Package: fabia

Version: 2.30.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:fabia.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings fabia_2.30.0.tar.gz

StartedAt: 2019-10-16 01:35:18 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:36:05 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 47.3 seconds

RetCode: 0

Status:  OK

CheckDir: fabia.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:fabia.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings fabia_2.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/fabia.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘2.30.0’
* 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 shell scripts ... 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 include directives in Makefiles ... NOTE
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/fabia.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL fabia
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘fabia’ ...
** using staged installation
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -g -O2 -Wall -fpic  -g -O2  -Wall -c fabiac.c -o fabiac.o
fabiac.c: In function ‘fabic’:
fabiac.c:605:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  for (i1=K-1;i1>=0;i1--)
  ^~~
fabiac.c:613:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
      for (i3 = 0; i3 < K; i3++) {
      ^~~
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o fabia.so fabiac.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-fabia/00new/fabia/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fabia)

name	user	system	elapsed
Factorization-class	0.964	0.012	0.976
estimateMode	0.032	0.000	0.032
extractBic	0.066	0.000	0.066
extractPlot	0.200	0.012	0.211
fabi	0.151	0.004	0.155
fabia	0.073	0.000	0.073
fabiaDemo	0.000	0.000	0.001
fabiaVersion	0.001	0.000	0.001
fabiap	0.077	0.000	0.078
fabias	0.070	0.000	0.069
fabiasp	0.430	0.024	0.454
makeFabiaData	0.048	0.004	0.052
makeFabiaDataBlocks	0.063	0.000	0.063
makeFabiaDataBlocksPos	0.058	0.000	0.059
makeFabiaDataPos	0.064	0.000	0.064
matrixImagePlot	0.056	0.004	0.060
mfsc	0.147	0.000	0.146
nmfdiv	0.087	0.000	0.087
nmfeu	0.075	0.012	0.087
nmfsc	0.087	0.004	0.091
plotBicluster	0.090	0.000	0.091
projFunc	0.001	0.000	0.002
projFuncPos	0.001	0.000	0.002
readSamplesSpfabia	0	0	0
samplesPerFeature	0	0	0
spfabia	0.030	0.008	0.038