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This page was generated on 2021-09-25 12:05:04 -0400 (Sat, 25 Sep 2021).

CHECK results for GeneStructureTools on nebbiolo2

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 719/2034HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.13.0  (landing page)
Beth Signal
Snapshot Date: 2021-09-24 14:50:08 -0400 (Fri, 24 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneStructureTools_1.13.0.tar.gz
StartedAt: 2021-09-24 20:03:27 -0400 (Fri, 24 Sep 2021)
EndedAt: 2021-09-24 20:09:15 -0400 (Fri, 24 Sep 2021)
EllapsedTime: 348.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneStructureTools_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 23.857  0.224  24.082
whippetTranscriptChangeSummary    16.805  0.111  16.917
replaceJunction                    6.995  0.025   7.020
alternativeIntronUsage             5.496  0.012   5.509
* 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:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL GeneStructureTools
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
DEXSeqIdsToGeneIds0.0020.0000.003
UTR2UTR532.2580.1682.427
addBroadTypes0.1750.0040.178
addIntronInTranscript2.7950.0192.815
alternativeIntronUsage5.4960.0125.509
annotateGeneModel0.9800.0000.981
attrChangeAltSpliced1.5850.0061.592
coordinates-methods0.0790.0050.084
diffSplicingResults-methods0.0700.0180.087
exonsToTranscripts0.3430.0040.347
filterGtfOverlap0.2300.0040.234
filterWhippetEvents0.0840.0130.098
findDEXexonType2.5150.0242.539
findExonContainingTranscripts0.4810.0240.504
findIntronContainingTranscripts0.8060.0250.832
findJunctionPairs1.7050.0351.739
formatWhippetEvents0.0190.0030.021
getOrfs0.7070.0080.715
getUOrfs0.5530.0120.565
junctions-methods0.1130.0170.129
leafcutterTranscriptChangeSummary23.857 0.22424.082
makeGeneModel0.1360.0000.137
maxLocation0.0030.0000.003
orfDiff1.9890.0342.022
orfSimilarity0.0000.0000.001
overlapTypes2.3650.0002.366
readCounts-methods0.0810.0140.095
readWhippetDIFFfiles0.0060.0020.008
readWhippetDataSet0.0740.0180.092
readWhippetJNCfiles0.0310.0080.038
readWhippetPSIfiles0.0180.0030.021
removeDuplicateTranscripts0.2350.0000.235
removeSameExon0.1970.0000.196
removeVersion000
reorderExonNumbers0.1850.0000.185
replaceJunction6.9950.0257.020
skipExonInTranscript2.0090.0192.028
summariseExonTypes2.5900.0122.601
transcriptChangeSummary1.8900.0171.908
whippetTranscriptChangeSummary16.805 0.11116.917