############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GenomicAlignments.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GenomicAlignments_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicAlignments.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘GenomicAlignments/DESCRIPTION’ ... OK * this is package ‘GenomicAlignments’ version ‘1.43.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'SummarizedExperiment', 'Biostrings', 'Rsamtools' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GenomicAlignments’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’ ‘Rsamtools’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Cannot process chunk/lines: version 1.18.0 Cannot process chunk/lines: No NEW FEATURES or SIGNIFICANT USER-VISIBLE CHANGES or BUG FIXES since Cannot process chunk/lines: version 1.16.0 Cannot process chunk/lines: The first version of GenomicAlignments was included in Bioconductor 2.14. Cannot process chunk/lines: The package was created from existing code in IRanges, ShortRead, Cannot process chunk/lines: Rsamtools and GenomicRanges. * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘Rsamtools:::.BamViews_delegate’ ‘Rsamtools:::.findMateWithinGroups’ ‘Rsamtools:::.load_bamcols_from_scanBam_res’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) coordinate-mapping-methods.Rd:69-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:84-101: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:102-114: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:115-120: Lost braces in \itemize; meant \describe ? checkRd: (-1) findSpliceOverlaps-methods.Rd:99-102: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) findSpliceOverlaps-methods.Rd:103-105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) findSpliceOverlaps-methods.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) intra-range-methods.Rd:52-60: Lost braces 52 | \item(){ | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: GAlignmentPairs-class.Rd: seqlevels, GRanges, GRangesList GAlignments-class.Rd: seqlevels, GRanges, GRangesList GAlignmentsList-class.Rd: GRanges, GRangesList coordinate-mapping-methods.Rd: GenomicRanges-class findCompatibleOverlaps-methods.Rd: GRangesList findOverlaps-methods.Rd: GRangesList, GRanges-class, GRangesList-class intra-range-methods.Rd: GRanges, GRangesList readGAlignments.Rd: scanBam, ScanBamParam-class sequenceLayer.Rd: XStringSet stackStringsFromGAlignments.Rd: scanBam, ScanBamParam summarizeOverlaps-methods.Rd: BamFile, ScanBamParam, register Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed readGAlignments 15.507 0.786 16.245 junctions-methods 11.831 0.311 12.179 summarizeOverlaps-methods 6.376 2.409 8.107 sequenceLayer 6.218 1.306 7.525 coordinate-mapping-methods 6.944 0.104 7.057 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GenomicAlignments.Rcheck/00check.log’ for details.