Package: qpgraph

Version: 1.15.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qpgraph_1.15.6.tar.gz

StartedAt: 2013-03-24 09:05:43 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:12:05 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 382.1 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/qpgraph.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'qpgraph/DESCRIPTION' ... OK
* this is package 'qpgraph' version '1.15.6'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'qpgraph' can be installed ... [38s/39s] 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 ... 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 ... [61s/62s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
qpNrr    22.216  0.176  22.673
qpGenNrr  9.476  0.075   9.800
* 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... i686-apple-darwin10.8.0
checking host system type... i686-apple-darwin10.8.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -pedantic -fPIC  -mtune=core2 -g -O2  -c cliquer.c -o cliquer.o
cliquer.c: In function 'clique_print_time':
cliquer.c:1788: warning: unused variable 'fp'
cliquer.c: In function 'clique_print_time_always':
cliquer.c:1837: warning: unused variable 'fp'
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -pedantic -fPIC  -mtune=core2 -g -O2  -c graph.c -o graph.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -pedantic -fPIC  -mtune=core2 -g -O2  -c qpgraph.c -o qpgraph.o
qpgraph.c: In function 'stat_mis':
qpgraph.c:4105: warning: unused variable 'k'
qpgraph.c:4105: warning: unused variable 'j'
qpgraph.c:4105: warning: unused variable 'i'
qpgraph.c: In function 'lr_em':
qpgraph.c:4147: warning: unused variable 'Y_j'
qpgraph.c: In function 'ssd_A':
qpgraph.c:7831: warning: unused variable 'm'
qpgraph.c:7831: warning: unused variable 'k'
qpgraph.c: In function 'qp_fast_rnd_graph':
qpgraph.c:7960: warning: assignment from incompatible pointer type
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -mtune=core2 -g -O2 -Wall -pedantic -fPIC  -mtune=core2 -g -O2  -c reorder.c -o reorder.o
llvm-gcc-4.2 -arch x86_64 -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/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/qpgraph.Rcheck/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function from function 'rmvnorm' in package 'qpgraph'
Creating a generic function from function 'sim.cross' in package 'qpgraph'
** help
*** installing help indices
** building package indices
** installing vignettes
   'qpTxRegNet.Rnw' 
   'qpgraphSimulate.Rnw' 
** testing if installed package can be loaded
* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.011	0.006	0.018
qpAllCItests	0.732	0.023	0.770
qpAnyGraph	0.170	0.015	0.185
qpAvgNrr	3.518	0.030	3.572
qpBoundary	0.866	0.020	0.898
qpCItest	0.065	0.012	0.076
qpClique	0.882	0.014	0.902
qpCliqueNumber	0.937	0.038	0.978
qpCov	0.155	0.019	0.176
qpEdgeNrr	0.060	0.012	0.072
qpFunctionalCoherence	0.024	0.018	0.043
qpG2Sigma	0.028	0.007	0.035
qpGenNrr	9.476	0.075	9.800
qpGetCliques	0.576	0.014	0.592
qpGraph	0.572	0.017	0.590
qpGraphDensity	0.864	0.017	0.883
qpHTF	0.192	0.019	0.214
qpHist	0.583	0.012	0.600
qpIPF	0.269	0.017	0.287
qpK2ParCor	0.074	0.010	0.083
qpNrr	22.216	0.176	22.673
qpPAC	0.763	0.034	0.804
qpPCC	0.185	0.015	0.201
qpPRscoreThreshold	0.430	0.013	0.452
qpPlotMap	0.174	0.033	0.207
qpPlotNetwork	0.223	0.013	0.236
qpPrecisionRecall	0.624	0.018	0.645
qpRndGraph	0.026	0.005	0.031
qpRndHMGM	0.010	0.003	0.013
qpRndWishart	0.045	0.010	0.056
qpSampleFromHMGM	0.010	0.003	0.014
qpTopPairs	0.007	0.003	0.010
qpUnifRndAssociation	0.028	0.004	0.032
qpUpdateCliquesRemoving	0.024	0.008	0.032