Package: fabia

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch fabia_1.5.0.tar.gz

StartedAt: 2011-05-09 14:22:41 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:23:54 -0700 (Mon, 09 May 2011)

EllapsedTime: 73.0 seconds

RetCode: 0

Status:  OK

CheckDir: fabia.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/fabia.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘1.5.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘fabia.pdf’ from 603Kb to 474Kb
  consider running tools::compactPDF() on these files
* 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 C++ compiler default output... 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 g++-4.2 -arch i386 accepts -g... yes
rm: conftest.dSYM: is a directory
checking how to run the C++ preprocessor... g++-4.2 -arch i386 -E
Building libRcpp.a in RcppSrc...
rm -f Rcpp.o libRcpp.a
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c Rcpp.cpp -o Rcpp.o
ar crs libRcpp.a Rcpp.o
rm -f Rcpp.o
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include   -I../RcppSrc -fPIC  -g -O2 -c fabiac.cpp -o fabiac.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o fabia.so fabiac.o -L../RcppSrc -lRcpp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/fabia.Rcheck/fabia/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
Creating a new generic function for "plot" in "fabia"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘fabia.Rnw’ 
** testing if installed package can be loaded

* DONE (fabia)

name	user	system	elapsed
estimateMode	0.069	0.008	0.077
extractBic	0.189	0.007	0.201
extractPlot	0.374	0.023	0.401
fabi	0.663	0.026	0.703
fabia	0.201	0.006	0.208
fabiaDemo	0.000	0.000	0.001
fabiaVersion	0.002	0.000	0.003
fabiap	0.207	0.007	0.223
fabias	0.199	0.007	0.207
fabiasp	1.423	0.057	1.489
makeFabiaData	0.063	0.012	0.162
makeFabiaDataBlocks	0.032	0.005	0.053
makeFabiaDataBlocksPos	0.037	0.007	0.060
makeFabiaDataPos	0.031	0.006	0.052
matrixImagePlot	0.033	0.006	0.055
mfsc	0.213	0.016	0.237
nmfdiv	0.196	0.108	0.310
nmfeu	0.146	0.070	0.219
nmfsc	0.071	0.015	0.088
plot-methods	1.323	0.031	1.420
plotBicluster	0.200	0.008	0.221
projFunc	0.002	0.000	0.002
projFuncPos	0.001	0.001	0.002
show-methods	0.231	0.008	0.274
showSelected-methods	0.213	0.006	0.224
summary-methods	0.240	0.006	0.246