Beth Signal
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: RELEASE_3_9 |
| Last Commit: 0263272 |
| Last Changed Date: 2019-05-02 11:54:10 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:40:45 -0400 (Wed, 16 Oct 2019).
| Package 641/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneStructureTools 1.4.0 Beth Signal
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GeneStructureTools |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneStructureTools_1.4.0.tar.gz |
| StartedAt: 2019-10-16 03:56:40 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:05:51 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 550.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GeneStructureTools_1.4.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneStructureTools.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneStructureTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneStructureTools' version '1.4.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
leafcutterTranscriptChangeSummary 14.78 0.63 15.41
whippetTranscriptChangeSummary 9.57 0.06 11.98
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
leafcutterTranscriptChangeSummary 26.60 0.70 27.30
whippetTranscriptChangeSummary 11.34 0.04 12.26
replaceJunction 4.08 0.05 5.41
addIntronInTranscript 2.03 0.03 18.56
filterWhippetEvents 0.08 0.02 5.07
* 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
GeneStructureTools.Rcheck/00install.out
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###
### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GeneStructureTools_1.4.0.tar.gz && rm -rf GeneStructureTools.buildbin-libdir && mkdir GeneStructureTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneStructureTools.buildbin-libdir GeneStructureTools_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools_1.4.0.zip && rm GeneStructureTools_1.4.0.tar.gz GeneStructureTools_1.4.0.zip
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install for i386
* installing *source* package 'GeneStructureTools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GeneStructureTools'
finding HTML links ... done
DEXSeqIdsToGeneIds html
UTR2UTR53 html
addBroadTypes html
addIntronInTranscript html
addSets html
alternativeIntronUsage html
annotateGeneModel html
attrChangeAltSpliced html
coordinates-methods html
cumsumANDpad html
diffSplicingResults-methods html
exonsToTranscripts html
filterGtfOverlap html
filterWhippetEvents html
findDEXexonType html
findExonContainingTranscripts html
findIntronContainingTranscripts html
findJunctionPairs html
formatWhippetEvents html
getOrfs html
getUOrfs html
junctions-methods html
leafcutterTranscriptChangeSummary html
makeGeneModel html
maxLocation html
orfDiff html
orfSimilarity html
overlapTypes html
readCounts-methods html
readWhippetDIFFfiles html
readWhippetDataSet html
readWhippetJNCfiles html
readWhippetPSIfiles html
removeDuplicateTranscripts html
removeSameExon html
removeVersion html
reorderExonNumbers html
replaceJunction html
skipExonInTranscript html
summariseExonTypes html
transcriptChangeSummary html
whippetDataSet-class html
whippetTranscriptChangeSummary html
** 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
install for x64
* installing *source* package 'GeneStructureTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneStructureTools' as GeneStructureTools_1.4.0.zip
* DONE (GeneStructureTools)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GeneStructureTools' successfully unpacked and MD5 sums checked
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GeneStructureTools.Rcheck/examples_i386/GeneStructureTools-Ex.timings
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GeneStructureTools.Rcheck/examples_x64/GeneStructureTools-Ex.timings
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