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This page was generated on 2022-01-14 13:06:22 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for fabia on tokay2


To the developers/maintainers of the fabia package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fabia.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 620/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fabia 2.40.0  (landing page)
Andreas Mitterecker
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/fabia
git_branch: RELEASE_3_14
git_last_commit: e5cd3a4
git_last_commit_date: 2021-10-26 11:56:21 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: fabia
Version: 2.40.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fabia.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings fabia_2.40.0.tar.gz
StartedAt: 2022-01-13 19:12:04 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 19:13:18 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 73.4 seconds
RetCode: 0
Status:   OK  
CheckDir: fabia.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fabia.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings fabia_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/fabia.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fabia/DESCRIPTION' ... OK
* this is package 'fabia' version '2.40.0'
* 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'.

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'
.onLoad: no visible global function definition for 'winMenuNames'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
plot,Factorization-missing: no visible global function definition for
  'dev.new'
Undefined global functions or variables:
  dev.new winMenuAdd winMenuAddItem winMenuNames
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem", "winMenuNames")
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 use of PKG_*FLAGS in Makefiles ... 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/fabia/libs/i386/fabia.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/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, nor use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/fabia.Rcheck/00check.log'
for details.



Installation output

fabia.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/fabia_2.40.0.tar.gz && rm -rf fabia.buildbin-libdir && mkdir fabia.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fabia.buildbin-libdir fabia_2.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL fabia_2.40.0.zip && rm fabia_2.40.0.tar.gz fabia_2.40.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7  205k    7 16227    0     0   193k      0  0:00:01 --:--:--  0:00:01  193k
100  205k  100  205k    0     0  1288k      0 --:--:-- --:--:-- --:--:-- 1289k

install for i386

* installing *source* package 'fabia' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
"C:/rtools40/mingw32/bin/"gcc  -c fabiac.c -o fabia.o -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -Wall -O3
"C:/rtools40/mingw32/bin/"gcc  -shared -s -static-libgcc fabia.o -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386"  -lR  -o fabia.dll 
rm -f fabia.o *.a *.o *.so
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/fabia.buildbin-libdir/00LOCK-fabia/00new/fabia/libs/i386
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'fabia'
    finding HTML links ... done
    Factorization-class                     html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/fabia.buildbin-libdir/00LOCK-fabia/00new/fabia/help/L.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/fabia.buildbin-libdir/00LOCK-fabia/00new/fabia/help/L+2CFactorization-method.html
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/fabia.buildbin-libdir/00LOCK-fabia/00new/fabia/help/L+3C-.html
    estimateMode                            html  
    extractBic                              html  
    extractPlot                             html  
    fabi                                    html  
    fabia                                   html  
    fabiaDemo                               html  
    fabiaVersion                            html  
    fabiap                                  html  
    fabias                                  html  
    fabiasp                                 html  
    makeFabiaData                           html  
    makeFabiaDataBlocks                     html  
    makeFabiaDataBlocksPos                  html  
    makeFabiaDataPos                        html  
    matrixImagePlot                         html  
    mfsc                                    html  
    nmfdiv                                  html  
    nmfeu                                   html  
    nmfsc                                   html  
    plotBicluster                           html  
    projFunc                                html  
    projFuncPos                             html  
    readSamplesSpfabia                      html  
    readSpfabiaResult                       html  
    samplesPerFeature                       html  
    spfabia                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'fabia' ...
** libs
  running 'src/Makefile.win' ...
rm -f fabia.o fabia.dll *.a *.o *.so *.dll
"C:/rtools40/mingw64/bin/"gcc  -c fabiac.c -o fabia.o -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -Wall -O3
"C:/rtools40/mingw64/bin/"gcc  -shared -s -static-libgcc fabia.o -L"C:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64"  -lR  -o fabia.dll 
rm -f fabia.o *.a *.o *.so
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/fabia.buildbin-libdir/fabia/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fabia' as fabia_2.40.0.zip
* DONE (fabia)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'fabia' successfully unpacked and MD5 sums checked

Tests output


Example timings

fabia.Rcheck/examples_i386/fabia-Ex.timings

nameusersystemelapsed
Factorization-class0.690.000.68
estimateMode000
extractBic0.040.000.05
extractPlot0.210.000.20
fabi0.090.000.09
fabia0.050.000.05
fabiaDemo000
fabiaVersion0.010.000.02
fabiap0.050.000.04
fabias0.050.000.05
fabiasp0.250.000.25
makeFabiaData0.110.000.11
makeFabiaDataBlocks0.070.020.09
makeFabiaDataBlocksPos0.070.030.10
makeFabiaDataPos0.040.030.07
matrixImagePlot0.070.030.10
mfsc0.090.000.09
nmfdiv0.060.020.08
nmfeu0.030.030.06
nmfsc0.070.000.07
plotBicluster0.090.000.09
projFunc0.020.000.01
projFuncPos000
readSamplesSpfabia000
samplesPerFeature000
spfabia0.030.030.07

fabia.Rcheck/examples_x64/fabia-Ex.timings

nameusersystemelapsed
Factorization-class0.70.00.7
estimateMode000
extractBic0.040.000.05
extractPlot0.250.000.25
fabi0.190.020.20
fabia0.090.000.09
fabiaDemo000
fabiaVersion000
fabiap0.090.000.09
fabias0.10.00.1
fabiasp0.390.000.39
makeFabiaData0.090.000.09
makeFabiaDataBlocks0.050.030.08
makeFabiaDataBlocksPos0.060.030.09
makeFabiaDataPos0.050.030.08
matrixImagePlot0.080.000.08
mfsc0.110.000.11
nmfdiv0.060.000.06
nmfeu0.060.020.08
nmfsc0.080.000.08
plotBicluster0.110.000.11
projFunc000
projFuncPos000
readSamplesSpfabia000
samplesPerFeature000
spfabia0.080.000.07