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This page was generated on 2025-10-18 12:03 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 827/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.29.0  (landing page)
Beth Signal
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 Oct 2025)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: devel
git_last_commit: 6d9702f
git_last_commit_date: 2025-04-15 11:19:16 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped


CHECK results for GeneStructureTools on nebbiolo2

To the developers/maintainers of the GeneStructureTools package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneStructureTools.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.

raw results


Summary

Package: GeneStructureTools
Version: 1.29.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GeneStructureTools_1.29.0.tar.gz
StartedAt: 2025-10-18 00:06:50 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 00:14:45 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 474.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GeneStructureTools_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneStructureTools’ version ‘1.29.0’
* 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 ‘GeneStructureTools’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
leafcutterTranscriptChangeSummary 19.843  0.203  20.046
whippetTranscriptChangeSummary    11.513  0.609  12.123
alternativeIntronUsage             4.933  0.102   5.035
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

GeneStructureTools.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GeneStructureTools’ ...
** this is package ‘GeneStructureTools’ version ‘1.29.0’
** using staged installation
** R
** 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 (GeneStructureTools)

Tests output


Example timings

GeneStructureTools.Rcheck/GeneStructureTools-Ex.timings

nameusersystemelapsed
DEXSeqIdsToGeneIds0.0020.0000.003
UTR2UTR532.0160.0962.112
addBroadTypes0.1550.0040.160
addIntronInTranscript1.6900.0351.726
alternativeIntronUsage4.9330.1025.035
annotateGeneModel0.7570.0650.824
attrChangeAltSpliced1.0450.0231.069
coordinates-methods0.0430.0180.060
diffSplicingResults-methods0.0400.0170.056
exonsToTranscripts0.2310.0040.234
filterGtfOverlap0.2290.0020.231
filterWhippetEvents0.0470.0140.062
findDEXexonType2.2690.0482.317
findExonContainingTranscripts0.3910.0200.410
findIntronContainingTranscripts0.5680.0190.586
findJunctionPairs1.1600.0441.205
formatWhippetEvents0.0100.0040.014
getOrfs0.6340.0180.652
getUOrfs0.4850.0170.502
junctions-methods0.0410.0210.061
leafcutterTranscriptChangeSummary19.843 0.20320.046
makeGeneModel0.1310.0060.137
maxLocation0.0020.0000.002
orfDiff1.4110.0311.442
orfSimilarity000
overlapTypes2.1080.0062.114
readCounts-methods0.0430.0170.060
readWhippetDIFFfiles0.0020.0040.005
readWhippetDataSet0.0430.0160.060
readWhippetJNCfiles0.0200.0090.029
readWhippetPSIfiles0.0080.0070.014
removeDuplicateTranscripts0.2250.0050.230
removeSameExon0.1890.0010.189
removeVersion000
reorderExonNumbers0.1440.0020.146
replaceJunction3.5400.0253.565
skipExonInTranscript1.2390.0271.266
summariseExonTypes2.2320.0042.237
transcriptChangeSummary1.3190.0321.350
whippetTranscriptChangeSummary11.513 0.60912.123