Konstantin Krismer
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/transite |
| Branch: RELEASE_3_9 |
| Last Commit: 9703392 |
| Last Changed Date: 2019-10-07 15:30:54 -0400 (Mon, 07 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:16:35 -0400 (Wed, 16 Oct 2019).
| Package 1667/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| transite 1.2.1 Konstantin Krismer
| 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: transite |
| Version: 1.2.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:transite.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings transite_1.2.1.tar.gz |
| StartedAt: 2019-10-16 05:30:54 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:34:48 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 234.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: transite.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:transite.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings transite_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/transite.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘transite/DESCRIPTION’ ... OK
* this is package ‘transite’ version ‘1.2.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘transite’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
runKmerSPMA 43.309 0.112 53.355
runKmerTSMA 41.082 0.008 45.659
calculateKmerEnrichment 7.495 0.012 7.506
runMatrixSPMA 3.037 0.016 5.056
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/transite.Rcheck/00check.log’
for details.
transite.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL transite ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘transite’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c scoring.cpp -o scoring.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o transite.so RcppExports.o scoring.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-transite/00new/transite/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (transite)
transite.Rcheck/transite-Ex.timings
| name | user | system | elapsed | |
| RBPMotif-class | 0.006 | 0.000 | 0.007 | |
| SpectrumScore-class | 0.002 | 0.000 | 0.002 | |
| calculateKmerEnrichment | 7.495 | 0.012 | 7.506 | |
| calculateKmerScores | 0.004 | 0.000 | 0.003 | |
| calculateLocalConsistency | 0.640 | 0.016 | 0.656 | |
| calculateMotifEnrichment | 1.516 | 0.004 | 1.520 | |
| calculateTranscriptMC | 0.006 | 0.000 | 0.006 | |
| checkKmers | 0.001 | 0.000 | 0.000 | |
| computeKmerEnrichment | 3.917 | 0.004 | 3.939 | |
| createKmerMotif | 0.004 | 0.000 | 0.004 | |
| createMatrixMotif | 0.003 | 0.000 | 0.003 | |
| drawVolcanoPlot | 0.631 | 0.008 | 0.639 | |
| empiricalEnrichmentMeanCDF | 0.005 | 0.000 | 0.005 | |
| generateIUPACByKmers | 0.001 | 0.000 | 0.000 | |
| generateIUPACByMatrix | 0.003 | 0.000 | 0.003 | |
| generateKmers | 0.152 | 0.000 | 0.152 | |
| generateKmersFromIUPAC | 0.003 | 0.000 | 0.004 | |
| geometricMean | 0.000 | 0.000 | 0.001 | |
| getMotifById | 0.002 | 0.004 | 0.006 | |
| getMotifByRBP | 0.007 | 0.000 | 0.007 | |
| getMotifs | 0 | 0 | 0 | |
| getPPM | 0.008 | 0.000 | 0.007 | |
| initIUPAClookupTable | 0.004 | 0.000 | 0.003 | |
| motifsMetaInfo | 0.024 | 0.000 | 0.023 | |
| pCombine | 0.000 | 0.000 | 0.001 | |
| runKmerSPMA | 43.309 | 0.112 | 53.355 | |
| runKmerTSMA | 41.082 | 0.008 | 45.659 | |
| runMatrixSPMA | 3.037 | 0.016 | 5.056 | |
| runMatrixTSMA | 0.018 | 0.000 | 0.018 | |
| scoreSequences | 0.004 | 0.004 | 0.007 | |
| scoreSpectrum | 1.256 | 0.030 | 1.287 | |
| scoreTranscripts | 0.01 | 0.00 | 0.01 | |
| setMotifs | 0.003 | 0.000 | 0.003 | |
| spectrumClassifier | 1.276 | 0.000 | 1.277 | |
| subdivideData | 0.005 | 0.000 | 0.005 | |