Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 1953/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
segmentSeq 2.42.0 (landing page) Samuel Granjeaud
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | 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: 2.42.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings segmentSeq_2.42.0.tar.gz |
StartedAt: 2025-10-15 12:08:53 -0400 (Wed, 15 Oct 2025) |
EndedAt: 2025-10-15 12:16:10 -0400 (Wed, 15 Oct 2025) |
EllapsedTime: 437.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: segmentSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings segmentSeq_2.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/segmentSeq.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘segmentSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘segmentSeq’ version ‘2.42.0’ * 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 ‘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 43.428 0.280 43.971 lociLikelihoods 20.581 0.124 25.348 heuristicSeg 20.165 0.109 22.303 plotGenome 10.533 0.086 12.186 getCounts 8.040 0.026 8.103 processAD 6.173 0.035 6.742 segmentSeq-package 5.878 0.034 6.796 findChunks 5.154 0.030 5.234 readMethods 5.099 0.024 5.706 getOverlaps 5.070 0.024 5.290 segData-class 4.972 0.060 6.079 normaliseNC 4.701 0.230 5.670 thresholdFinder 4.494 0.265 5.483 readMeths 4.471 0.230 5.161 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/segmentSeq.Rcheck/00check.log’ for details.
segmentSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL segmentSeq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘segmentSeq’ ... ** this is package ‘segmentSeq’ version ‘2.42.0’ ** 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 | 4.872 | 0.028 | 4.903 | |
classifySeg | 43.428 | 0.280 | 43.971 | |
findChunks | 5.154 | 0.030 | 5.234 | |
getCounts | 8.040 | 0.026 | 8.103 | |
getOverlaps | 5.070 | 0.024 | 5.290 | |
heuristicSeg | 20.165 | 0.109 | 22.303 | |
lociLikelihoods | 20.581 | 0.124 | 25.348 | |
normaliseNC | 4.701 | 0.230 | 5.670 | |
plotGenome | 10.533 | 0.086 | 12.186 | |
processAD | 6.173 | 0.035 | 6.742 | |
readMethods | 5.099 | 0.024 | 5.706 | |
readMeths | 4.471 | 0.230 | 5.161 | |
segData-class | 4.972 | 0.060 | 6.079 | |
segmentSeq-package | 5.878 | 0.034 | 6.796 | |
thresholdFinder | 4.494 | 0.265 | 5.483 | |