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This page was generated on 2024-03-28 11:32:21 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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

Package 807/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.22.0  (landing page)
Beth Signal
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: RELEASE_3_18
git_last_commit: 81b9c5e
git_last_commit_date: 2023-10-24 11:03:19 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for GeneStructureTools on kjohnson1


To the developers/maintainers of the GeneStructureTools package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GeneStructureTools
Version: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2024-03-27 14:07:30 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 14:15:11 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 460.6 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_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/GeneStructureTools.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneStructureTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneStructureTools’ version ‘1.22.0’
* 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 23.442  0.750  24.306
whippetTranscriptChangeSummary    12.053  0.278  12.433
* 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
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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
DEXSeqIdsToGeneIds0.0040.0010.005
UTR2UTR533.6550.1213.785
addBroadTypes0.2270.0130.241
addIntronInTranscript2.0110.1202.170
alternativeIntronUsage4.0810.0254.155
annotateGeneModel0.9520.0161.039
attrChangeAltSpliced1.3520.1271.539
coordinates-methods0.0780.0950.197
diffSplicingResults-methods0.0750.0790.176
exonsToTranscripts0.3050.0070.312
filterGtfOverlap0.2900.0070.298
filterWhippetEvents0.0840.0890.236
findDEXexonType2.3750.0202.400
findExonContainingTranscripts0.5000.1110.675
findIntronContainingTranscripts0.7370.0990.912
findJunctionPairs1.4070.1081.542
formatWhippetEvents0.0180.0110.030
getOrfs0.7500.0170.774
getUOrfs0.5630.0120.575
junctions-methods0.0740.0730.167
leafcutterTranscriptChangeSummary23.442 0.75024.306
makeGeneModel0.2090.0060.215
maxLocation0.0030.0000.003
orfDiff1.6550.1281.825
orfSimilarity0.0010.0000.001
overlapTypes2.1780.0142.193
readCounts-methods0.0720.0700.160
readWhippetDIFFfiles0.0070.0090.019
readWhippetDataSet0.0710.0740.165
readWhippetJNCfiles0.0370.0350.081
readWhippetPSIfiles0.0220.0350.066
removeDuplicateTranscripts0.3070.0070.315
removeSameExon0.2660.0070.278
removeVersion0.0000.0010.000
reorderExonNumbers0.1630.0080.210
replaceJunction3.2770.0823.459
skipExonInTranscript1.3810.0911.500
summariseExonTypes2.3630.0172.384
transcriptChangeSummary1.5170.1221.678
whippetTranscriptChangeSummary12.053 0.27812.433