Merge pull request #41 from pepkit/tximeta

v0.2.1

.Rbuildignore

@@ -3,4 +3,8 @@
 ^\.travis\.yml$
 ^_pkgdown.yaml
 ^docs
-^update_examples.sh
+^update_examples.sh
+^doc$
+^Meta$
+^\.github$
+long_vignettes

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/check-bioc.yml

@@ -0,0 +1,249 @@
+## Read more about GitHub actions the features of this GitHub Actions workflow
+## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
+##
+## For more details, check the biocthis developer notes vignette at
+## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
+##
+## You can add this workflow to other packages using:
+## > biocthis::use_bioc_github_action()
+##
+## Using GitHub Actions exposes you to many details about how R packages are
+## compiled and installed in several operating system.s
+### If you need help, please follow the steps listed at
+## https://github.com/r-lib/actions#where-to-find-help
+##
+## If you found an issue specific to biocthis's GHA workflow, please report it
+## with the information that will make it easier for others to help you.
+## Thank you!
+
+## Acronyms:
+## * GHA: GitHub Action
+## * OS: operating system
+
+on:
+  push: 
+    branches: [master, dev]
+  pull_request:
+    branches: [master, dev]
+
+name: R-CMD-check-bioc
+
+## These environment variables control whether to run GHA code later on that is
+## specific to testthat, covr, and pkgdown.
+##
+## If you need to clear the cache of packages, update the number inside
+## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
+## Note that you can always run a GHA test without the cache by using the word
+## "/nocache" in the commit message.
+env:
+  has_testthat: 'false'
+  run_covr: 'false'
+  run_pkgdown: 'false'
+  has_RUnit: 'false'
+  cache-version: 'cache-v1'
+
+jobs:
+  build-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    ## Environment variables unique to this job.
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: '4.0.2', cont: "bioconductor/bioconductor_docker:RELEASE_3_11", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.0.2'}
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      NOT_CRAN: true
+      TZ: UTC
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+
+      ## Set the R library to the directory matching the
+      ## R packages cache step further below when running on Docker (Linux).
+      - name: Set R Library home on Linux
+        if: runner.os == 'Linux'
+        run: |
+          mkdir /__w/_temp/Library
+          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
+
+      ## Most of these steps are the same as the ones in
+      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
+      ## If they update their steps, we will also need to update ours.
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      ## R is already included in the Bioconductor docker images
+      - name: Setup R from r-lib
+        if: runner.os != 'Linux'
+        uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      ## pandoc is already included in the Bioconductor docker images
+      - name: Setup pandoc from r-lib
+        if: runner.os != 'Linux'
+        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: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_11-r-4.0.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_11-r-4.0.2-
+
+      - name: Cache R packages on Linux
+        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
+        uses: actions/cache@v1
+        with:
+          path: /home/runner/work/_temp/Library
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_11-r-4.0.2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_11-r-4.0.2-
+
+      - name: Install Linux 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 macOS system dependencies
+        if: matrix.config.os == 'macOS-latest'
+        run: |
+          ## Enable installing XML from source if needed
+          brew install libxml2
+          echo "::set-env name=XML_CONFIG::/usr/local/opt/libxml2/bin/xml2-config"
+
+          ## Required to install magick as noted at
+          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
+          brew install imagemagick@6
+
+      - name: Install Windows system dependencies
+        if: runner.os == 'Windows'
+        run: |
+          ## Edit below if you have any Windows system dependencies
+        shell: Rscript {0}
+
+      - name: Install BiocManager
+        run: |
+          message(paste('****', Sys.time(), 'installing BiocManager ****'))
+          remotes::install_cran("BiocManager")
+        shell: Rscript {0}
+
+      - name: Set BiocVersion
+        run: |
+          BiocManager::install(version = "3.11", ask = FALSE)
+        shell: Rscript {0}
+
+      - name: Install dependencies
+        run: |
+          ## Try installing the package dependencies in steps. First the local
+          ## dependencies, then any remaining dependencies to avoid the
+          ## issues described at
+          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
+          ## https://github.com/r-lib/remotes/issues/296
+          ## Ideally, all dependencies should get installed in the first pass.
+          ## Pass #1 at installing dependencies
+          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+
+          ## Pass #2 at installing dependencies
+          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+
+          ## For running the checks
+          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+          remotes::install_cran("rcmdcheck")
+          BiocManager::install("BiocCheck")
+        shell: Rscript {0}
+
+      - name: Install BiocGenerics
+        if:  env.has_RUnit == 'true'
+        run: |
+          ## Install BiocGenerics
+          BiocManager::install("BiocGenerics")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Install pkgdown
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: |
+          remotes::install_cran("pkgdown")
+        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: Run CMD check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: |
+          rcmdcheck::rcmdcheck(
+              args = c("--no-build-vignettes", "--no-manual", "--timings"),
+              build_args = c("--no-manual", "--no-resave-data"),
+              error_on = "warning",
+              check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      ## Might need an to add this to the if:  && runner.os == 'Linux'
+      - name: Reveal testthat details
+        if:  env.has_testthat == 'true'
+        run: find . -name testthat.Rout -exec cat '{}' ';'
+
+      - name: Run RUnit tests
+        if:  env.has_RUnit == 'true'
+        run: |
+          BiocGenerics:::testPackage()
+        shell: Rscript {0}
+
+      - name: Run BiocCheck
+        run: |
+          BiocCheck::BiocCheck(
+              dir('check', 'tar.gz$', full.names = TRUE),
+              `quit-with-status` = TRUE,
+              `no-check-R-ver` = TRUE,
+              `no-check-bioc-help` = TRUE
+          )
+        shell: Rscript {0}
+
+      - name: Test coverage
+        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        run: |
+          covr::codecov()
+        shell: Rscript {0}
+
+      - name: Install package
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        run: R CMD INSTALL .
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-biocversion-RELEASE_3_11-r-4.0.2-results
+          path: check

.gitignore

@@ -1,7 +1,10 @@
+
 inst/doc
 .Rproj.user
 .Rhistory
 .RData
 .DS_Store
 docs
 *.RProj
+doc
+Meta

.travis.yml

@@ -1,13 +1,14 @@
-language: R
-sudo: false
+language: r
+branches:
+  only:
+  - master
+  - dev
+r: bioc-release
+os:
+  - linux
 cache: packages
 warnings_are_errors: false
 r_packages: devtools
-r_github_packages: 
-  - pepkit/pepr
+r_github_packages:
   - databio/simpleCache
-bioc_packages: 
-  - GenomicRanges
-  - BiocStyle
-  - BiocFileCache
-
+  - pepkit/pepr

DESCRIPTION

@@ -1,23 +1,18 @@
 Package: BiocProject
 Title: Bioconductor Management with Portable Encapsulated Project (PEP) Objects
-Version: 0.2
+Version: 0.2.1
 Authors@R: c(person("Michal", "Stolarczyk", email = "[email protected]",role = c("aut", "cre")), 
 	person("Nathan", "Sheffield", email = "[email protected]",role = c("aut")))
 Description: A Bioconductor-oriented project management class. It wraps the
 	generic pepr R package for project metadata. BiocProject allows you to read 
 	in project metadata and data for an entire project with a single line of R code.
-License: GPL-3
+License: BSD_2_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Depends: S4Vectors, pepr, methods
-Suggests:
-    knitr,
-    rmarkdown,
-    testthat,
-    yaml
-Enhances: BiocFileCache, simpleCache, GenomicRanges
+Suggests: testthat, yaml, BiocFileCache, simpleCache, GenomicRanges, knitr, BiocStyle, rmarkdown
 biocViews: DataImport, DataRepresentation
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 URL: https://github.com/pepkit/BiocProject
 BugReports: https://github.com/pepkit/BiocProject
 VignetteBuilder: knitr

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2018
+COPYRIGHT HOLDER: Nathan Sheffield

NAMESPACE

@@ -2,12 +2,12 @@
 
 export(.insertPEP)
 export(.setShowMethod)
-export(.updateList)
+export(.unionList)
 export(BiocProject)
 exportMethods(config)
 exportMethods(getProject)
 exportMethods(is)
-exportMethods(samples)
+exportMethods(sampleTable)
 import(S4Vectors)
 import(methods)
 import(pepr)

NEWS.md

@@ -1,3 +1,13 @@
+
+# BiocProject 0.2.1 - 2019-10-15
+
+## Added
+* added vignette: "Using BiocProject with tximeta"
+
+## Changed 
+* `subproject` argument to `amendments` in `BiocProject` function 
+* `Project` is not added as a first element in `Annotated@metadata`, it is appended to any existing ones
+
 # BiocProject 0.2 - 2019-04-19
 
 ## Added
@@ -71,4 +81,4 @@
 
 * make `BiocProject` class inherit from `pepr::Project` and `base::list`
 * the `initialize` method can read in the data with the provided `func`
-* the object constructor does not fail if the `pepr::Project` object is provided in the `funcArgs` arguments list
+* the object constructor does not fail if the `pepr::Project` object is provided in the `funcArgs` arguments list

R/constants.R

@@ -1,14 +1,10 @@
-# config section names
-# 
-# The YAML file looks like this:
-# 
-# MAIN_SECTION:
-#   FUNCTION_NAME: <name>
-#   FUNCTION_PATH: <path>
-#   FUNCTION_ARGS:
-#       <arg1>: <val1>
-#       <arg2>: <val2>
-MAIN_SECTION = "bioconductor"
+# config section names The YAML
+# file looks like this:
+# MAIN_SECTION: FUNCTION_NAME:
+# <name> FUNCTION_PATH: <path>
+# FUNCTION_ARGS: <arg1>: <val1>
+# <arg2>: <val2>
+BIOC_SECTION = "bioconductor"
 FUNCTION_ARGS = "funcArgs"
 FUNCTION_PATH = "readFunPath"
-FUNCTION_NAME = "readFunName"
+FUNCTION_NAME = "readFunName"