BioC 2.12: CHECK report for qpgraph on george2

Package: qpgraph

Version: 1.16.3

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings qpgraph_1.16.3.tar.gz

StartedAt: 2013-10-09 04:13:16 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:20:20 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 423.9 seconds

RetCode: 0

Status:  OK

CheckDir: qpgraph.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/qpgraph.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.16.3’
* 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 ... [48s/50s] 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 ... [31s/31s] 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-2.12-bioc/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include   -g -O2 -Wall -Wall -pedantic -fpic  -g -O2  -Wall -c cliquer.c -o cliquer.o
cliquer.c: In function ‘clique_print_time’:
cliquer.c:1788:8: warning: unused variable ‘fp’ [-Wunused-variable]
cliquer.c: In function ‘clique_print_time_always’:
cliquer.c:1837:8: warning: unused variable ‘fp’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -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-2.12-bioc/R/include -DNDEBUG -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 ‘stat_mis’:
qpgraph.c:4105:19: warning: unused variable ‘k’ [-Wunused-variable]
qpgraph.c:4105:17: warning: unused variable ‘j’ [-Wunused-variable]
qpgraph.c:4105:15: warning: unused variable ‘i’ [-Wunused-variable]
qpgraph.c: In function ‘lr_em’:
qpgraph.c:4147:15: warning: unused variable ‘Y_j’ [-Wunused-variable]
qpgraph.c:4145:39: warning: variable ‘sufStats_ij’ set but not used [-Wunused-but-set-variable]
qpgraph.c:4145:27: warning: variable ‘sufStats_j’ set but not used [-Wunused-but-set-variable]
qpgraph.c:4145:15: warning: variable ‘sufStats_i’ set but not used [-Wunused-but-set-variable]
qpgraph.c: In function ‘ssd_A’:
qpgraph.c:7831:17: warning: unused variable ‘m’ [-Wunused-variable]
qpgraph.c:7831:15: warning: unused variable ‘k’ [-Wunused-variable]
qpgraph.c: In function ‘qp_fast_rnd_graph’:
qpgraph.c:7960:5: warning: assignment from incompatible pointer type [enabled by default]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -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/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRblas -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRlapack -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/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	0.828	0.004	0.830
qpAllCItests	0.312	0.016	0.327
qpAnyGraph	0.224	0.004	0.229
qpAvgNrr	2.192	0.008	2.201
qpBoundary	0.428	0.000	0.429
qpCItest	0.096	0.004	0.106
qpClique	0.460	0.000	0.458
qpCliqueNumber	1.392	0.004	1.397
qpCov	0.164	0.016	0.180
qpEdgeNrr	0.064	0.020	0.084
qpFunctionalCoherence	0.064	0.004	0.067
qpG2Sigma	0.036	0.000	0.037
qpGenNrr	0.804	0.008	0.815
qpGetCliques	0.484	0.004	0.487
qpGraph	0.336	0.000	0.336
qpGraphDensity	0.428	0.004	0.440
qpHTF	0.184	0.016	0.206
qpHist	0.340	0.004	0.344
qpIPF	0.280	0.008	0.287
qpK2ParCor	0.088	0.000	0.090
qpNrr	0.284	0.000	0.287
qpPAC	0.572	0.012	0.588
qpPCC	1.084	0.004	1.092
qpPRscoreThreshold	0.236	0.008	0.244
qpPlotMap	0.148	0.008	0.154
qpPlotNetwork	0.224	0.004	0.264
qpPrecisionRecall	0.376	0.004	0.380
qpRndGraph	0.048	0.000	0.046
qpRndHMGM	0.016	0.000	0.015
qpRndWishart	0.056	0.000	0.055
qpSampleFromHMGM	0.012	0.004	0.016
qpTopPairs	0.020	0.004	0.022
qpUnifRndAssociation	0.028	0.000	0.030
qpUpdateCliquesRemoving	0.028	0.000	0.029