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BioC 3.5: CHECK report for fabia on veracruz2

This page was generated on 2017-08-16 13:28:55 -0400 (Wed, 16 Aug 2017).

Package 426/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fabia 2.22.0
Sepp Hochreiter
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/fabia
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: fabia
Version: 2.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings fabia_2.22.0.tar.gz
StartedAt: 2017-08-16 02:37:54 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:38:50 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 55.2 seconds
RetCode: 0
Status:  OK 
CheckDir: fabia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings fabia_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/fabia.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘2.22.0’
* 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.


fabia.Rcheck/00install.out:

* 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  -Wall -g -O2 -fPIC  -Wall -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)

fabia.Rcheck/fabia-Ex.timings:

nameusersystemelapsed
Factorization-class1.0700.0171.118
estimateMode0.0260.0020.028
extractBic0.0470.0020.049
extractPlot0.1810.0080.191
fabi0.1430.0040.147
fabia0.0550.0030.058
fabiaDemo0.0010.0000.001
fabiaVersion0.0010.0000.002
fabiap0.1190.0030.132
fabias0.0560.0020.059
fabiasp0.3780.0140.401
makeFabiaData0.0320.0020.034
makeFabiaDataBlocks0.0390.0070.049
makeFabiaDataBlocksPos0.0910.0070.100
makeFabiaDataPos0.0410.0070.048
matrixImagePlot0.0400.0080.048
mfsc0.1230.0070.133
nmfdiv0.0560.0070.064
nmfeu0.0440.0050.050
nmfsc0.1100.0060.117
plotBicluster0.1620.0030.168
projFunc0.0020.0010.003
projFuncPos0.0030.0000.003
readSamplesSpfabia0.0010.0010.000
samplesPerFeature0.0010.0000.001
spfabia0.0460.0080.054