BioC 2.13: CHECK report for fabia on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/fabia.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘2.8.0’
* 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 ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ‘fabia/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/fabia/fabia.html",     "\n\n", "FABIA 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking 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 files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/fabia.Rcheck/00check.log’
for details.

* installing *source* package ‘fabia’ ...
checking for gcc... llvm-gcc-4.2 -arch x86_64 -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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -fPIC  -mtune=core2 -g -O2 -Wall  -c fabiac.c -o fabiac.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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-2.13-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
** testing if installed package can be loaded
* DONE (fabia)

name	user	system	elapsed
Factorization-class	0.853	0.035	0.889
estimateMode	0.051	0.003	0.054
extractBic	0.123	0.003	0.127
extractPlot	0.350	0.015	0.369
fabi	0.279	0.014	0.294
fabia	0.315	0.008	0.324
fabiaDemo	0.006	0.000	0.007
fabiaVersion	0.008	0.000	0.009
fabiap	0.327	0.010	0.336
fabias	0.181	0.005	0.187
fabiasp	0.702	0.017	0.721
makeFabiaData	0.068	0.006	0.073
makeFabiaDataBlocks	0.086	0.013	0.100
makeFabiaDataBlocksPos	0.083	0.013	0.097
makeFabiaDataPos	0.079	0.014	0.096
matrixImagePlot	0.188	0.017	0.207
mfsc	0.278	0.025	0.303
nmfdiv	0.184	0.009	0.193
nmfeu	0.137	0.006	0.143
nmfsc	0.213	0.004	0.218
plotBicluster	0.172	0.009	0.183
projFunc	0.010	0.002	0.011
projFuncPos	0.018	0.003	0.021
readSamplesSpfabia	0.004	0.001	0.004
samplesPerFeature	0.010	0.002	0.012
spfabia	0.089	0.024	0.115

BioC 2.13: CHECK report for fabia on perceval

Summary

Command output