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This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).
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? 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 231/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEr 1.34.0 (landing page) Charles Plessy
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: CAGEr |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.34.0.tar.gz |
StartedAt: 2021-10-14 17:01:21 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 17:10:51 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 570.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CAGEr.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CAGEr_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.34.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... WARNING Missing link or links in documentation object 'CustomConsensusClusters.Rd': ‘.ConsensusClusters’ Missing link or links in documentation object 'clusterCTSS.Rd': ‘TagClusters’ Missing link or links in documentation object 'consensusClusters.Rd': ‘ConsensusClusters’ Missing link or links in documentation object 'tagClusters.Rd': ‘TagClusters’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'show' and siglist 'CTSS' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'CTSS-class' ‘.Object’ ‘...’ ‘bsgenomeName’ ‘seqnames’ ‘pos’ ‘strand’ ‘seqinfo’ ‘seqlengths’ ‘from’ ‘to’ ‘strict’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 importPublicData 34.819 1.138 45.438 scoreShift 32.768 0.091 32.887 quantilePositions 31.197 0.420 31.638 cumulativeCTSSdistribution 29.098 1.329 30.444 aggregateTagClusters 15.950 0.102 16.081 distclu-functions 7.552 0.198 7.758 clusterCTSS 6.822 0.157 6.982 CAGEexp-class 5.742 0.616 6.388 * 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: 3 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CAGEr.Rcheck/00check.log’ for details.
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 | 5.742 | 0.616 | 6.388 | |
CAGEr_Multicore | 0.917 | 0.023 | 0.945 | |
CAGEset-class | 0.002 | 0.001 | 0.003 | |
CTSS-class | 0.549 | 0.005 | 0.558 | |
CTSSclusteringMethod | 0.011 | 0.000 | 0.011 | |
CTSScoordinates | 0.185 | 0.002 | 0.188 | |
CTSSnormalizedTpm | 1.344 | 0.029 | 1.378 | |
CTSStagCount | 0.41 | 0.04 | 0.45 | |
CTSStagCountTable | 0.008 | 0.001 | 0.010 | |
CTSStoGenes | 1.115 | 0.007 | 1.127 | |
CustomConsensusClusters | 1.898 | 0.010 | 1.911 | |
GeneExpDESeq2 | 1.774 | 0.043 | 1.824 | |
GeneExpSE | 0.010 | 0.001 | 0.011 | |
QuantileWidthFunctions | 0.000 | 0.001 | 0.000 | |
aggregateTagClusters | 15.950 | 0.102 | 16.081 | |
annotateCTSS | 2.554 | 0.012 | 2.569 | |
byCtss | 0.007 | 0.001 | 0.008 | |
clusterCTSS | 6.822 | 0.157 | 6.982 | |
consensusClusterConvertors | 0.051 | 0.003 | 0.053 | |
consensusClusters | 3.509 | 0.227 | 3.738 | |
consensusClustersDESeq2 | 0.416 | 0.004 | 0.421 | |
consensusClustersTpm | 0.009 | 0.000 | 0.010 | |
coverage-functions | 4.538 | 0.310 | 4.852 | |
cumulativeCTSSdistribution | 29.098 | 1.329 | 30.444 | |
distclu-functions | 7.552 | 0.198 | 7.758 | |
exampleCAGEexp | 0.001 | 0.001 | 0.001 | |
exampleCAGEset | 0.013 | 0.001 | 0.014 | |
exportCTSStoBedGraph | 4.583 | 0.026 | 4.652 | |
exportToBed | 4.161 | 0.014 | 4.177 | |
expressionClasses | 0.003 | 0.001 | 0.003 | |
extractExpressionClass | 0.007 | 0.001 | 0.009 | |
genomeName | 0.000 | 0.000 | 0.001 | |
getCTSS | 0.217 | 0.011 | 0.228 | |
getExpressionProfiles | 0.679 | 0.002 | 0.682 | |
getShiftingPromoters | 0.009 | 0.003 | 0.011 | |
hanabi | 0.396 | 0.004 | 0.400 | |
hanabiPlot | 0.640 | 0.017 | 0.659 | |
import.CAGEscanMolecule | 0 | 0 | 0 | |
import.CTSS | 0.111 | 0.001 | 0.112 | |
import.bam | 0.000 | 0.001 | 0.000 | |
import.bedCTSS | 0 | 0 | 0 | |
import.bedScore | 0 | 0 | 0 | |
import.bedmolecule | 0 | 0 | 0 | |
importPublicData | 34.819 | 1.138 | 45.438 | |
inputFiles | 0.000 | 0.001 | 0.001 | |
inputFilesType | 0.000 | 0.001 | 0.001 | |
librarySizes | 0.001 | 0.001 | 0.001 | |
mapStats | 0.067 | 0.005 | 0.073 | |
mergeCAGEsets | 4.141 | 0.042 | 4.186 | |
mergeSamples | 1.428 | 0.004 | 1.432 | |
moleculesGR2CTSS | 0.231 | 0.001 | 0.232 | |
normalizeTagCount | 1.058 | 0.047 | 1.105 | |
parseCAGEscanBlocksToGrangeTSS | 0.045 | 0.001 | 0.047 | |
plotAnnot | 3.059 | 0.030 | 3.098 | |
plotCorrelation | 0.627 | 0.003 | 0.630 | |
plotExpressionProfiles | 0.155 | 0.004 | 0.160 | |
plotInterquantileWidth | 1.426 | 0.011 | 1.442 | |
plotReverseCumulatives | 0.849 | 0.007 | 0.859 | |
quantilePositions | 31.197 | 0.420 | 31.638 | |
ranges2annot | 0.411 | 0.002 | 0.413 | |
ranges2genes | 0.105 | 0.001 | 0.107 | |
ranges2names | 0.073 | 0.001 | 0.073 | |
sampleLabels | 0.000 | 0.000 | 0.001 | |
scoreShift | 32.768 | 0.091 | 32.887 | |
seqNameTotalsSE | 0.008 | 0.001 | 0.009 | |
setColors | 1.940 | 0.011 | 1.954 | |
strandInvaders | 1.338 | 0.056 | 1.405 | |
summariseChrExpr | 0.948 | 0.005 | 0.953 | |
tagClusterConvertors | 0.497 | 0.007 | 0.505 | |
tagClusters | 0.101 | 0.004 | 0.105 | |