Merge branch 'release/1.41.1'

ccagc · Jul 20, 2024 · ca72274 · ca72274
2 parents b8cc034 + 2cd55c8
commit ca72274
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diff --git a/.github/.travis.yml b/.github/.travis.yml
diff --git 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 }}
 
@@ -16,99 +16,86 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: release  }
-          - {os: macOS-latest,   r: devel    }
-#          - {os: macOS-latest,   r: release  } # QDNAseq.hg19, QDNAseq.mm10 not available
-          - {os: ubuntu-20.04,   r: devel    }
-          - {os: ubuntu-20.04,   r: release  }
-          - {os: ubuntu-20.04,   r: oldrel   }
-          - {os: ubuntu-20.04,   r: oldrel-1 }
-          - {os: ubuntu-20.04,   r: oldrel-2 }
-          - {os: ubuntu-20.04,   r: oldrel-3 }
-
+#          - {os: windows-latest, r: 'devel'    }
+#          - {os: windows-latest, r: 'release'  }
+#          - {os: windows-latest, r: 'oldrel'   }
+#          - {os: macOS-14,       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: '3.5'      }
+#          - {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__/focal/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_S3_METHODS_SHOW_POSSIBLE_ISSUES_: true
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-tinytex@v1
-
+      - uses: r-lib/actions/setup-tinytex@v2
       - name: Install additional LaTeX packages
         run: |
           tlmgr --version
           ## Additional LaTeX packages needed by BiocStyle:
           tlmgr install ae bera bibleref caption changepage enumitem everysel fancyhdr footmisc grfext hobsub marginfix mathtools nowidow parnotes parskip placeins preprint ragged2e setspace soul titlesec xstring
           tlmgr list --only-installed
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-
-      - name: Query R package dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - 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 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'
-        run: |
-          remotes::install_cran("rcmdcheck")
-          library(rcmdcheck)  ## triggers an error, if installation failed
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - name: Session info
         run: |
           options(width = 100)
           capabilities()
+          parallelly::availableCores(which = "all")
           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: |
           skip_vignettes <- (getRversion() < "4.0.0")
-          rcmdcheck::rcmdcheck(build_args = if (skip_vignettes) "--no-build-vignettes", args = c("--no-manual", "--as-cran", if (skip_vignettes) "--ignore-vignettes"), error_on = "warning", check_dir = "check")
+          rcmdcheck::rcmdcheck(
+            build_args = if (skip_vignettes) "--no-build-vignettes" else "--compact-vignettes=both",
+            args = c("--no-manual", "--as-cran", if (skip_vignettes) "--ignore-vignettes"),
+            error_on = "error",
+            check_dir = "check"
+          )
         shell: Rscript {0}
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        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
@@ -4,11 +4,11 @@ name: covr
 
 jobs:
   covr:
-    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"    
 
     timeout-minutes: 45
-    
-    runs-on: ubuntu-20.04
+
+    runs-on: ubuntu-latest
 
     name: covr
 
@@ -17,51 +17,34 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/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_CRAN_INCOMING_: false
+      _R_CHECK_SUGGESTS_ONLY_: true
+      _R_CHECK_THINGS_IN_TEMP_DIR_: true
+      RCMDCHECK_ERROR_ON: note
+      ## Specific to futures
+      R_FUTURE_RNG_ONMISUSE: error
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: release
+          use-public-rspm: true
 
-      - 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
-        uses: actions/cache@v1
+      - 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
-        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}
+          extra-packages: |
+            any::sessioninfo
+            any::covr
+          needs: check
 
       - name: Session info
         run: |
@@ -76,7 +59,7 @@ jobs:
           ##    https://app.codecov.io/gh/<org>/<repo>/settings
           ## 2. Set 'CODECOV_TOKEN' in GitHub Secrets:
           ##    https://github.com/<org>/<repo>/settings/environments/
-          coverage <- covr::package_coverage()
+          coverage <- covr::package_coverage(quiet = FALSE)
           print(coverage)
           covr::codecov(coverage = coverage, token="${{secrets.CODECOV_TOKEN}}")
         shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: QDNAseq
-Version: 1.41.0
+Version: 1.41.1
 Title: Quantitative DNA Sequencing for Chromosomal Aberrations
 Depends: R (>= 3.1.0)
 Imports:
@@ -44,4 +44,4 @@ biocViews: CopyNumberVariation, DNASeq, Genetics, GenomeAnnotation,
 License: GPL
 URL: https://github.com/ccagc/QDNAseq
 BugReports: https://github.com/ccagc/QDNAseq/issues
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,34 @@
-# Version 1.35.0 [2022-11-01]
+# Version 1.41.1 [2024-07-20]
+
+## Miscellaneous
+
+ * Fix markup typo in `help("exportBins")`.
+
+ * Add package test for `poolRuns()`.
+
+
+# Version 1.40.0 [2024-05-01]
 
 ## Release
 
- * The version number was bumped for the Bioconductor devel version,
-   which is now Bioconductor 3.17 for R-devel.
+ * The version number was bumped for the Bioconductor release version,
+     which is now Bioconductor 3.19 for R (>= 4.4.0).
+
+
+# Version 1.38.0 [2023-10-25]
+
+## Release
+
+ * The version number was bumped for the Bioconductor release version,
+   which is now Bioconductor 3.18 for R (>= 4.3.1).
+
+
+# Version 1.36.0 [2023-04-26]
+
+## Release
+
+ * The version number was bumped for the Bioconductor release version,
+   which is now Bioconductor 3.17 for R (>= 4.3.0).
 
 
 # Version 1.34.0 [2022-11-01]
@@ -549,5 +574,3 @@
 ## Release
 
  * Initial release as part of Bioconductor 2.14.
-
-
diff --git a/R/exportBins.R b/R/exportBins.R
@@ -25,7 +25,7 @@
 #     \item{filter}{If @TRUE, bins are filtered, otherwise not.}
 #     \item{logTransform}{If @TRUE (default), exported data will be log2
 #         transformed for \code{format} in \code{"tsv"}, \code{"igv"}, and
-#         \code{"bed"}.  This argument is ignored if code{type = "calls"}.}
+#         \code{"bed"}.  This argument is ignored if \code{type = "calls"}.}
 #     \item{digits}{The number of digits to round to. If not @numeric, no
 #         no rounding is performed.}
 #     \item{chromosomeReplacements}{A named character vector of chromosome name

diff --git a/R/poolRuns.R b/R/poolRuns.R
@@ -30,7 +30,7 @@
 # readCounts <- LGG150
 # # Note: the following command will "pool" data from a single run, which
 # # does not really make sense:
-# pooledReadCounts <- poolRuns(readCounts, "LGG150")
+# pooledReadCounts <- poolRuns(readCounts, samples = "LGG150")
 # }
 #
 # @author "IS"