |ecic |0.0.3 | | | | -|[econet](problems.md#econet)|1.0.0 | |1 | | +|[econet](problems.md#econet)|1.0.0.1 | |1 |1 | |[EFAtools](problems.md#efatools)|0.4.4 | | |3 | -|elevatr |0.4.5 | | | | -|[EpiNow2](problems.md#epinow2)|1.3.5 | | |2 | -|epwshiftr |0.1.3 | | | | -|fabletools |0.3.3 | | | | -|fastRhockey |0.4.0 | | | | +|EGAnet |2.0.8 | | | | +|elevatr |0.99.0 | | | | +|EpiForsk |0.1.1 | | | | +|[EpiModel](problems.md#epimodel)|2.5.0 | | |1 | +|[EpiNow2](problems.md#epinow2)|1.6.0 | | |4 | +|epwshiftr |0.1.4 | | | | +|fabletools |0.5.0 | | | | +|[fastRhockey](problems.md#fastrhockey)|0.4.0 | | |1 | |[fdacluster](problems.md#fdacluster)|0.3.0 | | |1 | -|ffsimulator |1.2.3 | | | | -|funGp |0.3.2 | | | | -|fxTWAPLS |0.1.2 | | | | -|[geocmeans](problems.md#geocmeans)|0.3.3 | | |1 | +|funGp |1.0.0 | | | | +|futureverse |0.1.0 | | | | +|fxTWAPLS |0.1.3 | | | | +|geocausal |0.3.2 | | | | +|[geocmeans](problems.md#geocmeans)|0.3.4 | | |1 | +|[GeoModels](problems.md#geomodels)|2.0.7 | | |1 | |gtfs2emis |0.1.0 | | | | -|gtfs2gps |2.1-1 | | | | -|hmer |1.5.0 | | | | -|hoopR |1.8.0 | | | | -|[ISAnalytics](problems.md#isanalytics)|1.10.2 | | |1 | -|isopam |1.1.0 | | | | -|lava |1.7.2.1 | | | | -|lightr |1.7.0 | | | | -|lmtp |1.3.2 | | | | -|LWFBrook90R |0.5.2 | | | | -|mcmcensemble |3.0.0 | | | | -|[metabolomicsR](problems.md#metabolomicsr)|1.0.0 | |1 |1 | -|mikropml |1.6.0 | | | | -|mlr3 |0.16.1 | | | | -|[modeltime.ensemble](problems.md#modeltimeensemble)|1.0.3 | | |1 | +|[gtfs2gps](problems.md#gtfs2gps)|2.1-2 |1 | | | +|[hbamr](problems.md#hbamr)|2.3.2 | | |2 | +|hmer |1.6.0 | | | | +|hoopR |2.1.0 | | | | +|[ISAnalytics](problems.md#isanalytics)|1.14.0 |1 | |2 | +|[kmeRtone](problems.md#kmertone)|1.0 | | |2 | +|[lava](problems.md#lava)|1.8.0 | | |1 | +|[lightr](problems.md#lightr)|1.7.1 | | |2 | +|lmtp |1.4.0 | | | | +|LWFBrook90R |0.6.1 | | | | +|[mapme.biodiversity](problems.md#mapmebiodiversity)|0.9.3 |1 | | | +|mcmcensemble |3.1.0 | | | | +|[mikropml](problems.md#mikropml)|1.6.1 | | |1 | +|mlr3 |0.21.1 | | | | |[modeltime.resample](problems.md#modeltimeresample)|0.2.3 | | |1 | -|mpathsenser |1.1.3 | | | | -|nflfastR |4.5.1 | | | | -|nflreadr |1.3.2 | | | | -|nflseedR |1.2.0 | | | | -|nlrx |0.4.4 | | | | +|mpathsenser |1.2.3 | | | | +|nflfastR |4.6.1 | | | | +|nflreadr |1.4.1 | | | | +|[nflseedR](problems.md#nflseedr)|1.2.0 | | |1 | +|nlrx |0.4.5 | | | | |[oddsapiR](problems.md#oddsapir)|0.0.3 | | |1 | -|opentripplanner |0.5.1 | | | | -|[pavo](problems.md#pavo)|2.8.0 | |1 | | +|opentripplanner |0.5.2 | | | | +|parseRPDR |1.1.1 | | | | +|[pavo](problems.md#pavo)|2.9.0 | |1 | | |plnr |2022.11.23 | | | | -|polle |1.3 | | | | -|poppr |2.9.4 | | | | -|powRICLPM |0.1.1 | | | | -|[RAINBOWR](problems.md#rainbowr)|0.1.32 | | |1 | +|polle |1.5 | | | | +|poppr |2.9.6 | | | | +|powRICLPM |0.2.1 | | | | +|[PWIR](problems.md#pwir)|0.0.3 | | |1 | +|[RAINBOWR](problems.md#rainbowr)|0.1.35 | | |1 | |rainette |0.3.1.1 | | | | |rangeMapper |2.0.3 | | | | -|receptiviti |0.1.4 | | | | +|readsdr |0.3.0 | | | | +|[receptiviti](problems.md#receptiviti)|0.1.8 |1 | | | +|rechaRge |1.0.0 | | | | |remiod |1.0.2 | | | | -|semPower |2.0.1 | | | | -|[sentopics](problems.md#sentopics)|0.7.2 | | |3 | -|[Seurat](problems.md#seurat)|4.3.0.1 | | |3 | -|[SeuratObject](problems.md#seuratobject)|4.1.3 | | |1 | -|simaerep |0.4.3 | | | | -|[SimDesign](problems.md#simdesign)|2.12 | | |1 | -|simfinapi |0.2.4 | | | | -|sims |0.0.3 | | | | -|[smoots](problems.md#smoots)|1.1.3 | | |1 | -|[sphunif](problems.md#sphunif)|1.0.1 | | |3 | -|[spNetwork](problems.md#spnetwork)|0.4.3.7 | | |1 | -|[SPQR](problems.md#spqr)|0.1.0 | | |2 | -|[squat](problems.md#squat)|0.2.1 | | |1 | -|survex |1.0.0 | | | | -|[targeted](problems.md#targeted)|0.3 | | |2 | -|terrainr |0.7.4 | | | | -|tidyfit |0.6.4 | | | | -|tidySEM |0.2.4 | | | | +|restriktor |0.5-90 | | | | +|rsi |0.3.1 | | | | +|[rTwig](problems.md#rtwig)|1.1.0 | | |1 | +|saeczi |0.2.0 | | | | +|semPower |2.1.1 | | | | +|semTests |0.5.0 | | | | +|[sentopics](problems.md#sentopics)|0.7.4 | | |3 | +|[Seurat](problems.md#seurat)|5.1.0 | | |3 | +|[SeuratObject](problems.md#seuratobject)|5.0.2 | | |3 | +|simaerep |0.6.0 | | | | +|[SimDesign](problems.md#simdesign)|2.17.1 | | |1 | +|sims |0.0.4 | | | | +|[skpr](problems.md#skpr)|1.7.1 | | |1 | +|[smoots](problems.md#smoots)|1.1.4 | | |1 | +|[sphunif](problems.md#sphunif)|1.4.0 | | |2 | +|[spNetwork](problems.md#spnetwork)|0.4.4.3 | | |1 | +|[squat](problems.md#squat)|0.3.0 | | |1 | +|[stppSim](problems.md#stppsim)|1.3.4 | |1 | | +|survex |1.2.0 | | | | +|[targeted](problems.md#targeted)|0.5 | | |1 | +|terrainr |0.7.5 | | | | +|tidyfit |0.7.2 | | | | +|tidySEM |0.2.7 | | | | +|[tsdistributions](problems.md#tsdistributions)|1.0.2 |1 | |1 | +|[tsgarch](problems.md#tsgarch)|1.0.3 | | |1 | +|[vital](problems.md#vital)|1.1.0 | | |1 | |[vmeasur](problems.md#vmeasur)|0.1.4 | |1 | | -|wehoop |1.5.0 | | | | -|[WeightedCluster](problems.md#weightedcluster)|1.6-4 | |1 | | +|wehoop |2.1.0 | | | | +|[WeightedCluster](problems.md#weightedcluster)|1.8-0 | |1 | | +|ycevo |0.2.1 | | | | diff --git a/revdep/cran.md b/revdep/cran.md index 08a8ef3..7f5d77a 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,6 +1,6 @@ ## revdepcheck results -We checked 82 reverse dependencies (79 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 110 reverse dependencies (107 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems * We failed to check 0 packages diff --git a/revdep/problems.md b/revdep/problems.md index 51c53d7..fa763a3 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -6,9 +6,9 @@ * GitHub: https://github.com/yqzhong7/AIPW * Source code: https://github.com/cran/AIPW * Date/Publication: 2021-06-11 09:30:02 UTC -* Number of recursive dependencies: 101 +* Number of recursive dependencies: 99 -Run `revdep_details(, "AIPW")` for more info +Run `revdepcheck::revdep_details(, "AIPW")` for more info @@ -26,13 +26,13 @@ Run `revdep_details(, "AIPW")` for more info
-* Version: 4.2.0 +* Version: 4.6.0 * GitHub: https://github.com/sipss/AlpsNMR * Source code: https://github.com/cran/AlpsNMR -* Date/Publication: 2023-04-25 -* Number of recursive dependencies: 172 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 174 -Run `revdep_details(, "AlpsNMR")` for more info +Run `revdepcheck::revdep_details(, "AlpsNMR")` for more info
@@ -41,17 +41,17 @@ Run `revdep_details(, "AlpsNMR")` for more info * checking re-building of vignette outputs ... ERROR ``` Error(s) in re-building vignettes: + ... --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown - ! LuaTeX error .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: b - ad argument #1 to 'insert' (table expected, got nil) - stack traceback: - [C]: in function 'insert' - .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: in main chunk - [C]: in function 'dofile' - [string "\directlua "]:6: in main chunk. - l.139 } + Error: processing vignette 'Vig01-introduction-to-alpsnmr.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/progressr/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01-introduction-to-alpsnmr.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. + --- failed re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ + + --- re-building ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’ using rmarkdown + Error: processing vignette 'Vig01b-introduction-to-alpsnmr-old-api.Rmd' failed with diagnostics: + LaTeX failed to compile /c4/home/henrik/repositories/progressr/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig01b-introduction-to-alpsnmr-old-api.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. ... - LaTeX failed to compile /c4/home/henrik/repositories/progressr/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Vig02-handling-metadata-and-annotations.log for more info. + LaTeX failed to compile /c4/home/henrik/repositories/progressr/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’ SUMMARY: processing the following files failed: @@ -63,6 +63,75 @@ Run `revdep_details(, "AlpsNMR")` for more info Execution halted ``` +# baskexact + +
+ +* Version: 1.0.1 +* GitHub: https://github.com/lbau7/baskexact +* Source code: https://github.com/cran/baskexact +* Date/Publication: 2024-04-09 13:30:02 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::revdep_details(, "baskexact")` for more info + +
+ +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘ggplot2’ + All declared Imports should be used. + ``` + +# bayesmove + +
+ +* Version: 0.2.1 +* GitHub: https://github.com/joshcullen/bayesmove +* Source code: https://github.com/cran/bayesmove +* Date/Publication: 2021-10-22 08:50:09 UTC +* Number of recursive dependencies: 166 + +Run `revdepcheck::revdep_details(, "bayesmove")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) insert_NAs.Rd:22: Lost braces; missing escapes or markup? + 22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed. + | ^ + ``` + +# crumble + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/crumble +* Date/Publication: 2024-09-18 11:50:05 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::revdep_details(, "crumble")` for more info + +
+ +## In both + +* checking package dependencies ... ERROR + ``` + Package required but not available: ‘Rsymphony’ + + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. + ``` + # cSEM
@@ -71,9 +140,9 @@ Run `revdep_details(, "AlpsNMR")` for more info * GitHub: https://github.com/M-E-Rademaker/cSEM * Source code: https://github.com/cran/cSEM * Date/Publication: 2022-11-24 17:50:05 UTC -* Number of recursive dependencies: 127 +* Number of recursive dependencies: 128 -Run `revdep_details(, "cSEM")` for more info +Run `revdepcheck::revdep_details(, "cSEM")` for more info
@@ -85,17 +154,47 @@ Run `revdep_details(, "cSEM")` for more info All declared Imports should be used. ``` +* checking Rd files ... NOTE + ``` + checkRd: (-1) calculateEffects.Rd:24: Lost braces; missing escapes or markup? + 24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between + | ^ + ``` + +# deseats + +
+ +* Version: 1.1.0 +* GitHub: NA +* Source code: https://github.com/cran/deseats +* Date/Publication: 2024-07-12 10:50:15 UTC +* Number of recursive dependencies: 115 + +Run `revdepcheck::revdep_details(, "deseats")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.6Mb + sub-directories of 1Mb or more: + libs 7.8Mb + ``` + # dipsaus
-* Version: 0.2.8 +* Version: 0.2.9 * GitHub: https://github.com/dipterix/dipsaus * Source code: https://github.com/cran/dipsaus -* Date/Publication: 2023-07-03 20:00:03 UTC +* Date/Publication: 2024-06-27 11:10:01 UTC * Number of recursive dependencies: 69 -Run `revdep_details(, "dipsaus")` for more info +Run `revdepcheck::revdep_details(, "dipsaus")` for more info
@@ -103,23 +202,23 @@ Run `revdep_details(, "dipsaus")` for more info * checking installed package size ... NOTE ``` - installed size is 5.9Mb + installed size is 6.7Mb sub-directories of 1Mb or more: doc 1.1Mb - libs 3.5Mb + libs 4.2Mb ``` # econet
-* Version: 1.0.0 +* Version: 1.0.0.1 * GitHub: NA * Source code: https://github.com/cran/econet -* Date/Publication: 2022-04-28 00:00:02 UTC +* Date/Publication: 2024-07-31 10:59:28 UTC * Number of recursive dependencies: 64 -Run `revdep_details(, "econet")` for more info +Run `revdepcheck::revdep_details(, "econet")` for more info
@@ -130,13 +229,13 @@ Run `revdep_details(, "econet")` for more info Error(s) in re-building vignettes: ... --- re-building ‘econet.tex’ using tex + Warning in texi2dvi(pathnameR, pdf = pdf, clean = clean, quiet = quiet, : + texi2dvi script/program not available, using emulation Error: processing vignette 'econet.tex' failed with diagnostics: - Running 'texi2dvi' on 'econet.tex' failed. + unable to run pdflatex on 'econet.tex' LaTeX errors: ! LaTeX Error: File `orcidlink.sty' not found. - Type X to quit or to proceed, - or enter new name. (Default extension: sty) ... l.5 \graphicspath {{Figures/}}^^M @@ -150,6 +249,15 @@ Run `revdep_details(, "econet")` for more info Execution halted ``` +* checking installed files from ‘inst/doc’ ... NOTE + ``` + The following files should probably not be installed: + ‘econet.tex’ + + Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, + or move the vignette sources from ‘inst/doc’ to ‘vignettes’. + ``` + # EFAtools
@@ -160,7 +268,7 @@ Run `revdep_details(, "econet")` for more info * Date/Publication: 2023-01-06 14:50:40 UTC * Number of recursive dependencies: 93 -Run `revdep_details(, "EFAtools")` for more info +Run `revdepcheck::revdep_details(, "EFAtools")` for more info
@@ -173,9 +281,9 @@ Run `revdep_details(, "EFAtools")` for more info * checking installed package size ... NOTE ``` - installed size is 7.2Mb + installed size is 7.5Mb sub-directories of 1Mb or more: - libs 6.0Mb + libs 6.2Mb ``` * checking dependencies in R code ... NOTE @@ -184,28 +292,63 @@ Run `revdep_details(, "EFAtools")` for more info All declared Imports should be used. ``` +# EpiModel + +
+ +* Version: 2.5.0 +* GitHub: https://github.com/EpiModel/EpiModel +* Source code: https://github.com/cran/EpiModel +* Date/Publication: 2024-10-11 17:50:02 UTC +* Number of recursive dependencies: 127 + +Run `revdepcheck::revdep_details(, "EpiModel")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + doc 2.8Mb + libs 1.2Mb + ``` + # EpiNow2
-* Version: 1.3.5 +* Version: 1.6.0 * GitHub: https://github.com/epiforecasts/EpiNow2 * Source code: https://github.com/cran/EpiNow2 -* Date/Publication: 2023-04-27 13:20:04 UTC -* Number of recursive dependencies: 129 +* Date/Publication: 2024-10-02 20:20:22 UTC +* Number of recursive dependencies: 132 -Run `revdep_details(, "EpiNow2")` for more info +Run `revdepcheck::revdep_details(, "EpiNow2")` for more info
## In both +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘cmdstanr’ + ``` + * checking installed package size ... NOTE ``` - installed size is 245.1Mb + installed size is 240.1Mb sub-directories of 1Mb or more: - help 1.4Mb - libs 242.9Mb + doc 1.4Mb + extdata 2.3Mb + libs 234.9Mb + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘cmdstanr’ ``` * checking for GNU extensions in Makefiles ... NOTE @@ -213,6 +356,30 @@ Run `revdep_details(, "EpiNow2")` for more info GNU make is a SystemRequirements. ``` +# fastRhockey + +
+ +* Version: 0.4.0 +* GitHub: https://github.com/sportsdataverse/fastRhockey +* Source code: https://github.com/cran/fastRhockey +* Date/Publication: 2022-10-25 20:55:15 UTC +* Number of recursive dependencies: 116 + +Run `revdepcheck::revdep_details(, "fastRhockey")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ? + checkRd: (-1) update_nhl_db.Rd:54-57: Lost braces in \itemize; meant \describe ? + checkRd: (-1) update_phf_db.Rd:51-53: Lost braces in \itemize; meant \describe ? + checkRd: (-1) update_phf_db.Rd:54-57: Lost braces in \itemize; meant \describe ? + ``` + # fdacluster
@@ -221,9 +388,9 @@ Run `revdep_details(, "EpiNow2")` for more info * GitHub: https://github.com/astamm/fdacluster * Source code: https://github.com/cran/fdacluster * Date/Publication: 2023-07-04 15:53:04 UTC -* Number of recursive dependencies: 121 +* Number of recursive dependencies: 127 -Run `revdep_details(, "fdacluster")` for more info +Run `revdepcheck::revdep_details(, "fdacluster")` for more info
@@ -231,25 +398,25 @@ Run `revdep_details(, "fdacluster")` for more info * checking installed package size ... NOTE ``` - installed size is 22.2Mb + installed size is 22.7Mb sub-directories of 1Mb or more: R 1.8Mb - doc 1.4Mb + doc 1.5Mb help 2.1Mb - libs 16.4Mb + libs 16.8Mb ``` # geocmeans
-* Version: 0.3.3 +* Version: 0.3.4 * GitHub: https://github.com/JeremyGelb/geocmeans * Source code: https://github.com/cran/geocmeans -* Date/Publication: 2023-02-07 01:02:31 UTC -* Number of recursive dependencies: 197 +* Date/Publication: 2023-09-12 03:10:02 UTC +* Number of recursive dependencies: 200 -Run `revdep_details(, "geocmeans")` for more info +Run `revdepcheck::revdep_details(, "geocmeans")` for more info
@@ -257,83 +424,305 @@ Run `revdep_details(, "geocmeans")` for more info * checking installed package size ... NOTE ``` - installed size is 14.5Mb + installed size is 14.3Mb sub-directories of 1Mb or more: - doc 1.7Mb extdata 3.0Mb - libs 8.2Mb + libs 9.0Mb + ``` + +# GeoModels + +
+ +* Version: 2.0.7 +* GitHub: https://github.com/vmoprojs/GeoModels +* Source code: https://github.com/cran/GeoModels +* Date/Publication: 2024-10-25 21:30:02 UTC +* Number of recursive dependencies: 55 + +Run `revdepcheck::revdep_details(, "GeoModels")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 6.2Mb + sub-directories of 1Mb or more: + R 1.0Mb + data 1.9Mb + libs 2.8Mb + ``` + +# gtfs2gps + +
+ +* Version: 2.1-2 +* GitHub: https://github.com/ipeaGIT/gtfs2gps +* Source code: https://github.com/cran/gtfs2gps +* Date/Publication: 2024-10-08 07:00:06 UTC +* Number of recursive dependencies: 86 + +Run `revdepcheck::revdep_details(, "gtfs2gps")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(gtfs2gps) + gtfs2gps version 2.1-2 is now loaded + NOTE: All filter functions from gtfs2gps were removed + Please replace them by similar functions from gtfstools + > + ... + 4. └─terra (local) .local(x, ...) + 5. ├─terra::makeValid(x) + 6. └─terra::makeValid(x) + 7. └─terra (local) .local(x, ...) + 8. └─terra:::messages(x) + 9. └─terra:::error(f, x@ptr$getError()) + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ] + Error: Test failures + Execution halted + ``` + +# hbamr + +
+ +* Version: 2.3.2 +* GitHub: https://github.com/jbolstad/hbamr +* Source code: https://github.com/cran/hbamr +* Date/Publication: 2024-09-23 12:20:07 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::revdep_details(, "hbamr")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 342.4Mb + sub-directories of 1Mb or more: + libs 340.7Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE + ``` + GNU make is a SystemRequirements. ``` # ISAnalytics
-* Version: 1.10.2 +* Version: 1.14.0 * GitHub: https://github.com/calabrialab/ISAnalytics * Source code: https://github.com/cran/ISAnalytics -* Date/Publication: 2023-07-24 -* Number of recursive dependencies: 172 +* Date/Publication: 2024-04-30 +* Number of recursive dependencies: 178 -Run `revdep_details(, "ISAnalytics")` for more info +Run `revdepcheck::revdep_details(, "ISAnalytics")` for more info
## In both +* checking examples ... ERROR + ``` + Running examples in ‘ISAnalytics-Ex.R’ failed + The error most likely occurred in: + + > ### Name: CIS_grubbs + > ### Title: Grubbs test for Common Insertion Sites (CIS). + > ### Aliases: CIS_grubbs + > + > ### ** Examples + > + > data("integration_matrices", package = "ISAnalytics") + > cis <- CIS_grubbs(integration_matrices) + Error in print.data.table(missing_genes, n = Inf) : + argument 2 matches multiple formal arguments + Calls: CIS_grubbs ... paste -> paste0 -> -> withVisible -> print + Execution halted + ``` + * checking installed package size ... NOTE ``` - installed size is 7.2Mb + installed size is 7.3Mb sub-directories of 1Mb or more: data 1.4Mb - doc 3.5Mb + doc 3.6Mb + ``` + +* checking Rd files ... NOTE + ``` + checkRd: (-1) refGenes_hg19.Rd:21: Lost braces; missing escapes or markup? + 21 | \item Download from {http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/} + | ^ ``` -# metabolomicsR +# kmeRtone
-* Version: 1.0.0 -* GitHub: https://github.com/XikunHan/metabolomicsR -* Source code: https://github.com/cran/metabolomicsR -* Date/Publication: 2022-04-29 07:40:02 UTC -* Number of recursive dependencies: 188 +* Version: 1.0 +* GitHub: https://github.com/SahakyanLab/kmeRtone +* Source code: https://github.com/cran/kmeRtone +* Date/Publication: 2024-08-30 10:50:06 UTC +* Number of recursive dependencies: 82 -Run `revdep_details(, "metabolomicsR")` for more info +Run `revdepcheck::revdep_details(, "kmeRtone")` for more info
## In both -* checking dependencies in R code ... WARNING +* checking installed package size ... NOTE + ``` + installed size is 9.9Mb + sub-directories of 1Mb or more: + libs 8.4Mb + ``` + +* checking for GNU extensions in Makefiles ... NOTE ``` - Missing or unexported object: ‘future::multiprocess’ + GNU make is a SystemRequirements. ``` +# lava + +
+ +* Version: 1.8.0 +* GitHub: https://github.com/kkholst/lava +* Source code: https://github.com/cran/lava +* Date/Publication: 2024-03-05 13:00:02 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::revdep_details(, "lava")` for more info + +
+ +## In both + * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘genuMet’ + Package suggested but not available for checking: ‘lavaSearch2’ ``` -# modeltime.ensemble +# lightr
-* Version: 1.0.3 -* GitHub: https://github.com/business-science/modeltime.ensemble -* Source code: https://github.com/cran/modeltime.ensemble -* Date/Publication: 2023-04-18 11:50:02 UTC -* Number of recursive dependencies: 226 +* Version: 1.7.1 +* GitHub: https://github.com/ropensci/lightr +* Source code: https://github.com/cran/lightr +* Date/Publication: 2024-03-21 21:50:10 UTC +* Number of recursive dependencies: 92 -Run `revdep_details(, "modeltime.ensemble")` for more info +Run `revdepcheck::revdep_details(, "lightr")` for more info
## In both -* checking dependencies in R code ... NOTE +* checking package dependencies ... NOTE ``` - Namespace in Imports field not imported from: ‘parsnip’ - All declared Imports should be used. + Package suggested but not available for checking: ‘pavo’ + ``` + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘pavo’ + ``` + +# mapme.biodiversity + +
+ +* Version: 0.9.3 +* GitHub: https://github.com/mapme-initiative/mapme.biodiversity +* Source code: https://github.com/cran/mapme.biodiversity +* Date/Publication: 2024-10-21 08:10:02 UTC +* Number of recursive dependencies: 107 + +Run `revdepcheck::revdep_details(, "mapme.biodiversity")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 50 lines of output: + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-calc_deforestation_drivers.R:16:3'): deforestation drivers works ── + `.check_single_asset(result)` produced warnings. + ── Failure ('test-calc_deforestation_drivers.R:17:3'): deforestation drivers works ── + unique(result$variable) (`actual`) not equal to c(...) (`expected`). + + ... + 12. │ └─jsonlite:::parseJSON(txt, bigint_as_char) + 13. │ └─jsonlite:::parse_string(txt, bigint_as_char) + 14. └─base::.handleSimpleError(...) + 15. └─purrr (local) h(simpleError(msg, call)) + 16. └─cli::cli_abort(...) + 17. └─rlang::abort(...) + + [ FAIL 5 | WARN 1 | SKIP 38 | PASS 560 ] + Error: Test failures + Execution halted + ``` + +# mikropml + +
+ +* Version: 1.6.1 +* GitHub: https://github.com/SchlossLab/mikropml +* Source code: https://github.com/cran/mikropml +* Date/Publication: 2023-08-21 15:10:05 UTC +* Number of recursive dependencies: 130 + +Run `revdepcheck::revdep_details(, "mikropml")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) create_grouped_data_partition.Rd:60: Lost braces; missing escapes or markup? + 60 | Zena Lapp, {zenalapp@umich.edu} + | ^ + checkRd: (-1) create_grouped_data_partition.Rd:62: Lost braces; missing escapes or markup? + 62 | Kelly Sovacool, {sovacool@umich.edu} + | ^ + checkRd: (-1) create_grouped_k_multifolds.Rd:30: Lost braces; missing escapes or markup? + 30 | Zena Lapp, {zenalapp@umich.edu} + | ^ + checkRd: (-1) get_partition_indices.Rd:58: Lost braces; missing escapes or markup? + 58 | Kelly Sovacool, {sovacool@umich.edu} + | ^ + checkRd: (-1) set_hparams_glmnet.Rd:16: Lost braces; missing escapes or markup? + 16 | Zena Lapp, {zenalapp@umich.edu} + | ^ ``` # modeltime.resample @@ -344,9 +733,9 @@ Run `revdep_details(, "modeltime.ensemble")` for more info * GitHub: https://github.com/business-science/modeltime.resample * Source code: https://github.com/cran/modeltime.resample * Date/Publication: 2023-04-12 15:50:02 UTC -* Number of recursive dependencies: 224 +* Number of recursive dependencies: 227 -Run `revdep_details(, "modeltime.resample")` for more info +Run `revdepcheck::revdep_details(, "modeltime.resample")` for more info @@ -359,6 +748,35 @@ Run `revdep_details(, "modeltime.resample")` for more info All declared Imports should be used. ``` +# nflseedR + +
+ +* Version: 1.2.0 +* GitHub: https://github.com/nflverse/nflseedR +* Source code: https://github.com/cran/nflseedR +* Date/Publication: 2023-01-05 21:50:31 UTC +* Number of recursive dependencies: 87 + +Run `revdepcheck::revdep_details(, "nflseedR")` for more info + +
+ +## In both + +* checking Rd files ... NOTE + ``` + checkRd: (-1) load_schedules.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly + checkRd: (-1) load_schedules.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly + ``` + # oddsapiR
@@ -367,9 +785,9 @@ Run `revdep_details(, "modeltime.resample")` for more info * GitHub: https://github.com/sportsdataverse/oddsapiR * Source code: https://github.com/cran/oddsapiR * Date/Publication: 2023-03-19 18:50:02 UTC -* Number of recursive dependencies: 119 +* Number of recursive dependencies: 120 -Run `revdep_details(, "oddsapiR")` for more info +Run `revdepcheck::revdep_details(, "oddsapiR")` for more info
@@ -384,13 +802,13 @@ Run `revdep_details(, "oddsapiR")` for more info
-* Version: 2.8.0 +* Version: 2.9.0 * GitHub: https://github.com/rmaia/pavo * Source code: https://github.com/cran/pavo -* Date/Publication: 2022-08-16 13:00:20 UTC -* Number of recursive dependencies: 93 +* Date/Publication: 2023-09-24 10:10:02 UTC +* Number of recursive dependencies: 103 -Run `revdep_details(, "pavo")` for more info +Run `revdepcheck::revdep_details(, "pavo")` for more info
@@ -403,17 +821,39 @@ Run `revdep_details(, "pavo")` for more info See ‘/c4/home/henrik/repositories/progressr/revdep/checks/pavo/new/pavo.Rcheck/00install.out’ for details. ``` +# PWIR + +
+ +* Version: 0.0.3 +* GitHub: NA +* Source code: https://github.com/cran/PWIR +* Date/Publication: 2023-10-20 09:50:02 UTC +* Number of recursive dependencies: 110 + +Run `revdepcheck::revdep_details(, "PWIR")` for more info + +
+ +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘progressr’ + All declared Imports should be used. + ``` + # RAINBOWR
-* Version: 0.1.32 +* Version: 0.1.35 * GitHub: NA * Source code: https://github.com/cran/RAINBOWR -* Date/Publication: 2023-08-09 04:20:10 UTC -* Number of recursive dependencies: 153 +* Date/Publication: 2024-03-03 09:12:36 UTC +* Number of recursive dependencies: 154 -Run `revdep_details(, "RAINBOWR")` for more info +Run `revdepcheck::revdep_details(, "RAINBOWR")` for more info
@@ -421,22 +861,86 @@ Run `revdep_details(, "RAINBOWR")` for more info * checking installed package size ... NOTE ``` - installed size is 38.0Mb + installed size is 42.9Mb sub-directories of 1Mb or more: - libs 36.6Mb + libs 41.5Mb + ``` + +# receptiviti + +
+ +* Version: 0.1.8 +* GitHub: https://github.com/Receptiviti/receptiviti-r +* Source code: https://github.com/cran/receptiviti +* Date/Publication: 2024-03-29 18:00:03 UTC +* Number of recursive dependencies: 66 + +Run `revdepcheck::revdep_details(, "receptiviti")` for more info + +
+ +## In both + +* checking tests ... + ``` + Running ‘testthat.R’ + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Complete output: + > library(testthat) + > library(receptiviti) + > + > test_check("receptiviti") + Status: ERROR + Message: Invalid header received from client. + ... + 7. └─receptiviti::receptiviti(...) + ── Failure ('test-receptiviti_status.R:5:3'): failures works ─────────────────── + receptiviti_status(...) is not NULL + + `actual` is a list + `expected` is NULL + + [ FAIL 2 | WARN 0 | SKIP 2 | PASS 6 ] + Error: Test failures + Execution halted + ``` + +# rTwig + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/aidanmorales/rTwig +* Source code: https://github.com/cran/rTwig +* Date/Publication: 2024-08-21 00:50:02 UTC +* Number of recursive dependencies: 148 + +Run `revdepcheck::revdep_details(, "rTwig")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 8.0Mb + sub-directories of 1Mb or more: + libs 6.1Mb ``` # sentopics
-* Version: 0.7.2 +* Version: 0.7.4 * GitHub: https://github.com/odelmarcelle/sentopics * Source code: https://github.com/cran/sentopics -* Date/Publication: 2023-05-28 09:50:02 UTC +* Date/Publication: 2024-09-20 12:20:02 UTC * Number of recursive dependencies: 172 -Run `revdep_details(, "sentopics")` for more info +Run `revdepcheck::revdep_details(, "sentopics")` for more info
@@ -444,7 +948,7 @@ Run `revdep_details(, "sentopics")` for more info * checking installed package size ... NOTE ``` - installed size is 8.1Mb + installed size is 8.3Mb sub-directories of 1Mb or more: data 1.2Mb libs 6.2Mb @@ -464,29 +968,29 @@ Run `revdep_details(, "sentopics")` for more info
-* Version: 4.3.0.1 +* Version: 5.1.0 * GitHub: https://github.com/satijalab/seurat * Source code: https://github.com/cran/Seurat -* Date/Publication: 2023-06-22 07:04:04 UTC -* Number of recursive dependencies: 254 +* Date/Publication: 2024-05-10 17:23:17 UTC +* Number of recursive dependencies: 267 -Run `revdep_details(, "Seurat")` for more info +Run `revdepcheck::revdep_details(, "Seurat")` for more info
## In both -* checking C++ specification ... NOTE +* checking package dependencies ... NOTE ``` - Specified C++11: please drop specification unless essential + Packages suggested but not available for checking: 'BPCells', 'presto' ``` * checking installed package size ... NOTE ``` - installed size is 14.6Mb + installed size is 16.0Mb sub-directories of 1Mb or more: - R 1.4Mb - libs 12.4Mb + R 1.7Mb + libs 13.5Mb ``` * checking Rd cross-references ... NOTE @@ -498,18 +1002,33 @@ Run `revdep_details(, "Seurat")` for more info
-* Version: 4.1.3 -* GitHub: https://github.com/mojaveazure/seurat-object +* Version: 5.0.2 +* GitHub: https://github.com/satijalab/seurat-object * Source code: https://github.com/cran/SeuratObject -* Date/Publication: 2022-11-07 18:50:02 UTC -* Number of recursive dependencies: 57 +* Date/Publication: 2024-05-08 13:40:06 UTC +* Number of recursive dependencies: 102 -Run `revdep_details(, "SeuratObject")` for more info +Run `revdepcheck::revdep_details(, "SeuratObject")` for more info
## In both +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘BPCells’ + + Package which this enhances but not available for checking: ‘Seurat’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 6.1Mb + sub-directories of 1Mb or more: + R 2.0Mb + libs 3.2Mb + ``` + * checking Rd cross-references ... NOTE ``` Package unavailable to check Rd xrefs: ‘plotly’ @@ -519,13 +1038,13 @@ Run `revdep_details(, "SeuratObject")` for more info
-* Version: 2.12 +* Version: 2.17.1 * GitHub: https://github.com/philchalmers/SimDesign * Source code: https://github.com/cran/SimDesign -* Date/Publication: 2023-07-07 16:40:02 UTC -* Number of recursive dependencies: 124 +* Date/Publication: 2024-08-17 05:00:02 UTC +* Number of recursive dependencies: 136 -Run `revdep_details(, "SimDesign")` for more info +Run `revdepcheck::revdep_details(, "SimDesign")` for more info
@@ -533,58 +1052,78 @@ Run `revdep_details(, "SimDesign")` for more info * checking installed package size ... NOTE ``` - installed size is 5.7Mb + installed size is 7.3Mb sub-directories of 1Mb or more: - doc 5.2Mb + doc 6.5Mb + ``` + +# skpr + +
+ +* Version: 1.7.1 +* GitHub: https://github.com/tylermorganwall/skpr +* Source code: https://github.com/cran/skpr +* Date/Publication: 2024-03-26 01:30:02 UTC +* Number of recursive dependencies: 153 + +Run `revdepcheck::revdep_details(, "skpr")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 59.6Mb + sub-directories of 1Mb or more: + libs 59.0Mb ``` # smoots
-* Version: 1.1.3 +* Version: 1.1.4 * GitHub: NA * Source code: https://github.com/cran/smoots -* Date/Publication: 2021-10-09 21:10:02 UTC -* Number of recursive dependencies: 77 +* Date/Publication: 2023-09-11 08:50:02 UTC +* Number of recursive dependencies: 75 -Run `revdep_details(, "smoots")` for more info +Run `revdepcheck::revdep_details(, "smoots")` for more info
## In both -* checking C++ specification ... NOTE +* checking installed package size ... NOTE ``` - Specified C++11: please drop specification unless essential + installed size is 5.2Mb + sub-directories of 1Mb or more: + libs 4.5Mb ``` # sphunif
-* Version: 1.0.1 +* Version: 1.4.0 * GitHub: https://github.com/egarpor/sphunif * Source code: https://github.com/cran/sphunif -* Date/Publication: 2021-09-02 07:40:02 UTC -* Number of recursive dependencies: 76 +* Date/Publication: 2024-05-24 21:50:01 UTC +* Number of recursive dependencies: 75 -Run `revdep_details(, "sphunif")` for more info +Run `revdepcheck::revdep_details(, "sphunif")` for more info
## In both -* checking C++ specification ... NOTE - ``` - Specified C++11: please drop specification unless essential - ``` - * checking installed package size ... NOTE ``` - installed size is 24.2Mb + installed size is 25.1Mb sub-directories of 1Mb or more: - libs 23.4Mb + libs 24.0Mb ``` * checking data for non-ASCII characters ... NOTE @@ -596,13 +1135,13 @@ Run `revdep_details(, "sphunif")` for more info
-* Version: 0.4.3.7 +* Version: 0.4.4.3 * GitHub: https://github.com/JeremyGelb/spNetwork * Source code: https://github.com/cran/spNetwork -* Date/Publication: 2023-04-11 15:50:02 UTC -* Number of recursive dependencies: 150 +* Date/Publication: 2024-06-21 21:40:02 UTC +* Number of recursive dependencies: 143 -Run `revdep_details(, "spNetwork")` for more info +Run `revdepcheck::revdep_details(, "spNetwork")` for more info
@@ -610,52 +1149,71 @@ Run `revdep_details(, "spNetwork")` for more info * checking installed package size ... NOTE ``` - installed size is 25.5Mb + installed size is 27.6Mb sub-directories of 1Mb or more: - doc 1.0Mb extdata 2.6Mb - libs 20.5Mb + libs 22.6Mb ``` -# SPQR +# squat
-* Version: 0.1.0 -* GitHub: https://github.com/stevengxu/SPQR -* Source code: https://github.com/cran/SPQR -* Date/Publication: 2022-05-02 20:02:03 UTC -* Number of recursive dependencies: 65 +* Version: 0.3.0 +* GitHub: https://github.com/LMJL-Alea/squat +* Source code: https://github.com/cran/squat +* Date/Publication: 2024-01-10 15:40:02 UTC +* Number of recursive dependencies: 141 -Run `revdep_details(, "SPQR")` for more info +Run `revdepcheck::revdep_details(, "squat")` for more info
## In both -* checking C++ specification ... NOTE +* checking installed package size ... NOTE ``` - Specified C++11: please drop specification unless essential + installed size is 19.9Mb + sub-directories of 1Mb or more: + data 1.1Mb + help 1.1Mb + libs 17.5Mb ``` -* checking dependencies in R code ... NOTE +# stppSim + +
+ +* Version: 1.3.4 +* GitHub: https://github.com/Manalytics/stppSim +* Source code: https://github.com/cran/stppSim +* Date/Publication: 2024-07-24 13:30:02 UTC +* Number of recursive dependencies: 131 + +Run `revdepcheck::revdep_details(, "stppSim")` for more info + +
+ +## In both + +* checking whether package ‘stppSim’ can be installed ... WARNING ``` - Namespaces in Imports field not imported from: - ‘Rcpp’ ‘progress’ - All declared Imports should be used. + Found the following significant warnings: + Warning: no DISPLAY variable so Tk is not available + See ‘/c4/home/henrik/repositories/progressr/revdep/checks/stppSim/new/stppSim.Rcheck/00install.out’ for details. ``` -# squat +# targeted
-* Version: 0.2.1 -* GitHub: https://github.com/LMJL-Alea/squat -* Source code: https://github.com/cran/squat -* Date/Publication: 2023-07-09 09:10:05 UTC -* Number of recursive dependencies: 134 +* Version: 0.5 +* GitHub: https://github.com/kkholst/targeted +* Source code: https://github.com/cran/targeted +* Date/Publication: 2024-02-22 10:00:21 UTC +* Number of recursive dependencies: 97 -Run `revdep_details(, "squat")` for more info +Run `revdepcheck::revdep_details(, "targeted")` for more info
@@ -663,39 +1221,105 @@ Run `revdep_details(, "squat")` for more info * checking installed package size ... NOTE ``` - installed size is 19.2Mb + installed size is 23.0Mb sub-directories of 1Mb or more: - data 1.1Mb - help 1.1Mb - libs 16.9Mb + doc 1.1Mb + libs 21.3Mb ``` -# targeted +# tsdistributions
-* Version: 0.3 -* GitHub: https://github.com/kkholst/targeted -* Source code: https://github.com/cran/targeted -* Date/Publication: 2022-10-25 20:30:02 UTC -* Number of recursive dependencies: 95 +* Version: 1.0.2 +* GitHub: https://github.com/tsmodels/tsdistributions +* Source code: https://github.com/cran/tsdistributions +* Date/Publication: 2024-08-23 04:20:02 UTC +* Number of recursive dependencies: 79 -Run `revdep_details(, "targeted")` for more info +Run `revdepcheck::revdep_details(, "tsdistributions")` for more info
## In both -* checking C++ specification ... NOTE +* checking re-building of vignette outputs ... ERROR ``` - Specified C++11: please drop specification unless essential + Error(s) in re-building vignettes: + ... + --- re-building ‘estimation_demo.Rmd’ using rmarkdown + --- finished re-building ‘estimation_demo.Rmd’ + + --- re-building ‘location_scale_distributions.Rmd’ using rmarkdown + ! Undefined control sequence. + l.56 \NewDocumentCommand + \citeproctext{}{} + + ... + --- finished re-building ‘profile_demo.Rmd’ + + --- re-building ‘spd_demo.Rmd’ using rmarkdown + --- finished re-building ‘spd_demo.Rmd’ + + SUMMARY: processing the following file failed: + ‘location_scale_distributions.Rmd’ + + Error: Vignette re-building failed. + Execution halted + ``` + +* checking installed package size ... NOTE + ``` + installed size is 42.8Mb + sub-directories of 1Mb or more: + libs 42.1Mb + ``` + +# tsgarch + +
+ +* Version: 1.0.3 +* GitHub: https://github.com/tsmodels/tsgarch +* Source code: https://github.com/cran/tsgarch +* Date/Publication: 2024-10-12 00:50:02 UTC +* Number of recursive dependencies: 100 + +Run `revdepcheck::revdep_details(, "tsgarch")` for more info + +
+ +## In both + +* checking installed package size ... NOTE + ``` + installed size is 144.2Mb + sub-directories of 1Mb or more: + libs 143.1Mb ``` +# vital + +
+ +* Version: 1.1.0 +* GitHub: https://github.com/robjhyndman/vital +* Source code: https://github.com/cran/vital +* Date/Publication: 2024-06-21 08:00:02 UTC +* Number of recursive dependencies: 201 + +Run `revdepcheck::revdep_details(, "vital")` for more info + +
+ +## In both + * checking installed package size ... NOTE ``` - installed size is 16.8Mb + installed size is 6.0Mb sub-directories of 1Mb or more: - libs 15.7Mb + data 4.4Mb + help 1.3Mb ``` # vmeasur @@ -706,9 +1330,9 @@ Run `revdep_details(, "targeted")` for more info * GitHub: NA * Source code: https://github.com/cran/vmeasur * Date/Publication: 2021-11-11 19:00:02 UTC -* Number of recursive dependencies: 118 +* Number of recursive dependencies: 107 -Run `revdep_details(, "vmeasur")` for more info +Run `revdepcheck::revdep_details(, "vmeasur")` for more info @@ -725,13 +1349,13 @@ Run `revdep_details(, "vmeasur")` for more info
-* Version: 1.6-4 +* Version: 1.8-0 * GitHub: NA * Source code: https://github.com/cran/WeightedCluster -* Date/Publication: 2023-07-07 07:50:02 UTC -* Number of recursive dependencies: 43 +* Date/Publication: 2024-10-02 15:30:02 UTC +* Number of recursive dependencies: 45 -Run `revdep_details(, "WeightedCluster")` for more info +Run `revdepcheck::revdep_details(, "WeightedCluster")` for more info
@@ -741,22 +1365,22 @@ Run `revdep_details(, "WeightedCluster")` for more info ``` Error(s) in re-building vignettes: --- re-building ‘WeightedCluster.Rnw’ using knitr + Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : + texi2dvi script/program not available, using emulation --- finished re-building ‘WeightedCluster.Rnw’ --- re-building ‘WeightedClusterFR.Rnw’ using knitr - --- finished re-building ‘WeightedClusterFR.Rnw’ - - --- re-building ‘WeightedClusterPreview.Rnw’ using knitr - Error: processing vignette 'WeightedClusterPreview.Rnw' failed with diagnostics: - Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed. + Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : + texi2dvi script/program not available, using emulation + Error: processing vignette 'WeightedClusterFR.Rnw' failed with diagnostics: ... l.85 \usepackage {tikz}^^M ! ==> Fatal error occurred, no output PDF file produced! --- failed re-building ‘WeightedClusterPreview.Rnw’ - SUMMARY: processing the following file failed: - ‘WeightedClusterPreview.Rnw’ + SUMMARY: processing the following files failed: + ‘WeightedClusterFR.Rnw’ ‘WeightedClusterPreview.Rnw’ Error: Vignette re-building failed. Execution halted diff --git a/tests/handler_filesize.R b/tests/handler_filesize.R new file mode 100644 index 0000000..a2664f4 --- /dev/null +++ b/tests/handler_filesize.R @@ -0,0 +1,22 @@ +source("incl/start.R") + +options(progressr.clear = FALSE) + +options(progressr.handlers = handler_filesize) + +message("handler_filesize() ...") + +for (x in list(integer(0), 1:10, 1L)) { + message("length(x): ", length(x)) + with_progress({ + progress <- progressor(along = x) + for (ii in x) { + Sys.sleep(getOption("progressr.demo.delay", 0.1)) + progress(message = sprintf("(%s)", paste(letters[1:ii], collapse=""))) + } + }) +} + +message("handler_filesize() ... done") + +source("incl/end.R") diff --git a/vignettes/progressr-intro.md b/vignettes/progressr-intro.md index 9ebd04d..6fbd026 100644 --- a/vignettes/progressr-intro.md +++ b/vignettes/progressr-intro.md @@ -620,8 +620,35 @@ my_fcn(1:5) ### foreach() with doFuture Here is an example that uses `foreach()` of the **[foreach]** package -to parallelize on the local machine (via **[doFuture]**) while at the -same time signaling progression updates: +together with `%dofuture%` of the **[doFuture]** package to +parallelize while reporting on progress. This example parallelizes on +the local machine, it works alsof for remote machines: + +```r +library(doFuture) ## %dofuture% +plan(multisession) + +library(progressr) +handlers(global = TRUE) +handlers("progress", "beepr") + +my_fcn <- function(xs) { + p <- progressor(along = xs) + foreach(x = xs) %dofuture% { + Sys.sleep(6.0-x) + p(sprintf("x=%g", x)) + sqrt(x) + } +} + +my_fcn(1:5) +# / [================>-----------------------------] 40% x=2 +``` + + +For existing code using the traditional `%dopar%` operators of the +**[foreach]** package, we can register the **[doFuture]** adaptor and +use the same **progressr** as above to progress updates; ```r library(doFuture) @@ -850,7 +877,7 @@ depends on it. The roadmap for developing the API is roughly: additional progression handlers For a more up-to-date view on what features might be added, see -. +. ## Appendix