Package: fabia

Version: 2.5.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings fabia_2.5.0.tar.gz

StartedAt: 2013-01-16 02:21:43 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:22:53 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 70.1 seconds

RetCode: 0

Status:  OK

CheckDir: fabia.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/fabia.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘2.5.0’
* 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 ‘fabia’ can be installed ... 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 ... 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘fabia’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -fpic  -g -O2  -c fabiac.c -o fabiac.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o fabia.so fabiac.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/fabia.Rcheck/fabia/libs
** R
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘fabia’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘fabia’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘fabia.Rnw’ 
** testing if installed package can be loaded

* DONE (fabia)

name	user	system	elapsed
Factorization-class	0.896	0.016	0.911
estimateMode	0.048	0.000	0.047
extractBic	0.204	0.004	0.206
extractPlot	0.276	0.008	0.284
fabi	0.252	0.008	0.263
fabia	0.268	0.004	0.272
fabiaDemo	0.008	0.000	0.006
fabiaVersion	0.008	0.000	0.007
fabiap	0.188	0.016	0.203
fabias	0.280	0.000	0.277
fabiasp	0.488	0.000	0.490
makeFabiaData	0.080	0.000	0.077
makeFabiaDataBlocks	0.08	0.00	0.08
makeFabiaDataBlocksPos	0.076	0.000	0.076
makeFabiaDataPos	0.168	0.012	0.182
matrixImagePlot	0.092	0.000	0.093
mfsc	0.340	0.008	0.345
nmfdiv	0.168	0.000	0.171
nmfeu	0.156	0.004	0.158
nmfsc	0.076	0.004	0.080
plotBicluster	0.268	0.000	0.271
projFunc	0.016	0.000	0.018
projFuncPos	0.032	0.000	0.032
readSamplesSpfabia	0.004	0.004	0.008
samplesPerFeature	0.008	0.000	0.009
spfabia	0.060	0.008	0.073