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CHECK report for transite on tokay2

This page was generated on 2019-04-09 12:42:31 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transite.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings transite_1.1.2.tar.gz
StartedAt: 2019-04-09 06:26:16 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:33:29 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 433.2 seconds
RetCode: 0
Status:  OK  
CheckDir: transite.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transite.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings transite_1.1.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/transite.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 '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 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
* 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/transite/libs/i386/transite.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/transite/libs/x64/transite.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
runKmerSPMA             55.00   0.01   61.12
runKmerTSMA             44.29   0.02   44.60
runMatrixSPMA            9.46   0.02   12.03
calculateKmerEnrichment  6.72   0.00    6.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
runKmerSPMA             48.58   0.00   49.63
runKmerTSMA             37.78   0.01   37.93
runMatrixSPMA            8.41   0.05   11.00
calculateKmerEnrichment  6.81   0.00    6.81
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/transite.Rcheck/00check.log'
for details.



Installation output

transite.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/transite_1.1.2.tar.gz && rm -rf transite.buildbin-libdir && mkdir transite.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transite.buildbin-libdir transite_1.1.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL transite_1.1.2.zip && rm transite_1.1.2.tar.gz transite_1.1.2.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  591k  100  591k    0     0  3986k      0 --:--:-- --:--:-- --:--:-- 4168k

install for i386

* installing *source* package 'transite' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c scoring.cpp -o scoring.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o transite.dll tmp.def RcppExports.o scoring.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/transite.buildbin-libdir/00LOCK-transite/00new/transite/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'transite'
    finding HTML links ... done
    RBPMotif-class                          html  
    SpectrumScore-class                     html  
    calculateKmerEnrichment                 html  
    calculateKmerScores                     html  
    calculateLocalConsistency               html  
    calculateMotifEnrichment                html  
    calculateTranscriptMC                   html  
    checkKmers                              html  
    computeKmerEnrichment                   html  
    computeMotifScore                       html  
    createKmerMotif                         html  
    createMatrixMotif                       html  
    drawVolcanoPlot                         html  
    empiricalEnrichmentMeanCDF              html  
    ge                                      html  
    generateIUPACByKmers                    html  
    generateIUPACByMatrix                   html  
    generateKmers                           html  
    generateKmersFromIUPAC                  html  
    generatePermutedEnrichments             html  
    geometricMean                           html  
    getMotifById                            html  
    getMotifByRBP                           html  
    getMotifs                               html  
    getPPM                                  html  
    homopolymerCorrection                   html  
    initIUPAClookupTable                    html  
    kmers.enrichment                        html  
    lookupKmerScores                        html  
    motifs                                  html  
    motifsMetaInfo                          html  
    pCombine                                html  
    permTestGeometricMean                   html  
    runKmerSPMA                             html  
    runKmerTSMA                             html  
    runMatrixSPMA                           html  
    runMatrixTSMA                           html  
    scoreSequences                          html  
    scoreSpectrum                           html  
    scoreTranscripts                        html  
    scoreTranscriptsSingleMotif             html  
    setMotifs                               html  
    spectrumClassifier                      html  
    subdivideData                           html  
    toy.motif.matrix                        html  
    transite                                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 'transite' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c scoring.cpp -o scoring.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o transite.dll tmp.def RcppExports.o scoring.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/transite.buildbin-libdir/transite/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transite' as transite_1.1.2.zip
* DONE (transite)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'transite' successfully unpacked and MD5 sums checked

Tests output


Example timings

transite.Rcheck/examples_i386/transite-Ex.timings

nameusersystemelapsed
RBPMotif-class000
SpectrumScore-class000
calculateKmerEnrichment6.720.006.72
calculateKmerScores000
calculateLocalConsistency0.530.080.61
calculateMotifEnrichment1.570.031.61
calculateTranscriptMC000
checkKmers000
computeKmerEnrichment3.050.003.05
createKmerMotif0.010.000.01
createMatrixMotif000
drawVolcanoPlot0.640.000.65
empiricalEnrichmentMeanCDF0.020.000.01
generateIUPACByKmers000
generateIUPACByMatrix000
generateKmers0.150.000.16
generateKmersFromIUPAC000
geometricMean000
getMotifById000
getMotifByRBP000
getMotifs000
getPPM000
initIUPAClookupTable000
motifsMetaInfo0.000.020.02
pCombine000
runKmerSPMA55.00 0.0161.12
runKmerTSMA44.29 0.0244.60
runMatrixSPMA 9.46 0.0212.03
runMatrixTSMA0.030.000.03
scoreSequences000
scoreSpectrum1.310.111.75
scoreTranscripts0.020.000.02
setMotifs0.010.000.01
spectrumClassifier0.910.030.94
subdivideData000

transite.Rcheck/examples_x64/transite-Ex.timings

nameusersystemelapsed
RBPMotif-class000
SpectrumScore-class000
calculateKmerEnrichment6.810.006.81
calculateKmerScores0.000.000.05
calculateLocalConsistency0.550.020.56
calculateMotifEnrichment1.530.051.60
calculateTranscriptMC000
checkKmers000
computeKmerEnrichment3.970.003.96
createKmerMotif0.010.000.02
createMatrixMotif000
drawVolcanoPlot0.350.030.38
empiricalEnrichmentMeanCDF000
generateIUPACByKmers000
generateIUPACByMatrix000
generateKmers0.120.000.12
generateKmersFromIUPAC000
geometricMean000
getMotifById000
getMotifByRBP000
getMotifs000
getPPM0.020.000.02
initIUPAClookupTable000
motifsMetaInfo0.010.000.01
pCombine000
runKmerSPMA48.58 0.0049.63
runKmerTSMA37.78 0.0137.93
runMatrixSPMA 8.41 0.0511.00
runMatrixTSMA0.010.000.02
scoreSequences0.020.000.02
scoreSpectrum1.300.051.34
scoreTranscripts000
setMotifs0.020.000.02
spectrumClassifier1.420.011.44
subdivideData0.010.000.01