Back to Multiple platform build/check report for BioC 3.14
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-18 12:06:39 -0400 (Sat, 18 Sep 2021).

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? here 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 719/2029HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.13.0  (landing page)
Beth Signal
Snapshot Date: 2021-09-17 14:50:09 -0400 (Fri, 17 Sep 2021)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: master
git_last_commit: b6fe688
git_last_commit_date: 2021-05-19 12:33:53 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / 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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2021-09-18 03:16:18 -0400 (Sat, 18 Sep 2021)
EndedAt: 2021-09-18 03:24:48 -0400 (Sat, 18 Sep 2021)
EllapsedTime: 509.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.13.0’
* 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 41.944  0.701  42.727
whippetTranscriptChangeSummary    26.458  0.216  26.728
replaceJunction                   10.099  0.082  10.208
alternativeIntronUsage             8.189  0.035   8.242
findDEXexonType                    5.538  0.068   5.656
* 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/4.1/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
UTR2UTR534.1330.2074.350
addBroadTypes0.3030.0050.310
addIntronInTranscript3.9390.0724.197
alternativeIntronUsage8.1890.0358.242
annotateGeneModel1.6720.0141.688
attrChangeAltSpliced2.5700.0792.660
coordinates-methods0.0990.0500.155
diffSplicingResults-methods0.0970.0510.154
exonsToTranscripts0.3850.0080.394
filterGtfOverlap0.4050.0050.411
filterWhippetEvents0.1190.0520.178
findDEXexonType5.5380.0685.656
findExonContainingTranscripts0.9170.0570.982
findIntronContainingTranscripts1.4000.0541.462
findJunctionPairs3.0110.0573.080
formatWhippetEvents0.0370.0070.045
getOrfs1.3330.0161.350
getUOrfs1.0730.0111.085
junctions-methods0.1240.0550.189
leafcutterTranscriptChangeSummary41.944 0.70142.727
makeGeneModel0.2650.0060.272
maxLocation0.0050.0010.006
orfDiff3.3020.0873.403
orfSimilarity0.0010.0010.002
overlapTypes3.9750.0173.995
readCounts-methods0.1090.0530.170
readWhippetDIFFfiles0.0080.0070.015
readWhippetDataSet0.1030.0500.158
readWhippetJNCfiles0.0520.0240.081
readWhippetPSIfiles0.0200.0240.047
removeDuplicateTranscripts0.4120.0060.419
removeSameExon0.3820.0050.388
removeVersion0.0000.0000.001
reorderExonNumbers0.3750.0060.381
replaceJunction10.099 0.08210.208
skipExonInTranscript3.1010.0693.239
summariseExonTypes4.3980.0224.431
transcriptChangeSummary3.0630.0743.152
whippetTranscriptChangeSummary26.458 0.21626.728