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BioC 2.13: CHECK report for fabia on moscato1

This page was generated on 2014-04-05 09:50:06 -0700 (Sat, 05 Apr 2014).

Package 238/750HostnameOS / ArchBUILDCHECKBUILD BIN
fabia 2.8.0
Sepp Hochreiter
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/fabia
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: fabia
Version: 2.8.0
Command: rm -rf fabia.buildbin-libdir && mkdir fabia.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=fabia.buildbin-libdir fabia_2.8.0.tar.gz >fabia-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=fabia.buildbin-libdir --install="check:fabia-install.out" --force-multiarch --no-vignettes --timings fabia_2.8.0.tar.gz && mv fabia.buildbin-libdir/* fabia.Rcheck/ && rmdir fabia.buildbin-libdir
StartedAt: 2014-04-05 03:45:59 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:47:34 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 95.4 seconds
RetCode: 0
Status:  OK  
CheckDir: fabia.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/fabia.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.13-bioc/meat/fabia.buildbin-libdir/fabia/libs/i386/fabia.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/fabia.buildbin-libdir/fabia/libs/x64/fabia.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [5s] OK
** running examples for arch 'x64' ... [6s] 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 were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/fabia.Rcheck/00check.log'
for details.

fabia.Rcheck/00install.out:


install for i386

* installing *source* package 'fabia' ...
** libs
  running 'src/Makefile.win' ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
gcc -m32 -c fabiac.c -o fabia.o -I"D:/biocbld/BBS-2˜1.13-/R/include" -Wall -O3
gcc -m32 -shared -s -static-libgcc fabia.o -L"D:/biocbld/BBS-2˜1.13-/R/bin/i386"  -lR  -o fabia.dll 
rm -f fabia.o *.a *.o *.so
installing to D:/biocbld/bbs-2.13-bioc/meat/fabia.buildbin-libdir/fabia/libs/i386
** 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

install for x64

* installing *source* package 'fabia' ...
** libs
  running 'src/Makefile.win' ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
gcc -m64 -c fabiac.c -o fabia.o -I"D:/biocbld/BBS-2˜1.13-/R/include" -Wall -O3
gcc -m64 -shared -s -static-libgcc fabia.o -L"D:/biocbld/BBS-2˜1.13-/R/bin/x64"  -lR  -o fabia.dll 
rm -f fabia.o *.a *.o *.so
installing to D:/biocbld/bbs-2.13-bioc/meat/fabia.buildbin-libdir/fabia/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fabia' as fabia_2.8.0.zip
* DONE (fabia)

fabia.Rcheck/examples_i386/fabia-Ex.timings:

nameusersystemelapsed
Factorization-class0.810.000.87
estimateMode0.030.000.03
extractBic0.120.000.12
extractPlot0.270.000.27
fabi0.20.00.2
fabia0.170.000.17
fabiaDemo0.000.020.02
fabiaVersion000
fabiap0.110.000.11
fabias0.140.000.14
fabiasp0.420.000.42
makeFabiaData0.160.000.16
makeFabiaDataBlocks0.090.030.12
makeFabiaDataBlocksPos0.080.030.13
makeFabiaDataPos0.080.030.11
matrixImagePlot0.110.030.14
mfsc0.130.000.13
nmfdiv0.120.000.12
nmfeu0.090.000.10
nmfsc0.030.000.03
plotBicluster0.140.000.14
projFunc0.010.000.02
projFuncPos000
readSamplesSpfabia0.020.000.01
samplesPerFeature000
spfabia0.050.010.06

fabia.Rcheck/examples_x64/fabia-Ex.timings:

nameusersystemelapsed
Factorization-class0.780.000.78
estimateMode0.050.000.05
extractBic0.140.000.14
extractPlot0.260.000.26
fabi0.240.000.24
fabia0.180.000.19
fabiaDemo0.020.000.01
fabiaVersion000
fabiap0.190.000.19
fabias0.180.000.19
fabiasp0.490.000.48
makeFabiaData0.180.000.19
makeFabiaDataBlocks0.160.030.18
makeFabiaDataBlocksPos0.110.040.14
makeFabiaDataPos0.090.010.11
matrixImagePlot0.100.020.11
mfsc0.200.000.21
nmfdiv0.090.000.09
nmfeu0.090.000.10
nmfsc0.050.000.05
plotBicluster0.170.000.17
projFunc000
projFuncPos000
readSamplesSpfabia000
samplesPerFeature000
spfabia0.060.000.06