Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:38 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 245/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BSgenome 1.72.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the BSgenome package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BSgenome.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: BSgenome |
Version: 1.72.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BSgenome_1.72.0.tar.gz |
StartedAt: 2024-08-11 21:12:45 -0400 (Sun, 11 Aug 2024) |
EndedAt: 2024-08-11 21:19:22 -0400 (Sun, 11 Aug 2024) |
EllapsedTime: 397.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BSgenome.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BSgenome_1.72.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BSgenome.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘BSgenome/DESCRIPTION’ ... OK * this is package ‘BSgenome’ version ‘1.72.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'Biostrings', 'BiocIO', 'rtracklayer' 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 ‘BSgenome’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: R 1.3Mb extdata 5.3Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * 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 ':::' calls which should be '::': ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’ ‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’ 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘OnDiskLongTable_old’ ‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’ ‘getBatchesByOverlapsFromOnDiskLongTable’ ‘getBatchesBySeqnameFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’ ‘getRowsByIdFromOnDiskLongTable’ ‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’ ‘saveAsOnDiskLongTable_old’ ‘saveRowidsForOnDiskLongTable_old’ ‘spatialIndex’ ‘writeOnDiskLongTable’ ‘writeOnDiskLongTableRowids’ Undocumented S4 classes: ‘OnDiskLongTable_old’ ‘GRanges_OR_NULL’ ‘MaskedBSgenome’ ‘OnDiskLongTable’ Undocumented S4 methods: generic '[' and siglist 'XStringSet,GRangesList,ANY,ANY' generic '[' and siglist 'XStringSet,GenomicRanges,ANY,ANY' generic '[[' and siglist 'BSgenome,ANY,ANY' generic 'batchsizes' and siglist 'OnDiskLongTable' generic 'blocksizes' and siglist 'OnDiskLongTable_old' generic 'breakpoints' and siglist 'OnDiskLongTable' generic 'breakpoints' and siglist 'OnDiskLongTable_old' generic 'coerce' and siglist 'RdsCollection,RdsNamedSequences' generic 'dim' and siglist 'OnDiskLongTable' generic 'dim' and siglist 'OnDiskLongTable_old' generic 'dimnames' and siglist 'OnDiskLongTable' generic 'dimnames' and siglist 'OnDiskLongTable_old' generic 'dimnames' and siglist 'XtraSNPlocs' generic 'extractAt' and siglist 'BSgenome' generic 'length' and siglist 'OnDiskNamedSequences' generic 'names' and siglist 'FastaNamedSequences' generic 'names' and siglist 'TwobitNamedSequences' generic 'seqinfo' and siglist 'FastaNamedSequences' generic 'seqinfo' and siglist 'RdaNamedSequences' generic 'seqinfo' and siglist 'RdsNamedSequences' generic 'seqinfo' and siglist 'TwobitNamedSequences' generic 'seqnames' and siglist 'OnDiskNamedSequences' generic 'show' and siglist 'OnDiskLongTable' generic 'show' and siglist 'OnDiskLongTable_old' generic 'show' and siglist 'OnDiskNamedSequences' generic 'spatialIndex' and siglist 'OnDiskLongTable' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SNPlocs-class 37.662 3.925 42.787 BSgenome-utils 19.984 0.380 20.367 BSgenomeViews-class 12.802 4.017 16.824 BSgenome-class 11.942 0.879 12.836 injectSNPs 8.996 2.387 11.467 XtraSNPlocs-class 5.661 0.408 6.095 getSeq-methods 5.329 0.684 6.014 export-methods 4.245 0.904 5.149 bsapply 4.572 0.420 5.001 * 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: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/BSgenome.Rcheck/00check.log’ for details.
BSgenome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BSgenome ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘BSgenome’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BSgenome)
BSgenome.Rcheck/BSgenome-Ex.timings
name | user | system | elapsed | |
BSgenome-class | 11.942 | 0.879 | 12.836 | |
BSgenome-utils | 19.984 | 0.380 | 20.367 | |
BSgenomeViews-class | 12.802 | 4.017 | 16.824 | |
SNPlocs-class | 37.662 | 3.925 | 42.787 | |
XtraSNPlocs-class | 5.661 | 0.408 | 6.095 | |
available.genomes | 0.546 | 0.152 | 0.939 | |
bsapply | 4.572 | 0.420 | 5.001 | |
export-methods | 4.245 | 0.904 | 5.149 | |
getSeq-methods | 5.329 | 0.684 | 6.014 | |
injectSNPs | 8.996 | 2.387 | 11.467 | |