Merge branch 'release/3.2.2'

HenrikBengtsson · Feb 18, 2024 · 4e3d784 · 4e3d784
2 parents b6bf76f + 0102e41
commit 4e3d784
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -22,13 +22,13 @@ jobs:
           - {os: macOS-latest,   r: 'devel'    }
           - {os: macOS-latest,   r: 'release'  }
           - {os: macOS-latest,   r: 'oldrel'   }
-          - {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: 'release'  , language: ko,    label: ko    }
-#          - {os: ubuntu-20.04,   r: 'release'  , language: zh_CN, label: zh_CN }
-#          - {os: ubuntu-20.04,   r: 'release'  , language: zh_TW, label: zh_TW }
+          - {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: '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 }}
       R_KEEP_PKG_SOURCE: yes
@@ -43,7 +43,7 @@ jobs:
       _R_CHECK_SUGGESTS_ONLY_: true
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -81,7 +81,7 @@ jobs:
 
       - 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
@@ -8,7 +8,7 @@ jobs:
 
     timeout-minutes: 45
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     name: covr
 
@@ -17,7 +17,7 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      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
@@ -26,7 +26,7 @@ jobs:
       _R_CHECK_CRAN_INCOMING_: false
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -42,7 +42,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: aroma.affymetrix
-Version: 3.2.1
+Version: 3.2.2
 Depends:
   R (>= 3.2.0),
   R.utils (>= 2.9.0),

diff --git a/NEWS b/NEWS
@@ -1,7 +1,14 @@
 Package: aroma.affymetrix
 =========================
 
-Version: 3.2.0-9000 [2019-12-14]
+Version: 3.2.2 [2024-02-18]
+
+DOCUMENTATION:
+
+ * Fix minor Rd help-page issues.
+
+
+Version: 3.2.1 [2022-07-18]
 
 PERFORMANCE:
 

diff --git a/R/AffymetrixCdfFile.R b/R/AffymetrixCdfFile.R
@@ -420,7 +420,6 @@ setMethodS3("hasUnitTypes", "AffymetrixCdfFile", function(this, types, ..., verb
 #
 # \arguments{
 #   \item{units}{The units of interest. If @NULL, all units are considered.}
-#   \item{map}{A @character string specifying the mapping used.}
 #   \item{...}{Not used.}
 # }
 #
@@ -834,7 +833,6 @@ setMethodS3("restruct", "AffymetrixCdfFile", function(this, cdf, ..., verbose=FA
 # @synopsis
 #
 # \arguments{
-#   \item{units}{The units of interest. If @NULL, all units are considered.}
 #   \item{...}{Additional arguments passed to
 #      @see "affxparser::readCdfCellIndices".}
 # }

diff --git a/R/AffymetrixCdfFile.getAlleleProbePairs.R b/R/AffymetrixCdfFile.getAlleleProbePairs.R
@@ -25,7 +25,7 @@
 #
 # \section{Benchmarking}{
 #   On an IBM Thinkpad A31 with 1.8GHz and 1GB RAM:
-#   \itemize{
+#   \describe{
 #    \item{Mapping10K_Xba142}{10208 units & 432964 cells: 11 seconds.}
 #    \item{Mapping50K_Xba240}{58960 SNPs & 589,600 (PMA,PMB) probe pairs: 11 seconds.}
 #   }

diff --git a/R/AffymetrixCdfFile.getAlleleProbePairs3.R b/R/AffymetrixCdfFile.getAlleleProbePairs3.R
@@ -25,7 +25,7 @@
 #
 # \section{Benchmarking}{
 #   On an IBM Thinkpad A31 with 1.8GHz and 1GB RAM:
-#   \itemize{
+#   \describe{
 #    \item{Mapping10K_Xba142}{10208 units & 432964 cells: 11 seconds.}
 #    \item{Mapping50K_Xba240}{58960 SNPs & 589,600 (PMA,PMB) probe pairs: 11 seconds.}
 #   }

diff --git a/R/AffymetrixCelFile.PLOT.R b/R/AffymetrixCelFile.PLOT.R
@@ -313,8 +313,8 @@ setMethodS3("smoothScatterMvsA", "AffymetrixCelFile", function(this, reference,
 #   \item{x}{The other variable.  A @double @vector.}
 #   \item{indices}{Indices of the probe signals to be plotted.}
 #   \item{pch}{The plot symbol.}
-#   \item{xlim,ylim}{The range of the x and the y axes.}
-#   \item{xlab,ylab}{The labels on the x and the y axes.}
+#   \item{ylim}{The range of the y axes.}
+#   \item{ylab}{The labels on the y axes.}
 #   \item{...}{Additional arguments passed to @see "graphics::plot".}
 #   \item{annotate}{If @TRUE, the plot is annotated with information about
 #     the data plotted, otherwise not.}
@@ -495,7 +495,6 @@ setMethodS3("image270", "AffymetrixCelFile", function(this, xrange=c(0,Inf), yra
 #      \code{stdvs}, or \code{pixels}.}
 #   \item{zoom}{A @numeric scale factor in (0,+Inf) for resizing the
 #     imaging. If \code{1}, no resizing is done.}
-#   \item{palette}{An optional @vector of color code.}
 #   \item{...}{Additional arguments passed to
 #      @seemethod "readRawDataRectangle" and more function.}
 #   \item{readRectFcn}{A @function taking arguments 'xrange' and 'yrange',

diff --git a/R/AffymetrixCelSet.R b/R/AffymetrixCelSet.R
@@ -1,5 +1,6 @@
 ###########################################################################/**
 # @RdocClass AffymetrixCelSet
+# @alias nbrOfArrays.AffymetrixCelSet
 #
 # @title "The AffymetrixCelSet class"
 #
@@ -450,7 +451,7 @@ setMethodS3("findByName", "AffymetrixCelSet", function(static, ..., chipType=NUL
 
   # Arguments 'paths':
   if (is.null(paths)) {
-    paths <- eval(formals(findByName.AffymetrixCelSet)[["paths"]])
+    paths <- eval(formals(findByName.AffymetrixCelSet)[["paths"]], enclos = baseenv())
   }
 
   # Call the "next" method

diff --git a/R/AffymetrixCnChpSet.R b/R/AffymetrixCnChpSet.R
@@ -103,7 +103,7 @@ setMethodS3("findByName", "AffymetrixCnChpSet", function(static, ..., paths="chp
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # Arguments 'paths':
   if (is.null(paths)) {
-    paths <- eval(formals(findByName.AffymetrixCnChpSet)[["paths"]])
+    paths <- eval(formals(findByName.AffymetrixCnChpSet)[["paths"]], enclos = baseenv())
   }
 
   NextMethod("findByName", paths=paths)

diff --git a/R/AromaChipTypeAnnotationFile.R b/R/AromaChipTypeAnnotationFile.R
@@ -229,8 +229,6 @@ setMethodS3("getDefaultExtension", "AromaChipTypeAnnotationFile", function(stati
 # @synopsis
 #
 # \arguments{
-#  \item{chipType}{A @character string.}
-#  \item{tags}{An optional @character @vector of tags.}
 #  \item{...}{Additional arguments.}
 # }
 #

diff --git a/R/AromaUnitTabularBinaryFile.AFFX.R b/R/AromaUnitTabularBinaryFile.AFFX.R
@@ -86,11 +86,6 @@ setMethodS3("getCdf", "AromaUnitTabularBinaryFile", function(this, ..., force=FA
 # \arguments{
 #   \item{cdf}{The @see "AffymetrixCdfFile" used as a template and from
 #      which the (full) chip type is taken.}
-#   \item{path}{The path where to store the new file.}
-#   \item{tags}{A @character @vector of optional tags appended to
-#      the filename.}
-#   \item{footer}{A nested named @list structure of additional attributes
-#      that are saved in the file footer after the mandatory ones.}
 #   \item{...}{Additional arguments passed to \code{allocate()} of
 #      @see "aroma.core::AromaTabularBinaryFile".}
 # }

diff --git a/R/ArrayExplorer.R b/R/ArrayExplorer.R
@@ -180,8 +180,6 @@ setMethodS3("getArraysOfInput", "ArrayExplorer", function(this, ...) {
 # @synopsis
 #
 # \arguments{
-#   \item{arrays}{A @character (or @integer) @vector of arrays to be
-#      considered. If @NULL, all arrays of the data set are considered.}
 #   \item{...}{Not used.}
 # }
 #

diff --git a/R/BackgroundCorrection.R b/R/BackgroundCorrection.R
@@ -69,9 +69,6 @@ setMethodS3("getParameters", "BackgroundCorrection", function(this, ...) {
 #
 # \arguments{
 #   \item{...}{Not used.}
-#   \item{force}{If @TRUE, data already processed is re-processed,
-#       otherwise not.}
-#   \item{verbose}{See @see "R.utils::Verbose".}
 # }
 #
 # \value{

diff --git a/R/ChipEffectSet.R b/R/ChipEffectSet.R
@@ -64,7 +64,7 @@ setMethodS3("findByName", "ChipEffectSet", function(static, ..., paths="plmData(
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # Arguments 'paths':
   if (is.null(paths)) {
-    paths <- eval(formals(findByName.ChipEffectSet)[["paths"]])
+    paths <- eval(formals(findByName.ChipEffectSet)[["paths"]], enclos = baseenv())
   }
 
   NextMethod("findByName", paths=paths)

diff --git a/R/CnPlm.R b/R/CnPlm.R
@@ -36,7 +36,7 @@
 # \section{Requirements}{
 #   Classes inheriting from this @see "R.oo::Interface" must provide the
 #   following fields, in addition to the ones according to @see "SnpPlm":
-#   \itemize{
+#   \describe{
 #    \item{combineAlleles}{A @logical indicating if total or allele-specific
 #      copy numbers should be estimated according to the above averaging.}
 #   }

diff --git a/R/CnagCfhFile.R b/R/CnagCfhFile.R
@@ -356,8 +356,6 @@ setMethodS3("getChipType", "CnagCfhFile", function(this, ...) {
 #
 # \arguments{
 #   \item{units}{The units to be read. If @NULL, all units are read.}
-#   \item{cdf}{An alternative CDF structure to be used.  This overrides
-#     the \code{units} arguments.}
 #   \item{...}{Arguments passed to \code{getUnits()} of the
 #     @see "AffymetrixCdfFile" class (if \code{cdf} was not specified),
 #     but also to the @see "affxparser::readCelUnits" methods.}

diff --git a/R/CnagCfhSet.R b/R/CnagCfhSet.R
@@ -302,7 +302,7 @@ setMethodS3("findByName", "CnagCfhSet", function(static, ..., paths="cnagData(|,
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # Arguments 'paths':
   if (is.null(paths)) {
-    paths <- eval(formals(findByName.CnagCfhSet)[["paths"]])
+    paths <- eval(formals(findByName.CnagCfhSet)[["paths"]], enclos = baseenv())
   }
 
   NextMethod("findByName", paths=paths)

diff --git a/R/DChipDcpSet.R b/R/DChipDcpSet.R
@@ -103,7 +103,7 @@ setMethodS3("findByName", "DChipDcpSet", function(static, ..., paths=c("rawData(
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # Arguments 'paths':
   if (is.null(paths)) {
-    paths <- eval(formals(findByName.DChipDcpSet)[["paths"]])
+    paths <- eval(formals(findByName.DChipDcpSet)[["paths"]], enclos = baseenv())
   }
 
   NextMethod("findByName", paths=paths)

diff --git a/R/DChipSnpInformation.R b/R/DChipSnpInformation.R
@@ -94,14 +94,9 @@ setMethodS3("findByChipType", "DChipSnpInformation", function(static, chipType,
 #
 # \arguments{
 #  \item{chipType}{A @character string.}
-#  \item{rootPath}{A @character string specifying the root path, i.e.
-#    the annotation directory.}
 #  \item{version}{An optional @character string specifying the version
 #    string, if more than one version is available.}
-#  \item{pattern}{An optional filename pattern used to locate the
-#    dChip genome file.  If @NULL, a default pattern is used.}
-#  \item{...}{Not used.}
-#  \item{verbose}{See @see "R.utils::Verbose".}
+#  \item{...}{Additional arguments passed to @seemethod "findByChipType".}
 # }
 #
 # \value{

diff --git a/R/ExonChipEffectFile.R b/R/ExonChipEffectFile.R
@@ -59,8 +59,6 @@ setMethodS3("getParameters", "ExonChipEffectFile", function(this, ...) {
 # @synopsis
 #
 # \arguments{
-#  \item{units}{Unit indices to be retrieved.
-#               If @NULL, all units are considered.}
 #  \item{...}{Additional arguments passed to \code{getCellIndices()}
 #             of @see "ChipEffectFile".}
 #  \item{unlist}{If @TRUE, the cell indices are returned as a @vector.}

diff --git a/R/FirmaModel.R b/R/FirmaModel.R
@@ -263,7 +263,6 @@ setMethodS3("getFirmaScores", "FirmaModel", function(this, ...) {
 #
 # \arguments{
 #   \item{...}{Not used.}
-#   \item{verbose}{A @logical or a @see "R.utils::Verbose".}
 # }
 #
 # \value{

diff --git a/R/FragmentEquivalentClassNormalization.R b/R/FragmentEquivalentClassNormalization.R
@@ -687,7 +687,9 @@ setMethodS3("normalizeOneArrayVector", "FragmentEquivalentClassNormalization", f
     delta <- deltas[[ee]]
 
     # Identify the class IDs, e.g. 0x14
-    classIds <- sapply(names(delta), FUN=function(x) eval(parse(text=x)))
+    classIds <- sapply(names(delta), FUN=function(x) {
+      eval(parse(text = x), enclos = baseenv())
+    })
 
     # Normalize on log2-scale?
     if (log2) {

diff --git a/R/SmoothMultiarrayModel.fit.R b/R/SmoothMultiarrayModel.fit.R
@@ -14,9 +14,6 @@ setMethodS3("getFitUnitGroupFunction", "SmoothMultiarrayModel", abstract=TRUE, p
 # @synopsis
 #
 # \arguments{
-#   \item{data}{A @data.frame with columns \code{M} (log-ratio) and
-#      \code{x} (locus position).
-#   }
 #   \item{chromosome}{An @integer specifying the index of the chromosome to
 #      be fitted.}
 #   \item{...}{Additional arguments passed down to the internal fit function.}

diff --git a/R/SnpPlm.R b/R/SnpPlm.R
@@ -23,7 +23,7 @@
 # \section{Requirements}{
 #   Classes inheriting from this @see "R.oo::Interface" must provide the
 #   following fields:
-#   \itemize{
+#   \describe{
 #    \item{mergeStrands}{A @logical value indicating if strands should be
 #       merged or not.}
 #   }

diff --git a/R/Transform.R b/R/Transform.R
@@ -31,7 +31,6 @@ setMethodS3("getOutputFiles", "Transform", function(this, pattern=NULL, ...) {
 #
 # \arguments{
 #   \item{...}{Not used.}
-#   \item{force}{If @TRUE, any in-memory cached results are ignored.}
 #   \item{verbose}{See @see "R.utils::Verbose".}
 # }
 #

diff --git a/R/UgpGenomeInformation.R b/R/UgpGenomeInformation.R
@@ -68,9 +68,7 @@ setMethodS3("findByChipType", "UgpGenomeInformation", function(static, ...) {
 # \arguments{
 #  \item{chipType}{A @character string.}
 #  \item{tags}{...}
-#  \item{version}{An optional @character string specifying the version
-#    string, if more than one version is available.}
-#  \item{...}{Not used.}
+#  \item{...}{Additional arguments passed to @see "UgpGenomeInformation".}
 #  \item{verbose}{See @see "R.utils::Verbose".}
 # }
 #

diff --git a/R/fitPlasqUnit.R b/R/fitPlasqUnit.R
@@ -17,7 +17,7 @@ plasqGaussian <- function(link="exponential") {
   if (!is.character(linktemp)) {
     linktemp <- deparse(linktemp)
     if (linktemp == "link")
-      linktemp <- eval(link)
+      linktemp <- eval(link, enclos = baseenv())
   }
 
   if (linktemp == "exponential") {

diff --git a/R/setupExampleData.R b/R/setupExampleData.R
@@ -1,6 +1,7 @@
 ###########################################################################/**
 # @set class=AromaAffymetrix
 # @RdocMethod setupExampleData
+# @alias setupExampleData
 #
 # @title "Setups example data in the current directory"
 #