BioC 3.2: CHECK report for NetPathMiner on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings NetPathMiner_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/NetPathMiner.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.6.0’
* 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/25s] 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 ... NOTE
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RCytoscape’ ‘graph’ ‘rBiopaxParser’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotCytoscape: no visible global function definition for
  ‘cy2.edge.names’
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘NetPathMiner/libs/NetPathMiner.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘methods.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotPaths       15.424  0.053  15.663
plotAllNetworks 13.462  0.055  13.548
* 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/NetPathMiner.Rcheck/00check.log’
for details.

* 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.
Package /usr/local/lib/pkgconfig/libsbml.pc.bak was not found in the pkg-config search path.
Perhaps you should add the directory containing `/usr/local/lib/pkgconfig/libsbml.pc.bak.pc'
to the PKG_CONFIG_PATH environment variable
No package '/usr/local/lib/pkgconfig/libsbml.pc.bak' found
Package /usr/local/lib/pkgconfig/libsbml.pc.bak was not found in the pkg-config search path.
Perhaps you should add the directory containing `/usr/local/lib/pkgconfig/libsbml.pc.bak.pc'
to the PKG_CONFIG_PATH environment variable
No package '/usr/local/lib/pkgconfig/libsbml.pc.bak' found
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/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -fPIC  -Wall -mtune=core2 -g -O2  -c PathRanker.cpp -o PathRanker.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 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/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -fPIC  -Wall -mtune=core2 -g -O2  -c kgml_interface.cpp -o kgml_interface.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/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -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/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -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/MacOSX10.10.sdk/usr/include/libxml2 -DHAVE_SBML  -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/Library/Frameworks/R.framework/Resources/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 -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-3.2-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	0.315	0.005	0.330
MIRIAM	0.367	0.005	0.372
NPMdefaults	0.014	0.002	0.016
SBML2igraph	0.371	0.007	0.378
assignEdgeWeights	0.558	0.009	0.568
biopax2igraph	0.752	0.015	0.787
colorVertexByAttr	0.216	0.004	0.221
ex_biopax	0.027	0.001	0.029
ex_kgml_sig	0.270	0.005	0.278
ex_microarray	0.005	0.000	0.005
ex_sbml	1.346	0.008	1.357
extractPathNetwork	2.005	0.011	2.018
getAttr	0.035	0.003	0.039
getGeneSetNetworks	0.007	0.001	0.008
getGeneSets	0.074	0.002	0.076
getPathsAsEIDs	1.948	0.006	1.955
layoutVertexByAttr	0.456	0.008	0.467
makeGeneNetwork	0.192	0.001	0.194
makeReactionNetwork	0.101	0.002	0.102
pathClassifier	0.903	0.013	0.971
pathCluster	0.424	0.005	0.429
pathRanker	1.099	0.014	1.114
pathsToBinary	0.849	0.007	0.857
plotAllNetworks	13.462	0.055	13.548
plotClusters	1.281	0.007	1.293
plotCytoscape	0.495	0.007	0.503
plotNetwork	0.979	0.013	0.997
plotPathClassifier	1.171	0.008	1.183
plotPathCluster	0.411	0.003	0.413
plotPaths	15.424	0.053	15.663
predictPathClassifier	0.852	0.003	0.856
predictPathCluster	0.442	0.007	0.448
rmSmallCompounds	0.129	0.000	0.130
samplePaths	0.856	0.009	0.865
simplifyReactionNetwork	0.293	0.002	0.294
toGraphNEL	0.687	0.004	0.693
vertexDeleteReconnect	0.167	0.002	0.169

BioC 3.2: CHECK report for NetPathMiner on oaxaca

Summary

Command output