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This page was generated on 2022-12-03 11:09:07 -0500 (Sat, 03 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4277
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-11-30 r83393 ucrt) -- "Unsuffered Consequences" 4152
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-30 r83393) -- "Unsuffered Consequences" 4236
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 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? 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 757/2155HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.19.0  (landing page)
Beth Signal
Snapshot Date: 2022-12-02 14:00:12 -0500 (Fri, 02 Dec 2022)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: master
git_last_commit: bb48912
git_last_commit_date: 2022-11-01 11:17:16 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'Gviz' which is not available

Summary

Package: GeneStructureTools
Version: 1.19.0
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_1.19.0.tar.gz
StartedAt: 2022-12-03 01:41:38 -0500 (Sat, 03 Dec 2022)
EndedAt: 2022-12-03 01:57:28 -0500 (Sat, 03 Dec 2022)
EllapsedTime: 950.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GeneStructureTools.Rcheck’
* using R Under development (unstable) (2022-11-30 r83393)
* 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 ‘1.19.0’
* 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 54.663  0.911  73.061
whippetTranscriptChangeSummary    28.089  0.236  36.266
alternativeIntronUsage             9.891  0.037  13.152
replaceJunction                    8.927  0.082  11.148
UTR2UTR53                          7.623  0.302  10.500
findDEXexonType                    6.892  0.033   9.140
summariseExonTypes                 6.706  0.027   8.843
overlapTypes                       6.205  0.031   7.890
addIntronInTranscript              4.103  0.121   5.473
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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
DEXSeqIdsToGeneIds0.0050.0010.005
UTR2UTR53 7.623 0.30210.500
addBroadTypes0.3520.0060.455
addIntronInTranscript4.1030.1215.473
alternativeIntronUsage 9.891 0.03713.152
annotateGeneModel1.8770.0122.626
attrChangeAltSpliced2.7480.0724.101
coordinates-methods0.1060.0530.210
diffSplicingResults-methods0.1060.0530.198
exonsToTranscripts0.5500.0080.708
filterGtfOverlap0.5360.0070.685
filterWhippetEvents0.1280.0550.236
findDEXexonType6.8920.0339.140
findExonContainingTranscripts0.9120.0621.290
findIntronContainingTranscripts1.4280.0652.157
findJunctionPairs3.0420.0704.099
formatWhippetEvents0.0280.0070.046
getOrfs1.5700.0202.215
getUOrfs1.2470.0161.775
junctions-methods0.1060.0570.222
leafcutterTranscriptChangeSummary54.663 0.91173.061
makeGeneModel0.3180.0060.408
maxLocation0.0050.0010.005
orfDiff3.3950.1054.445
orfSimilarity0.0020.0000.001
overlapTypes6.2050.0317.890
readCounts-methods0.1070.0520.216
readWhippetDIFFfiles0.0070.0060.019
readWhippetDataSet0.1050.0520.192
readWhippetJNCfiles0.0530.0240.091
readWhippetPSIfiles0.0230.0240.062
removeDuplicateTranscripts0.5350.0060.639
removeSameExon0.4620.0070.579
removeVersion000
reorderExonNumbers0.3560.0080.446
replaceJunction 8.927 0.08211.148
skipExonInTranscript3.1720.0664.118
summariseExonTypes6.7060.0278.843
transcriptChangeSummary3.3210.0834.248
whippetTranscriptChangeSummary28.089 0.23636.266