Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:37 -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 |
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To the developers/maintainers of the CAGEr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.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 242/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEr 2.5.0 (landing page) Charles Plessy
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: CAGEr |
Version: 2.5.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CAGEr_2.5.0.tar.gz |
StartedAt: 2023-02-27 22:32:46 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 22:46:30 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 823.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CAGEr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CAGEr_2.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CAGEr.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 ‘CAGEr/DESCRIPTION’ ... OK * this is package ‘CAGEr’ version ‘2.5.0’ * package encoding: UTF-8 * 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 ‘CAGEr’ can be installed ... OK * checking installed package size ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cumulativeCTSSdistribution 55.064 6.152 61.221 clusterCTSS 45.573 0.576 46.152 exportToTrack 41.739 0.180 41.920 quantilePositions 25.732 0.044 25.776 aggregateTagClusters 9.285 0.080 9.364 plotExpressionProfiles 6.993 0.040 7.034 distclu-functions 6.195 0.600 6.792 coverage-functions 5.224 0.360 5.585 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘CAGE_Resources.Rmd’ using ‘UTF-8’... OK ‘CAGEexp.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘CAGEr’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (CAGEr)
CAGEr.Rcheck/CAGEr-Ex.timings
name | user | system | elapsed | |
CAGEexp-class | 3.939 | 0.220 | 4.168 | |
CAGEr_Multicore | 3.136 | 0.056 | 3.192 | |
CTSS-class | 0.404 | 0.004 | 0.408 | |
CTSSclusteringMethod | 0.001 | 0.000 | 0.001 | |
CTSScoordinates | 0.106 | 0.000 | 0.106 | |
CTSSnormalizedTpm | 0.999 | 0.052 | 1.050 | |
CTSStagCount | 1.148 | 0.040 | 1.188 | |
CTSStoGenes | 0.512 | 0.004 | 0.516 | |
CustomConsensusClusters | 1.261 | 0.012 | 1.272 | |
GeneExpDESeq2 | 0.625 | 0.036 | 0.661 | |
GeneExpSE | 0.006 | 0.000 | 0.006 | |
QuantileWidthFunctions | 0.152 | 0.000 | 0.152 | |
aggregateTagClusters | 9.285 | 0.080 | 9.364 | |
annotateCTSS | 1.983 | 0.020 | 2.004 | |
byCtss | 0.006 | 0.000 | 0.006 | |
clusterCTSS | 45.573 | 0.576 | 46.152 | |
consensusClusters | 0.171 | 0.000 | 0.171 | |
consensusClustersDESeq2 | 0.250 | 0.000 | 0.251 | |
consensusClustersTpm | 0.008 | 0.000 | 0.007 | |
coverage-functions | 5.224 | 0.360 | 5.585 | |
cumulativeCTSSdistribution | 55.064 | 6.152 | 61.221 | |
distclu-functions | 6.195 | 0.600 | 6.792 | |
exampleCAGEexp | 0.001 | 0.000 | 0.000 | |
exportToTrack | 41.739 | 0.180 | 41.920 | |
expressionClasses | 0.016 | 0.003 | 0.020 | |
genomeName | 0 | 0 | 0 | |
getCTSS | 1.440 | 0.045 | 1.484 | |
getExpressionProfiles | 2.303 | 0.015 | 2.319 | |
getShiftingPromoters | 0 | 0 | 0 | |
hanabi | 0.319 | 0.016 | 0.335 | |
hanabiPlot | 0.392 | 0.020 | 0.412 | |
import.CAGEscanMolecule | 0 | 0 | 0 | |
import.CTSS | 0.109 | 0.000 | 0.109 | |
import.bam | 0 | 0 | 0 | |
import.bedCTSS | 0 | 0 | 0 | |
import.bedScore | 0.000 | 0.000 | 0.001 | |
import.bedmolecule | 0 | 0 | 0 | |
inputFiles | 0.000 | 0.001 | 0.002 | |
inputFilesType | 0.002 | 0.000 | 0.002 | |
librarySizes | 0.002 | 0.000 | 0.002 | |
mapStats | 0.072 | 0.000 | 0.072 | |
mergeCAGEsets | 3.002 | 0.016 | 3.018 | |
mergeSamples | 0.679 | 0.000 | 0.680 | |
moleculesGR2CTSS | 0.17 | 0.00 | 0.17 | |
normalizeTagCount | 0.690 | 0.000 | 0.686 | |
parseCAGEscanBlocksToGrangeTSS | 0.030 | 0.000 | 0.031 | |
plotAnnot | 3.689 | 0.068 | 3.757 | |
plotCorrelation | 0.342 | 0.016 | 0.357 | |
plotExpressionProfiles | 6.993 | 0.040 | 7.034 | |
plotInterquantileWidth | 2.956 | 0.012 | 2.971 | |
plotReverseCumulatives | 0.422 | 0.000 | 0.412 | |
quantilePositions | 25.732 | 0.044 | 25.776 | |
ranges2annot | 0.482 | 0.004 | 0.486 | |
ranges2genes | 0.075 | 0.000 | 0.075 | |
ranges2names | 0.073 | 0.000 | 0.074 | |
sampleLabels | 0.006 | 0.000 | 0.005 | |
scoreShift | 0.001 | 0.000 | 0.000 | |
seqNameTotalsSE | 0.005 | 0.000 | 0.005 | |
setColors | 0.548 | 0.004 | 0.552 | |
strandInvaders | 0.885 | 0.044 | 0.946 | |
summariseChrExpr | 0.638 | 0.000 | 0.638 | |
tagClusters | 0.120 | 0.000 | 0.121 | |