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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for GeneStructureTools on nebbiolo1

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 727/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.12.0  (landing page)
Beth Signal
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: RELEASE_3_13
git_last_commit: 1b05c47
git_last_commit_date: 2021-05-19 12:33:53 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneStructureTools
Version: 1.12.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneStructureTools_1.12.0.tar.gz
StartedAt: 2021-10-14 09:57:36 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:03:21 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 345.5 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-3.13-bioc/R/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneStructureTools_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-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 ‘1.12.0’
* 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 25.725  0.328  26.060
whippetTranscriptChangeSummary    16.088  0.090  16.178
replaceJunction                    5.951  0.023   5.978
* 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:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GeneStructureTools
###
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* installing to library ‘/home/biocbuild/bbs-3.13-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
DEXSeqIdsToGeneIds0.0030.0000.003
UTR2UTR532.4140.1392.555
addBroadTypes0.1610.0040.165
addIntronInTranscript2.6380.0172.657
alternativeIntronUsage4.7900.0044.797
annotateGeneModel0.9280.0080.936
attrChangeAltSpliced1.4990.0261.524
coordinates-methods0.0710.0200.090
diffSplicingResults-methods0.0730.0090.081
exonsToTranscripts0.2340.0040.238
filterGtfOverlap0.2180.0080.226
filterWhippetEvents0.0790.0110.091
findDEXexonType2.6710.0082.681
findExonContainingTranscripts0.5020.0290.532
findIntronContainingTranscripts0.8730.0130.885
findJunctionPairs2.8490.0282.877
formatWhippetEvents0.0210.0000.021
getOrfs0.7130.0120.725
getUOrfs0.60.00.6
junctions-methods0.0750.0180.093
leafcutterTranscriptChangeSummary25.725 0.32826.060
makeGeneModel0.1420.0000.143
maxLocation0.0040.0000.003
orfDiff2.3330.0542.387
orfSimilarity0.0010.0000.001
overlapTypes2.5770.0042.581
readCounts-methods0.0740.0110.085
readWhippetDIFFfiles0.0050.0030.009
readWhippetDataSet0.0830.0110.094
readWhippetJNCfiles0.0380.0050.042
readWhippetPSIfiles0.0140.0100.024
removeDuplicateTranscripts0.2580.0040.263
removeSameExon0.2080.0000.208
removeVersion0.0000.0000.001
reorderExonNumbers0.1930.0110.204
replaceJunction5.9510.0235.978
skipExonInTranscript2.0780.0052.098
summariseExonTypes2.8820.0042.887
transcriptChangeSummary2.4050.0222.435
whippetTranscriptChangeSummary16.088 0.09016.178