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BioC 2.13: CHECK report for fabia on zin1

This page was generated on 2014-04-05 09:47:55 -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: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings fabia_2.8.0.tar.gz
StartedAt: 2014-04-05 01:03:10 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:03:57 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 47.6 seconds
RetCode: 0
Status:  OK 
CheckDir: fabia.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/fabia.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fabia/DESCRIPTION’ ... OK
* this is package ‘fabia’ version ‘2.8.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘fabia’ can be installed ... [6s/7s] 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'.
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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 was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/fabia.Rcheck/00check.log’
for details.

fabia.Rcheck/00install.out:

* installing *source* package ‘fabia’ ...
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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 ‘readSpfabicResult’:
fabiac.c:3569:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3577:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3600:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3604:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3607:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3610:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3613:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3644:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3650:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3671:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3674:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3689:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3705:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3708:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c: In function ‘readSamplesSpfabic’:
fabiac.c:3348:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3356:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3383:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3386:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3389:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3391:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3394:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3416:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3418:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3420:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3422:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3424:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3427:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3430:16: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3433:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3435:16: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3438:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c: In function ‘samplesPerFeature’:
fabiac.c:3114:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3122:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3158:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3161:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3164:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3166:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3169:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3191:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3193:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3195:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3197:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3199:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3202:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3205:16: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3208:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3210:16: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:3213:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c: In function ‘spfabic’:
fabiac.c:1592:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1600:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1616:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1621:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1624:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1626:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1629:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1641:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1643:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1645:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1647:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1649:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1652:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1657:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1660:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1662:14: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fabiac.c:1665:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -shared -L/usr/local/lib -o fabia.so fabiac.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/fabia.Rcheck/fabia/libs
** 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
* DONE (fabia)

fabia.Rcheck/fabia-Ex.timings:

nameusersystemelapsed
Factorization-class0.5520.0040.558
estimateMode0.0320.0000.030
extractBic0.1120.0000.116
extractPlot0.1640.0040.169
fabi0.2200.0000.221
fabia0.0920.0040.098
fabiaDemo0.0040.0000.002
fabiaVersion0.0040.0000.003
fabiap0.1360.0040.141
fabias0.0840.0040.091
fabiasp0.4000.0000.399
makeFabiaData0.0480.0000.045
makeFabiaDataBlocks0.0520.0000.051
makeFabiaDataBlocksPos0.0520.0000.051
makeFabiaDataPos0.0520.0000.052
matrixImagePlot0.0520.0000.052
mfsc0.1480.0080.154
nmfdiv0.1040.0000.104
nmfeu0.0800.0080.091
nmfsc0.0360.0000.037
plotBicluster0.1080.0000.109
projFunc0.0080.0000.006
projFuncPos0.0520.0000.049
readSamplesSpfabia0.0040.0000.003
samplesPerFeature0.0000.0000.003
spfabia0.0400.0040.045