BioC 3.0: CHECK report for NetPathMiner on zin1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings NetPathMiner_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/NetPathMiner.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.2.0’
* 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 ... [18s/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’ ‘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 ... WARNING
'library' or 'require' calls not declared from:
  ‘ALL’ ‘GSEABase’ ‘clipper’ ‘graphite’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [36s/38s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotPaths       13.433  0.012  13.704
plotAllNetworks  5.617  0.004   5.762
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/NetPathMiner.Rcheck/00check.log’
for details.

* installing *source* package ‘NetPathMiner’ ...
checking for gcc... gcc -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 gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -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
g++ -I/home/biocbuild/bbs-3.0-bioc/R/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  -g -O2  -Wall -c PathRanker.cpp -o PathRanker.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c handlesegfault.c -o handlesegfault.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c hme3m.c -o hme3m.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/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  -g -O2  -Wall -c kgml_interface.cpp -o kgml_interface.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/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  -g -O2  -Wall -c methods.cpp -o methods.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/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  -g -O2  -Wall -c pathScope.cpp -o pathScope.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/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  -g -O2  -Wall -c sbml_interface.cpp -o sbml_interface.o
g++ -shared -L/home/biocbuild/bbs-3.0-bioc/R/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 -L/usr/lib/x86_64-linux-gnu -lxml2 -lsbml -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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	0.268	0.008	0.574
MIRIAM	0.076	0.004	0.080
NPMdefaults	0.008	0.004	0.011
SBML2igraph	0.396	0.000	0.446
assignEdgeWeights	0.428	0.000	0.456
biopax2igraph	0.996	0.020	1.166
colorVertexByAttr	0.328	0.004	0.336
ex_biopax	0.024	0.000	0.023
ex_kgml_sig	0.412	0.000	0.415
ex_microarray	0.004	0.000	0.004
ex_sbml	3.020	0.000	3.098
extractPathNetwork	0.952	0.012	0.966
getAttr	0.024	0.000	0.022
getGeneSetNetworks	0.004	0.004	0.007
getGeneSets	0.032	0.000	0.032
getPathsAsEIDs	0.876	0.008	0.887
layoutVertexByAttr	0.788	0.004	0.840
makeGeneNetwork	0.152	0.000	0.155
makeReactionNetwork	0.056	0.000	0.068
pathClassifier	0.716	0.004	0.794
pathCluster	0.260	0.004	0.304
pathRanker	0.792	0.000	0.828
pathsToBinary	0.556	0.000	0.592
plotAllNetworks	5.617	0.004	5.762
plotClusters	0.872	0.004	0.989
plotCytoscape	0.612	0.000	0.646
plotNetwork	1.032	0.004	1.041
plotPathClassifier	0.692	0.000	0.758
plotPathCluster	0.268	0.000	0.267
plotPaths	13.433	0.012	13.704
predictPathClassifier	0.536	0.000	0.538
predictPathCluster	0.268	0.000	0.269
rmSmallCompounds	0.076	0.000	0.078
samplePaths	0.668	0.008	0.676
simplifyReactionNetwork	0.076	0.004	0.081
toGraphNEL	0.452	0.004	0.459
vertexDeleteReconnect	0.036	0.004	0.040

BioC 3.0: CHECK report for NetPathMiner on zin1

Summary

Command output