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This page was generated on 2021-09-20 15:04:49 -0400 (Mon, 20 Sep 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: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 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: 2021-09-19 09:55:27 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 10:01:18 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 351.4 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 25.528  0.650  26.200
whippetTranscriptChangeSummary    15.875  0.053  15.930
replaceJunction                    6.294  0.066   6.361
alternativeIntronUsage             5.398  0.275   5.675
* 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
UTR2UTR532.4780.2032.684
addBroadTypes0.1770.0080.185
addIntronInTranscript2.9440.0833.027
alternativeIntronUsage5.3980.2755.675
annotateGeneModel1.0630.0911.156
attrChangeAltSpliced1.7390.2581.997
coordinates-methods0.0910.0150.105
diffSplicingResults-methods0.0790.0210.099
exonsToTranscripts0.2770.0120.290
filterGtfOverlap0.2950.0160.311
filterWhippetEvents0.0880.0070.095
findDEXexonType2.9280.0082.941
findExonContainingTranscripts0.4980.0330.531
findIntronContainingTranscripts0.8890.0250.913
findJunctionPairs3.0510.5913.641
formatWhippetEvents0.0190.0030.022
getOrfs0.7620.0040.766
getUOrfs0.5480.0160.564
junctions-methods0.0790.0090.088
leafcutterTranscriptChangeSummary25.528 0.65026.200
makeGeneModel0.1170.0160.134
maxLocation0.0000.0030.003
orfDiff1.9970.0392.035
orfSimilarity0.0010.0000.001
overlapTypes2.7550.0042.765
readCounts-methods0.0870.0100.120
readWhippetDIFFfiles0.0080.0010.011
readWhippetDataSet0.0840.0160.108
readWhippetJNCfiles0.0410.0000.041
readWhippetPSIfiles0.0140.0080.020
removeDuplicateTranscripts0.2400.0040.245
removeSameExon0.1910.0120.204
removeVersion000
reorderExonNumbers0.1910.0070.198
replaceJunction6.2940.0666.361
skipExonInTranscript2.2540.0142.269
summariseExonTypes2.7760.0202.796
transcriptChangeSummary1.9620.0522.015
whippetTranscriptChangeSummary15.875 0.05315.930