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Package 283/609HostnameOS / ArchBUILDCHECKBUILD BIN
hapFabia 1.0.6
Sepp Hochreiter
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/hapFabia
Last Changed Rev: 73724 / Revision: 74773
Last Changed Date: 2013-02-25 03:12:31 -0800 (Mon, 25 Feb 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: hapFabia
Version: 1.0.6
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings hapFabia_1.0.6.tar.gz
StartedAt: 2013-03-25 02:04:38 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:06:03 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 85.9 seconds
RetCode: 0
Status:  OK 
CheckDir: hapFabia.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/hapFabia.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.0.6’
* 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 whether package ‘hapFabia’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
iterateIntervals 7.344   0.18   7.586
* 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

hapFabia.Rcheck/00install.out:

* installing *source* package ‘hapFabia’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-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/lib64 -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
gcc -std=gnu99 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2  -Wall
gcc -std=gnu99 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2  -Wall
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
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 /loc/home/biocbuild/bbs-2.11-bioc/meat/hapFabia.Rcheck/hapFabia/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘hapfabia.Rnw’ 
** testing if installed package can be loaded

* DONE (hapFabia)

hapFabia.Rcheck/hapFabia-Ex.timings:

nameusersystemelapsed
IBDsegment-class0.3520.0320.485
IBDsegmentList-class0.0160.0000.041
IBDsegmentList2excel0.0120.0000.011
analyzeIBDsegments0.0040.0000.001
compareIBDsegmentLists0.1320.0040.137
extractIBDsegments0.0760.0000.077
findDenseRegions0.0000.0040.005
hapFabia4.4880.0764.698
hapFabiaVersion0.0000.0040.000
identifyDuplicates0.0000.0000.001
iterateIntervals7.3440.1807.586
makePipelineFile0.0080.0000.022
matrixPlot0.0040.0040.005
mergeIBDsegmentLists0.0200.0000.022
plotIBDsegment0.3000.0160.373
setAnnotation0.0680.0040.071
setStatistics0.0720.0000.076
sim000
simulateIBDsegments000
simulateIBDsegmentsFabia2.5130.0282.541
split_sparse_matrix0.0040.0000.000
toolsFactorizationClass1.3040.0241.449
vcftoFABIA000