Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-02-04 11:40 -0500 (Tue, 04 Feb 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4716 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
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 1128/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LymphoSeq 1.35.0 (landing page) David Coffey
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | OK | 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: 1.35.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings LymphoSeq_1.35.0.tar.gz |
StartedAt: 2025-02-03 23:49:05 -0500 (Mon, 03 Feb 2025) |
EndedAt: 2025-02-03 23:52:56 -0500 (Mon, 03 Feb 2025) |
EllapsedTime: 231.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LymphoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings LymphoSeq_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/LymphoSeq.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * 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 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘LymphoSeq/DESCRIPTION’ ... OK * this is package ‘LymphoSeq’ version ‘1.35.0’ * 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 ... OK * 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 26.131 1.714 27.852 productiveSeq 14.634 1.406 16.046 * 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-3.21-bioc/R/bin/R CMD INSTALL LymphoSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘LymphoSeq’ ... ** this is package ‘LymphoSeq’ version ‘1.35.0’ ** 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 | 0.674 | 0.047 | 0.728 | |
bhattacharyyaCoefficient | 0.147 | 0.006 | 0.167 | |
bhattacharyyaMatrix | 0.170 | 0.005 | 0.174 | |
chordDiagramVDJ | 0.765 | 0.027 | 0.792 | |
clonalRelatedness | 0.715 | 0.006 | 0.383 | |
clonality | 0.051 | 0.007 | 0.058 | |
cloneTrack | 26.131 | 1.714 | 27.852 | |
commonSeqs | 0.158 | 0.026 | 0.184 | |
commonSeqsBar | 0.817 | 0.163 | 0.981 | |
commonSeqsPlot | 0.364 | 0.056 | 0.420 | |
commonSeqsVenn | 0.723 | 0.106 | 0.822 | |
differentialAbundance | 2.517 | 0.172 | 2.689 | |
exportFasta | 0.215 | 0.005 | 0.221 | |
geneFreq | 0.942 | 0.018 | 0.960 | |
lorenzCurve | 0.889 | 0.006 | 0.896 | |
mergeFiles | 0.072 | 0.005 | 0.078 | |
pairwisePlot | 1.415 | 0.002 | 1.417 | |
phyloTree | 3.238 | 0.037 | 3.276 | |
productive | 0.054 | 0.003 | 0.057 | |
productiveSeq | 14.634 | 1.406 | 16.046 | |
readImmunoSeq | 0.047 | 0.002 | 0.049 | |
removeSeq | 0.054 | 0.002 | 0.055 | |
searchPublished | 0.153 | 0.008 | 0.161 | |
searchSeq | 0.884 | 0.006 | 0.889 | |
seqMatrix | 2.493 | 0.171 | 2.664 | |
similarityMatrix | 0.159 | 0.003 | 0.162 | |
similarityScore | 0.151 | 0.002 | 0.153 | |
topFreq | 1.188 | 0.116 | 1.303 | |
topSeqs | 0.749 | 0.033 | 0.782 | |
topSeqsPlot | 0.385 | 0.003 | 0.387 | |
uniqueSeqs | 0.183 | 0.003 | 0.185 | |