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This page was generated on 2022-08-12 13:21:30 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 palomino3


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: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 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 20.04.4 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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GeneStructureTools_1.16.0.tar.gz
StartedAt: 2022-08-12 01:09:35 -0400 (Fri, 12 Aug 2022)
EndedAt: 2022-08-12 01:16:36 -0400 (Fri, 12 Aug 2022)
EllapsedTime: 420.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneStructureTools.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GeneStructureTools_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/GeneStructureTools.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 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 26.07   1.72   28.00
whippetTranscriptChangeSummary    13.27   0.31   14.98
replaceJunction                    4.11   0.10    5.32
* 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:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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
DEXSeqIdsToGeneIds0.000.020.01
UTR2UTR533.080.194.43
addBroadTypes0.260.000.26
addIntronInTranscript1.940.042.99
alternativeIntronUsage4.260.074.32
annotateGeneModel1.000.031.05
attrChangeAltSpliced1.360.052.36
coordinates-methods0.040.021.10
diffSplicingResults-methods0.060.011.10
exonsToTranscripts0.310.030.34
filterGtfOverlap0.310.030.35
filterWhippetEvents0.070.021.07
findDEXexonType3.760.093.88
findExonContainingTranscripts0.520.001.61
findIntronContainingTranscripts0.730.001.84
findJunctionPairs2.310.003.39
formatWhippetEvents0.030.000.14
getOrfs0.860.020.87
getUOrfs0.680.010.69
junctions-methods0.040.031.30
leafcutterTranscriptChangeSummary26.07 1.7228.00
makeGeneModel0.390.000.39
maxLocation000
orfDiff2.100.173.55
orfSimilarity0.000.010.01
overlapTypes2.810.022.83
readCounts-methods0.040.051.16
readWhippetDIFFfiles0.000.010.12
readWhippetDataSet0.040.051.13
readWhippetJNCfiles0.030.010.54
readWhippetPSIfiles0.010.040.44
removeDuplicateTranscripts0.570.000.56
removeSameExon0.340.000.35
removeVersion000
reorderExonNumbers0.280.010.29
replaceJunction4.110.105.32
skipExonInTranscript1.640.032.71
summariseExonTypes3.900.033.93
transcriptChangeSummary1.860.083.05
whippetTranscriptChangeSummary13.27 0.3114.98