Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-17 11:37 -0400 (Tue, 17 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
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 1114/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LymphoSeq 1.33.0 (landing page) David Coffey
| teran2 | Linux (Ubuntu 24.04.1 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 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.33.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings LymphoSeq_1.33.0.tar.gz |
StartedAt: 2024-09-17 02:35:32 -0400 (Tue, 17 Sep 2024) |
EndedAt: 2024-09-17 02:38:44 -0400 (Tue, 17 Sep 2024) |
EllapsedTime: 192.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LymphoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings LymphoSeq_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/LymphoSeq.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘LymphoSeq/DESCRIPTION’ ... OK * this is package ‘LymphoSeq’ version ‘1.33.0’ * 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 ... NOTE 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 21.198 1.697 22.95 productiveSeq 21.333 1.402 22.74 * 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 NOTE See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/LymphoSeq.Rcheck/00check.log’ for details.
LymphoSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL LymphoSeq ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘LymphoSeq’ ... ** 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 | 0.468 | 0.039 | 0.547 | |
bhattacharyyaCoefficient | 0.110 | 0.013 | 0.162 | |
bhattacharyyaMatrix | 0.119 | 0.005 | 0.125 | |
chordDiagramVDJ | 0.553 | 0.058 | 0.612 | |
clonalRelatedness | 0.542 | 0.001 | 0.287 | |
clonality | 0.038 | 0.003 | 0.040 | |
cloneTrack | 21.198 | 1.697 | 22.950 | |
commonSeqs | 0.106 | 0.025 | 0.132 | |
commonSeqsBar | 1.327 | 0.160 | 1.487 | |
commonSeqsPlot | 0.252 | 0.002 | 0.254 | |
commonSeqsVenn | 0.500 | 0.019 | 0.512 | |
differentialAbundance | 1.284 | 0.090 | 1.375 | |
exportFasta | 0.151 | 0.035 | 0.186 | |
geneFreq | 1.436 | 0.115 | 1.551 | |
lorenzCurve | 0.589 | 0.003 | 0.591 | |
mergeFiles | 0.055 | 0.001 | 0.056 | |
pairwisePlot | 0.453 | 0.002 | 0.454 | |
phyloTree | 2.766 | 0.004 | 2.771 | |
productive | 0.045 | 0.000 | 0.045 | |
productiveSeq | 21.333 | 1.402 | 22.740 | |
readImmunoSeq | 0.04 | 0.00 | 0.04 | |
removeSeq | 0.039 | 0.002 | 0.041 | |
searchPublished | 0.105 | 0.003 | 0.108 | |
searchSeq | 0.480 | 0.005 | 0.485 | |
seqMatrix | 2.573 | 0.131 | 2.704 | |
similarityMatrix | 0.113 | 0.002 | 0.114 | |
similarityScore | 0.103 | 0.003 | 0.106 | |
topFreq | 3.554 | 0.162 | 3.715 | |
topSeqs | 0.105 | 0.004 | 0.109 | |
topSeqsPlot | 0.282 | 0.003 | 0.284 | |
uniqueSeqs | 0.139 | 0.003 | 0.142 | |