Package: fabia

Version: 2.3.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch fabia_2.3.0.tar.gz

StartedAt: 2012-06-20 23:37:16 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 23:38:48 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 92.2 seconds

RetCode: 0

Status:  OK

CheckDir: fabia.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/fabia.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '2.3.0'
* 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 whether package 'fabia' 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 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 sizes of PDF files under 'inst/doc' ... 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 -arch i386 -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 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -arch i386 -std=gnu99 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic  -c fabiac.c -o fabiac.o
fabiac.c: In function 'spfabic':
fabiac.c:1528: warning: ordered comparison of pointer with integer zero
fabiac.c: In function 'samplesPerFeature':
fabiac.c:3026: warning: ordered comparison of pointer with integer zero
fabiac.c: In function 'readSamplesSpfabic':
fabiac.c:3260: warning: ordered comparison of pointer with integer zero
fabiac.c: In function 'readSpfabicResult':
fabiac.c:3480: warning: ordered comparison of pointer with integer zero
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o fabia.so fabiac.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/fabia.Rcheck/fabia/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
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
estimateMode	0.049	0.009	0.058
extractBic	0.136	0.007	0.144
extractPlot	0.399	0.034	0.439
fabi	0.391	0.028	0.428
fabia	0.122	0.007	0.138
fabiaDemo	0	0	0
fabiaVersion	0.001	0.000	0.001
fabiap	0.127	0.007	0.133
fabias	0.172	0.007	0.181
fabiasp	0.758	0.053	0.821
makeFabiaData	0.076	0.010	0.087
makeFabiaDataBlocks	0.078	0.027	0.106
makeFabiaDataBlocksPos	0.077	0.027	0.105
makeFabiaDataPos	0.077	0.027	0.106
matrixImagePlot	0.079	0.027	0.107
mfsc	0.154	0.015	0.175
nmfdiv	0.211	0.116	0.335
nmfeu	0.151	0.070	0.221
nmfsc	0.063	0.014	0.077
plot-methods	0.625	0.027	0.657
plotBicluster	0.179	0.014	0.193
projFunc	0.001	0.001	0.002
projFuncPos	0.001	0.001	0.002
readSamplesSpfabia	0	0	0
samplesPerFeature	0.000	0.001	0.001
show-methods	0.146	0.008	0.159
showSelected-methods	0.129	0.006	0.137
spfabia	0.069	0.020	0.145
summary-methods	0.138	0.005	0.147