Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-12 11:41:04 -0400 (Tue, 12 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-06 r86056) -- "Unsuffered Consequences" | 4471 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-06 r86056 ucrt) -- "Unsuffered Consequences" | 4417 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-04 r86048) -- "Unsuffered Consequences" | 4444 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4430 |
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 1898/2257 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Thomas J. Hardcastle
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 2.37.1 |
Command: /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings segmentSeq_2.37.1.tar.gz |
StartedAt: 2024-03-12 09:02:03 -0000 (Tue, 12 Mar 2024) |
EndedAt: 2024-03-12 09:09:36 -0000 (Tue, 12 Mar 2024) |
EllapsedTime: 452.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: segmentSeq.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings segmentSeq_2.37.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/segmentSeq.Rcheck’ * using R Under development (unstable) (2024-01-16 r85812) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 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 ‘segmentSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘segmentSeq’ version ‘2.37.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘segmentSeq’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor Warning: Package 'segmentSeq' is deprecated and will be removed from See ‘/home/biocbuild/bbs-3.19-bioc/meat/segmentSeq.Rcheck/00install.out’ for details. * 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 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 ... NOTE heuristicSeg : <anonymous>: no visible binding for global variable ‘sDP’ Undefined global functions or variables: sDP * 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 ... NOTE Argument items with no description in Rd file 'plotMeth.Rd': ‘loci’ * 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 42.879 0.148 43.114 lociLikelihoods 19.228 0.012 19.281 heuristicSeg 18.863 0.016 18.917 plotGenome 9.952 0.012 9.983 getCounts 7.034 0.008 7.056 processAD 5.634 0.008 5.654 segmentSeq-package 5.555 0.008 5.575 segData-class 5.507 0.020 5.537 normaliseNC 5.045 0.060 5.119 * 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 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/segmentSeq.Rcheck/00check.log’ for details.
segmentSeq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD INSTALL segmentSeq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library’ * installing *source* package ‘segmentSeq’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning message: Package 'baySeq' is deprecated and will be removed from Bioconductor version 3.19 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor version 3.19 Warning: Package 'segmentSeq' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor version 3.19 Warning: Package 'segmentSeq' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (segmentSeq)
segmentSeq.Rcheck/segmentSeq-Ex.timings
name | user | system | elapsed | |
alignmentData-class | 4.527 | 0.015 | 4.556 | |
classifySeg | 42.879 | 0.148 | 43.114 | |
findChunks | 4.502 | 0.000 | 4.511 | |
getCounts | 7.034 | 0.008 | 7.056 | |
getOverlaps | 4.629 | 0.000 | 4.639 | |
heuristicSeg | 18.863 | 0.016 | 18.917 | |
lociLikelihoods | 19.228 | 0.012 | 19.281 | |
normaliseNC | 5.045 | 0.060 | 5.119 | |
plotGenome | 9.952 | 0.012 | 9.983 | |
processAD | 5.634 | 0.008 | 5.654 | |
readMethods | 4.562 | 0.000 | 4.571 | |
readMeths | 3.974 | 0.048 | 4.030 | |
segData-class | 5.507 | 0.020 | 5.537 | |
segmentSeq-package | 5.555 | 0.008 | 5.575 | |
thresholdFinder | 4.003 | 0.044 | 4.055 | |