BioC 3.1: 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 NetPathMiner_1.4.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.4.1’
* 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 ... [19s/21s] 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 ... [48s/49s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotPaths       14.289  0.817  15.135
plotAllNetworks 11.868  0.351  12.310
* 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-3.1-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-3.1-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	0.263	0.019	0.297
MIRIAM	0.300	0.004	0.303
NPMdefaults	0.013	0.003	0.017
SBML2igraph	0.307	0.026	0.333
assignEdgeWeights	0.542	0.117	0.661
biopax2igraph	0.689	0.106	0.821
colorVertexByAttr	0.174	0.004	0.179
ex_biopax	0.019	0.001	0.019
ex_kgml_sig	0.273	0.007	0.282
ex_microarray	0.004	0.002	0.006
ex_sbml	1.351	0.052	1.420
extractPathNetwork	2.052	0.107	2.160
getAttr	0.034	0.005	0.039
getGeneSetNetworks	0.007	0.001	0.008
getGeneSets	0.074	0.001	0.074
getPathsAsEIDs	1.868	0.119	1.987
layoutVertexByAttr	0.576	0.091	0.677
makeGeneNetwork	0.168	0.001	0.169
makeReactionNetwork	0.104	0.001	0.104
pathClassifier	0.948	0.053	1.004
pathCluster	0.337	0.003	0.340
pathRanker	0.961	0.084	1.046
pathsToBinary	0.775	0.038	0.813
plotAllNetworks	11.868	0.351	12.310
plotClusters	1.159	0.005	1.171
plotCytoscape	0.418	0.036	0.455
plotNetwork	0.807	0.018	0.830
plotPathClassifier	1.034	0.059	1.097
plotPathCluster	0.452	0.069	0.523
plotPaths	14.289	0.817	15.135
predictPathClassifier	0.857	0.077	0.935
predictPathCluster	0.452	0.008	0.460
rmSmallCompounds	0.160	0.001	0.161
samplePaths	0.963	0.023	0.988
simplifyReactionNetwork	0.238	0.029	0.267
toGraphNEL	0.636	0.043	0.680
vertexDeleteReconnect	0.107	0.001	0.109

BioC 3.1: CHECK report for NetPathMiner on morelia

Summary

Command output