Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:43 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 |
To the developers/maintainers of the LymphoSeq package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1055/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
LymphoSeq 1.27.0 (landing page) David Coffey
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: LymphoSeq |
Version: 1.27.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings LymphoSeq_1.27.0.tar.gz |
StartedAt: 2023-02-28 07:03:34 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 07:08:40 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 306.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: LymphoSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:LymphoSeq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings LymphoSeq_1.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/LymphoSeq.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘LymphoSeq/DESCRIPTION’ ... OK * this is package ‘LymphoSeq’ version ‘1.27.0’ * 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 R 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 cloneTrack 31.564 1.571 33.179 productiveSeq 28.820 1.195 30.017 phyloTree 6.616 0.128 6.745 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘LymphoSeq.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/LymphoSeq.Rcheck/00check.log’ for details.
LymphoSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL LymphoSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 | 0.807 | 0.021 | 0.855 | |
bhattacharyyaCoefficient | 0.209 | 0.012 | 0.253 | |
bhattacharyyaMatrix | 0.219 | 0.008 | 0.227 | |
chordDiagramVDJ | 1.561 | 0.112 | 1.673 | |
clonalRelatedness | 1.073 | 0.004 | 0.573 | |
clonality | 0.068 | 0.000 | 0.068 | |
cloneTrack | 31.564 | 1.571 | 33.179 | |
commonSeqs | 0.169 | 0.036 | 0.204 | |
commonSeqsBar | 1.086 | 0.124 | 1.211 | |
commonSeqsPlot | 0.460 | 0.088 | 0.548 | |
commonSeqsVenn | 0.888 | 0.109 | 0.980 | |
differentialAbundance | 4.764 | 0.168 | 4.931 | |
exportFasta | 0.265 | 0.008 | 0.273 | |
geneFreq | 2.065 | 0.032 | 2.097 | |
lorenzCurve | 3.345 | 0.056 | 3.401 | |
mergeFiles | 0.092 | 0.000 | 0.092 | |
pairwisePlot | 0.944 | 0.000 | 0.945 | |
phyloTree | 6.616 | 0.128 | 6.745 | |
productive | 0.064 | 0.012 | 0.076 | |
productiveSeq | 28.820 | 1.195 | 30.017 | |
readImmunoSeq | 0.043 | 0.012 | 0.055 | |
removeSeq | 1.668 | 0.068 | 1.737 | |
searchPublished | 0.192 | 0.024 | 0.217 | |
searchSeq | 0.448 | 0.020 | 0.468 | |
seqMatrix | 2.397 | 0.108 | 2.506 | |
similarityMatrix | 0.190 | 0.016 | 0.206 | |
similarityScore | 0.178 | 0.008 | 0.187 | |
topFreq | 1.821 | 0.120 | 1.941 | |
topSeqs | 0.177 | 0.019 | 0.197 | |
topSeqsPlot | 0.561 | 0.020 | 0.580 | |
uniqueSeqs | 1.848 | 0.072 | 1.920 | |