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This page was generated on 2021-09-20 15:05:42 -0400 (Mon, 20 Sep 2021).

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? here 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 727/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneStructureTools 1.12.0  (landing page)
Beth Signal
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/GeneStructureTools
git_branch: RELEASE_3_13
git_last_commit: 1b05c47
git_last_commit_date: 2021-05-19 12:33:53 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneStructureTools_1.12.0.tar.gz
StartedAt: 2021-09-19 19:18:52 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 19:27:03 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 491.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneStructureTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneStructureTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneStructureTools_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneStructureTools.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 42.551  0.644  43.250
whippetTranscriptChangeSummary    25.879  0.151  26.073
replaceJunction                    9.188  0.082   9.287
alternativeIntronUsage             7.694  0.055   7.759
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/GeneStructureTools.Rcheck/00check.log’
for details.



Installation output

GeneStructureTools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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
DEXSeqIdsToGeneIds0.0020.0000.004
UTR2UTR533.9180.2214.154
addBroadTypes0.2630.0070.271
addIntronInTranscript4.2680.1004.572
alternativeIntronUsage7.6940.0557.759
annotateGeneModel1.5760.0081.584
attrChangeAltSpliced2.3320.0602.399
coordinates-methods0.1100.0490.167
diffSplicingResults-methods0.1080.0510.163
exonsToTranscripts0.3410.0070.349
filterGtfOverlap0.4400.0060.448
filterWhippetEvents0.1260.0490.183
findDEXexonType4.3120.0324.349
findExonContainingTranscripts0.7470.0510.807
findIntronContainingTranscripts1.2290.0661.303
findJunctionPairs4.0020.0804.100
formatWhippetEvents0.0350.0080.044
getOrfs1.3680.0081.377
getUOrfs0.9020.0060.909
junctions-methods0.0930.0450.144
leafcutterTranscriptChangeSummary42.551 0.64443.250
makeGeneModel0.2260.0060.233
maxLocation0.0040.0010.004
orfDiff3.1530.0853.253
orfSimilarity0.0010.0000.001
overlapTypes4.0080.0094.018
readCounts-methods0.1070.0480.163
readWhippetDIFFfiles0.0070.0050.013
readWhippetDataSet0.0950.0490.151
readWhippetJNCfiles0.0550.0210.078
readWhippetPSIfiles0.0200.0200.043
removeDuplicateTranscripts0.3680.0070.374
removeSameExon0.2690.0080.278
removeVersion0.0010.0000.001
reorderExonNumbers0.2500.0040.254
replaceJunction9.1880.0829.287
skipExonInTranscript3.4250.0663.504
summariseExonTypes4.4810.0324.525
transcriptChangeSummary3.0500.0593.117
whippetTranscriptChangeSummary25.879 0.15126.073