Beth Signal
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/GeneStructureTools |
| Branch: RELEASE_3_12 |
| Last Commit: 61bb2b5 |
| Last Changed Date: 2020-10-27 11:32:49 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:31:26 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the GeneStructureTools package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 701/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GeneStructureTools 1.10.0 (landing page) Beth Signal
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: GeneStructureTools |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneStructureTools_1.10.0.tar.gz |
| StartedAt: 2021-05-06 03:03:50 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:16:03 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 732.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneStructureTools.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GeneStructureTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings GeneStructureTools_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/GeneStructureTools.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.10.0'
* 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 (user + system) or elapsed time > 5s
user system elapsed
leafcutterTranscriptChangeSummary 24.75 0.89 25.91
whippetTranscriptChangeSummary 14.97 0.06 16.61
alternativeIntronUsage 6.05 0.02 6.06
replaceJunction 4.88 0.08 6.61
UTR2UTR53 4.16 0.33 5.39
skipExonInTranscript 2.65 0.04 5.31
junctions-methods 0.06 0.00 17.13
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
leafcutterTranscriptChangeSummary 40.16 0.80 40.97
whippetTranscriptChangeSummary 21.79 0.02 22.33
alternativeIntronUsage 5.58 0.02 5.59
replaceJunction 5.11 0.04 5.66
addIntronInTranscript 3.81 0.00 6.82
* 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 http://172.29.0.3/BBS/3.12/bioc/src/contrib/GeneStructureTools_1.10.0.tar.gz && rm -rf GeneStructureTools.buildbin-libdir && mkdir GeneStructureTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GeneStructureTools.buildbin-libdir GeneStructureTools_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL GeneStructureTools_1.10.0.zip && rm GeneStructureTools_1.10.0.tar.gz GeneStructureTools_1.10.0.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 987k 100 987k 0 0 36.6M 0 --:--:-- --:--:-- --:--:-- 38.5M
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_1.10.0.zip
* DONE (GeneStructureTools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-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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