BioC 3.6: CHECK report for motifcounter on veracruz1

Package: motifcounter

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifcounter_1.1.0.tar.gz

StartedAt: 2017-08-16 05:51:07 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:56:33 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 325.4 seconds

RetCode: 0

Status:  OK

CheckDir: motifcounter.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifcounter_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/motifcounter.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.1.0’
* 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 ‘motifcounter’ 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 loading without being on the library search path ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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

* installing *source* package ‘motifcounter’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rbackground.c -o Rbackground.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rcombinatorial.c -o Rcombinatorial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rminmaxscore.c -o Rminmaxscore.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Roption.c -o Roption.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Roverlap.c -o Roverlap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rscore1d.c -o Rscore1d.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rsequence.c -o Rsequence.o
Rsequence.c:28:9: warning: unused variable 'i' [-Wunused-variable]
    int i;
        ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c Rsimulate.c -o Rsimulate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c background.c -o background.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c combinatorial.c -o combinatorial.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c compoundpoisson.c -o compoundpoisson.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c markovchain.c -o markovchain.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c matrix.c -o matrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c mdist_register.c -o mdist_register.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c minmaxscore.c -o minmaxscore.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c overlap.c -o overlap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c score1d.c -o score1d.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c score2d.c -o score2d.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c scorefunctions.c -o scorefunctions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c sequence.c -o sequence.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -DIN_R -fPIC  -Wall -g -O2  -c simulate.c -o simulate.o
clang -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 motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/motifcounter.Rcheck/motifcounter/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifcounter)

name	user	system	elapsed
combinatorialDist	0.579	0.005	0.590
compoundPoissonDist	0.451	0.017	0.470
generateDNAString	0.105	0.001	0.106
generateDNAStringSet	0.137	0.001	0.138
lenSequences	0.058	0.000	0.058
motifAndBackgroundValid	0.064	0.001	0.067
motifEnrichment	3.895	0.027	3.960
motifHitProfile	0.114	0.003	0.118
motifHits	0.070	0.001	0.073
motifValid	0.002	0.000	0.002
motifcounter-package	1.160	0.009	1.197
motifcounterOptions	0.001	0.000	0.001
normalizeMotif	0.002	0.000	0.005
numMotifHits	0.941	0.007	0.964
probOverlapHit	0.261	0.005	0.272
readBackground	0.06	0.00	0.06
revcompMotif	0.002	0.000	0.003
scoreDist	0.059	0.001	0.061
scoreDistBf	0.075	0.000	0.076
scoreDistEmpirical	2.976	0.020	3.060
scoreHistogram	0.298	0.006	0.318
scoreHistogramSingleSeq	0.054	0.003	0.058
scoreProfile	0.343	0.001	0.362
scoreSequence	0.061	0.001	0.062
scoreStrand	0.070	0.001	0.071
scoreThreshold	0.062	0.000	0.063
sigLevel	0.000	0.001	0.001
simulateNumHitsDist	2.046	0.006	2.101