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 11:05:27 -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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CAGEr_2.4.0.tar.gz |
StartedAt: 2023-04-10 23:36:12 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 23:43:47 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 455.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CAGEr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CAGEr.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings CAGEr_2.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/CAGEr.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (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 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 38.49 2.13 40.62 clusterCTSS 34.03 0.54 34.57 exportToTrack 29.58 0.24 29.82 quantilePositions 18.03 0.36 18.39 aggregateTagClusters 7.63 0.11 7.74 CAGEexp-class 5.27 1.46 6.87 plotExpressionProfiles 5.33 0.17 5.50 * 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: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-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 | 5.27 | 1.46 | 6.87 | |
CAGEr_Multicore | 0.06 | 0.00 | 0.07 | |
CTSS-class | 0.29 | 0.05 | 0.35 | |
CTSSclusteringMethod | 0.02 | 0.00 | 0.01 | |
CTSScoordinates | 0.06 | 0.00 | 0.06 | |
CTSSnormalizedTpm | 0.67 | 0.02 | 0.69 | |
CTSStagCount | 1.00 | 0.01 | 1.02 | |
CTSStoGenes | 0.40 | 0.00 | 0.39 | |
CustomConsensusClusters | 1.33 | 0.00 | 1.33 | |
GeneExpDESeq2 | 1.25 | 0.06 | 1.41 | |
GeneExpSE | 0 | 0 | 0 | |
QuantileWidthFunctions | 0.12 | 0.00 | 0.12 | |
aggregateTagClusters | 7.63 | 0.11 | 7.74 | |
annotateCTSS | 1.94 | 0.04 | 1.97 | |
byCtss | 0 | 0 | 0 | |
clusterCTSS | 34.03 | 0.54 | 34.57 | |
consensusClusters | 0.11 | 0.00 | 0.11 | |
consensusClustersDESeq2 | 0.14 | 0.00 | 0.14 | |
consensusClustersTpm | 0 | 0 | 0 | |
coverage-functions | 4.19 | 0.08 | 4.27 | |
cumulativeCTSSdistribution | 38.49 | 2.13 | 40.62 | |
distclu-functions | 3.89 | 0.15 | 4.05 | |
exampleCAGEexp | 0 | 0 | 0 | |
exportToTrack | 29.58 | 0.24 | 29.82 | |
expressionClasses | 0.02 | 0.00 | 0.01 | |
genomeName | 0 | 0 | 0 | |
getCTSS | 1.26 | 0.01 | 1.28 | |
getExpressionProfiles | 2.27 | 0.03 | 2.30 | |
getShiftingPromoters | 0 | 0 | 0 | |
hanabi | 0.32 | 0.02 | 0.34 | |
hanabiPlot | 0.43 | 0.05 | 0.47 | |
import.CAGEscanMolecule | 0 | 0 | 0 | |
import.CTSS | 0.10 | 0.00 | 0.09 | |
import.bam | 0 | 0 | 0 | |
import.bedCTSS | 0 | 0 | 0 | |
import.bedScore | 0 | 0 | 0 | |
import.bedmolecule | 0 | 0 | 0 | |
inputFiles | 0 | 0 | 0 | |
inputFilesType | 0 | 0 | 0 | |
librarySizes | 0 | 0 | 0 | |
mapStats | 0.04 | 0.00 | 0.04 | |
mergeCAGEsets | 2.55 | 0.05 | 2.60 | |
mergeSamples | 1.58 | 0.00 | 1.58 | |
moleculesGR2CTSS | 0.12 | 0.00 | 0.12 | |
normalizeTagCount | 0.42 | 0.01 | 0.44 | |
parseCAGEscanBlocksToGrangeTSS | 0.02 | 0.00 | 0.01 | |
plotAnnot | 2.87 | 0.07 | 2.97 | |
plotCorrelation | 0.30 | 0.01 | 0.31 | |
plotExpressionProfiles | 5.33 | 0.17 | 5.50 | |
plotInterquantileWidth | 2.37 | 0.02 | 2.39 | |
plotReverseCumulatives | 0.3 | 0.0 | 0.3 | |
quantilePositions | 18.03 | 0.36 | 18.39 | |
ranges2annot | 0.39 | 0.00 | 0.39 | |
ranges2genes | 0.06 | 0.00 | 0.07 | |
ranges2names | 0.05 | 0.00 | 0.04 | |
sampleLabels | 0 | 0 | 0 | |
scoreShift | 0 | 0 | 0 | |
seqNameTotalsSE | 0.01 | 0.00 | 0.02 | |
setColors | 0.40 | 0.00 | 0.39 | |
strandInvaders | 0.82 | 0.14 | 1.02 | |
summariseChrExpr | 0.62 | 0.00 | 0.63 | |
tagClusters | 0.10 | 0.00 | 0.09 | |