Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:05 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 1140/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LymphoSeq 1.37.0 (landing page) David Coffey
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the LymphoSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LymphoSeq.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: LymphoSeq |
Version: 1.37.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LymphoSeq_1.37.0.tar.gz |
StartedAt: 2025-08-03 23:49:28 -0400 (Sun, 03 Aug 2025) |
EndedAt: 2025-08-03 23:53:13 -0400 (Sun, 03 Aug 2025) |
EllapsedTime: 225.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LymphoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings LymphoSeq_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/LymphoSeq.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘LymphoSeq/DESCRIPTION’ ... OK * this is package ‘LymphoSeq’ version ‘1.37.0’ * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘LymphoSeq’ can be installed ... OK * checking installed package size ... INFO installed size is 5.7Mb sub-directories of 1Mb or more: extdata 5.5Mb * 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 ... OK * 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 ... OK * 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 cloneTrack 21.732 1.588 23.358 productiveSeq 17.565 1.382 18.947 * 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: OK
LymphoSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL LymphoSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘LymphoSeq’ ... ** this is package ‘LymphoSeq’ version ‘1.37.0’ ** 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 (LymphoSeq)
LymphoSeq.Rcheck/LymphoSeq-Ex.timings
name | user | system | elapsed | |
alignSeq | 0.701 | 0.008 | 0.718 | |
bhattacharyyaCoefficient | 0.148 | 0.006 | 0.163 | |
bhattacharyyaMatrix | 0.157 | 0.003 | 0.160 | |
chordDiagramVDJ | 0.819 | 0.039 | 0.857 | |
clonalRelatedness | 0.717 | 0.000 | 0.378 | |
clonality | 0.052 | 0.002 | 0.053 | |
cloneTrack | 21.732 | 1.588 | 23.358 | |
commonSeqs | 0.141 | 0.025 | 0.166 | |
commonSeqsBar | 0.807 | 0.176 | 0.983 | |
commonSeqsPlot | 0.345 | 0.056 | 0.401 | |
commonSeqsVenn | 0.692 | 0.101 | 0.787 | |
differentialAbundance | 2.581 | 0.113 | 2.695 | |
exportFasta | 0.203 | 0.008 | 0.212 | |
geneFreq | 0.936 | 0.009 | 0.944 | |
lorenzCurve | 1.569 | 0.029 | 1.598 | |
mergeFiles | 0.073 | 0.000 | 0.072 | |
pairwisePlot | 0.639 | 0.017 | 0.656 | |
phyloTree | 2.999 | 0.064 | 3.065 | |
productive | 0.058 | 0.002 | 0.059 | |
productiveSeq | 17.565 | 1.382 | 18.947 | |
readImmunoSeq | 0.041 | 0.003 | 0.044 | |
removeSeq | 0.052 | 0.002 | 0.054 | |
searchPublished | 0.152 | 0.001 | 0.153 | |
searchSeq | 0.760 | 0.001 | 0.761 | |
seqMatrix | 2.223 | 0.166 | 2.389 | |
similarityMatrix | 0.154 | 0.009 | 0.163 | |
similarityScore | 0.146 | 0.006 | 0.151 | |
topFreq | 1.256 | 0.124 | 1.379 | |
topSeqs | 0.144 | 0.002 | 0.147 | |
topSeqsPlot | 0.387 | 0.012 | 0.399 | |
uniqueSeqs | 0.175 | 0.002 | 0.177 | |