BioC 2.14: CHECK report for NetPathMiner on petty

Package: NetPathMiner

Version: 1.0.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NetPathMiner_1.0.4.tar.gz

StartedAt: 2014-10-07 23:11:58 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:15:13 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 194.8 seconds

RetCode: 0

Status:  OK

CheckDir: NetPathMiner.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch NetPathMiner_1.0.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/NetPathMiner.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [29s/38s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [64s/91s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotPaths       19.736  0.079  30.332
plotAllNetworks  9.812  0.053  14.308
* 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... llvm-gcc-4.2 -arch x86_64 -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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2 -Wall  -c PathRanker.cpp -o PathRanker.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c handlesegfault.c -o handlesegfault.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c hme3m.c -o hme3m.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c init.c -o init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2 -Wall  -c kgml_interface.cpp -o kgml_interface.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2 -Wall  -c methods.cpp -o methods.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2 -Wall  -c pathScope.cpp -o pathScope.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/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  -mtune=core2 -g -O2 -Wall  -c sbml_interface.cpp -o sbml_interface.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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 -lxml2 -lz -lpthread -licucore -lm -lsbml -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -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-2.14-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	0.533	0.007	0.548
MIRIAM	0.161	0.008	0.169
NPMdefaults	0.024	0.005	0.029
SBML2igraph	0.825	0.011	0.839
assignEdgeWeights	0.852	0.011	0.865
biopax2igraph	2.192	0.046	2.248
colorVertexByAttr	0.508	0.007	0.520
ex_biopax	0.049	0.002	0.051
ex_kgml_sig	0.624	0.008	0.637
ex_microarray	0.008	0.000	0.009
ex_sbml	4.356	0.018	4.391
extractPathNetwork	2.253	0.017	3.831
getAttr	0.040	0.005	0.099
getGeneSetNetworks	0.014	0.001	0.035
getGeneSets	0.015	0.001	0.035
getPathsAsEIDs	2.233	0.014	4.319
layoutVertexByAttr	1.237	0.019	2.419
makeGeneNetwork	0.273	0.002	0.547
makeReactionNetwork	0.127	0.000	0.240
pathClassifier	1.775	0.019	3.495
pathCluster	0.636	0.006	1.304
pathRanker	1.823	0.018	3.511
pathsToBinary	1.315	0.009	2.627
plotAllNetworks	9.812	0.053	14.308
plotClusters	1.917	0.015	1.943
plotCytoscape	0.002	0.000	0.002
plotNetwork	1.662	0.020	1.835
plotPathClassifier	1.708	0.015	2.557
plotPathCluster	0.626	0.005	1.108
plotPaths	19.736	0.079	30.332
predictPathClassifier	1.323	0.009	1.333
predictPathCluster	0.625	0.003	0.629
rmSmallCompounds	0.165	0.001	0.181
samplePaths	1.448	0.014	1.479
simplifyReactionNetwork	0.263	0.004	0.269
toGraphNEL	0.833	0.015	0.861
vertexDeleteReconnect	0.235	0.004	0.239