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This page was generated on 2025-09-25 11:42 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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: 2025-09-22 13:40 -0400 (Mon, 22 Sep 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: GeneStructureTools
Version: 1.28.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GeneStructureTools_1.28.0.tar.gz
StartedAt: 2025-09-23 10:06:32 -0000 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 10:15:16 -0000 (Tue, 23 Sep 2025)
EllapsedTime: 523.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --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 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 ‘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 32.550  0.260  32.900
whippetTranscriptChangeSummary    17.430  0.124  17.600
replaceJunction                    6.853  0.143   7.015
alternativeIntronUsage             5.774  0.072   5.876
* 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: OK


Installation output

GeneStructureTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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
DEXSeqIdsToGeneIds0.0040.0000.004
UTR2UTR533.1030.1603.277
addBroadTypes0.2290.0120.241
addIntronInTranscript3.6000.1053.731
alternativeIntronUsage5.7740.0725.876
annotateGeneModel1.1400.0121.155
attrChangeAltSpliced1.5770.0451.624
coordinates-methods0.0770.0210.096
diffSplicingResults-methods0.0770.0200.097
exonsToTranscripts0.3630.0040.368
filterGtfOverlap0.3140.0160.330
filterWhippetEvents0.0970.0080.104
findDEXexonType3.3630.0283.402
findExonContainingTranscripts0.5710.0180.590
findIntronContainingTranscripts0.8940.0280.926
findJunctionPairs1.8970.0261.928
formatWhippetEvents0.0160.0070.021
getOrfs0.9620.0240.988
getUOrfs0.7350.0070.744
junctions-methods0.0750.0230.098
leafcutterTranscriptChangeSummary32.55 0.2632.90
makeGeneModel0.2000.0040.205
maxLocation0.0040.0000.004
orfDiff2.1390.0512.196
orfSimilarity0.0010.0000.001
overlapTypes3.2890.0243.321
readCounts-methods0.0670.0330.100
readWhippetDIFFfiles0.0040.0050.009
readWhippetDataSet0.0730.0250.096
readWhippetJNCfiles0.0400.0050.046
readWhippetPSIfiles0.0170.0110.027
removeDuplicateTranscripts0.3500.0000.351
removeSameExon0.2860.0080.295
removeVersion0.0010.0000.001
reorderExonNumbers0.2240.0080.232
replaceJunction6.8530.1437.015
skipExonInTranscript1.9590.0622.024
summariseExonTypes3.5590.0083.576
transcriptChangeSummary2.1180.0732.198
whippetTranscriptChangeSummary17.430 0.12417.600