Devel

.Rbuildignore

@@ -7,3 +7,5 @@
 ^Makefile$
 ^coverage\.txt$
 ^coverage\.r$
+^\.github$
+^NEWS$

.github/.gitignore

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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,33 @@
+on:
+  push:
+    branches:
+      - master
+      - devel
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck any::pkgdown
+          needs: check
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/standard-ci-workflow.yml

@@ -22,65 +22,38 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: macOS-latest, r: 'devel'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          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)
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         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:
-          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
+          needs: check
 
-      - name: Install Bioconductor
-        run: |
-          install.packages("BiocManager")
-          BiocManager::install()
-        shell: Rscript {0}
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
-          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}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"warning"'
+          upload-snapshots: true
 
       - 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

DESCRIPTION

@@ -1,16 +1,21 @@
 Package: ribiosExpression
 Type: Package
-Title: Expression Analysis with RibiosExpression
+Title: Data Structures and Utilities for Gene Expression Analysis
 Version: 1.3.5
-Date: 2025-01-30
 Authors@R:
   person(given = "Jitao David",
          family = "Zhang",
-         role = c("aut", "cre", "ctb"),
+         role = c("aut", "cre"),
          email = "jitao_david.zhang@roche.com",
          comment = c(ORCID="0000-0002-3085-0909"))
-Description: Data structures and functions for expression analysis.
-Depends: R (>= 3.5.0)
+Description: Provides data structures and utility functions for gene expression
+    analysis. It includes the DesignContrast class for representing study
+    designs and contrasts used in differential expression analysis, functions
+    for importing and exporting expression data in GCT/CLS formats, tools for
+    probeset summarization and filtering, and interfaces to limma-based
+    differential gene expression workflows. The package works with Biobase
+    ExpressionSet objects and integrates with the limma framework.
+Depends: R (>= 4.4.0)
 Imports:
     methods,
     stats,
@@ -28,9 +33,17 @@ Imports:
     openxlsx
 Suggests:
     testthat,
-    grid
+    grid,
+    BiocStyle,
+    knitr,
+    rmarkdown
 License: GPL-3
 Encoding: UTF-8
+URL: https://github.com/bedapub/ribiosExpression
+BugReports: https://github.com/bedapub/ribiosExpression/issues
+biocViews: GeneExpression, DifferentialExpression, Microarray,
+    DataImport, Visualization
+VignetteBuilder: knitr
 RoxygenNote: 7.3.2
 Collate: 
     'AllClasses.R'

NEWS.md

@@ -0,0 +1,175 @@
+# Changes in ribiosExpression
+
+## Changes in version 1.3.5
+
+### Bioconductor preparation
+- Added `biocViews` to DESCRIPTION.
+- Added BiocStyle vignette.
+- Updated R dependency to >= 4.4.0.
+- Added `@return` tags to all exported functions.
+- Fixed typos in documentation.
+- Replaced `class(x) %in%` with `is.numeric()`.
+- Converted NEWS to NEWS.md format.
+
+## Changes in version 1.0-39
+
+- `parseDesignContrast` adds new parameter `expSampleNames` to allow sample
+  name consistency check with input matrix.
+
+## Changes in version 1.0-34
+
+- `DesignContrast` prints error message if validity is violated.
+- `parseDesignContrastFile` fixes a mistake of assigning group levels.
+- `parseDesignContrastFile` now accepts the `dispLevelStr` option.
+
+## Changes in version 1.0-33
+
+- `parseDesignContrastStr` fixes two errors.
+
+## Changes in version 1.0-32
+
+- Add `DesignContrast` object.
+
+## Changes in version 1.0-29
+
+- Add new functionality in keepMaxMeanProbes.Rscript: able to read from .CHIP
+  file.
+- keepMaxMeanProbes.Rscript now does not depend on the S4 class ExpressionSet
+  anymore, therefore much faster.
+
+## Changes in version 1.0-28
+
+- Debug keepMaxMeanProbes.Rscript: `extname` returns NA if not found, therefore
+  an additional check is added.
+
+## Changes in version 1.0-27
+
+- Function extension in `ChipFetcher2ExpressionSet`: now non-Affymetrix
+  probesets are supported as well.
+
+## Changes in version 1.0-26
+
+- The main body of `readCls` has been moved to `ribiosIO::read_cls`. `readCls`
+  becomes a synonym for compatibility.
+
+## Changes in version 1.0-25
+
+- Improvement in `readCls`: error messages provide more informative details for
+  mal-formatted files.
+
+## Changes in version 1.0-24
+
+- Bug fix in `writeEset`: expression matrix is written without quotes.
+- New script: keepMaxMeanProbes.Rscript filters duplicated genes by taking the
+  one with maximum average expression.
+
+## Changes in version 1.0-23
+
+- Bug fix in `readGct`: if input feature names have duplicates, the exprs
+  matrix row names are changed.
+
+## Changes in version 1.0-22
+
+- Move exprsMat2gct.Rscript to the ribiosIO package.
+- `writeGct` has been refactored for matrix in ribiosIO, and re-implemented as
+  an S4-method for matrix and ExpressionSet.
+
+## Changes in version 1.0-21
+
+- Add exprsMat2gct.Rscript to convert between expression matrix files and GCT
+  files.
+
+## Changes in version 1.0-20
+
+- `ChipFetcher2ExpressionSet`: add option orthologue.
+- `keepMaxStatProbe` uses `function(x) mean(x, na.rm=TRUE)` as default
+  function.
+
+## Changes in version 1.0-19
+
+- limma2gsea.Rscript is updated.
+
+## Changes in version 1.0-18
+
+- Refactor GSEA-related functions that are not dependent on the Biobase data
+  structure to the ribiosGSEA package.
+
+## Changes in version 1.0-17
+
+- limma2gsea.Rscript guarantees no replicated gene symbols after orthologue
+  mapping.
+
+## Changes in version 1.0-16
+
+- Add limma2gsea.Rscript to inst/Rscript.
+
+## Changes in version 1.0-15
+
+- The ribiosAnnotation package has been removed from the dependency list.
+- Add comp_diff.Rscript to inst/Rscript.
+
+## Changes in version 1.0-14
+
+- The deprecation message of `remainHighestVarProbe` and `keepHighestVarProbe`
+  have been updated.
+
+## Changes in version 1.0-13
+
+- The `rowscale` method warns if the input ExpressionSet does not have
+  'lockedEnvironment' as storageMode.
+
+## Changes in version 1.0-12
+
+- Low-level functions for computational drug repositioning refactored into
+  ribiosReposition.
+
+## Changes in version 1.0-11
+
+- Add feature in `summarizeProbesets`: option `keep.featureNames`.
+- Rename and rewrite `sprintGmt` to `formatGmt` as S4 method.
+
+## Changes in version 1.0-10
+
+- Bugfix in `readEset` for numeric column names.
+- Add `annotate` and `reannotate` methods.
+- Add documentation for the `ribios.ExpressionSet` object.
+
+## Changes in version 1.0-9
+
+- Add `kendallW` function and `kendallWmat` S4-method.
+
+## Changes in version 1.0-8
+
+- PCA-related data structures and functions are refactored into the ribiosPCA
+  package.
+
+## Changes in version 1.0-7
+
+- Add `summarizeProbesets` to summarize probesets.
+- NAMESPACE are now explicitly stated.
+
+## Changes in version 1.0-6
+
+- Add dependency on the ribiosAnnotation package.
+- Add `writeEset` and `readEset` functions.
+- `readFKdata` was renamed as `readFKtable`.
+
+## Changes in version 1.0-5
+
+- Add git version control.
+
+## Changes in version 1.0-4
+
+- Move data.frame and matrix functions to the ribiosUtils package.
+
+## Changes in version 1.0-3
+
+- Refactor `read_gct` into ribiosIO for efficiency.
+
+## Changes in version 1.0-2
+
+- Change `keepHighestVarProbe` to more generalized `keepMaxStatProbe`.
+
+## Changes in version 1.0-1
+
+- Remove the path option from the `readGctCls` function.