BioC 3.5: CHECK report for fabia on oaxaca

Package: fabia

Version: 2.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings fabia_2.21.0.tar.gz

StartedAt: 2017-03-04 02:39:00 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:39:58 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 57.1 seconds

RetCode: 0

Status:  OK

CheckDir: fabia.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings fabia_2.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/fabia.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘2.21.0’
* 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 ‘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'.

plot,Factorization-missing: warning in symbols(ll[isel, 1], ll[isel,
  2], circle = sqs[isel], inches = FALSE, lwd = 3, add = TRUE, fg =
  colors[2]): partial argument match of 'circle' to 'circles'
plot,Factorization-missing: warning in symbols(zz[ii, 1], zz[ii, 2],
  square = sqs, inches = FALSE, lwd = 3, add = TRUE, fg = colors[2 +
  iGroup[i]]): partial argument match of 'square' to 'squares'
plot,Factorization-missing: no visible global function definition for
  ‘dev.new’
Undefined global functions or variables:
  dev.new
Consider adding
  importFrom("grDevices", "dev.new")
to your NAMESPACE file.
* 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 GNU extensions in Makefiles ... 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 ... 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
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/fabia.Rcheck/00check.log’
for details.

* installing *source* package ‘fabia’ ...
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ANSI C... none needed
checking how to run the C preprocessor... clang -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -Wall -mtune=core2 -g -O2 -fPIC  -Wall -mtune=core2 -g -O2  -c fabiac.c -o fabiac.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-3.5-bioc/meat/fabia.Rcheck/fabia/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (fabia)

name	user	system	elapsed
Factorization-class	1.248	0.019	1.268
estimateMode	0.032	0.002	0.034
extractBic	0.058	0.002	0.060
extractPlot	0.199	0.008	0.212
fabi	0.117	0.005	0.122
fabia	0.068	0.002	0.069
fabiaDemo	0.000	0.000	0.001
fabiaVersion	0.001	0.000	0.001
fabiap	0.142	0.003	0.147
fabias	0.072	0.002	0.075
fabiasp	0.338	0.013	0.351
makeFabiaData	0.024	0.002	0.026
makeFabiaDataBlocks	0.035	0.007	0.045
makeFabiaDataBlocksPos	0.107	0.007	0.116
makeFabiaDataPos	0.042	0.007	0.052
matrixImagePlot	0.042	0.008	0.052
mfsc	0.119	0.006	0.125
nmfdiv	0.054	0.003	0.057
nmfeu	0.059	0.006	0.066
nmfsc	0.136	0.006	0.141
plotBicluster	0.245	0.003	0.251
projFunc	0.003	0.001	0.003
projFuncPos	0.003	0.000	0.003
readSamplesSpfabia	0.001	0.001	0.001
samplesPerFeature	0.001	0.000	0.001
spfabia	0.045	0.009	0.055