motifcounter 1.0.0
Wolfgang Kopp
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/motifcounter | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings motifcounter_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/motifcounter.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rbackground.c -o Rbackground.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rcombinatorial.c -o Rcombinatorial.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rcompoundpoisson.c -o Rcompoundpoisson.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rminmaxscore.c -o Rminmaxscore.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Roption.c -o Roption.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Roverlap.c -o Roverlap.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rscore1d.c -o Rscore1d.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rsequence.c -o Rsequence.o
Rsequence.c: In function ‘Rscoresequence’:
Rsequence.c:28:9: warning: unused variable ‘i’ [-Wunused-variable]
int i;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c Rsimulate.c -o Rsimulate.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c background.c -o background.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c combinatorial.c -o combinatorial.o
combinatorial.c: In function ‘multipleShortSequenceProbability’:
combinatorial.c:419:12: warning: variable ‘sum’ set but not used [-Wunused-but-set-variable]
double sum;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c compoundpoisson.c -o compoundpoisson.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c markovchain.c -o markovchain.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c matrix.c -o matrix.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c mdist_register.c -o mdist_register.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c minmaxscore.c -o minmaxscore.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c overlap.c -o overlap.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c score1d.c -o score1d.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c score2d.c -o score2d.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c scorefunctions.c -o scorefunctions.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c sequence.c -o sequence.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -DIN_R -fpic -g -O2 -Wall -c simulate.c -o simulate.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/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 -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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)