From a96148ec7dd49cc31b6d82305fa39279e2134412 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Fri, 3 Jul 2020 10:51:07 -0400 Subject: [PATCH 01/24] try R check workflow --- .github/workflow/build-R.yml | 51 ++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 .github/workflow/build-R.yml diff --git a/.github/workflow/build-R.yml b/.github/workflow/build-R.yml new file mode 100644 index 0000000..cd0e1a0 --- /dev/null +++ b/.github/workflow/build-R.yml @@ -0,0 +1,51 @@ +name: R-CMD-check + +on: + push: + branches: [master, dev] + pull_request: + branches: [master, dev] + +jobs: + R-CMD-check: + runs-on: ${{ matrix.os }} + name: ${{ matrix.os }} (${{ matrix.r }}) + + strategy: + fail-fast: false + matrix: + r: ['release', 'devel'] + os: [ubuntu-latest, macos-latest, windows-latest] + + env: + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@master + with: + r-version: ${{ matrix.r }} + + - uses: r-lib/actions/setup-pandoc@master + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + shell: Rscript {0} + + - name: Install dependencies + run: | + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("devtools") + remotes::install_cran("covr") + shell: Rscript {0} + + - name: Check package + run: devtools::check() + shell: Rscript {0} + + - name: Report test coverage + run: covr::codecov() + shell: Rscript {0} From 47b5fcc17e890148f8149c465e9dde7236aa22a1 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Fri, 3 Jul 2020 10:52:31 -0400 Subject: [PATCH 02/24] correct dir name --- .github/{workflow => workflows}/build-R.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/{workflow => workflows}/build-R.yml (100%) diff --git a/.github/workflow/build-R.yml b/.github/workflows/build-R.yml similarity index 100% rename from .github/workflow/build-R.yml rename to .github/workflows/build-R.yml From 9c8861ce4ae7ea566027e358d8b28eaeab2940cd Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Fri, 3 Jul 2020 11:15:28 -0400 Subject: [PATCH 03/24] add rspm --- .github/workflows/build-R.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index cd0e1a0..4f0fce7 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -19,6 +19,7 @@ jobs: env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + RSPM: https://packagemanager.rstudio.com/cran/__linux__/xenial/latest steps: - uses: actions/checkout@v2 From 1dca719ff18b9236e7edb9be23ac3fcacf3184d5 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Mon, 6 Jul 2020 08:40:21 -0400 Subject: [PATCH 04/24] try installing os deps --- .github/workflows/build-R.yml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index 4f0fce7..67d9aaf 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -36,7 +36,16 @@ jobs: saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} - - name: Install dependencies + - name: Install system dependencies + 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" + + - name: Install R dependencies run: | remotes::install_deps(dependencies = TRUE) remotes::install_cran("devtools") From fae9694a50741966cee1469cf131181b9de8e8a8 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Mon, 6 Jul 2020 08:42:02 -0400 Subject: [PATCH 05/24] fix indentation --- .github/workflows/build-R.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index 67d9aaf..a4d06ce 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -36,7 +36,7 @@ jobs: saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} - - name: Install system dependencies + - name: Install system dependencies if: runner.os == 'Linux' env: RHUB_PLATFORM: linux-x86_64-ubuntu-gcc From a0f431125f2a2b1ac230dbf9af2de80092c4ea38 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Mon, 6 Jul 2020 09:09:04 -0400 Subject: [PATCH 06/24] no r devel --- .github/workflows/build-R.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index a4d06ce..b8dbaef 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - r: ['release', 'devel'] + r: [release] os: [ubuntu-latest, macos-latest, windows-latest] env: @@ -36,6 +36,14 @@ jobs: saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} + - name: Cache R packages + if: runner.os != 'Windows' + uses: actions/cache@v1 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1- + - name: Install system dependencies if: runner.os == 'Linux' env: From a3e31c9a73d93817fbad678f0cdf59077207a8ca Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Mon, 3 Aug 2020 12:15:00 -0400 Subject: [PATCH 07/24] add multi subsample tables example dataset --- .../example_subtable1/project_config.yaml | 3 ++- .../example_subtable2/project_config.yaml | 5 +++-- .../example_subtable3/project_config.yaml | 5 +++-- .../example_subtable4/project_config.yaml | 5 +++-- .../example_subtable5/project_config.yaml | 5 +++-- 5 files changed, 14 insertions(+), 9 deletions(-) diff --git a/inst/extdata/example_peps-master/example_subtable1/project_config.yaml b/inst/extdata/example_peps-master/example_subtable1/project_config.yaml index 1a61fa8..44dc31a 100644 --- a/inst/extdata/example_peps-master/example_subtable1/project_config.yaml +++ b/inst/extdata/example_peps-master/example_subtable1/project_config.yaml @@ -1,4 +1,5 @@ pep_version: "2.0.0" sample_table: sample_table.csv subsample_table: subsample_table.csv -output_dir: $HOME/example_results +looper: + output_dir: $HOME/example_results diff --git a/inst/extdata/example_peps-master/example_subtable2/project_config.yaml b/inst/extdata/example_peps-master/example_subtable2/project_config.yaml index f8dc65b..80824aa 100644 --- a/inst/extdata/example_peps-master/example_subtable2/project_config.yaml +++ b/inst/extdata/example_peps-master/example_subtable2/project_config.yaml @@ -1,8 +1,9 @@ pep_version: "2.0.0" sample_table: sample_table.csv subsample_table: subsample_table.csv -output_dir: $HOME/hello_looper_results -pipeline_interfaces: [../pipeline/pipeline_interface.yaml] +looper: + output_dir: $HOME/hello_looper_results + pipeline_interfaces: [../pipeline/pipeline_interface.yaml] sample_modifiers: derive: diff --git a/inst/extdata/example_peps-master/example_subtable3/project_config.yaml b/inst/extdata/example_peps-master/example_subtable3/project_config.yaml index ee3cad6..34b4e26 100644 --- a/inst/extdata/example_peps-master/example_subtable3/project_config.yaml +++ b/inst/extdata/example_peps-master/example_subtable3/project_config.yaml @@ -1,8 +1,9 @@ pep_version: "2.0.0" sample_table: sample_table.csv subsample_table: subsample_table.csv -output_dir: $HOME/hello_looper_results -pipeline_interfaces: [../pipeline/pipeline_interface.yaml] +looper: + output_dir: $HOME/hello_looper_results + pipeline_interfaces: [../pipeline/pipeline_interface.yaml] sample_modifiers: derive: diff --git a/inst/extdata/example_peps-master/example_subtable4/project_config.yaml b/inst/extdata/example_peps-master/example_subtable4/project_config.yaml index aad9eae..8a9e87d 100644 --- a/inst/extdata/example_peps-master/example_subtable4/project_config.yaml +++ b/inst/extdata/example_peps-master/example_subtable4/project_config.yaml @@ -1,6 +1,7 @@ pep_version: "2.0.0" sample_table: sample_table.csv subsample_table: subsample_table.csv -output_dir: $HOME/hello_looper_results -pipeline_interfaces: [../pipeline/pipeline_interface.yaml] +looper: + output_dir: $HOME/hello_looper_results + pipeline_interfaces: [../pipeline/pipeline_interface.yaml] diff --git a/inst/extdata/example_peps-master/example_subtable5/project_config.yaml b/inst/extdata/example_peps-master/example_subtable5/project_config.yaml index 28f3472..227aea3 100644 --- a/inst/extdata/example_peps-master/example_subtable5/project_config.yaml +++ b/inst/extdata/example_peps-master/example_subtable5/project_config.yaml @@ -1,8 +1,9 @@ pep_version: "2.0.0" sample_table: sample_table.csv subsample_table: subsample_table.csv -output_dir: $HOME/hello_looper_results -pipeline_interfaces: [../pipeline/pipeline_interface.yaml] +looper: + output_dir: $HOME/hello_looper_results + pipeline_interfaces: [../pipeline/pipeline_interface.yaml] sample_modifiers: derive: From 55df57b1772c7778c0cb1d44c8322c70bea867ff Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Mon, 3 Aug 2020 12:15:27 -0400 Subject: [PATCH 08/24] add multi subsample tables example dataset --- .../example_subtables/project_config.yaml | 5 +++++ .../example_peps-master/example_subtables/sample_table.csv | 4 ++++ .../example_subtables/subsample_table.csv | 6 ++++++ .../example_subtables/subsample_table1.csv | 2 ++ 4 files changed, 17 insertions(+) create mode 100644 inst/extdata/example_peps-master/example_subtables/project_config.yaml create mode 100644 inst/extdata/example_peps-master/example_subtables/sample_table.csv create mode 100644 inst/extdata/example_peps-master/example_subtables/subsample_table.csv create mode 100644 inst/extdata/example_peps-master/example_subtables/subsample_table1.csv diff --git a/inst/extdata/example_peps-master/example_subtables/project_config.yaml b/inst/extdata/example_peps-master/example_subtables/project_config.yaml new file mode 100644 index 0000000..05743a3 --- /dev/null +++ b/inst/extdata/example_peps-master/example_subtables/project_config.yaml @@ -0,0 +1,5 @@ +pep_version: "2.0.0" +sample_table: sample_table.csv +subsample_table: [subsample_table.csv, subsample_table1.csv] +looper: + output_dir: $HOME/example_results diff --git a/inst/extdata/example_peps-master/example_subtables/sample_table.csv b/inst/extdata/example_peps-master/example_subtables/sample_table.csv new file mode 100644 index 0000000..a800e04 --- /dev/null +++ b/inst/extdata/example_peps-master/example_subtables/sample_table.csv @@ -0,0 +1,4 @@ +sample_name,protocol,file +frog_1,anySampleType,multi +frog_2,anySampleType,multi +frog_3,anySampleType,multi diff --git a/inst/extdata/example_peps-master/example_subtables/subsample_table.csv b/inst/extdata/example_peps-master/example_subtables/subsample_table.csv new file mode 100644 index 0000000..158761c --- /dev/null +++ b/inst/extdata/example_peps-master/example_subtables/subsample_table.csv @@ -0,0 +1,6 @@ +sample_name,subsample_name,file +frog_1,sub_a,data/frog1a_data.txt +frog_1,sub_b,data/frog1b_data.txt +frog_1,sub_c,data/frog1c_data.txt +frog_2,sub_a,data/frog2a_data.txt +frog_2,sub_b,data/frog2b_data.txt \ No newline at end of file diff --git a/inst/extdata/example_peps-master/example_subtables/subsample_table1.csv b/inst/extdata/example_peps-master/example_subtables/subsample_table1.csv new file mode 100644 index 0000000..da94637 --- /dev/null +++ b/inst/extdata/example_peps-master/example_subtables/subsample_table1.csv @@ -0,0 +1,2 @@ +sample_name,subsample_name,desc +frog_3,sub_a,TEST3a \ No newline at end of file From 667081b267a3cb7bdf3d79c21fa125d5c8472a7f Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Mon, 3 Aug 2020 12:16:12 -0400 Subject: [PATCH 09/24] implement multi subsample table support; #40 --- R/project.R | 37 ++++++++++++++++++++++++----------- tests/testthat/test_project.R | 22 +++++++++++++++++++++ 2 files changed, 48 insertions(+), 11 deletions(-) diff --git a/R/project.R b/R/project.R index 9e613e0..0187618 100644 --- a/R/project.R +++ b/R/project.R @@ -479,40 +479,37 @@ setMethod( } -#' Merge samples defined in sample table with ones in subsample table +#' Load single subsample annotation #' #' @param .Object an object of \code{"\linkS4class{Project}"} +#' @param path string, a path to the subsample table to read and incorporate #' #' @return an object of \code{"\linkS4class{Project}"} -.mergeAttrs = function(.Object){ - cfg = config(.Object) - if (!CFG_SUBSAMPLE_TABLE_KEY %in% names(cfg)) return(.Object) - sampleSubannotationPath = cfg[[CFG_SUBSAMPLE_TABLE_KEY]] - samples = sampleTable(.Object) - samples = .listifyDF(samples) - if (.safeFileExists(sampleSubannotationPath)) { - samplesSubannotation = data.table::fread(sampleSubannotationPath) +.loadSubsampleAnnotation = function(.Object, path) { + if (.safeFileExists(path)) { + samplesSubannotation = data.table::fread(path) } else{ samplesSubannotation = data.table::data.table() } subNames = unique(samplesSubannotation$sample_name) + samples = sampleTable(.Object) + samples = .listifyDF(samples) rowNum = nrow(samples) # Creating a list to be populated in the loop and inserted # into the samples data.table as a column. This way the "cells" # in the samples table can consist of multiple elements - colList = vector("list", rowNum) for (iName in subNames) { whichNames = which(samplesSubannotation$sample_name == iName) subTable = samplesSubannotation[whichNames,] dropCol = which(names(samplesSubannotation[whichNames,]) == "sample_name") subTable = subset(subTable, select = -dropCol) + colList = vector("list", rowNum) for (iColumn in seq_len(ncol(subTable))) { colName = names(subset(subTable, select = iColumn)) if (!any(names(samples) == colName)) { # The column doesn't exist, creating samples[, colName] = NULL } else{ - # colList=as.list(unname(samples[, ..colName]))[[1]] colList = samples[[colName]] } # The column exists @@ -532,3 +529,21 @@ setMethod( .Object@samples = samples return(.Object) } + + + +#' Merge samples defined in sample table with ones in subsample table(s) +#' +#' @param .Object an object of \code{"\linkS4class{Project}"} +#' +#' @return an object of \code{"\linkS4class{Project}"} +.mergeAttrs = function(.Object){ + cfg = config(.Object) + if (!CFG_SUBSAMPLE_TABLE_KEY %in% names(cfg)) return(.Object) + sampleSubannotationPath = cfg[[CFG_SUBSAMPLE_TABLE_KEY]] + for(p in sampleSubannotationPath){ + .Object = .loadSubsampleAnnotation(.Object, p) + print(.Object@samples) + } + return(.Object) +} diff --git a/tests/testthat/test_project.R b/tests/testthat/test_project.R index dfef280..3ba0f5e 100644 --- a/tests/testthat/test_project.R +++ b/tests/testthat/test_project.R @@ -35,6 +35,14 @@ cfgSubtable = system.file( package = "pepr" ) +cfgSubtableMulti = system.file( + "extdata", + paste0("example_peps-",branch), + "example_subtables", + "project_config.yaml", + package = "pepr" +) + cfgBioc = system.file( "extdata", paste0("example_peps-",branch), @@ -184,3 +192,17 @@ test_that("Version number is required", { expect_error(Project(file = path)) }) + +test_that("Subsample table works", { + p=Project(file=cfgSubtable) + expect_true("subsample_name" %in% colnames(p@samples)) + expect_equal(length(p@samples$file[[1]]), 3) +}) + + +test_that("Subsample table works for multiple subtables", { + p=Project(file=cfgSubtableMulti) + expect_true("desc" %in% colnames(p@samples)) +}) + + From 3816b8e31d0387fb8fb25ddd8a657c6f33ccc484 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Mon, 3 Aug 2020 12:32:00 -0400 Subject: [PATCH 10/24] remove diagnostic msg --- R/project.R | 1 - README.md | 4 ++-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/R/project.R b/R/project.R index 0187618..d8e6c62 100644 --- a/R/project.R +++ b/R/project.R @@ -543,7 +543,6 @@ setMethod( sampleSubannotationPath = cfg[[CFG_SUBSAMPLE_TABLE_KEY]] for(p in sampleSubannotationPath){ .Object = .loadSubsampleAnnotation(.Object, p) - print(.Object@samples) } return(.Object) } diff --git a/README.md b/README.md index 3acaf6a..50e8fa1 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/pepr)](http://cranlogs.r-pkg.org/badges/grand-total/pepr) [![CRAN](http://www.r-pkg.org/badges/version-last-release/pepr)](http://www.r-pkg.org/badges/version-last-release/pepr) -[![Build Status](https://travis-ci.org/pepkit/pepr.svg?branch=master)](https://travis-ci.org/pepkit/pepr) -[![Coverage Status](https://coveralls.io/repos/github/pepkit/pepr/badge.svg?branch=dev)](https://coveralls.io/github/pepkit/pepr?branch=dev&service=github) +![R-CMD-check](https://github.com/pepkit/pepr/workflows/R-CMD-check/badge.svg) +[![codecov](https://codecov.io/gh/pepkit/pepr/branch/master/graph/badge.svg)](https://codecov.io/gh/pepkit/pepr) [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io) # The `pepr` package: Portable Encapsulated Projects in R From a91159230e64c38caafa2852ef7dc45b75c88dbf Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Mon, 3 Aug 2020 12:36:28 -0400 Subject: [PATCH 11/24] install stringi on linux --- .github/workflows/build-R.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index b8dbaef..6af8f63 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -49,6 +49,7 @@ jobs: env: RHUB_PLATFORM: linux-x86_64-ubuntu-gcc run: | + sudo apt install r-cran-stringi Rscript -e "remotes::install_github('r-hub/sysreqs')" sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") sudo -s eval "$sysreqs" From 2a97ca854cd1e4dc4c7e072b663c69953b2b99ee Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Wed, 30 Sep 2020 13:50:26 -0400 Subject: [PATCH 12/24] use preprocessed path for Config obj init --- R/project.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/project.R b/R/project.R index d8e6c62..1afa16e 100644 --- a/R/project.R +++ b/R/project.R @@ -25,7 +25,7 @@ setMethod("initialize", "Project", function(.Object, ...) { # check if file path provided .Object@file = .makeAbsPath(ellipsis$file, parent = path.expand(getwd())) # instantiate config object and stick it in the config slot - .Object@config = Config(ellipsis$file, ellipsis$amendments) + .Object@config = Config(.Object@file, ellipsis$amendments) .Object = .loadSampleAnnotation(.Object) .Object = .modifySamples(.Object) } From b0e2c765eaf7f5b5a022dece2e9d22eaa57c5231 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 18:09:01 -0400 Subject: [PATCH 13/24] determine dollar matches by the beginning of the string --- .travis.yml | 9 - R/config.R | 4 +- .../other_pipeline1/sample1_GSM2471255_1.bw | 1339 +++++++++++++++++ .../other_pipeline1/sample1_GSM2471255_2.bw | 1187 +++++++++++++++ .../sample1/pipeline1/sample1_GSM2471255_1.bw | 1302 ++++++++++++++++ .../sample1/pipeline1/sample1_GSM2471255_2.bw | 1298 ++++++++++++++++ .../other_pipeline1/sample2_GSM2471300_1.bw | 1339 +++++++++++++++++ .../other_pipeline1/sample2_GSM2471300_2.bw | 1311 ++++++++++++++++ .../sample2/pipeline1/sample2_GSM2471300_1.bw | 1234 +++++++++++++++ .../sample2/pipeline1/sample2_GSM2471300_2.bw | 97 ++ .../other_pipeline2/sample3_GSM2471249_1.bw | 1302 ++++++++++++++++ .../other_pipeline2/sample3_GSM2471249_2.bw | 1339 +++++++++++++++++ .../sample3/pipeline2/sample3_GSM2471249_1.bw | 896 +++++++++++ .../sample3/pipeline2/sample3_GSM2471249_2.bw | 111 ++ 14 files changed, 12757 insertions(+), 11 deletions(-) delete mode 100644 .travis.yml create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_1.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_2.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample1/pipeline1/sample1_GSM2471255_1.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample1/pipeline1/sample1_GSM2471255_2.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample2/other_pipeline1/sample2_GSM2471300_1.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample2/other_pipeline1/sample2_GSM2471300_2.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample2/pipeline1/sample2_GSM2471300_1.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample2/pipeline1/sample2_GSM2471300_2.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample3/other_pipeline2/sample3_GSM2471249_1.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample3/other_pipeline2/sample3_GSM2471249_2.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_1.bw create mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_2.bw diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 7d86e60..0000000 --- a/.travis.yml +++ /dev/null @@ -1,9 +0,0 @@ -language: r -os: "linux" -warnings_are_errors: false -cache: packages -r_packages: devtools -r_github_packages: - - r-lib/covr -after_success: - - Rscript -e 'covr::coveralls()' \ No newline at end of file diff --git a/R/config.R b/R/config.R index aacd6f3..4f24f9f 100644 --- a/R/config.R +++ b/R/config.R @@ -129,12 +129,12 @@ setMethod("[[", "Config", function(x, i) { .DollarNames.Config <- function(x, pattern = "") - grep(pattern, grep(names(x), value=TRUE)) + grep(paste0("^", pattern), grep(names(x), value=TRUE)) #' @rdname select-config #' @export setMethod("$", "Config", function(x, name){ - matches = grep(name, names(x)) + matches = grep(paste0("^", name), names(x)) if(length(matches) == 0) return(NULL) hits = x[[matches]] diff --git a/inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_1.bw b/inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_1.bw new file mode 100644 index 0000000..326b41a --- /dev/null +++ b/inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_1.bw @@ -0,0 +1,1339 @@ +chr1 3190581 3191428 +chr1 8130439 8131887 +chr1 10593123 10594209 +chr1 10732070 10733118 +chr1 10757664 10758631 +chr1 10781239 10781744 +chr1 10851570 10852173 +chr1 10925202 10925728 +chr1 10965129 10966144 +chr1 27049620 27050905 +chr1 32510030 32510913 +chr1 33722494 33723960 +chr1 33828789 33830947 +chr1 38494689 38495688 +chr1 38560194 38561606 +chr1 38627529 38629265 +chr1 38656780 38657626 +chr1 38662809 38664040 +chr1 38735942 38737376 +chr1 38791998 38793333 +chr1 38801888 38802630 +chr1 38819171 38820577 +chr1 39192609 39194134 +chr1 39248757 39250129 +chr1 39291500 39292441 +chr1 41710596 41712937 +chr1 44500383 44503337 +chr1 44715420 44716129 +chr1 44989824 44991149 +chr1 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b/inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_2.bw new file mode 100644 index 0000000..a540b28 --- /dev/null +++ b/inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_2.bw @@ -0,0 +1,111 @@ +chr1 3190581 3191428 +chr1 8130439 8131887 +chr1 10593123 10594209 +chr1 10732070 10733118 +chr1 10757664 10758631 +chr1 10781239 10781744 +chr1 10851570 10852173 +chr1 10925202 10925728 +chr1 10965129 10966144 +chr1 27049620 27050905 +chr1 32510030 32510913 +chr1 33722494 33723960 +chr1 33828789 33830947 +chr1 38494689 38495688 +chr1 38560194 38561606 +chr1 38627529 38629265 +chr1 38656780 38657626 +chr1 38662809 38664040 +chr1 38735942 38737376 +chr1 38791998 38793333 +chr1 38801888 38802630 +chr1 38819171 38820577 +chr1 39192609 39194134 +chr1 39248757 39250129 +chr1 39291500 39292441 +chr1 41710596 41712937 +chr1 44500383 44503337 +chr1 44715420 44716129 +chr1 44989824 44991149 +chr1 49112757 49113363 +chr1 51006090 51007314 +chr1 51034546 51036289 +chr1 51098841 51099913 +chr1 51165195 51166786 +chr1 54925046 54928826 +chr1 59522325 59524092 +chr1 60102624 60105491 +chr1 61086857 61087871 +chr1 61917795 61920190 +chr1 62045460 62048159 +chr1 62053433 62055908 +chr1 63369349 63370894 +chr1 63443534 63444884 +chr1 63464282 63465717 +chr1 63665219 63666122 +chr1 82557436 82558140 +chr1 82663553 82664196 +chr1 82664608 82665419 +chr1 83220709 83221363 +chr1 83252219 83253218 +chr1 83310680 83311769 +chr1 83345366 83346271 +chr1 83360512 83361298 +chr1 83411289 83412040 +chr1 83878319 83879217 +chr1 87795192 87796737 +chr1 87803415 87805212 +chr1 87821621 87823082 +chr1 87821793 87822910 +chr1 88028658 88029378 +chr1 88065041 88066530 +chr1 88108084 88109396 +chr1 88183654 88184961 +chr1 88402821 88404888 +chr1 88535719 88538390 +chr1 88577535 88578821 +chr1 88595049 88596320 +chr1 88615687 88616927 +chr1 88646698 88648145 +chr1 88686076 88687740 +chr1 88841735 88843091 +chr1 88875731 88877192 +chr1 88926796 88928508 +chr1 91305562 91307215 +chr1 92271540 92273987 +chr1 97610491 97611741 +chr1 113540056 113542020 +chr1 119028026 119029955 +chr1 119452558 119453594 +chr1 163359231 163360494 +chr1 163441941 163442842 +chr1 163507965 163509139 +chr1 163939700 163940637 +chr1 164023244 164024214 +chr1 164197827 164199172 +chr1 164620038 164621164 +chr1 164637575 164639037 +chr1 164668592 164669823 +chr1 164672787 164674206 +chr1 164700259 164701522 +chr1 167296954 167299046 +chr1 169910396 169913079 +chr1 181121049 181123654 +chr1 198263562 198265742 +chr1 198339402 198341607 +chr1 204423958 204424935 +chr1 209064233 209067059 +chr1 209989050 209989824 +chr1 210433698 210437258 +chr1 213498112 213501134 +chr1 213597964 213599524 +chr1 215888921 215890374 +chr1 216772416 216773458 +chr1 217766122 217767351 +chr1 218207432 218208498 +chr1 218222277 218224086 +chr1 221906778 221908480 +chr1 232753930 232757436 +chr1 243876467 243877893 +chr1 243895796 243896468 +chr1 244217325 244218426 \ No newline at end of file From ef098b8fbf90f4459d8112deb4a805073c2fa263 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 18:46:35 -0400 Subject: [PATCH 14/24] remove data, account for multiple path expansions scenario --- R/config.R | 2 + R/utils.R | 24 +- .../example_peps-master/data/frog1_data.txt | 4 - .../example_peps-master/data/frog1a_data.txt | 2 - .../example_peps-master/data/frog1a_data2.txt | 2 - .../example_peps-master/data/frog1b_data.txt | 3 - .../example_peps-master/data/frog1b_data2.txt | 3 - .../example_peps-master/data/frog1c_data.txt | 2 - .../example_peps-master/data/frog1c_data2.txt | 2 - .../example_peps-master/data/frog2_data.txt | 7 - .../example_peps-master/data/frog2a_data.txt | 3 - .../example_peps-master/data/frog2b_data.txt | 3 - .../example_peps-master/data/frog3_data.txt | 7 - .../example_peps-master/data/frog4_data.txt | 7 - .../other_pipeline1/sample1_GSM2471255_1.bw | 1339 ----------------- .../other_pipeline1/sample1_GSM2471255_2.bw | 1187 --------------- .../sample1/pipeline1/sample1_GSM2471255_1.bw | 1302 ---------------- .../sample1/pipeline1/sample1_GSM2471255_2.bw | 1298 ---------------- .../other_pipeline1/sample2_GSM2471300_1.bw | 1339 ----------------- .../other_pipeline1/sample2_GSM2471300_2.bw | 1311 ---------------- .../sample2/pipeline1/sample2_GSM2471300_1.bw | 1234 --------------- .../sample2/pipeline1/sample2_GSM2471300_2.bw | 97 -- .../other_pipeline2/sample3_GSM2471249_1.bw | 1302 ---------------- .../other_pipeline2/sample3_GSM2471249_2.bw | 1339 ----------------- .../sample3/pipeline2/sample3_GSM2471249_1.bw | 896 ----------- .../sample3/pipeline2/sample3_GSM2471249_2.bw | 111 -- 26 files changed, 16 insertions(+), 12810 deletions(-) delete mode 100644 inst/extdata/example_peps-master/data/frog1_data.txt delete mode 100644 inst/extdata/example_peps-master/data/frog1a_data.txt delete mode 100644 inst/extdata/example_peps-master/data/frog1a_data2.txt delete mode 100644 inst/extdata/example_peps-master/data/frog1b_data.txt delete mode 100644 inst/extdata/example_peps-master/data/frog1b_data2.txt delete mode 100644 inst/extdata/example_peps-master/data/frog1c_data.txt delete mode 100644 inst/extdata/example_peps-master/data/frog1c_data2.txt delete mode 100644 inst/extdata/example_peps-master/data/frog2_data.txt delete mode 100644 inst/extdata/example_peps-master/data/frog2a_data.txt delete mode 100644 inst/extdata/example_peps-master/data/frog2b_data.txt delete mode 100644 inst/extdata/example_peps-master/data/frog3_data.txt delete mode 100644 inst/extdata/example_peps-master/data/frog4_data.txt delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_1.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_2.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample1/pipeline1/sample1_GSM2471255_1.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample1/pipeline1/sample1_GSM2471255_2.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample2/other_pipeline1/sample2_GSM2471300_1.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample2/other_pipeline1/sample2_GSM2471300_2.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample2/pipeline1/sample2_GSM2471300_1.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample2/pipeline1/sample2_GSM2471300_2.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample3/other_pipeline2/sample3_GSM2471249_1.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample3/other_pipeline2/sample3_GSM2471249_2.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_1.bw delete mode 100644 inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_2.bw diff --git a/R/config.R b/R/config.R index 4f24f9f..74691f0 100644 --- a/R/config.R +++ b/R/config.R @@ -60,6 +60,8 @@ setMethod( .expandList <- function(x) { if(is.list(x)) return(lapply(x, .expandList)) + if(length(x) > 1) + return(unname(sapply(x, .expandList))) return(suppressWarnings(.expandPath(x))) } diff --git a/R/utils.R b/R/utils.R index e40ba89..a76c4f7 100644 --- a/R/utils.R +++ b/R/utils.R @@ -126,17 +126,21 @@ #' @export #' @return Target itself if already absolute, else target nested within parent. .makeAbsPath = function(perhapsRelative, parent) { - if (!.isDefined(perhapsRelative)) return(perhapsRelative) - perhapsRelative = .expandPath(perhapsRelative) - if (.isAbsolute(perhapsRelative)) { - abspath = perhapsRelative - } else { - abspath = file.path(path.expand(parent), perhapsRelative) + res = c() + for(pR in perhapsRelative){ + if (!.isDefined(pR)) return(pR) + pR = .expandPath(pR) + if (.isAbsolute(pR)) { + abspath = pR + } else { + abspath = file.path(path.expand(parent), pR) + } + if (!.isAbsolute(abspath)) + stop("Relative path ", pR, " and parent ", parent , + " failed to create absolute path: ", abspath) + res = append(res, abspath) } - if (!.isAbsolute(abspath)) - stop("Relative path ", perhapsRelative, " and parent ", parent , - " failed to create absolute path: ", abspath) - return(abspath) + return(res) } # Must test for is.null first, since is.na(NULL) returns a logical(0) which is diff --git a/inst/extdata/example_peps-master/data/frog1_data.txt b/inst/extdata/example_peps-master/data/frog1_data.txt deleted file mode 100644 index 17cadc8..0000000 --- a/inst/extdata/example_peps-master/data/frog1_data.txt +++ /dev/null @@ -1,4 +0,0 @@ -ribbit -ribbit -ribbit -CROAK! \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog1a_data.txt b/inst/extdata/example_peps-master/data/frog1a_data.txt deleted file mode 100644 index b05e765..0000000 --- a/inst/extdata/example_peps-master/data/frog1a_data.txt +++ /dev/null @@ -1,2 +0,0 @@ -ribbit -ribbit \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog1a_data2.txt b/inst/extdata/example_peps-master/data/frog1a_data2.txt deleted file mode 100644 index b05e765..0000000 --- a/inst/extdata/example_peps-master/data/frog1a_data2.txt +++ /dev/null @@ -1,2 +0,0 @@ -ribbit -ribbit \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog1b_data.txt b/inst/extdata/example_peps-master/data/frog1b_data.txt deleted file mode 100644 index 019fcf4..0000000 --- a/inst/extdata/example_peps-master/data/frog1b_data.txt +++ /dev/null @@ -1,3 +0,0 @@ -ribbit -ribbit -ribbit \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog1b_data2.txt b/inst/extdata/example_peps-master/data/frog1b_data2.txt deleted file mode 100644 index 019fcf4..0000000 --- a/inst/extdata/example_peps-master/data/frog1b_data2.txt +++ /dev/null @@ -1,3 +0,0 @@ -ribbit -ribbit -ribbit \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog1c_data.txt b/inst/extdata/example_peps-master/data/frog1c_data.txt deleted file mode 100644 index 16ab2fe..0000000 --- a/inst/extdata/example_peps-master/data/frog1c_data.txt +++ /dev/null @@ -1,2 +0,0 @@ -ribbit -CROAK! \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog1c_data2.txt b/inst/extdata/example_peps-master/data/frog1c_data2.txt deleted file mode 100644 index 16ab2fe..0000000 --- a/inst/extdata/example_peps-master/data/frog1c_data2.txt +++ /dev/null @@ -1,2 +0,0 @@ -ribbit -CROAK! \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog2_data.txt b/inst/extdata/example_peps-master/data/frog2_data.txt deleted file mode 100644 index bc2c035..0000000 --- a/inst/extdata/example_peps-master/data/frog2_data.txt +++ /dev/null @@ -1,7 +0,0 @@ -ribbit -ribbit -ribbit - -ribbit, ribbit -ribbit, ribbit -CROAK! \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog2a_data.txt b/inst/extdata/example_peps-master/data/frog2a_data.txt deleted file mode 100644 index 8bd2e54..0000000 --- a/inst/extdata/example_peps-master/data/frog2a_data.txt +++ /dev/null @@ -1,3 +0,0 @@ -ribbit -ribbit -ribbit diff --git a/inst/extdata/example_peps-master/data/frog2b_data.txt b/inst/extdata/example_peps-master/data/frog2b_data.txt deleted file mode 100644 index c5c3a54..0000000 --- a/inst/extdata/example_peps-master/data/frog2b_data.txt +++ /dev/null @@ -1,3 +0,0 @@ -ribbit, ribbit -ribbit, ribbit -CROAK! \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog3_data.txt b/inst/extdata/example_peps-master/data/frog3_data.txt deleted file mode 100644 index bc2c035..0000000 --- a/inst/extdata/example_peps-master/data/frog3_data.txt +++ /dev/null @@ -1,7 +0,0 @@ -ribbit -ribbit -ribbit - -ribbit, ribbit -ribbit, ribbit -CROAK! \ No newline at end of file diff --git a/inst/extdata/example_peps-master/data/frog4_data.txt b/inst/extdata/example_peps-master/data/frog4_data.txt deleted file mode 100644 index bc2c035..0000000 --- a/inst/extdata/example_peps-master/data/frog4_data.txt +++ /dev/null @@ -1,7 +0,0 @@ -ribbit -ribbit -ribbit - -ribbit, ribbit -ribbit, ribbit -CROAK! \ No newline at end of file diff --git a/inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_1.bw b/inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_1.bw deleted file mode 100644 index 326b41a..0000000 --- a/inst/extdata/example_peps-master/output/results_pipeline/sample1/other_pipeline1/sample1_GSM2471255_1.bw +++ /dev/null @@ -1,1339 +0,0 @@ -chr1 3190581 3191428 -chr1 8130439 8131887 -chr1 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180436427 180437958 -chr3 180461825 180462874 -chr3 180773639 180775802 -chr3 181958774 181961127 -chr3 188857183 188858023 -chr3 189233649 189234301 -chr3 193660817 193662478 -chr3 193677518 193680170 \ No newline at end of file diff --git a/inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_2.bw b/inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_2.bw deleted file mode 100644 index a540b28..0000000 --- a/inst/extdata/example_peps-master/output/results_pipeline/sample3/pipeline2/sample3_GSM2471249_2.bw +++ /dev/null @@ -1,111 +0,0 @@ -chr1 3190581 3191428 -chr1 8130439 8131887 -chr1 10593123 10594209 -chr1 10732070 10733118 -chr1 10757664 10758631 -chr1 10781239 10781744 -chr1 10851570 10852173 -chr1 10925202 10925728 -chr1 10965129 10966144 -chr1 27049620 27050905 -chr1 32510030 32510913 -chr1 33722494 33723960 -chr1 33828789 33830947 -chr1 38494689 38495688 -chr1 38560194 38561606 -chr1 38627529 38629265 -chr1 38656780 38657626 -chr1 38662809 38664040 -chr1 38735942 38737376 -chr1 38791998 38793333 -chr1 38801888 38802630 -chr1 38819171 38820577 -chr1 39192609 39194134 -chr1 39248757 39250129 -chr1 39291500 39292441 -chr1 41710596 41712937 -chr1 44500383 44503337 -chr1 44715420 44716129 -chr1 44989824 44991149 -chr1 49112757 49113363 -chr1 51006090 51007314 -chr1 51034546 51036289 -chr1 51098841 51099913 -chr1 51165195 51166786 -chr1 54925046 54928826 -chr1 59522325 59524092 -chr1 60102624 60105491 -chr1 61086857 61087871 -chr1 61917795 61920190 -chr1 62045460 62048159 -chr1 62053433 62055908 -chr1 63369349 63370894 -chr1 63443534 63444884 -chr1 63464282 63465717 -chr1 63665219 63666122 -chr1 82557436 82558140 -chr1 82663553 82664196 -chr1 82664608 82665419 -chr1 83220709 83221363 -chr1 83252219 83253218 -chr1 83310680 83311769 -chr1 83345366 83346271 -chr1 83360512 83361298 -chr1 83411289 83412040 -chr1 83878319 83879217 -chr1 87795192 87796737 -chr1 87803415 87805212 -chr1 87821621 87823082 -chr1 87821793 87822910 -chr1 88028658 88029378 -chr1 88065041 88066530 -chr1 88108084 88109396 -chr1 88183654 88184961 -chr1 88402821 88404888 -chr1 88535719 88538390 -chr1 88577535 88578821 -chr1 88595049 88596320 -chr1 88615687 88616927 -chr1 88646698 88648145 -chr1 88686076 88687740 -chr1 88841735 88843091 -chr1 88875731 88877192 -chr1 88926796 88928508 -chr1 91305562 91307215 -chr1 92271540 92273987 -chr1 97610491 97611741 -chr1 113540056 113542020 -chr1 119028026 119029955 -chr1 119452558 119453594 -chr1 163359231 163360494 -chr1 163441941 163442842 -chr1 163507965 163509139 -chr1 163939700 163940637 -chr1 164023244 164024214 -chr1 164197827 164199172 -chr1 164620038 164621164 -chr1 164637575 164639037 -chr1 164668592 164669823 -chr1 164672787 164674206 -chr1 164700259 164701522 -chr1 167296954 167299046 -chr1 169910396 169913079 -chr1 181121049 181123654 -chr1 198263562 198265742 -chr1 198339402 198341607 -chr1 204423958 204424935 -chr1 209064233 209067059 -chr1 209989050 209989824 -chr1 210433698 210437258 -chr1 213498112 213501134 -chr1 213597964 213599524 -chr1 215888921 215890374 -chr1 216772416 216773458 -chr1 217766122 217767351 -chr1 218207432 218208498 -chr1 218222277 218224086 -chr1 221906778 221908480 -chr1 232753930 232757436 -chr1 243876467 243877893 -chr1 243895796 243896468 -chr1 244217325 244218426 \ No newline at end of file From 5965e7b5a4c4df6c783e948c5f0a204c759fbcae Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 18:50:25 -0400 Subject: [PATCH 15/24] update workflow --- .github/workflows/build-R.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index 6af8f63..3c2c77d 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -49,6 +49,7 @@ jobs: env: RHUB_PLATFORM: linux-x86_64-ubuntu-gcc run: | + sudo apt install -y r-api-3.4 sudo apt install r-cran-stringi Rscript -e "remotes::install_github('r-hub/sysreqs')" sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") From 94f29961b4934bf79909f93000f3814df3638391 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 18:56:36 -0400 Subject: [PATCH 16/24] update workflow --- .github/workflows/build-R.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index 3c2c77d..b8dbaef 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -49,8 +49,6 @@ jobs: env: RHUB_PLATFORM: linux-x86_64-ubuntu-gcc run: | - sudo apt install -y r-api-3.4 - sudo apt install r-cran-stringi Rscript -e "remotes::install_github('r-hub/sysreqs')" sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") sudo -s eval "$sysreqs" From f64493491e440074326f7c3bb65a91b2f7ce624a Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 19:07:38 -0400 Subject: [PATCH 17/24] update workflow --- .github/workflows/build-R.yml | 2 +- DESCRIPTION | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index b8dbaef..6ef9ebe 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -15,7 +15,7 @@ jobs: fail-fast: false matrix: r: [release] - os: [ubuntu-latest, macos-latest, windows-latest] + os: [ubuntu-20.04, macos-latest, windows-latest] env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true diff --git a/DESCRIPTION b/DESCRIPTION index db921f5..74efb6c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: pepr Type: Package Title: Reading Portable Encapsulated Projects -Version: 0.3.2 +Version: 0.4.0 Date: 2020-06-03 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org", role = c("aut", "cph")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut","cre"))) From d73ded8895d770d4c305c4407e89583c874c3a58 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 19:15:58 -0400 Subject: [PATCH 18/24] update workflow --- .github/workflows/build-R.yml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml index 6ef9ebe..7a39429 100644 --- a/.github/workflows/build-R.yml +++ b/.github/workflows/build-R.yml @@ -46,12 +46,11 @@ jobs: - name: Install system dependencies 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" + while read -r cmd + do + eval sudo $cmd + done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - name: Install R dependencies run: | From b6321bd2989654922d0bb37b2e1b23f202457c9d Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 19:20:15 -0400 Subject: [PATCH 19/24] add new worflow --- .github/workflows/new-build-R.yml | 81 +++++++++++++++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 .github/workflows/new-build-R.yml diff --git a/.github/workflows/new-build-R.yml b/.github/workflows/new-build-R.yml new file mode 100644 index 0000000..ecbd593 --- /dev/null +++ b/.github/workflows/new-build-R.yml @@ -0,0 +1,81 @@ +# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. +# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions +on: + push: + branches: + - master + pull_request: + branches: + - master + +name: new-R-CMD-check + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: windows-latest, r: 'release'} + - {os: macOS-latest, r: 'release'} + - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + + env: + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + RSPM: ${{ matrix.config.rspm }} + + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@master + with: + r-version: ${{ matrix.config.r }} + + - uses: r-lib/actions/setup-pandoc@master + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Cache R packages + if: runner.os != 'Windows' + uses: actions/cache@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 + if: runner.os == 'Linux' + run: | + while read -r cmd + do + eval sudo $cmd + done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') + + - name: Install dependencies + run: | + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("rcmdcheck") + shell: Rscript {0} + + - name: Check + env: + _R_CHECK_CRAN_INCOMING_REMOTE_: false + run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") + shell: Rscript {0} + + - name: Upload check results + if: failure() + uses: actions/upload-artifact@main + with: + name: ${{ runner.os }}-r${{ matrix.config.r }}-results + path: check \ No newline at end of file From b3bcf2729a8390292be6c68b0aa0acaa0f842136 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 19:27:12 -0400 Subject: [PATCH 20/24] update date, upload test covrage --- .github/workflows/build-R.yml | 68 ------------------------------- .github/workflows/new-build-R.yml | 6 ++- DESCRIPTION | 2 +- 3 files changed, 6 insertions(+), 70 deletions(-) delete mode 100644 .github/workflows/build-R.yml diff --git a/.github/workflows/build-R.yml b/.github/workflows/build-R.yml deleted file mode 100644 index 7a39429..0000000 --- a/.github/workflows/build-R.yml +++ /dev/null @@ -1,68 +0,0 @@ -name: R-CMD-check - -on: - push: - branches: [master, dev] - pull_request: - branches: [master, dev] - -jobs: - R-CMD-check: - runs-on: ${{ matrix.os }} - name: ${{ matrix.os }} (${{ matrix.r }}) - - strategy: - fail-fast: false - matrix: - r: [release] - os: [ubuntu-20.04, macos-latest, windows-latest] - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: https://packagemanager.rstudio.com/cran/__linux__/xenial/latest - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@master - with: - r-version: ${{ matrix.r }} - - - uses: r-lib/actions/setup-pandoc@master - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v1 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1- - - - name: Install system dependencies - if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - - - name: Install R dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("devtools") - remotes::install_cran("covr") - shell: Rscript {0} - - - name: Check package - run: devtools::check() - shell: Rscript {0} - - - name: Report test coverage - run: covr::codecov() - shell: Rscript {0} diff --git a/.github/workflows/new-build-R.yml b/.github/workflows/new-build-R.yml index ecbd593..25b4d04 100644 --- a/.github/workflows/new-build-R.yml +++ b/.github/workflows/new-build-R.yml @@ -78,4 +78,8 @@ jobs: uses: actions/upload-artifact@main with: name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check \ No newline at end of file + path: check + + - name: Report test coverage + run: covr::codecov() + shell: Rscript {0} \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index 74efb6c..9d1efa1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pepr Type: Package Title: Reading Portable Encapsulated Projects Version: 0.4.0 -Date: 2020-06-03 +Date: 2020-10-14 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org", role = c("aut", "cph")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut","cre"))) Maintainer: Michal Stolarczyk From 4a68edab385e0f487b720422379cca0b323ae1c2 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 19:30:37 -0400 Subject: [PATCH 21/24] install dep --- .github/workflows/new-build-R.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/new-build-R.yml b/.github/workflows/new-build-R.yml index 25b4d04..1c2a41a 100644 --- a/.github/workflows/new-build-R.yml +++ b/.github/workflows/new-build-R.yml @@ -8,7 +8,7 @@ on: branches: - master -name: new-R-CMD-check +name: R-CMD-check jobs: R-CMD-check: @@ -63,6 +63,7 @@ jobs: - name: Install dependencies run: | + remotes::install_cran("covr") remotes::install_deps(dependencies = TRUE) remotes::install_cran("rcmdcheck") shell: Rscript {0} From 9627e4ee0493fa8cf936bde1e3886e2725482db7 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Tue, 13 Oct 2020 19:35:02 -0400 Subject: [PATCH 22/24] skip ubuut devel --- .github/workflows/new-build-R.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/new-build-R.yml b/.github/workflows/new-build-R.yml index 1c2a41a..4d2665c 100644 --- a/.github/workflows/new-build-R.yml +++ b/.github/workflows/new-build-R.yml @@ -23,7 +23,6 @@ jobs: - {os: windows-latest, r: 'release'} - {os: macOS-latest, r: 'release'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true From fe11c659630143be69bcdc9c70aa2991b58acdac Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Wed, 14 Oct 2020 18:24:17 -0400 Subject: [PATCH 23/24] prep release --- DESCRIPTION | 2 +- NEWS.md | 10 ++++++++++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9d1efa1..58b4f12 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pepr Type: Package Title: Reading Portable Encapsulated Projects Version: 0.4.0 -Date: 2020-10-14 +Date: 2020-10-15 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org", role = c("aut", "cph")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut","cre"))) Maintainer: Michal Stolarczyk diff --git a/NEWS.md b/NEWS.md index cadbc8b..2c626d7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,13 @@ +# pepr 0.4.0 - 2020-10-14 + +## Changed + +* added multiple subsample_table support + +## Fixed + +* issues with config file determination + # pepr 0.3.2 - 2020-06-03 ## Changed From 2e231a8ddf372bebed1b40976f2f721ef0773764 Mon Sep 17 00:00:00 2001 From: Michal Stolarczyk Date: Wed, 14 Oct 2020 18:28:00 -0400 Subject: [PATCH 24/24] update readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 50e8fa1..aad478b 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ Load a project and explore metadata like this: library("pepr") cfgPath = system.file( "extdata", - paste0("example_peps-master"), + "example_peps-master", "example_basic", "project_config.yaml", package = "pepr"