diff --git a/.github/workflows/R-CMD-build_check.yml b/.github/workflows/R-CMD-build_check.yml index 5df78ab9..464c5bde 100644 --- a/.github/workflows/R-CMD-build_check.yml +++ b/.github/workflows/R-CMD-build_check.yml @@ -4,10 +4,10 @@ on: push: branches: - - master + - devel pull_request: branches: - - master + - devel name: R-CMD-check @@ -22,9 +22,9 @@ jobs: fail-fast: false matrix: config: - - {os: ubuntu-20.04, r: '4.1.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: macOS-latest, r: '4.1.3'} - - {os: windows-latest, r: '4.1.3'} + - {os: ubuntu-20.04, r: '4.3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: '4.3.3'} + - {os: windows-latest, r: '4.3.3'} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true @@ -38,7 +38,7 @@ jobs: with: r-version: ${{ matrix.config.r }} - - uses: r-lib/actions/setup-pandoc@master + - uses: r-lib/actions/setup-pandoc@v2 - name: Query dependencies run: | diff --git a/DESCRIPTION b/DESCRIPTION index 37bf5d79..8c6b41d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -13,7 +13,8 @@ Imports: GenomicRanges, SummarizedExperiment, ggplot2, Suggests: BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, - batchtools, GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11) + batchtools, GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11), + txdbmaker VignetteBuilder: knitr SystemRequirements: systemPipeR can be used to run external command-line software (e.g. short read aligners), but the diff --git a/man/SYSargs2-class.Rd b/man/SYSargs2-class.Rd index fa8113ef..f8f2d151 100644 --- a/man/SYSargs2-class.Rd +++ b/man/SYSargs2-class.Rd @@ -82,7 +82,7 @@ Objects can be created by calls of the form \code{new("SYSargs2", ...)}. \item{\code{modules}:}{Object of class \code{"list"} storing software versions from module system } \item{\code{wf}:}{Object of class \code{"list"} storing data from Workflow \code{CWL parameters} file } \item{\code{clt}:}{Object of class \code{"list"} storing data from each \code{CommandLineTool} - substep in the Workflow or the single code{CommandLineTool} \code{CWL parameters} file } + substep in the Workflow or the single \code{CommandLineTool} \code{CWL parameters} file } \item{\code{yamlinput}:}{Object of class \code{"list"} storing data from \code{input (*.yml)} file } \item{\code{cmdlist}:}{Object of class \code{"list"} storing all command-line used to execute external software } \item{\code{input}:}{Object of class \code{"list"} storing data from each target defined in \code{inputvars} } diff --git a/man/runDiff.Rd b/man/runDiff.Rd index 133a71b0..828d144b 100644 --- a/man/runDiff.Rd +++ b/man/runDiff.Rd @@ -36,7 +36,7 @@ runDiff(args, outfiles=NULL, diffFct, targets, cmp, dbrfilter, ...) targets \code{data.frame} } \item{cmp}{ - code{character matrix} where comparisons are defined in two columns. This matrix should be generated with \code{readComp()} from the targets file. Values used for comparisons need to match those in the \code{Factor} column of the targets file. + \code{character matrix} where comparisons are defined in two columns. This matrix should be generated with \code{readComp()} from the targets file. Values used for comparisons need to match those in the \code{Factor} column of the targets file. } \item{dbrfilter}{ Named vector with filter cutoffs of format \code{c(Fold=2, FDR=1)} where \code{Fold} refers to the fold change cutoff (unlogged) and \code{FDR} to the p-value cutoff. Those values are passed on to the \code{filterDEGs} function. diff --git a/man/seeFastq.Rd b/man/seeFastq.Rd index c1986f97..e1bed717 100644 --- a/man/seeFastq.Rd +++ b/man/seeFastq.Rd @@ -16,7 +16,7 @@ instance, constant length clipping of the reads on either end or variable length clipping on the 3' end maintains this relationship, while variable length clipping on the 5' end without reversing the reads erases it. -The function {seeFastq} computes the summary stats and stores them in a relatively +The function \code{seeFastq} computes the summary stats and stores them in a relatively small list object that can be saved to disk with \code{save()} and reloaded with \code{load()} for later plotting. The argument 'klength' specifies the k-mer length and 'batchsize' the number of reads to random sample from each fastq file. }