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This page was generated on 2021-12-06 13:05:56 -0500 (Mon, 06 Dec 2021).

CHECK results for fabia on machv2

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: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
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 20.04.3 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fabia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fabia_2.40.0.tar.gz
StartedAt: 2021-12-05 14:29:20 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 14:30:29 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 68.5 seconds
RetCode: 0
Status:   OK  
CheckDir: fabia.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fabia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fabia_2.40.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/fabia.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 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 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 is not available
* checking sizes of PDF files under ‘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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/fabia.Rcheck/00check.log’
for details.



Installation output

fabia.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL fabia
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘fabia’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fabiac.c -o fabiac.o
clang -mmacosx-version-min=10.13 -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 /Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output


Example timings

fabia.Rcheck/fabia-Ex.timings

nameusersystemelapsed
Factorization-class1.0170.0451.066
estimateMode0.0030.0000.003
extractBic0.0980.0060.105
extractPlot0.2060.0170.224
fabi0.1600.0090.169
fabia0.0920.0060.100
fabiaDemo0.0010.0000.001
fabiaVersion0.0010.0000.001
fabiap0.0830.0070.090
fabias0.0860.0030.092
fabiasp0.4390.0440.483
makeFabiaData0.0370.0050.042
makeFabiaDataBlocks0.0440.0140.058
makeFabiaDataBlocksPos0.0490.0180.066
makeFabiaDataPos0.0500.0170.068
matrixImagePlot0.0510.0150.066
mfsc0.1610.0160.178
nmfdiv0.0780.0200.098
nmfeu0.0690.0200.089
nmfsc0.0880.0150.103
plotBicluster0.1270.0060.134
projFunc0.0020.0010.004
projFuncPos0.0020.0020.003
readSamplesSpfabia0.0000.0010.000
samplesPerFeature000
spfabia0.0650.0330.098