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This page was generated on 2022-08-08 13:20:21 -0400 (Mon, 08 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4362
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4180
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

CHECK results for GeneStructureTools on merida1


To the developers/maintainers of the GeneStructureTools package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 757/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.16.0  (landing page)
Beth Signal
Snapshot Date: 2022-08-07 13:55:12 -0400 (Sun, 07 Aug 2022)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: RELEASE_3_15
git_last_commit: 25bbb44
git_last_commit_date: 2022-04-26 11:47:45 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneStructureTools
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2022-08-08 02:41:25 -0400 (Mon, 08 Aug 2022)
EndedAt: 2022-08-08 02:52:40 -0400 (Mon, 08 Aug 2022)
EllapsedTime: 674.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneStructureTools’ version ‘1.16.0’
* 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 R 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 51.742  0.848  53.722
whippetTranscriptChangeSummary    27.143  0.217  27.549
alternativeIntronUsage             9.976  0.082  10.070
replaceJunction                    8.119  0.087   8.236
findDEXexonType                    6.615  0.022   6.651
UTR2UTR53                          6.279  0.269   6.639
summariseExonTypes                 6.298  0.021   6.330
overlapTypes                       6.013  0.019   6.061
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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
DEXSeqIdsToGeneIds0.0040.0010.004
UTR2UTR536.2790.2696.639
addBroadTypes0.3580.0080.375
addIntronInTranscript3.9360.0734.080
alternativeIntronUsage 9.976 0.08210.070
annotateGeneModel1.7630.0121.778
attrChangeAltSpliced2.5200.0682.602
coordinates-methods0.1130.0560.178
diffSplicingResults-methods0.1040.0560.168
exonsToTranscripts0.5100.0070.516
filterGtfOverlap0.5140.0060.521
filterWhippetEvents0.1230.0510.185
findDEXexonType6.6150.0226.651
findExonContainingTranscripts0.8490.0560.923
findIntronContainingTranscripts2.4300.0792.523
findJunctionPairs2.7760.0962.887
formatWhippetEvents0.0260.0070.032
getOrfs1.4470.0131.462
getUOrfs1.1270.0111.139
junctions-methods0.1010.0490.158
leafcutterTranscriptChangeSummary51.742 0.84853.722
makeGeneModel0.2910.0080.298
maxLocation0.0050.0010.005
orfDiff3.3290.0783.432
orfSimilarity0.0010.0000.002
overlapTypes6.0130.0196.061
readCounts-methods0.1050.0530.166
readWhippetDIFFfiles0.0090.0060.016
readWhippetDataSet0.1110.0530.172
readWhippetJNCfiles0.0470.0240.074
readWhippetPSIfiles0.0230.0230.051
removeDuplicateTranscripts0.5080.0060.515
removeSameExon0.4380.0060.445
removeVersion000
reorderExonNumbers0.3440.0060.352
replaceJunction8.1190.0878.236
skipExonInTranscript2.9600.0773.057
summariseExonTypes6.2980.0216.330
transcriptChangeSummary3.2690.0783.377
whippetTranscriptChangeSummary27.143 0.21727.549