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This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 801/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.27.0  (landing page)
Beth Signal
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: devel
git_last_commit: 001986b
git_last_commit_date: 2024-10-29 10:26:11 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for GeneStructureTools on lconway

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: 1.27.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneStructureTools_1.27.0.tar.gz
StartedAt: 2024-12-23 20:36:43 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 20:44:12 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 449.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneStructureTools_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeneStructureTools.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneStructureTools’ version ‘1.27.0’
* 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 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 26.977  1.200  28.410
whippetTranscriptChangeSummary    13.819  0.244  14.287
* 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

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘GeneStructureTools’ ...
** 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
DEXSeqIdsToGeneIds0.0030.0010.004
UTR2UTR532.3030.0942.411
addBroadTypes0.1920.0050.199
addIntronInTranscript1.9040.0942.161
alternativeIntronUsage4.2860.0344.345
annotateGeneModel0.8930.0150.918
attrChangeAltSpliced1.2040.0841.419
coordinates-methods0.0690.0670.236
diffSplicingResults-methods0.0680.0650.230
exonsToTranscripts0.2520.0060.263
filterGtfOverlap0.3290.0090.339
filterWhippetEvents0.0810.0720.259
findDEXexonType2.5290.0242.571
findExonContainingTranscripts0.4560.0760.636
findIntronContainingTranscripts0.7220.0840.964
findJunctionPairs1.6040.0911.836
formatWhippetEvents0.0180.0100.047
getOrfs0.7420.0150.764
getUOrfs0.6120.0130.629
junctions-methods0.0750.0700.244
leafcutterTranscriptChangeSummary26.977 1.20028.410
makeGeneModel0.1800.0060.186
maxLocation0.0030.0010.003
orfDiff1.8050.1192.188
orfSimilarity0.0010.0010.002
overlapTypes2.4660.0222.503
readCounts-methods0.0720.0760.246
readWhippetDIFFfiles0.0060.0080.025
readWhippetDataSet0.0750.0770.267
readWhippetJNCfiles0.0360.0330.116
readWhippetPSIfiles0.0200.0340.102
removeDuplicateTranscripts0.2920.0080.304
removeSameExon0.2520.0060.261
removeVersion000
reorderExonNumbers0.1950.0080.206
replaceJunction4.2840.1044.511
skipExonInTranscript1.4340.0791.619
summariseExonTypes2.6930.0212.729
transcriptChangeSummary1.6230.1021.852
whippetTranscriptChangeSummary13.819 0.24414.287