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This page was generated on 2022-10-19 13:22:59 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 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 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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: 2022-10-19 02:46:15 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 02:57:11 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 656.6 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_1.16.0.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 49.889  0.800  51.031
whippetTranscriptChangeSummary    26.109  0.214  26.425
alternativeIntronUsage             8.639  0.029   8.681
replaceJunction                    7.954  0.080   8.061
UTR2UTR53                          7.210  0.284   7.504
findDEXexonType                    6.616  0.046   6.726
summariseExonTypes                 5.768  0.021   5.798
overlapTypes                       5.584  0.025   5.622
* 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

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


* 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
DEXSeqIdsToGeneIds0.0040.0010.005
UTR2UTR537.2100.2847.504
addBroadTypes0.3040.0050.309
addIntronInTranscript3.6080.1063.750
alternativeIntronUsage8.6390.0298.681
annotateGeneModel1.7850.0131.801
attrChangeAltSpliced2.6030.0782.702
coordinates-methods0.0980.0460.155
diffSplicingResults-methods0.1000.0440.150
exonsToTranscripts0.5140.0070.522
filterGtfOverlap0.4830.0060.489
filterWhippetEvents0.1230.0540.185
findDEXexonType6.6160.0466.726
findExonContainingTranscripts0.9230.0681.011
findIntronContainingTranscripts1.3760.0701.497
findJunctionPairs2.9040.0783.039
formatWhippetEvents0.0260.0070.034
getOrfs1.4340.0181.460
getUOrfs1.1020.0121.115
junctions-methods0.1020.0500.178
leafcutterTranscriptChangeSummary49.889 0.80051.031
makeGeneModel0.3060.0050.311
maxLocation0.0050.0000.005
orfDiff3.3100.1083.455
orfSimilarity0.0020.0000.002
overlapTypes5.5840.0255.622
readCounts-methods0.1010.0480.156
readWhippetDIFFfiles0.0080.0050.013
readWhippetDataSet0.1010.0530.163
readWhippetJNCfiles0.0510.0200.074
readWhippetPSIfiles0.0210.0210.045
removeDuplicateTranscripts0.5090.0070.518
removeSameExon0.4190.0070.425
removeVersion0.0000.0000.001
reorderExonNumbers0.3180.0050.324
replaceJunction7.9540.0808.061
skipExonInTranscript2.6620.0582.730
summariseExonTypes5.7680.0215.798
transcriptChangeSummary2.9970.0873.106
whippetTranscriptChangeSummary26.109 0.21426.425