Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1126/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LymphoSeq 1.34.0 (landing page) David Coffey
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.34.0 |
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_1.34.0.tar.gz |
StartedAt: 2024-12-20 01:57:25 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 02:04:23 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 418.4 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_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/LymphoSeq.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 ‘1.34.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 17.462 1.605 19.109 productiveSeq 15.482 1.320 16.802 * 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 ‘/home/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 ‘/home/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 | 0.607 | 0.034 | 0.651 | |
bhattacharyyaCoefficient | 0.138 | 0.007 | 0.154 | |
bhattacharyyaMatrix | 0.150 | 0.003 | 0.153 | |
chordDiagramVDJ | 0.674 | 0.053 | 0.727 | |
clonalRelatedness | 0.711 | 0.001 | 0.375 | |
clonality | 0.048 | 0.001 | 0.049 | |
cloneTrack | 17.462 | 1.605 | 19.109 | |
commonSeqs | 0.136 | 0.020 | 0.156 | |
commonSeqsBar | 1.284 | 0.172 | 1.456 | |
commonSeqsPlot | 0.321 | 0.015 | 0.337 | |
commonSeqsVenn | 0.688 | 0.029 | 0.711 | |
differentialAbundance | 1.670 | 0.127 | 1.797 | |
exportFasta | 0.181 | 0.030 | 0.211 | |
geneFreq | 1.434 | 0.105 | 1.540 | |
lorenzCurve | 0.752 | 0.007 | 0.759 | |
mergeFiles | 0.066 | 0.000 | 0.067 | |
pairwisePlot | 0.58 | 0.01 | 0.59 | |
phyloTree | 3.401 | 0.082 | 3.483 | |
productive | 0.046 | 0.005 | 0.052 | |
productiveSeq | 15.482 | 1.320 | 16.802 | |
readImmunoSeq | 0.037 | 0.006 | 0.043 | |
removeSeq | 0.049 | 0.002 | 0.051 | |
searchPublished | 0.139 | 0.008 | 0.147 | |
searchSeq | 0.789 | 0.009 | 0.798 | |
seqMatrix | 2.069 | 0.155 | 2.224 | |
similarityMatrix | 0.142 | 0.000 | 0.142 | |
similarityScore | 0.128 | 0.006 | 0.134 | |
topFreq | 2.809 | 0.162 | 2.971 | |
topSeqs | 0.134 | 0.001 | 0.135 | |
topSeqsPlot | 0.342 | 0.002 | 0.344 | |
uniqueSeqs | 0.174 | 0.001 | 0.174 | |