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This page was generated on 2025-10-06 11:38 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 822/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.28.0  (landing page)
Beth Signal
Snapshot Date: 2025-10-02 13:40 -0400 (Thu, 02 Oct 2025)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: RELEASE_3_21
git_last_commit: f23a47c
git_last_commit_date: 2025-04-15 11:19:16 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GeneStructureTools on nebbiolo1

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: 1.28.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeneStructureTools_1.28.0.tar.gz
StartedAt: 2025-10-05 23:28:48 -0400 (Sun, 05 Oct 2025)
EndedAt: 2025-10-05 23:37:10 -0400 (Sun, 05 Oct 2025)
EllapsedTime: 502.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeneStructureTools_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.28.0’
* 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 20.611  0.154  20.768
whippetTranscriptChangeSummary    11.106  0.152  11.261
* 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-3.21-bioc/R/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GeneStructureTools’ ...
** this is package ‘GeneStructureTools’ version ‘1.28.0’
** 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
DEXSeqIdsToGeneIds0.0030.0000.003
UTR2UTR532.2880.1892.478
addBroadTypes0.1710.0020.173
addIntronInTranscript2.9790.1783.159
alternativeIntronUsage4.0670.0374.104
annotateGeneModel0.7850.0050.790
attrChangeAltSpliced1.1850.0601.244
coordinates-methods0.0460.0200.065
diffSplicingResults-methods0.0680.0160.084
exonsToTranscripts0.2580.0150.272
filterGtfOverlap0.2330.0190.252
filterWhippetEvents0.0580.0180.077
findDEXexonType2.5560.0662.627
findExonContainingTranscripts0.3950.0290.425
findIntronContainingTranscripts0.6490.0640.712
findJunctionPairs1.3080.0581.366
formatWhippetEvents0.0130.0030.015
getOrfs0.6790.0190.698
getUOrfs0.5420.0100.552
junctions-methods0.0520.0220.074
leafcutterTranscriptChangeSummary20.611 0.15420.768
makeGeneModel0.1380.0040.142
maxLocation0.0020.0000.002
orfDiff1.3940.0421.435
orfSimilarity0.0000.0000.001
overlapTypes3.0150.1123.127
readCounts-methods0.0450.0160.061
readWhippetDIFFfiles0.0040.0020.006
readWhippetDataSet0.0410.0200.063
readWhippetJNCfiles0.0220.0100.031
readWhippetPSIfiles0.0100.0060.017
removeDuplicateTranscripts0.2310.0080.238
removeSameExon0.2000.0040.204
removeVersion0.0000.0000.001
reorderExonNumbers0.1440.0040.149
replaceJunction3.6200.0283.663
skipExonInTranscript1.2560.0261.283
summariseExonTypes2.2630.0072.270
transcriptChangeSummary1.3120.0321.344
whippetTranscriptChangeSummary11.106 0.15211.261