Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-06-16 11:47 -0400 (Mon, 16 Jun 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4838 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4578 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4602 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4556 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4576 |
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 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: segmentSeq |
Version: 2.42.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings segmentSeq_2.42.0.tar.gz |
StartedAt: 2025-06-13 14:22:39 -0000 (Fri, 13 Jun 2025) |
EndedAt: 2025-06-13 14:31:16 -0000 (Fri, 13 Jun 2025) |
EllapsedTime: 517.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: segmentSeq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings segmentSeq_2.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/segmentSeq.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * 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 loading without being on the library search path ... 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 47.278 0.132 54.100 lociLikelihoods 20.844 0.000 22.963 heuristicSeg 20.648 0.000 21.994 plotGenome 10.955 0.016 11.557 getCounts 7.900 0.000 9.250 segmentSeq-package 6.286 0.000 7.072 processAD 6.175 0.004 6.432 segData-class 6.109 0.012 6.505 alignmentData-class 5.410 0.008 6.150 normaliseNC 5.187 0.059 6.204 getOverlaps 5.112 0.000 5.394 findChunks 5.066 0.000 5.981 readMethods 4.981 0.000 5.702 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/segmentSeq.Rcheck/00check.log’ for details.
segmentSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL segmentSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-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 | 5.410 | 0.008 | 6.150 | |
classifySeg | 47.278 | 0.132 | 54.100 | |
findChunks | 5.066 | 0.000 | 5.981 | |
getCounts | 7.90 | 0.00 | 9.25 | |
getOverlaps | 5.112 | 0.000 | 5.394 | |
heuristicSeg | 20.648 | 0.000 | 21.994 | |
lociLikelihoods | 20.844 | 0.000 | 22.963 | |
normaliseNC | 5.187 | 0.059 | 6.204 | |
plotGenome | 10.955 | 0.016 | 11.557 | |
processAD | 6.175 | 0.004 | 6.432 | |
readMethods | 4.981 | 0.000 | 5.702 | |
readMeths | 4.005 | 0.032 | 4.324 | |
segData-class | 6.109 | 0.012 | 6.505 | |
segmentSeq-package | 6.286 | 0.000 | 7.072 | |
thresholdFinder | 4.104 | 0.039 | 4.326 | |