Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:01 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 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 246/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEr 2.4.0 (landing page) Charles Plessy
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: CAGEr |
Version: 2.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.4.0.tar.gz |
StartedAt: 2023-04-10 19:12:16 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:18:46 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 389.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CAGEr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/CAGEr.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAGEr/DESCRIPTION’ ... OK * this is package ‘CAGEr’ version ‘2.4.0’ * 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 31.863 2.397 34.369 clusterCTSS 25.905 0.299 26.268 exportToTrack 23.591 0.167 23.785 quantilePositions 15.837 0.081 15.981 aggregateTagClusters 5.850 0.039 5.905 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 | 3.226 | 0.713 | 3.960 | |
CAGEr_Multicore | 0.894 | 0.007 | 0.903 | |
CTSS-class | 0.235 | 0.003 | 0.237 | |
CTSSclusteringMethod | 0.001 | 0.000 | 0.001 | |
CTSScoordinates | 0.064 | 0.002 | 0.065 | |
CTSSnormalizedTpm | 0.618 | 0.039 | 0.658 | |
CTSStagCount | 0.683 | 0.037 | 0.722 | |
CTSStoGenes | 0.339 | 0.002 | 0.341 | |
CustomConsensusClusters | 0.949 | 0.008 | 0.959 | |
GeneExpDESeq2 | 1.060 | 0.027 | 1.089 | |
GeneExpSE | 0.005 | 0.000 | 0.005 | |
QuantileWidthFunctions | 0.114 | 0.002 | 0.140 | |
aggregateTagClusters | 5.850 | 0.039 | 5.905 | |
annotateCTSS | 1.500 | 0.011 | 1.516 | |
byCtss | 0.004 | 0.000 | 0.004 | |
clusterCTSS | 25.905 | 0.299 | 26.268 | |
consensusClusters | 0.109 | 0.001 | 0.110 | |
consensusClustersDESeq2 | 0.134 | 0.001 | 0.135 | |
consensusClustersTpm | 0.005 | 0.000 | 0.008 | |
coverage-functions | 3.648 | 0.230 | 3.894 | |
cumulativeCTSSdistribution | 31.863 | 2.397 | 34.369 | |
distclu-functions | 3.225 | 0.166 | 3.398 | |
exampleCAGEexp | 0.000 | 0.000 | 0.001 | |
exportToTrack | 23.591 | 0.167 | 23.785 | |
expressionClasses | 0.015 | 0.001 | 0.014 | |
genomeName | 0.000 | 0.001 | 0.001 | |
getCTSS | 0.950 | 0.013 | 0.966 | |
getExpressionProfiles | 2.070 | 0.015 | 2.091 | |
getShiftingPromoters | 0.000 | 0.001 | 0.000 | |
hanabi | 0.172 | 0.008 | 0.180 | |
hanabiPlot | 0.268 | 0.015 | 0.284 | |
import.CAGEscanMolecule | 0 | 0 | 0 | |
import.CTSS | 0.074 | 0.001 | 0.075 | |
import.bam | 0 | 0 | 0 | |
import.bedCTSS | 0 | 0 | 0 | |
import.bedScore | 0.000 | 0.000 | 0.001 | |
import.bedmolecule | 0 | 0 | 0 | |
inputFiles | 0.002 | 0.000 | 0.002 | |
inputFilesType | 0.001 | 0.001 | 0.002 | |
librarySizes | 0.001 | 0.000 | 0.001 | |
mapStats | 0.042 | 0.002 | 0.044 | |
mergeCAGEsets | 1.933 | 0.019 | 1.955 | |
mergeSamples | 0.452 | 0.002 | 0.455 | |
moleculesGR2CTSS | 0.132 | 0.001 | 0.134 | |
normalizeTagCount | 0.434 | 0.002 | 0.437 | |
parseCAGEscanBlocksToGrangeTSS | 0.024 | 0.000 | 0.024 | |
plotAnnot | 2.349 | 0.053 | 2.409 | |
plotCorrelation | 0.230 | 0.002 | 0.234 | |
plotExpressionProfiles | 4.005 | 0.117 | 4.131 | |
plotInterquantileWidth | 1.759 | 0.008 | 1.772 | |
plotReverseCumulatives | 0.285 | 0.004 | 0.290 | |
quantilePositions | 15.837 | 0.081 | 15.981 | |
ranges2annot | 0.341 | 0.002 | 0.344 | |
ranges2genes | 0.053 | 0.000 | 0.052 | |
ranges2names | 0.048 | 0.000 | 0.048 | |
sampleLabels | 0.003 | 0.001 | 0.004 | |
scoreShift | 0 | 0 | 0 | |
seqNameTotalsSE | 0.003 | 0.001 | 0.003 | |
setColors | 0.402 | 0.004 | 0.408 | |
strandInvaders | 0.608 | 0.060 | 0.685 | |
summariseChrExpr | 0.408 | 0.002 | 0.410 | |
tagClusters | 0.103 | 0.002 | 0.105 | |