Package: qpgraph

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qpgraph_1.6.2.tar.gz

StartedAt: 2011-03-31 07:21:24 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 07:26:34 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 310.1 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/qpgraph.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qpgraph/DESCRIPTION’ ... OK
* this is package ‘qpgraph’ version ‘1.6.2’
* 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 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 data for non-ASCII characters ... 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 package vignettes in ‘inst/doc’ ... 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... i686-apple-darwin9.8.0
checking host system type... i686-apple-darwin9.8.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic -c cliquer.c -o cliquer.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic -c graph.c -o graph.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic -c qpgraph.c -o qpgraph.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -Wall -pedantic -fPIC  -g -O2 -Wall -pedantic -c reorder.c -o reorder.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/i386 -lRblas -L/Library/Frameworks/R.framework/Versions/2.12/Resources/lib/i386 -lRlapack -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/qpgraph.Rcheck/qpgraph/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.127	0.006	0.133
qpAnyGraph	0.327	0.126	0.456
qpAvgNrr	7.926	0.164	8.253
qpCItest	0.058	0.003	0.061
qpClique	0.987	0.145	1.229
qpCliqueNumber	0.196	0.007	0.205
qpCov	0.322	0.202	0.534
qpEdgeNrr	0.058	0.003	0.061
qpFunctionalCoherence	73.950	3.433	82.080
qpG2Sigma	0.085	0.003	0.088
qpGenNrr	9.219	0.306	9.641
qpGetCliques	0.626	0.012	0.643
qpGraph	0.683	0.125	0.812
qpGraphDensity	0.946	0.126	1.082
qpHist	0.693	0.121	0.823
qpIPF	0.489	0.308	0.825
qpK2ParCor	0.083	0.002	0.086
qpNrr	25.138	0.425	25.819
qpPAC	1.020	0.266	1.300
qpPCC	0.383	0.177	0.565
qpPRscoreThreshold	0.515	0.122	0.644
qpPlotNetwork	0.517	0.022	0.586
qpPrecisionRecall	0.677	0.123	0.807
qpRndGraph	0.019	0.001	0.020
qpRndWishart	0.018	0.002	0.020
qpTopPairs	0.006	0.000	0.007
qpUnifRndAssociation	0.009	0.002	0.011
qpUpdateCliquesRemoving	23.537	0.655	24.514