Merge branch 'release/3.2.1'

.Rbuildignore

@@ -4,6 +4,7 @@
 ^.svn
 ^.git
 ^.make
+^.local
 INSTALL[.]md
 OVERVIEW[.]md
 README[.]md

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,87 @@
+on: [push, pull_request]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"    
+
+    timeout-minutes: 30
+
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.label }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'devel'    }
+          - {os: windows-latest, r: 'release'  }
+          - {os: windows-latest, r: 'oldrel'   }
+          - {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 }
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      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
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          capabilities()
+          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: |
+          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@v3
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/covr.yaml

@@ -0,0 +1,82 @@
+on: [push]
+
+name: covr
+
+jobs:
+  covr:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"    
+
+    timeout-minutes: 45
+
+    runs-on: ubuntu-20.04
+
+    name: covr
+
+    strategy:
+      fail-fast: false
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      ## R CMD check
+      _R_CHECK_LENGTH_1_CONDITION_: true
+      _R_CHECK_LENGTH_1_LOGIC2_: true
+      _R_CHECK_MATRIX_DATA_: true
+      _R_CHECK_CRAN_INCOMING_: false
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v3
+        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}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: |
+          ## 1. Get 'Repository Upload Token' from Codecov:
+          ##    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()
+          print(coverage)
+          covr::codecov(coverage = coverage, token="${{secrets.CODECOV_TOKEN}}")
+        shell: Rscript {0}

.gitignore

@@ -6,4 +6,5 @@
 *Data
 .Rproj.user
 .make
+.local
 revdep/

DESCRIPTION

@@ -1,20 +1,20 @@
 Package: aroma.affymetrix
-Version: 3.2.0
+Version: 3.2.1
 Depends:
   R (>= 3.2.0),
   R.utils (>= 2.9.0),
   aroma.core (>= 3.2.0)
 Imports:
   methods,
   R.methodsS3 (>= 1.7.1),
-  R.oo (>= 1.21.0),
-  R.cache (>= 0.13.0),
-  R.devices (>= 2.16.0),
+  R.oo (>= 1.23.0),
+  R.cache (>= 0.14.0),
+  R.devices (>= 2.16.1),
   R.filesets (>= 2.13.0),
   aroma.apd (>= 0.6.0),
   MASS,
   splines,
-  matrixStats (>= 0.54.0),
+  matrixStats (>= 0.55.0),
   listenv,
   future
 Suggests:
@@ -59,4 +59,3 @@ URL: https://www.aroma-project.org/, https://github.com/HenrikBengtsson/aroma.af
 BugReports: https://github.com/HenrikBengtsson/aroma.affymetrix/issues
 LazyLoad: TRUE
 biocViews: Infrastructure, ProprietaryPlatforms, ExonArray, Microarray, OneChannel, GUI, DataImport, DataRepresentation, Preprocessing, QualityControl, Visualization, ReportWriting, aCGH, CopyNumberVariants, DifferentialExpression, GeneExpression, SNP, Transcription
-

NAMESPACE

@@ -1,7 +1,7 @@
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # IMPORTS
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-importFrom("R.methodsS3", "throw")
+importFrom("R.oo", "throw")
 importFrom("R.methodsS3", "setMethodS3")
 importFrom("R.oo", "setConstructorS3")
 importFrom("R.oo", "extend")
@@ -206,6 +206,7 @@ importFrom("matrixStats", "rowAnys")
 importFrom("matrixStats", "rowMads")
 importFrom("matrixStats", "rowMedians") ## Multi-sources: matrixStats, Biobase
 importFrom("matrixStats", "rowSds")
+importFrom("matrixStats", "rowSums2")
 importFrom("methods", "new")
 importFrom("R.cache", "getChecksum") ## Multi-sources: R.cache, R.filesets
 importFrom("R.cache", "loadCache")
@@ -301,7 +302,6 @@ importFrom("R.utils", "CmdArgsFunction")
 ## importFrom("base", "readLines") ## Multi-sources: R.filesets, base
 ## importFrom("base", "gc") ## Multi-sources: R.oo, base
 ## importFrom("base", "warnings") ## Multi-sources: R.utils, base
-## importFrom("inherits", "inherits") ## Multi-sources: R.utils, base
 
 ## Importing other objects
 importFrom("aroma.core", "aromaSettings")

NEWS

@@ -1,7 +1,16 @@
 Package: aroma.affymetrix
 =========================
 
-Version: 3.2.0 [2018-06-22]
+Version: 3.2.0-9000 [2019-12-14]
+
+PERFORMANCE:
+
+ * MEMORY: Some parameter estimates where pre-allocated as logical (NA)
+   values, instead of as numeric (NA_real_) values, which would result in
+   an unnecessary coercion from logical to numeric.
+
+
+Version: 3.2.0 [2019-06-22]
 
 NEW FEATURES:
 

R/999.package.R

@@ -31,7 +31,7 @@
 #   The releases of this package is licensed under
 #   LGPL version 2.1 or newer.
 #
-#   The development code of the packages is under a private licence
+#   The development code of the packages is under a private license
 #   (where applicable) and patches sent to the author fall under the
 #   latter license, but will be, if incorporated, released under the
 #   "release" license above.

R/AffineCnPlm.R

@@ -12,7 +12,7 @@
 # \arguments{
 #   \item{...}{Arguments passed to @see "AffineSnpPlm".}
 #   \item{combineAlleles}{If @FALSE, allele A and allele B are treated
-#      seperately, otherwise together.}
+#      separately, otherwise together.}
 # }
 #
 # \section{Fields and Methods}{

R/AffinePlm.R

@@ -7,7 +7,7 @@
 # \description{
 #  @classhierarchy
 #
-#  This class represents affine model in Bengtsson \& Hossjer (2006).
+#  This class represents affine model in Bengtsson & Hossjer (2006).
 # }
 #
 # @synopsis
@@ -44,7 +44,7 @@
 # @author "HB"
 #
 # \references{
-#   Bengtsson \& Hossjer (2006). \cr
+#   Bengtsson & Hossjer (2006). \cr
 # }
 #*/###########################################################################
 setConstructorS3("AffinePlm", function(..., background=TRUE) {

R/AffymetrixCdfFile.computeAffinities.R

@@ -193,7 +193,7 @@ setMethodS3("computeAffinities", "AffymetrixCdfFile", function(this, safe=TRUE,
   dimension <- NULL; # Not needed anymore
 
   # Allocate empty vector of affinities
-  naValue <- as.double(NA)
+  naValue <- NA_real_
   affinities <- rep(naValue, times=nbrOfCells)
 
   if(isPMMMChip) {
@@ -259,7 +259,7 @@ setMethodS3("computeAffinities", "AffymetrixCdfFile", function(this, safe=TRUE,
     # new code to compute affinities from the MM probes
     # (antigenomic or whatever) on PM-only arrays  -- MR 2009-03-28
     # ---------------------------------------------------------
-    naValue <- as.double(NA)
+    naValue <- NA_real_
     apm <- rep(naValue, times=nbrOfSequences)
 
     indexAll <- sequenceInfo$cell
@@ -465,7 +465,7 @@ setMethodS3("computeAffinitiesByACS", "AffymetrixCdfFile", function(this, ..., m
   verbose && enter(verbose, "Calculating chip-type specific gcRMA probe affinities")
 
   # Allocate empty vector of affinities
-  naValue <- as.double(NA)
+  naValue <- NA_real_
   affinities <- rep(naValue, times=nbrOfCells)
 
   if (method == "v1") {