Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-06-24 12:07:09 -0400 (Fri, 24 Jun 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4380 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" | 4156 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4221 |
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 243/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEr 2.2.0 (landing page) Charles Plessy
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: CAGEr |
Version: 2.2.0 |
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_2.2.0.tar.gz |
StartedAt: 2022-06-24 00:19:35 -0400 (Fri, 24 Jun 2022) |
EndedAt: 2022-06-24 00:33:48 -0400 (Fri, 24 Jun 2022) |
EllapsedTime: 853.5 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_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CAGEr.Rcheck’ * using R version 4.2.0 (2022-04-22) * 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 ‘2.2.0’ * 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 clusterCTSS 72.563 0.432 75.057 cumulativeCTSSdistribution 69.764 1.938 73.536 exportToTrack 63.410 0.129 64.181 quantilePositions 38.165 0.097 38.666 aggregateTagClusters 14.888 0.058 15.195 plotExpressionProfiles 9.162 0.213 9.520 CAGEexp-class 7.396 0.703 8.691 distclu-functions 6.631 0.338 7.164 coverage-functions 5.830 0.303 6.157 plotInterquantileWidth 5.781 0.031 5.853 mergeCAGEsets 5.121 0.026 5.190 * 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 | 7.396 | 0.703 | 8.691 | |
CAGEr_Multicore | 1.167 | 0.019 | 1.310 | |
CTSS-class | 0.650 | 0.003 | 0.709 | |
CTSSclusteringMethod | 0.002 | 0.000 | 0.002 | |
CTSScoordinates | 0.160 | 0.002 | 0.182 | |
CTSSnormalizedTpm | 1.593 | 0.042 | 1.843 | |
CTSStagCount | 1.825 | 0.104 | 2.047 | |
CTSStoGenes | 0.901 | 0.004 | 0.911 | |
CustomConsensusClusters | 2.045 | 0.010 | 2.110 | |
GeneExpDESeq2 | 2.431 | 0.041 | 2.514 | |
GeneExpSE | 0.009 | 0.000 | 0.009 | |
QuantileWidthFunctions | 0.263 | 0.002 | 0.270 | |
aggregateTagClusters | 14.888 | 0.058 | 15.195 | |
annotateCTSS | 3.200 | 0.012 | 3.249 | |
byCtss | 0.009 | 0.000 | 0.009 | |
clusterCTSS | 72.563 | 0.432 | 75.057 | |
consensusClusters | 0.279 | 0.002 | 0.295 | |
consensusClustersDESeq2 | 0.387 | 0.002 | 0.447 | |
consensusClustersTpm | 0.011 | 0.000 | 0.012 | |
coverage-functions | 5.830 | 0.303 | 6.157 | |
cumulativeCTSSdistribution | 69.764 | 1.938 | 73.536 | |
distclu-functions | 6.631 | 0.338 | 7.164 | |
exampleCAGEexp | 0.000 | 0.000 | 0.001 | |
exportToTrack | 63.410 | 0.129 | 64.181 | |
expressionClasses | 0.031 | 0.001 | 0.033 | |
genomeName | 0.001 | 0.000 | 0.000 | |
getCTSS | 2.354 | 0.016 | 2.424 | |
getExpressionProfiles | 4.730 | 0.013 | 4.771 | |
getShiftingPromoters | 0 | 0 | 0 | |
hanabi | 0.442 | 0.005 | 0.450 | |
hanabiPlot | 0.567 | 0.023 | 0.592 | |
import.CAGEscanMolecule | 0.001 | 0.000 | 0.000 | |
import.CTSS | 0.171 | 0.002 | 0.173 | |
import.bam | 0.001 | 0.000 | 0.000 | |
import.bedCTSS | 0.000 | 0.000 | 0.001 | |
import.bedScore | 0 | 0 | 0 | |
import.bedmolecule | 0 | 0 | 0 | |
inputFiles | 0.003 | 0.001 | 0.002 | |
inputFilesType | 0.002 | 0.000 | 0.002 | |
librarySizes | 0.002 | 0.000 | 0.002 | |
mapStats | 0.118 | 0.002 | 0.119 | |
mergeCAGEsets | 5.121 | 0.026 | 5.190 | |
mergeSamples | 1.252 | 0.004 | 1.263 | |
moleculesGR2CTSS | 0.271 | 0.001 | 0.275 | |
normalizeTagCount | 1.209 | 0.003 | 1.219 | |
parseCAGEscanBlocksToGrangeTSS | 0.048 | 0.001 | 0.049 | |
plotAnnot | 4.430 | 0.030 | 4.487 | |
plotCorrelation | 0.571 | 0.004 | 0.580 | |
plotExpressionProfiles | 9.162 | 0.213 | 9.520 | |
plotInterquantileWidth | 5.781 | 0.031 | 5.853 | |
plotReverseCumulatives | 0.630 | 0.004 | 0.644 | |
quantilePositions | 38.165 | 0.097 | 38.666 | |
ranges2annot | 0.777 | 0.002 | 0.790 | |
ranges2genes | 0.126 | 0.000 | 0.127 | |
ranges2names | 0.119 | 0.001 | 0.120 | |
sampleLabels | 0.009 | 0.001 | 0.009 | |
scoreShift | 0 | 0 | 0 | |
seqNameTotalsSE | 0.008 | 0.000 | 0.008 | |
setColors | 0.912 | 0.005 | 0.920 | |
strandInvaders | 1.470 | 0.092 | 1.583 | |
summariseChrExpr | 1.126 | 0.003 | 1.141 | |
tagClusters | 0.190 | 0.002 | 0.200 | |