Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-01 12:07 -0400 (Wed, 01 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4843 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4631 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4575 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
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 1153/2337 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LymphoSeq 1.37.0 (landing page) David Coffey
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: LymphoSeq |
Version: 1.37.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings LymphoSeq_1.37.0.tar.gz |
StartedAt: 2025-09-30 09:44:59 -0000 (Tue, 30 Sep 2025) |
EndedAt: 2025-09-30 09:49:08 -0000 (Tue, 30 Sep 2025) |
EllapsedTime: 249.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LymphoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings LymphoSeq_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/LymphoSeq.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 32.305 1.389 33.846 productiveSeq 22.261 0.348 22.641 phyloTree 6.063 0.184 6.257 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
LymphoSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL LymphoSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/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 | 0.825 | 0.039 | 0.907 | |
bhattacharyyaCoefficient | 0.295 | 0.047 | 0.389 | |
bhattacharyyaMatrix | 0.565 | 0.112 | 0.679 | |
chordDiagramVDJ | 1.147 | 0.067 | 1.218 | |
clonalRelatedness | 1.255 | 0.007 | 0.669 | |
clonality | 0.063 | 0.004 | 0.067 | |
cloneTrack | 32.305 | 1.389 | 33.846 | |
commonSeqs | 0.174 | 0.020 | 0.195 | |
commonSeqsBar | 1.572 | 0.147 | 1.724 | |
commonSeqsPlot | 2.672 | 0.108 | 2.786 | |
commonSeqsVenn | 0.853 | 0.032 | 0.890 | |
differentialAbundance | 2.887 | 0.100 | 2.996 | |
exportFasta | 0.250 | 0.027 | 0.279 | |
geneFreq | 3.165 | 0.128 | 3.298 | |
lorenzCurve | 1.625 | 0.040 | 1.668 | |
mergeFiles | 0.081 | 0.000 | 0.081 | |
pairwisePlot | 1.356 | 0.004 | 1.363 | |
phyloTree | 6.063 | 0.184 | 6.257 | |
productive | 0.059 | 0.004 | 0.063 | |
productiveSeq | 22.261 | 0.348 | 22.641 | |
readImmunoSeq | 0.048 | 0.000 | 0.049 | |
removeSeq | 0.062 | 0.004 | 0.066 | |
searchPublished | 0.186 | 0.008 | 0.194 | |
searchSeq | 0.443 | 0.012 | 0.456 | |
seqMatrix | 4.005 | 0.155 | 4.167 | |
similarityMatrix | 0.188 | 0.000 | 0.188 | |
similarityScore | 0.171 | 0.000 | 0.171 | |
topFreq | 1.451 | 0.052 | 1.505 | |
topSeqs | 0.179 | 0.000 | 0.179 | |
topSeqsPlot | 0.861 | 0.000 | 0.863 | |
uniqueSeqs | 0.213 | 0.000 | 0.213 | |