Package: hapFabia

Version: 1.1.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch hapFabia_1.1.7.tar.gz

StartedAt: 2013-03-25 03:01:13 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:03:06 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 112.6 seconds

RetCode: 0

Status:  OK

CheckDir: hapFabia.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'hapFabia/DESCRIPTION' ... OK
* this is package 'hapFabia' version '1.1.7'
* 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 'hapFabia' can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... NOTE
File 'hapFabia/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("+--------------------------+          #    #    ##    #####     \n",     "|#.....#...#.......#.#....#|          #    #   #  #   #    #    \n",     "|#.....#...#.......#.#....#|          ######  #    #  #    #    \n",     "|#.....#...#...............|          #    #  ######  #####     \n",     "|#.....#...#.......#.#....#|          #    #  #    #  #         \n",     "|#.....#...#...............|          #    #  #    #  #         \n",     "|#.....#...#.......#.#....#|  #######                           \n",     "|..................#.#....#|  #         ##    #####   #    ##   \n",     "|#.....#...#.......#.#....#|  #        #  #   #    #  #   #  #  \n",     "|..................#.#....#|  #####   #    #  #####   #  #    # \n",     "|#.....#...#.......#.#....#|  #       ######  #    #  #  ###### \n",     "|#.....#...#.......#.#....#|  #       #    #  #    #  #  #    # \n",     "+--------------------------+  #       #    #  #####   #  #    # \n")
    packageStartupMessage("Citation: S. Hochreiter et al.,", "\n",     "FABIA: Factor Analysis for Bicluster Acquisition,", "\n",     "Bioinformatics 26(12):1520-1527, 2010.", "\n", "BibTex: enter 'toBibtex(citation(\"fabia\"))'",     "\n\n", "Homepage: http://www.bioinf.jku.at/software/hapFabia/hapFabia.html",     "\n\n", "hapFabia Package Version ", version, "\n")

See section 'Good practice' in '?.onAttach'.
* 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 line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [28s/30s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
iterateIntervals 10.110  0.978  11.790
hapFabia          7.029  0.210   7.765
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck/00check.log'
for details.

* installing *source* package 'hapFabia' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c interfaceR.c -o interfaceR.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c vcftoFABIAB.c -o vcftoFABIAB.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
gcc -arch i386 -std=gnu99 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 -Wall -pedantic 
gcc -arch i386 -std=gnu99 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 -Wall -pedantic 
gcc -arch i386 -std=gnu99 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine//i386
gcc -arch i386 -std=gnu99 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 -Wall -pedantic 
gcc -arch i386 -std=gnu99 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 -Wall -pedantic 
gcc -arch i386 -std=gnu99 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine//i386
installing to /Users/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck/hapFabia/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'hapfabia.Rnw' 
** testing if installed package can be loaded
* DONE (hapFabia)

name	user	system	elapsed
IBDsegment-class	0.604	0.135	0.984
IBDsegmentList-class	0.071	0.028	0.100
IBDsegmentList2excel	0.038	0.013	0.050
analyzeIBDsegments	0.064	0.062	0.126
compareIBDsegmentLists	0.057	0.015	0.071
extractIBDsegments	0.168	0.026	0.193
findDenseRegions	0.023	0.009	0.032
hapFabia	7.029	0.210	7.765
hapFabiaVersion	0.006	0.006	0.011
identifyDuplicates	0.057	0.069	0.126
iterateIntervals	10.110	0.978	11.790
makePipelineFile	0.014	0.014	0.030
matrixPlot	0.017	0.015	0.034
mergeIBDsegmentLists	0.040	0.017	0.057
plotIBDsegment	0.439	0.091	0.742
setAnnotation	0.105	0.030	0.151
setStatistics	0.112	0.017	0.130
sim	0.006	0.008	0.014
simulateIBDsegments	0.007	0.010	0.016
simulateIBDsegmentsFabia	3.407	0.078	3.705
split_sparse_matrix	0.034	0.047	0.081
toolsFactorizationClass	1.450	0.082	1.540
vcftoFABIA	0.037	0.046	0.083