Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:14:54 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 240/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEfightR 1.19.0 (landing page) Malte Thodberg
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: CAGEfightR |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CAGEfightR_1.19.0.tar.gz |
StartedAt: 2023-02-06 19:57:22 -0000 (Mon, 06 Feb 2023) |
EndedAt: 2023-02-06 20:06:15 -0000 (Mon, 06 Feb 2023) |
EllapsedTime: 533.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: CAGEfightR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings CAGEfightR_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CAGEfightR.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘CAGEfightR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAGEfightR’ version ‘1.19.0’ * 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 7.02 0.874 7.523 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Introduction_to_CAGEfightR.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘Introduction_to_CAGEfightR.Rmd’ using rmarkdown Killed * checking PDF version of manual ... OK * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.17-bioc/meat/CAGEfightR.Rcheck/00check.log’ for details.
CAGEfightR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL CAGEfightR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 | 3.528 | 0.080 | 3.622 | |
assignMissingID | 2.562 | 0.008 | 2.572 | |
assignTxID | 1.124 | 0.014 | 1.139 | |
assignTxType | 0.000 | 0.000 | 0.001 | |
balanceBC | 0.001 | 0.000 | 0.001 | |
balanceD | 0.001 | 0.000 | 0.001 | |
bwCommonGenome | 0.039 | 0.007 | 0.050 | |
bwGenomeCompatibility | 0.017 | 0.004 | 0.021 | |
bwValid | 0.009 | 0.000 | 0.010 | |
calcBidirectionality | 0.575 | 0.008 | 0.583 | |
calcComposition | 1.878 | 0.008 | 1.887 | |
calcPooled | 0.128 | 0.000 | 0.128 | |
calcShape | 3.418 | 0.124 | 3.902 | |
calcSupport | 0.154 | 0.000 | 0.154 | |
calcTPM | 0.173 | 0.004 | 0.177 | |
calcTotalTags | 0.086 | 0.004 | 0.090 | |
checkCTSSs | 0.388 | 0.004 | 0.394 | |
checkPeaked | 0.088 | 0.000 | 0.088 | |
checkPooled | 0.078 | 0.004 | 0.082 | |
clusterBidirectionally | 0 | 0 | 0 | |
clusterUnidirectionally | 1.831 | 0.004 | 1.835 | |
combineClusters | 1.060 | 0.004 | 1.063 | |
convertBAM2BigWig | 0.001 | 0.000 | 0.000 | |
convertBED2BigWig | 0.001 | 0.000 | 0.000 | |
convertGRanges2GPos | 0.107 | 0.000 | 0.107 | |
exampleDesign | 0.003 | 0.004 | 0.006 | |
findLinks | 7.020 | 0.874 | 7.523 | |
findStretches | 0.504 | 0.068 | 0.573 | |
quantifyCTSSs | 0 | 0 | 0 | |
quantifyCTSSs2 | 0 | 0 | 0 | |
quantifyClusters | 0.524 | 0.068 | 0.593 | |
quantifyGenes | 1.624 | 0.136 | 1.761 | |
quickEnhancers | 0 | 0 | 0 | |
quickGenes | 0 | 0 | 0 | |
quickTSSs | 0 | 0 | 0 | |
shapeEntropy | 0 | 0 | 0 | |
shapeIQR | 0.000 | 0.000 | 0.001 | |
shapeMean | 0.001 | 0.000 | 0.001 | |
shapeMultimodality | 0 | 0 | 0 | |
subsetByBidirectionality | 0.585 | 0.008 | 0.593 | |
subsetByComposition | 1.653 | 0.036 | 1.885 | |
subsetBySupport | 0.103 | 0.000 | 0.104 | |
swapRanges | 0.230 | 0.004 | 0.234 | |
swapScores | 0.132 | 0.012 | 0.144 | |
trackBalance | 0.000 | 0.000 | 0.001 | |
trackCTSS | 3.867 | 0.264 | 4.133 | |
trackClusters | 2.571 | 0.000 | 2.572 | |
trackLinks | 1.147 | 0.477 | 1.445 | |
trimToPeak | 0.928 | 0.155 | 1.085 | |
trimToPercentiles | 2.564 | 0.056 | 2.624 | |
tuneTagClustering | 0.000 | 0.000 | 0.001 | |
utilsAggregateRows | 0.346 | 0.176 | 0.523 | |
utilsDeStrand | 0.166 | 0.000 | 0.166 | |
utilsScoreOverlaps | 0.085 | 0.000 | 0.084 | |
utilsSimplifyTxDb | 0 | 0 | 0 | |