BioC 2.12: CHECK report for qpgraph on petty

Package: qpgraph

Version: 1.16.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch qpgraph_1.16.3.tar.gz

StartedAt: 2013-10-08 23:33:35 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:40:25 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 409.3 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 3.0.1 (2013-05-16)
* 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 '1.16.3'
* 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 ... [45s/46s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [35s/35s] 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... 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 -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
** testing if installed package can be loaded
* DONE (qpgraph)

name	user	system	elapsed
EcoliOxygen	0.018	0.004	0.022
qpAllCItests	0.339	0.020	0.359
qpAnyGraph	0.654	0.019	0.683
qpAvgNrr	3.760	0.020	3.801
qpBoundary	0.930	0.015	0.954
qpCItest	0.070	0.011	0.081
qpClique	0.988	0.017	1.010
qpCliqueNumber	0.895	0.029	0.931
qpCov	0.174	0.017	0.193
qpEdgeNrr	0.069	0.011	0.081
qpFunctionalCoherence	0.026	0.014	0.039
qpG2Sigma	0.035	0.005	0.040
qpGenNrr	1.653	0.023	1.724
qpGetCliques	0.638	0.015	0.656
qpGraph	0.601	0.015	0.618
qpGraphDensity	0.952	0.012	1.019
qpHTF	0.201	0.014	0.216
qpHist	0.612	0.010	0.623
qpIPF	0.304	0.015	0.320
qpK2ParCor	0.070	0.007	0.078
qpNrr	0.511	0.014	0.526
qpPAC	0.904	0.027	0.933
qpPCC	0.213	0.012	0.226
qpPRscoreThreshold	0.466	0.009	0.476
qpPlotMap	0.131	0.023	0.154
qpPlotNetwork	0.747	0.010	0.774
qpPrecisionRecall	0.651	0.014	0.666
qpRndGraph	0.023	0.004	0.027
qpRndHMGM	0.006	0.003	0.010
qpRndWishart	0.032	0.008	0.040
qpSampleFromHMGM	0.002	0.003	0.005
qpTopPairs	0.011	0.004	0.015
qpUnifRndAssociation	0.016	0.005	0.021
qpUpdateCliquesRemoving	0.013	0.007	0.021