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CHECK report for transite on malbec2

This page was generated on 2019-04-09 11:52:04 -0400 (Tue, 09 Apr 2019).

Package 1631/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transite 1.1.2
Konstantin Krismer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/transite
Branch: master
Last Commit: 801359e
Last Changed Date: 2019-02-22 14:08:40 -0400 (Fri, 22 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: transite
Version: 1.1.2
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_1.1.2.tar.gz
StartedAt: 2019-04-09 04:07:01 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:10:55 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 234.1 seconds
RetCode: 0
Status:  OK 
CheckDir: transite.Rcheck
Warnings: 0

Command output

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### Running 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_1.1.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/transite.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.1.2’
* 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             51.110  0.133  64.283
runKmerTSMA             46.423  0.017  46.444
calculateKmerEnrichment  6.361  0.004   6.369
runMatrixSPMA            3.280  0.028   5.314
* 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.



Installation output

transite.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL transite
###
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* 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)

Tests output


Example timings

transite.Rcheck/transite-Ex.timings

nameusersystemelapsed
RBPMotif-class0.0040.0000.004
SpectrumScore-class0.0010.0000.002
calculateKmerEnrichment6.3610.0046.369
calculateKmerScores0.0040.0000.004
calculateLocalConsistency0.7080.0360.744
calculateMotifEnrichment1.2540.0001.254
calculateTranscriptMC0.0040.0000.004
checkKmers000
computeKmerEnrichment3.3420.0163.359
createKmerMotif0.0030.0000.003
createMatrixMotif0.0040.0000.004
drawVolcanoPlot0.5860.0160.602
empiricalEnrichmentMeanCDF0.0050.0000.005
generateIUPACByKmers0.0000.0000.001
generateIUPACByMatrix0.0030.0000.003
generateKmers0.160.000.16
generateKmersFromIUPAC0.0040.0000.004
geometricMean000
getMotifById0.0060.0000.006
getMotifByRBP0.0080.0000.008
getMotifs000
getPPM0.0080.0000.008
initIUPAClookupTable0.0030.0000.003
motifsMetaInfo0.0220.0040.026
pCombine0.0000.0010.001
runKmerSPMA51.110 0.13364.283
runKmerTSMA46.423 0.01746.444
runMatrixSPMA3.2800.0285.314
runMatrixTSMA0.0170.0000.017
scoreSequences0.0070.0000.007
scoreSpectrum1.2010.0001.201
scoreTranscripts0.0060.0000.006
setMotifs0.0020.0000.002
spectrumClassifier0.8660.0000.866
subdivideData0.0020.0030.004