Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:07 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 1931/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
segmentSeq 2.43.1 (landing page) Samuel Granjeaud
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the segmentSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/segmentSeq.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. |
Package: segmentSeq |
Version: 2.43.1 |
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:segmentSeq.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings segmentSeq_2.43.1.tar.gz |
StartedAt: 2025-08-04 06:38:21 -0400 (Mon, 04 Aug 2025) |
EndedAt: 2025-08-04 06:45:21 -0400 (Mon, 04 Aug 2025) |
EllapsedTime: 420.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: segmentSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:segmentSeq.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings segmentSeq_2.43.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/segmentSeq.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'segmentSeq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'segmentSeq' version '2.43.1' * 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 'segmentSeq' 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 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: averageMethylationRegions.Rd: GRanges-class findChunks.Rd: GRanges-class, GRanges lociData-class.Rd: countData, countData-class methData-class.Rd: countData, countData-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 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 classifySeg 41.21 0.23 41.47 lociLikelihoods 18.02 0.05 18.31 heuristicSeg 15.89 0.00 15.90 plotGenome 9.54 0.00 9.55 getCounts 7.05 0.03 7.08 processAD 5.49 0.07 5.64 segData-class 5.46 0.01 5.47 segmentSeq-package 5.39 0.00 5.39 * 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: 1 NOTE See 'F:/biocbuild/bbs-3.22-bioc/meat/segmentSeq.Rcheck/00check.log' for details.
segmentSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL segmentSeq ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'segmentSeq' ... ** this is package 'segmentSeq' version '2.43.1' ** using staged installation ** R ** data ** 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 (segmentSeq)
segmentSeq.Rcheck/segmentSeq-Ex.timings
name | user | system | elapsed | |
alignmentData-class | 4.52 | 0.00 | 4.51 | |
classifySeg | 41.21 | 0.23 | 41.47 | |
findChunks | 4.45 | 0.02 | 4.47 | |
getCounts | 7.05 | 0.03 | 7.08 | |
getOverlaps | 4.45 | 0.00 | 4.45 | |
heuristicSeg | 15.89 | 0.00 | 15.90 | |
lociLikelihoods | 18.02 | 0.05 | 18.31 | |
normaliseNC | 4.16 | 0.18 | 4.84 | |
plotGenome | 9.54 | 0.00 | 9.55 | |
processAD | 5.49 | 0.07 | 5.64 | |
readMethods | 4.34 | 0.00 | 4.34 | |
readMeths | 3.29 | 0.28 | 3.61 | |
segData-class | 5.46 | 0.01 | 5.47 | |
segmentSeq-package | 5.39 | 0.00 | 5.39 | |
thresholdFinder | 3.79 | 0.19 | 3.98 | |