Package: qpgraph

Version: 1.9.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_1.9.0.tar.gz

StartedAt: 2011-05-09 13:49:09 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:53:15 -0700 (Mon, 09 May 2011)

EllapsedTime: 246.1 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/qpgraph.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘1.9.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘qpgraph’ 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘qpgraph’ ...
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2 -Wall -c cliquer.c -o cliquer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2 -Wall -c graph.c -o graph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2 -Wall -c qpgraph.c -o qpgraph.o
qpgraph.c: In function ‘qp_ci_test_hmgm’:
qpgraph.c:2089:17: warning: unused variable ‘m’
qpgraph.c: In function ‘ssd_A’:
qpgraph.c:4703:15: warning: unused variable ‘k’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2 -Wall -c reorder.c -o reorder.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.9-bioc/R/lib -lRlapack -lgfortran -lm -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘qpTxRegNet.Rnw’ 
** testing if installed package can be loaded

* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.068	0.000	0.066
qpAnyGraph	0.532	0.008	0.538
qpAvgNrr	2.212	0.008	2.218
qpCItest	0.036	0.004	0.038
qpClique	0.796	0.000	0.794
qpCliqueNumber	0.136	0.008	0.142
qpCov	0.160	0.004	0.163
qpEdgeNrr	0.032	0.000	0.032
qpFunctionalCoherence	60.024	0.996	61.221
qpG2Sigma	0.024	0.000	0.026
qpGenNrr	6.824	0.024	6.889
qpGetCliques	0.420	0.000	0.421
qpGraph	0.556	0.012	0.569
qpGraphDensity	0.676	0.000	0.674
qpHist	1.160	0.000	1.163
qpIPF	0.236	0.004	0.245
qpK2ParCor	0.056	0.000	0.057
qpNrr	17.774	0.000	17.874
qpPAC	1.060	0.008	1.071
qpPCC	0.204	0.004	0.212
qpPRscoreThreshold	0.384	0.000	0.386
qpPlotNetwork	0.348	0.012	0.360
qpPrecisionRecall	0.532	0.000	0.533
qpRndGraph	0.204	0.000	0.204
qpRndHMGM	0.064	0.000	0.066
qpRndWishart	0.008	0.000	0.011
qpSampleFromHMGM	0.072	0.000	0.075
qpTopPairs	0.004	0.000	0.005
qpUnifRndAssociation	0.008	0.000	0.007
qpUpdateCliquesRemoving	25.313	0.120	25.467