BioC 3.5: CHECK report for motifcounter on veracruz2

Package: motifcounter

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings motifcounter_1.0.0.tar.gz

StartedAt: 2017-08-16 05:34:34 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:40:06 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 331.5 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-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 ‘1.0.0’
* 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-3.5-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	0.558	0.004	0.575
compoundPoissonDist	0.414	0.016	0.440
generateDNAString	0.093	0.001	0.098
generateDNAStringSet	0.110	0.002	0.111
lenSequences	0.050	0.000	0.051
motifAndBackgroundValid	0.065	0.000	0.070
motifEnrichment	3.940	0.027	4.029
motifHitProfile	0.121	0.003	0.126
motifHits	0.072	0.001	0.075
motifValid	0.003	0.000	0.003
motifcounter-package	1.118	0.008	1.154
motifcounterOptions	0.001	0.001	0.000
normalizeMotif	0.002	0.000	0.002
numMotifHits	0.930	0.009	0.953
probOverlapHit	0.272	0.005	0.290
readBackground	0.062	0.001	0.064
revcompMotif	0.006	0.001	0.007
scoreDist	0.074	0.001	0.077
scoreDistBf	0.109	0.001	0.115
scoreDistEmpirical	3.033	0.024	3.108
scoreHistogram	0.164	0.005	0.172
scoreHistogramSingleSeq	0.069	0.003	0.074
scoreProfile	0.410	0.002	0.416
scoreSequence	0.069	0.001	0.071
scoreStrand	0.075	0.001	0.077
scoreThreshold	0.060	0.001	0.060
sigLevel	0.001	0.000	0.000
simulateNumHitsDist	1.991	0.010	2.034