Package: transite

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transite.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transite_1.1.2.tar.gz

StartedAt: 2019-04-09 04:11:14 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:15:43 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 268.8 seconds

RetCode: 0

Status:  OK

CheckDir: transite.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:transite.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings transite_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/transite.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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             58.125  0.659  69.089
runKmerTSMA             56.037  0.147  61.605
calculateKmerEnrichment  8.099  0.019   8.200
runMatrixSPMA            3.087  0.040   5.360
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/transite.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL transite
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘transite’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c scoring.cpp -o scoring.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o transite.so RcppExports.o scoring.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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
* DONE (transite)

name	user	system	elapsed
RBPMotif-class	0.007	0.001	0.009
SpectrumScore-class	0.003	0.000	0.003
calculateKmerEnrichment	8.099	0.019	8.200
calculateKmerScores	0.004	0.001	0.004
calculateLocalConsistency	1.042	0.036	1.085
calculateMotifEnrichment	1.473	0.040	1.524
calculateTranscriptMC	0.01	0.00	0.01
checkKmers	0.001	0.000	0.000
computeKmerEnrichment	3.803	0.006	3.845
createKmerMotif	0.004	0.000	0.004
createMatrixMotif	0.004	0.000	0.005
drawVolcanoPlot	0.460	0.012	0.478
empiricalEnrichmentMeanCDF	0.004	0.000	0.005
generateIUPACByKmers	0.001	0.001	0.001
generateIUPACByMatrix	0.002	0.000	0.003
generateKmers	0.168	0.002	0.171
generateKmersFromIUPAC	0.003	0.000	0.004
geometricMean	0.001	0.000	0.001
getMotifById	0.004	0.001	0.004
getMotifByRBP	0.008	0.002	0.010
getMotifs	0.001	0.000	0.001
getPPM	0.009	0.001	0.010
initIUPAClookupTable	0.002	0.000	0.002
motifsMetaInfo	0.027	0.008	0.035
pCombine	0.001	0.000	0.002
runKmerSPMA	58.125	0.659	69.089
runKmerTSMA	56.037	0.147	61.605
runMatrixSPMA	3.087	0.040	5.360
runMatrixTSMA	0.014	0.001	0.014
scoreSequences	0.006	0.001	0.006
scoreSpectrum	1.525	0.034	1.569
scoreTranscripts	0.007	0.000	0.007
setMotifs	0.002	0.000	0.003
spectrumClassifier	1.444	0.022	1.475
subdivideData	0.003	0.000	0.004