BioC 2.14: CHECK report for NetPathMiner on zin2

Package: NetPathMiner

Version: 1.0.4

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings NetPathMiner_1.0.4.tar.gz

StartedAt: 2014-10-08 01:25:07 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:26:38 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 90.4 seconds

RetCode: 0

Status:  OK

CheckDir: NetPathMiner.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings NetPathMiner_1.0.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/NetPathMiner.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.0.4’
* 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 ‘NetPathMiner’ can be installed ... [20s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 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 files in ‘vignettes’ ... OK
* checking examples ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotPaths       14.261  0.012  14.572
plotAllNetworks  6.001  0.004   6.115
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘NetPathMiner’ ...
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... yes
untarring boost include tree...
libSBML found, finding configuration...
pkg-config tool found
libsbml.pc found. Using pkg-config to extract it.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fpic  -g -O2  -Wall -c PathRanker.cpp -o PathRanker.o
PathRanker.cpp: In function ‘SEXPREC* pathranker(SEXP, SEXP, SEXP, SEXP, SEXP)’:
PathRanker.cpp:249:10: warning: variable ‘e_temp’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c handlesegfault.c -o handlesegfault.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hme3m.c -o hme3m.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fpic  -g -O2  -Wall -c kgml_interface.cpp -o kgml_interface.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fpic  -g -O2  -Wall -c methods.cpp -o methods.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fpic  -g -O2  -Wall -c pathScope.cpp -o pathScope.o
g++ -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG  -I/usr/local/include   -I . -I/usr/local/include -DHAVE_XML -I/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fpic  -g -O2  -Wall -c sbml_interface.cpp -o sbml_interface.o
g++ -shared -L/usr/local/lib -o NetPathMiner.so PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -lsbml -lxml2 -L/usr/lib/x86_64-linux-gnu -lxml2 -lsbml -L/home/biocbuild/bbs-2.14-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.14-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-bioc/meat/NetPathMiner.Rcheck/NetPathMiner/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (NetPathMiner)

name	user	system	elapsed
KGML2igraph	0.280	0.004	0.296
MIRIAM	0.076	0.004	0.082
NPMdefaults	0.004	0.004	0.010
SBML2igraph	0.388	0.004	0.445
assignEdgeWeights	0.428	0.000	0.447
biopax2igraph	1.108	0.024	1.228
colorVertexByAttr	0.348	0.000	0.350
ex_biopax	0.016	0.000	0.029
ex_kgml_sig	0.420	0.000	0.454
ex_microarray	0.004	0.000	0.005
ex_sbml	3.248	0.000	3.288
extractPathNetwork	0.948	0.004	1.212
getAttr	0.012	0.004	0.016
getGeneSetNetworks	0.004	0.000	0.006
getGeneSets	0.008	0.000	0.006
getPathsAsEIDs	0.896	0.000	0.926
layoutVertexByAttr	0.824	0.008	0.852
makeGeneNetwork	0.116	0.000	0.118
makeReactionNetwork	0.060	0.004	0.075
pathClassifier	0.796	0.008	0.809
pathCluster	0.284	0.000	0.285
pathRanker	0.772	0.004	0.781
pathsToBinary	0.596	0.004	0.602
plotAllNetworks	6.001	0.004	6.115
plotClusters	0.848	0.004	0.857
plotCytoscape	0.000	0.000	0.001
plotNetwork	1.176	0.012	1.196
plotPathClassifier	0.824	0.004	0.845
plotPathCluster	0.280	0.000	0.281
plotPaths	14.261	0.012	14.572
predictPathClassifier	0.54	0.00	0.54
predictPathCluster	0.284	0.000	0.281
rmSmallCompounds	0.076	0.000	0.077
samplePaths	0.664	0.000	0.666
simplifyReactionNetwork	0.132	0.000	0.137
toGraphNEL	0.396	0.000	0.397
vertexDeleteReconnect	0.104	0.000	0.105