Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:03 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 machv2


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 736/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.14.0  (landing page)
Beth Signal
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: RELEASE_3_14
git_last_commit: 2d82a8c
git_last_commit_date: 2021-10-26 12:42:28 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2022-04-12 13:36:58 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 13:46:23 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 565.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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### Running 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.14.0’
* 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 43.730  0.788  44.611
whippetTranscriptChangeSummary    29.453  0.204  29.698
replaceJunction                   10.206  0.124  10.387
alternativeIntronUsage             9.826  0.047   9.990
findDEXexonType                    5.105  0.063   5.173
addIntronInTranscript              5.074  0.087   5.360
* 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/4.1/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
DEXSeqIdsToGeneIds0.0040.0020.006
UTR2UTR534.6300.2184.852
addBroadTypes0.3540.0250.380
addIntronInTranscript5.0740.0875.360
alternativeIntronUsage9.8260.0479.990
annotateGeneModel1.8500.0141.867
attrChangeAltSpliced2.8950.0682.972
coordinates-methods0.1100.0510.169
diffSplicingResults-methods0.1260.0550.190
exonsToTranscripts0.4420.0090.450
filterGtfOverlap0.4600.0080.468
filterWhippetEvents0.1440.0550.207
findDEXexonType5.1050.0635.173
findExonContainingTranscripts0.9070.0740.987
findIntronContainingTranscripts1.2800.0661.352
findJunctionPairs4.5660.0594.635
formatWhippetEvents0.0360.0070.043
getOrfs1.5330.0151.549
getUOrfs1.0710.0111.086
junctions-methods0.1150.0550.179
leafcutterTranscriptChangeSummary43.730 0.78844.611
makeGeneModel0.2900.0070.298
maxLocation0.0040.0010.006
orfDiff3.6050.0863.703
orfSimilarity0.0010.0010.002
overlapTypes4.4570.0484.530
readCounts-methods0.1170.0530.179
readWhippetDIFFfiles0.0080.0070.017
readWhippetDataSet0.1060.0530.164
readWhippetJNCfiles0.0610.0260.090
readWhippetPSIfiles0.0210.0240.049
removeDuplicateTranscripts0.4690.0100.481
removeSameExon0.3680.0110.381
removeVersion0.0000.0000.001
reorderExonNumbers0.3600.0110.373
replaceJunction10.206 0.12410.387
skipExonInTranscript3.5220.0613.596
summariseExonTypes4.0690.0204.098
transcriptChangeSummary3.2170.0723.302
whippetTranscriptChangeSummary29.453 0.20429.698