BioC 2.11: CHECK report for hapFabia on perceval

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/hapFabia.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.0.6'
* 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 whether package 'hapFabia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... 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 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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iterateIntervals 7.175  0.892   8.332
* 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

* 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-2.11-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	0.375	0.058	0.458
IBDsegmentList-class	0.018	0.002	0.021
IBDsegmentList2excel	0.013	0.002	0.017
analyzeIBDsegments	0.001	0.001	0.002
compareIBDsegmentLists	0.092	0.003	0.095
extractIBDsegments	0.082	0.005	0.088
findDenseRegions	0.005	0.001	0.007
hapFabia	4.554	0.137	4.733
hapFabiaVersion	0.000	0.000	0.001
identifyDuplicates	0.001	0.001	0.002
iterateIntervals	7.175	0.892	8.332
makePipelineFile	0.004	0.004	0.010
matrixPlot	0.006	0.002	0.007
mergeIBDsegmentLists	0.025	0.001	0.027
plotIBDsegment	0.333	0.053	0.462
setAnnotation	0.084	0.005	0.103
setStatistics	0.075	0.003	0.079
sim	0.001	0.000	0.001
simulateIBDsegments	0.000	0.001	0.000
simulateIBDsegmentsFabia	2.580	0.091	2.722
split_sparse_matrix	0.000	0.001	0.002
toolsFactorizationClass	1.470	0.084	1.595
vcftoFABIA	0.001	0.001	0.002

Summary

Command output