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This page was generated on 2024-03-27 11:37:38 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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: 2024-03-25 14:05:07 -0400 (Mon, 25 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)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for GeneStructureTools on merida1


To the developers/maintainers of the GeneStructureTools package:
- 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 Troubleshooting Build Report for more information.
- 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: 2024-03-26 03:00:28 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 03:14:13 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 824.7 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_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 Monterey 12.7.1
* 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 55.160  1.463  59.323
whippetTranscriptChangeSummary    27.889  0.403  30.305
alternativeIntronUsage             9.781  0.079  10.344
replaceJunction                    8.891  0.141  10.000
UTR2UTR53                          6.429  0.289   6.856
findDEXexonType                    5.803  0.089   6.401
summariseExonTypes                 5.606  0.039   6.287
overlapTypes                       5.187  0.051   5.795
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneStructureTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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
DEXSeqIdsToGeneIds0.0050.0020.006
UTR2UTR536.4290.2896.856
addBroadTypes0.3700.0090.381
addIntronInTranscript4.1180.1384.636
alternativeIntronUsage 9.781 0.07910.344
annotateGeneModel1.8430.0211.964
attrChangeAltSpliced2.7550.1203.180
coordinates-methods0.1130.0770.210
diffSplicingResults-methods0.1120.0780.213
exonsToTranscripts0.5860.0180.632
filterGtfOverlap0.5750.0160.647
filterWhippetEvents0.1400.0940.253
findDEXexonType5.8030.0896.401
findExonContainingTranscripts0.8930.0871.041
findIntronContainingTranscripts1.3870.0981.569
findJunctionPairs3.0310.1113.349
formatWhippetEvents0.0340.0120.052
getOrfs1.6610.0231.777
getUOrfs1.2660.0211.323
junctions-methods0.1120.0850.211
leafcutterTranscriptChangeSummary55.160 1.46359.323
makeGeneModel0.3370.0090.351
maxLocation0.0060.0010.007
orfDiff3.4120.1303.902
orfSimilarity0.0020.0010.005
overlapTypes5.1870.0515.795
readCounts-methods0.1180.0880.240
readWhippetDIFFfiles0.0090.0110.033
readWhippetDataSet0.1140.0880.235
readWhippetJNCfiles0.0610.0430.128
readWhippetPSIfiles0.0280.0370.072
removeDuplicateTranscripts0.5470.0110.570
removeSameExon0.4790.0090.525
removeVersion0.0000.0000.001
reorderExonNumbers0.3590.0080.376
replaceJunction 8.891 0.14110.000
skipExonInTranscript3.1920.1133.742
summariseExonTypes5.6060.0396.287
transcriptChangeSummary3.300.133.80
whippetTranscriptChangeSummary27.889 0.40330.305