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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 791/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.25.0  (landing page)
Beth Signal
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: devel
git_last_commit: 59cccd6
git_last_commit_date: 2024-04-30 11:04:32 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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


CHECK results for GeneStructureTools on merida1

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: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2024-06-10 03:59:46 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 04:15:00 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 913.9 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneStructureTools’ version ‘1.25.0’
* 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 61.596  1.673  71.280
whippetTranscriptChangeSummary    31.151  0.414  36.088
alternativeIntronUsage            11.019  0.075  12.709
replaceJunction                    9.674  0.162  11.578
findDEXexonType                    6.370  0.059   7.120
summariseExonTypes                 6.291  0.050   7.198
UTR2UTR53                          5.818  0.264   6.792
overlapTypes                       5.623  0.046   6.039
addIntronInTranscript              4.427  0.150   5.192
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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
DEXSeqIdsToGeneIds0.0050.0020.009
UTR2UTR535.8180.2646.792
addBroadTypes0.4330.0110.497
addIntronInTranscript4.4270.1505.192
alternativeIntronUsage11.019 0.07512.709
annotateGeneModel2.0790.0252.521
attrChangeAltSpliced3.0630.1643.714
coordinates-methods0.1320.0930.256
diffSplicingResults-methods0.1270.0940.265
exonsToTranscripts0.6970.0190.754
filterGtfOverlap0.6040.0170.686
filterWhippetEvents0.1540.0990.282
findDEXexonType6.3700.0597.120
findExonContainingTranscripts1.0110.1001.228
findIntronContainingTranscripts1.5170.1111.779
findJunctionPairs3.3050.1113.721
formatWhippetEvents0.0320.0110.050
getOrfs1.7760.0261.978
getUOrfs1.4080.0231.552
junctions-methods0.1340.1050.278
leafcutterTranscriptChangeSummary61.596 1.67371.280
makeGeneModel0.3550.0100.425
maxLocation0.0070.0020.009
orfDiff3.8270.1584.465
orfSimilarity0.0020.0010.003
overlapTypes5.6230.0466.039
readCounts-methods0.1220.0930.254
readWhippetDIFFfiles0.0110.0110.028
readWhippetDataSet0.1220.0870.244
readWhippetJNCfiles0.0580.0410.112
readWhippetPSIfiles0.0290.0380.075
removeDuplicateTranscripts0.5770.0150.598
removeSameExon0.5040.0090.518
removeVersion0.0000.0000.001
reorderExonNumbers0.3770.0090.392
replaceJunction 9.674 0.16211.578
skipExonInTranscript3.3780.1203.787
summariseExonTypes6.2910.0507.198
transcriptChangeSummary3.6350.1364.435
whippetTranscriptChangeSummary31.151 0.41436.088