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BioC 2.12: CHECK report for hapFabia on george2

This page was generated on 2013-10-09 09:37:56 -0700 (Wed, 09 Oct 2013).

Package 307/671HostnameOS / ArchBUILDCHECKBUILD BIN
hapFabia 1.2.2
Sepp Hochreiter
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/hapFabia
Last Changed Rev: 77740 / Revision: 81334
Last Changed Date: 2013-06-19 22:40:09 -0700 (Wed, 19 Jun 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: hapFabia
Version: 1.2.2
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings hapFabia_1.2.2.tar.gz
StartedAt: 2013-10-09 02:30:49 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:32:52 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 122.4 seconds
RetCode: 0
Status:  OK 
CheckDir: hapFabia.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hapFabia/DESCRIPTION’ ... OK
* this is package ‘hapFabia’ version ‘1.2.2’
* 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 ‘hapFabia’ can be installed ... [12s/12s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ‘hapFabia/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/hapFabia/hapFabia.html",     "\n\n", "hapFabia 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable 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 examples ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
iterateIntervals 13.129  0.232  14.056
hapFabia          6.420  0.116   6.545
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck/00check.log’
for details.

hapFabia.Rcheck/00install.out:

* installing *source* package ‘hapFabia’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c interfaceR.c -o interfaceR.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c split_sparse_matrixB.c -o split_sparse_matrixB.o
split_sparse_matrixB.c: In function ‘split_sparse_matrixB’:
split_sparse_matrixB.c:95:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:96:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:161:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:163:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:164:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:166:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:167:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:279:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:280:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:335:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c vcftoFABIAB.c -o vcftoFABIAB.o
gcc -std=gnu99 -shared -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
gcc -std=gnu99 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2  -Wall
./commandLine/split_sparse_matrix.c: In function ‘Rprintf’:
./commandLine/split_sparse_matrix.c:9:3: warning: format not a string literal and no format arguments [-Wformat-security]
gcc -std=gnu99 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2  -Wall
split_sparse_matrixB.c: In function ‘split_sparse_matrixB’:
split_sparse_matrixB.c:95:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:96:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:161:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:163:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:164:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:166:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:167:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:279:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:280:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
split_sparse_matrixB.c:335:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine/
gcc -std=gnu99 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2  -Wall
./commandLine/vcftoFABIA.c: In function ‘Rprintf’:
./commandLine/vcftoFABIA.c:10:3: warning: format not a string literal and no format arguments [-Wformat-security]
gcc -std=gnu99 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2  -Wall
gcc -std=gnu99 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine/
installing to /home/biocbuild/bbs-2.12-bioc/meat/hapFabia.Rcheck/hapFabia/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hapFabia)

hapFabia.Rcheck/hapFabia-Ex.timings:

nameusersystemelapsed
IBDsegment-class0.9720.0681.039
IBDsegmentList-class0.0760.0000.074
IBDsegmentList2excel0.0320.0000.034
analyzeIBDsegments0.2480.0000.251
compareIBDsegmentLists0.0600.0040.063
extractIBDsegments0.1480.0000.146
findDenseRegions0.0240.0040.028
hapFabia6.4200.1166.545
hapFabiaVersion0.0080.0000.008
identifyDuplicates0.0840.0080.090
iterateIntervals13.129 0.23214.056
makePipelineFile0.0120.0080.021
matrixPlot0.0320.0000.033
mergeIBDsegmentLists0.0600.0000.059
plotIBDsegment0.5000.0160.515
setAnnotation0.1480.0080.154
setStatistics0.1120.0040.118
sim0.1640.0040.176
simulateIBDsegments0.0120.0000.010
simulateIBDsegmentsFabia3.4120.0163.526
split_sparse_matrix0.0840.0080.091
toolsFactorizationClass3.2760.0043.292
vcftoFABIA0.1000.0040.105