Package: qpgraph

Version: 1.6.2

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_1.6.2.tar.gz

StartedAt: 2011-04-07 08:24:23 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 08:27:53 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 209.7 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/qpgraph.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.6.2’
* 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... 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-2.7-bioc/R/include -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2 -c cliquer.c -o cliquer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2 -c graph.c -o graph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2 -c qpgraph.c -o qpgraph.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -pedantic -fpic  -g -O2 -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-2.7-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.7-bioc/R/lib -lRlapack -lgfortran -lm -L/home/biocbuild/bbs-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** 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	0.052	0.000	0.050
qpAnyGraph	0.180	0.008	0.185
qpAvgNrr	4.700	0.000	4.699
qpCItest	0.040	0.000	0.039
qpClique	0.380	0.004	0.387
qpCliqueNumber	0.128	0.004	0.131
qpCov	0.176	0.000	0.174
qpEdgeNrr	0.040	0.000	0.037
qpFunctionalCoherence	53.747	0.184	54.040
qpG2Sigma	0.084	0.000	0.085
qpGenNrr	6.077	0.016	6.100
qpGetCliques	0.376	0.008	0.384
qpGraph	0.324	0.004	0.330
qpGraphDensity	0.396	0.000	0.396
qpHist	0.312	0.004	0.316
qpIPF	0.280	0.008	0.292
qpK2ParCor	0.064	0.000	0.064
qpNrr	17.729	0.004	17.731
qpPAC	0.520	0.012	0.529
qpPCC	0.252	0.000	0.252
qpPRscoreThreshold	0.204	0.000	0.206
qpPlotNetwork	0.424	0.008	0.453
qpPrecisionRecall	0.320	0.000	0.321
qpRndGraph	0.012	0.000	0.014
qpRndWishart	0.048	0.000	0.051
qpTopPairs	0.004	0.000	0.005
qpUnifRndAssociation	0.008	0.000	0.006
qpUpdateCliquesRemoving	22.886	0.116	23.024