Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-31 19:29:04 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 1098/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LymphoSeq 1.33.0 (landing page) David Coffey
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.33.0 |
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: 2024-05-31 05:11:21 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 05:15:05 -0400 (Fri, 31 May 2024) |
EllapsedTime: 224.4 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_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/LymphoSeq.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 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 20.157 1.508 21.707 productiveSeq 19.546 1.248 20.794 * 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 | 0.657 | 0.043 | 0.709 | |
bhattacharyyaCoefficient | 0.157 | 0.020 | 0.187 | |
bhattacharyyaMatrix | 0.171 | 0.004 | 0.175 | |
chordDiagramVDJ | 0.746 | 0.024 | 0.770 | |
clonalRelatedness | 0.708 | 0.008 | 0.379 | |
clonality | 0.054 | 0.000 | 0.054 | |
cloneTrack | 20.157 | 1.508 | 21.707 | |
commonSeqs | 0.148 | 0.016 | 0.164 | |
commonSeqsBar | 1.430 | 0.184 | 1.614 | |
commonSeqsPlot | 0.342 | 0.004 | 0.345 | |
commonSeqsVenn | 0.729 | 0.016 | 0.730 | |
differentialAbundance | 1.694 | 0.068 | 1.762 | |
exportFasta | 0.222 | 0.052 | 0.274 | |
geneFreq | 1.651 | 0.156 | 1.807 | |
lorenzCurve | 0.806 | 0.012 | 0.818 | |
mergeFiles | 0.073 | 0.004 | 0.078 | |
pairwisePlot | 0.605 | 0.004 | 0.609 | |
phyloTree | 3.432 | 0.088 | 3.520 | |
productive | 0.058 | 0.000 | 0.058 | |
productiveSeq | 19.546 | 1.248 | 20.794 | |
readImmunoSeq | 0.045 | 0.004 | 0.049 | |
removeSeq | 0.050 | 0.004 | 0.054 | |
searchPublished | 0.156 | 0.000 | 0.155 | |
searchSeq | 0.726 | 0.000 | 0.727 | |
seqMatrix | 2.414 | 0.136 | 2.550 | |
similarityMatrix | 0.159 | 0.000 | 0.159 | |
similarityScore | 0.149 | 0.000 | 0.149 | |
topFreq | 3.442 | 0.180 | 3.623 | |
topSeqs | 0.153 | 0.000 | 0.154 | |
topSeqsPlot | 0.363 | 0.004 | 0.367 | |
uniqueSeqs | 0.199 | 0.000 | 0.200 | |