BioC 3.1: CHECK report for NetPathMiner on petty

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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 Patched (2015-08-14 r69078)
* 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 ‘1.4.1’
* 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 ... [24s/40s] 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:
  ‘graph’ ‘rBiopaxParser’ ‘RCurl’ ‘RCytoscape’
  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 ... [73s/74s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotPaths       23.510  0.083  23.687
plotAllNetworks 17.701  0.082  17.801
* 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... 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/Library/Frameworks/R.framework/Resources/lib -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-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	0.507	0.010	0.581
MIRIAM	0.538	0.010	0.549
NPMdefaults	0.026	0.006	0.031
SBML2igraph	0.789	0.011	0.822
assignEdgeWeights	0.816	0.017	0.833
biopax2igraph	1.131	0.029	1.352
colorVertexByAttr	0.322	0.005	0.341
ex_biopax	0.038	0.001	0.040
ex_kgml_sig	0.424	0.007	0.434
ex_microarray	0.007	0.001	0.008
ex_sbml	2.262	0.012	2.279
extractPathNetwork	2.849	0.009	2.858
getAttr	0.035	0.003	0.038
getGeneSetNetworks	0.020	0.001	0.021
getGeneSets	0.101	0.002	0.104
getPathsAsEIDs	2.731	0.010	2.741
layoutVertexByAttr	0.893	0.014	0.913
makeGeneNetwork	0.329	0.002	0.331
makeReactionNetwork	0.210	0.001	0.212
pathClassifier	1.384	0.024	1.410
pathCluster	0.615	0.003	0.621
pathRanker	1.540	0.014	1.555
pathsToBinary	1.286	0.012	1.300
plotAllNetworks	17.701	0.082	17.801
plotClusters	1.666	0.009	1.686
plotCytoscape	0.645	0.002	0.647
plotNetwork	1.329	0.022	1.366
plotPathClassifier	1.517	0.013	1.627
plotPathCluster	0.779	0.008	0.789
plotPaths	23.510	0.083	23.687
predictPathClassifier	1.142	0.004	1.147
predictPathCluster	0.788	0.007	0.796
rmSmallCompounds	0.218	0.002	0.221
samplePaths	1.668	0.021	1.691
simplifyReactionNetwork	0.299	0.002	0.301
toGraphNEL	1.112	0.008	1.122
vertexDeleteReconnect	0.204	0.002	0.207

BioC 3.1: CHECK report for NetPathMiner on petty

Summary

Command output