Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-04 11:44 -0400 (Thu, 04 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4411 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4413 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4395 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4390 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
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 |
Package 259/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEfightR 1.25.0 (landing page) Malte Thodberg
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the CAGEfightR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: CAGEfightR |
Version: 1.25.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CAGEfightR_1.25.0.tar.gz |
StartedAt: 2024-07-04 03:13:51 -0000 (Thu, 04 Jul 2024) |
EndedAt: 2024-07-04 03:22:08 -0000 (Thu, 04 Jul 2024) |
EllapsedTime: 496.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CAGEfightR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CAGEfightR_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CAGEfightR.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAGEfightR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAGEfightR’ version ‘1.25.0’ * 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 code 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 7.356 1.061 7.683 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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/R/R/bin/R CMD INSTALL CAGEfightR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.0/site-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 | 4.693 | 0.043 | 4.763 | |
assignMissingID | 1.418 | 0.016 | 1.437 | |
assignTxID | 1.109 | 0.004 | 1.116 | |
assignTxType | 0.001 | 0.000 | 0.000 | |
balanceBC | 0.000 | 0.001 | 0.001 | |
balanceD | 0.000 | 0.000 | 0.001 | |
bwCommonGenome | 0.040 | 0.008 | 0.054 | |
bwGenomeCompatibility | 0.022 | 0.000 | 0.022 | |
bwValid | 0.01 | 0.00 | 0.01 | |
calcBidirectionality | 0.605 | 0.004 | 0.611 | |
calcComposition | 1.813 | 0.008 | 1.826 | |
calcPooled | 1.391 | 0.049 | 1.443 | |
calcShape | 3.325 | 0.140 | 3.472 | |
calcSupport | 0.137 | 0.004 | 0.141 | |
calcTPM | 0.168 | 0.000 | 0.169 | |
calcTotalTags | 0.079 | 0.004 | 0.083 | |
checkCTSSs | 0.352 | 0.000 | 0.355 | |
checkPeaked | 0.078 | 0.004 | 0.083 | |
checkPooled | 0.079 | 0.004 | 0.083 | |
clusterBidirectionally | 0 | 0 | 0 | |
clusterUnidirectionally | 1.770 | 0.012 | 1.786 | |
combineClusters | 0.988 | 0.008 | 0.999 | |
convertBAM2BigWig | 0 | 0 | 0 | |
convertBED2BigWig | 0 | 0 | 0 | |
convertGRanges2GPos | 0.1 | 0.0 | 0.1 | |
exampleDesign | 0.005 | 0.000 | 0.004 | |
findLinks | 7.356 | 1.061 | 7.683 | |
findStretches | 0.501 | 0.083 | 0.586 | |
quantifyCTSSs | 0.001 | 0.000 | 0.000 | |
quantifyCTSSs2 | 0.001 | 0.000 | 0.000 | |
quantifyClusters | 0.598 | 0.040 | 0.639 | |
quantifyGenes | 1.590 | 0.199 | 1.793 | |
quickEnhancers | 0 | 0 | 0 | |
quickGenes | 0 | 0 | 0 | |
quickTSSs | 0.001 | 0.000 | 0.000 | |
shapeEntropy | 0.001 | 0.000 | 0.000 | |
shapeIQR | 0.000 | 0.001 | 0.000 | |
shapeMean | 0.000 | 0.001 | 0.001 | |
shapeMultimodality | 0.000 | 0.001 | 0.000 | |
subsetByBidirectionality | 0.574 | 0.016 | 0.591 | |
subsetByComposition | 1.701 | 0.064 | 1.768 | |
subsetBySupport | 0.101 | 0.013 | 0.114 | |
swapRanges | 0.231 | 0.008 | 0.239 | |
swapScores | 0.133 | 0.000 | 0.133 | |
trackBalance | 0 | 0 | 0 | |
trackCTSS | 4.120 | 0.587 | 4.717 | |
trackClusters | 2.721 | 0.176 | 2.903 | |
trackLinks | 1.230 | 0.532 | 1.447 | |
trimToPeak | 1.061 | 0.145 | 1.208 | |
trimToPercentiles | 2.814 | 0.048 | 2.870 | |
tuneTagClustering | 0.000 | 0.000 | 0.001 | |
utilsAggregateRows | 0.392 | 0.099 | 0.493 | |
utilsDeStrand | 0.154 | 0.019 | 0.175 | |
utilsScoreOverlaps | 0.092 | 0.000 | 0.093 | |
utilsSimplifyTxDb | 0.000 | 0.000 | 0.001 | |