Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the CAGEfightR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEfightR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 230/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEfightR 1.12.0 (landing page) Malte Thodberg
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: CAGEfightR |
Version: 1.12.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CAGEfightR_1.12.0.tar.gz |
StartedAt: 2021-10-14 09:07:17 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:12:37 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 319.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CAGEfightR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CAGEfightR_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CAGEfightR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAGEfightR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAGEfightR’ version ‘1.12.0’ * 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 ‘CAGEfightR’ 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 findLinks 4.437 0.919 4.484 * 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
CAGEfightR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CAGEfightR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘CAGEfightR’ ... ** 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 (CAGEfightR)
CAGEfightR.Rcheck/CAGEfightR-Ex.timings
name | user | system | elapsed | |
assignGeneID | 3.990 | 0.119 | 4.110 | |
assignMissingID | 1.166 | 0.011 | 1.178 | |
assignTxID | 0.951 | 0.027 | 0.979 | |
assignTxType | 0.000 | 0.000 | 0.001 | |
balanceBC | 0.000 | 0.001 | 0.000 | |
balanceD | 0.000 | 0.001 | 0.000 | |
bwCommonGenome | 0.048 | 0.001 | 0.054 | |
bwGenomeCompatibility | 0.019 | 0.003 | 0.022 | |
bwValid | 0.006 | 0.004 | 0.010 | |
calcBidirectionality | 0.526 | 0.004 | 0.530 | |
calcComposition | 2.429 | 0.072 | 2.501 | |
calcPooled | 0.176 | 0.000 | 0.175 | |
calcShape | 2.551 | 0.144 | 2.695 | |
calcSupport | 0.162 | 0.012 | 0.174 | |
calcTPM | 0.197 | 0.004 | 0.202 | |
calcTotalTags | 0.097 | 0.008 | 0.105 | |
checkCTSSs | 0.298 | 0.000 | 0.299 | |
checkPeaked | 0.196 | 0.000 | 0.196 | |
checkPooled | 0.066 | 0.000 | 0.066 | |
clusterBidirectionally | 0.000 | 0.001 | 0.000 | |
clusterUnidirectionally | 1.395 | 0.019 | 1.414 | |
combineClusters | 1.015 | 0.012 | 1.027 | |
convertBAM2BigWig | 0.000 | 0.001 | 0.000 | |
convertBED2BigWig | 0.000 | 0.001 | 0.001 | |
convertGRanges2GPos | 0.082 | 0.001 | 0.084 | |
exampleDesign | 0.005 | 0.000 | 0.005 | |
findLinks | 4.437 | 0.919 | 4.484 | |
findStretches | 0.506 | 0.084 | 0.591 | |
quantifyCTSSs | 0.001 | 0.000 | 0.001 | |
quantifyCTSSs2 | 0.001 | 0.000 | 0.001 | |
quantifyClusters | 0.557 | 0.080 | 0.636 | |
quantifyGenes | 1.346 | 0.052 | 1.398 | |
quickEnhancers | 0 | 0 | 0 | |
quickGenes | 0 | 0 | 0 | |
quickTSSs | 0.001 | 0.000 | 0.000 | |
shapeEntropy | 0.000 | 0.000 | 0.001 | |
shapeIQR | 0.000 | 0.001 | 0.001 | |
shapeMean | 0.000 | 0.001 | 0.001 | |
shapeMultimodality | 0.000 | 0.001 | 0.000 | |
subsetByBidirectionality | 0.504 | 0.016 | 0.520 | |
subsetByComposition | 1.404 | 0.016 | 1.420 | |
subsetBySupport | 0.132 | 0.004 | 0.136 | |
swapRanges | 0.257 | 0.008 | 0.265 | |
swapScores | 0.143 | 0.012 | 0.156 | |
trackBalance | 0.000 | 0.000 | 0.001 | |
trackCTSS | 3.146 | 0.148 | 3.294 | |
trackClusters | 2.202 | 0.036 | 2.238 | |
trackLinks | 1.014 | 0.641 | 1.101 | |
trimToPeak | 1.081 | 0.076 | 1.157 | |
trimToPercentiles | 2.973 | 0.044 | 3.018 | |
tuneTagClustering | 0.001 | 0.000 | 0.001 | |
utilsAggregateRows | 0.396 | 0.480 | 0.876 | |
utilsDeStrand | 0.144 | 0.004 | 0.148 | |
utilsScoreOverlaps | 0.068 | 0.000 | 0.068 | |
utilsSimplifyTxDb | 0.001 | 0.000 | 0.001 | |