Beth Signal
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: master |
| Last Commit: 74bed05 |
| Last Changed Date: 2019-01-04 13:34:09 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:36:56 -0400 (Tue, 09 Apr 2019).
| Package 632/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneStructureTools 1.3.1 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: GeneStructureTools |
| Version: 1.3.1 |
| 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_1.3.1.tar.gz |
| StartedAt: 2019-04-09 02:58:15 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:17:52 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 1176.6 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_1.3.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GeneStructureTools.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.3.1'
* 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 19.51 0.80 20.31
whippetTranscriptChangeSummary 12.03 0.06 18.15
replaceJunction 5.56 0.01 18.25
UTR2UTR53 4.35 0.64 5.71
readWhippetDataSet 0.06 0.01 11.39
coordinates-methods 0.02 0.01 5.70
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
leafcutterTranscriptChangeSummary 17.75 0.75 18.50
whippetTranscriptChangeSummary 9.62 0.05 19.28
replaceJunction 3.16 0.00 15.29
orfDiff 1.50 0.14 143.10
transcriptChangeSummary 1.44 0.05 15.08
findJunctionPairs 1.11 0.06 63.83
findIntronContainingTranscripts 0.84 0.04 55.89
findExonContainingTranscripts 0.60 0.03 95.47
readWhippetDataSet 0.07 0.03 5.54
readCounts-methods 0.06 0.01 32.80
junctions-methods 0.06 0.00 112.12
coordinates-methods 0.05 0.00 5.80
filterWhippetEvents 0.03 0.00 15.92
diffSplicingResults-methods 0.02 0.00 22.23
* 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:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GeneStructureTools_1.3.1.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_1.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools_1.3.1.zip && rm GeneStructureTools_1.3.1.tar.gz GeneStructureTools_1.3.1.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 984k 100 984k 0 0 6680k 0 --:--:-- --:--:-- --:--:-- 7032k
install for i386
* installing *source* package 'GeneStructureTools' ...
** 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_1.3.1.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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