BioC 2.14: CHECK report for NetPathMiner on morelia

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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-darwin13.1.0 (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 ... [15s/42s] 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 loading without being on the library search path ... 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 ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
plotPaths       9.261  0.024   9.561
plotAllNetworks 5.087  0.026   5.207
* 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... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -Wall -mtune=core2 -g -O2  -c PathRanker.cpp -o PathRanker.o
PathRanker.cpp:249:10: warning: unused variable 'e_temp' [-Wunused-variable]
    Edge e_temp = edge(p.sequence[0],p.sequence[1],g).first;
         ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c hme3m.c -o hme3m.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -Wall -mtune=core2 -g -O2  -c kgml_interface.cpp -o kgml_interface.o
kgml_interface.cpp:384:23: warning: variable 'xpathCtx' is uninitialized when used here [-Wuninitialized]
                xmlXPathFreeContext(xpathCtx);
                                    ^˜˜˜˜˜˜˜
kgml_interface.cpp:355:29: note: initialize the variable 'xpathCtx' to silence this warning
        xmlXPathContextPtr xpathCtx;
                                   ^
                                    = NULL
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -Wall -mtune=core2 -g -O2  -c methods.cpp -o methods.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -Wall -mtune=core2 -g -O2  -c pathScope.cpp -o pathScope.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -I . -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -DHAVE_XML -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -DHAVE_SBML -I/usr/local/include -I/usr/include/libxml2   -fPIC  -Wall -mtune=core2 -g -O2  -c sbml_interface.cpp -o sbml_interface.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -lsbml -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -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	0.300	0.005	0.305
MIRIAM	0.093	0.004	0.097
NPMdefaults	0.015	0.003	0.018
SBML2igraph	0.441	0.006	0.513
assignEdgeWeights	0.441	0.006	0.447
biopax2igraph	1.154	0.026	1.219
colorVertexByAttr	0.271	0.003	0.283
ex_biopax	0.031	0.002	0.032
ex_kgml_sig	0.347	0.006	0.369
ex_microarray	0.004	0.000	0.005
ex_sbml	2.166	0.009	2.178
extractPathNetwork	1.248	0.011	1.261
getAttr	0.019	0.002	0.021
getGeneSetNetworks	0.007	0.001	0.008
getGeneSets	0.008	0.000	0.009
getPathsAsEIDs	1.161	0.008	1.171
layoutVertexByAttr	0.617	0.010	0.640
makeGeneNetwork	0.123	0.001	0.125
makeReactionNetwork	0.065	0.001	0.065
pathClassifier	0.916	0.011	0.930
pathCluster	0.355	0.004	0.359
pathRanker	0.819	0.011	0.834
pathsToBinary	0.617	0.005	0.623
plotAllNetworks	5.087	0.026	5.207
plotClusters	1.117	0.006	1.124
plotCytoscape	0.001	0.000	0.001
plotNetwork	0.893	0.012	0.927
plotPathClassifier	0.900	0.006	0.984
plotPathCluster	0.438	0.003	0.443
plotPaths	9.261	0.024	9.561
predictPathClassifier	0.676	0.002	0.679
predictPathCluster	0.270	0.002	0.271
rmSmallCompounds	0.068	0.000	0.068
samplePaths	0.666	0.008	0.674
simplifyReactionNetwork	0.089	0.001	0.090
toGraphNEL	0.521	0.007	0.527
vertexDeleteReconnect	0.051	0.001	0.053

BioC 2.14: CHECK report for NetPathMiner on morelia

Summary

Command output