Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-07 20:27 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1134/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LymphoSeq 1.32.0 (landing page) David Coffey
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | 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 | |||||||||
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: 1.32.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LymphoSeq_1.32.0.tar.gz |
StartedAt: 2024-06-05 21:17:35 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 21:21:17 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 221.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LymphoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LymphoSeq_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/LymphoSeq.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘LymphoSeq/DESCRIPTION’ ... OK * this is package ‘LymphoSeq’ version ‘1.32.0’ * 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 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 productiveSeq 26.776 0.673 27.540 cloneTrack 25.571 1.068 26.699 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/LymphoSeq.Rcheck/00check.log’ for details.
LymphoSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LymphoSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 1.248 | 0.039 | 1.303 | |
bhattacharyyaCoefficient | 0.194 | 0.017 | 0.227 | |
bhattacharyyaMatrix | 0.152 | 0.010 | 0.161 | |
chordDiagramVDJ | 0.930 | 0.040 | 0.973 | |
clonalRelatedness | 0.678 | 0.008 | 0.688 | |
clonality | 0.062 | 0.006 | 0.068 | |
cloneTrack | 25.571 | 1.068 | 26.699 | |
commonSeqs | 0.192 | 0.022 | 0.215 | |
commonSeqsBar | 2.091 | 0.160 | 2.258 | |
commonSeqsPlot | 0.446 | 0.010 | 0.458 | |
commonSeqsVenn | 0.702 | 0.033 | 0.740 | |
differentialAbundance | 2.162 | 0.061 | 2.229 | |
exportFasta | 0.249 | 0.029 | 0.280 | |
geneFreq | 2.176 | 0.132 | 2.316 | |
lorenzCurve | 0.955 | 0.017 | 0.976 | |
mergeFiles | 0.089 | 0.005 | 0.094 | |
pairwisePlot | 0.736 | 0.013 | 0.751 | |
phyloTree | 2.661 | 0.027 | 2.696 | |
productive | 0.056 | 0.004 | 0.060 | |
productiveSeq | 26.776 | 0.673 | 27.540 | |
readImmunoSeq | 0.050 | 0.005 | 0.055 | |
removeSeq | 0.063 | 0.005 | 0.068 | |
searchPublished | 0.196 | 0.010 | 0.208 | |
searchSeq | 0.526 | 0.011 | 0.539 | |
seqMatrix | 3.042 | 0.082 | 3.130 | |
similarityMatrix | 0.187 | 0.007 | 0.195 | |
similarityScore | 0.183 | 0.006 | 0.191 | |
topFreq | 2.742 | 0.048 | 2.798 | |
topSeqs | 0.159 | 0.004 | 0.164 | |
topSeqsPlot | 0.431 | 0.007 | 0.441 | |
uniqueSeqs | 0.220 | 0.009 | 0.227 | |