Package: NetPathMiner

Version: 1.19.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NetPathMiner_1.19.5.tar.gz

StartedAt: 2019-04-09 03:56:58 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:58:33 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 95.1 seconds

RetCode: 0

Status:  OK

CheckDir: NetPathMiner.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NetPathMiner_1.19.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/NetPathMiner.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.19.5’
* package encoding: UTF-8
* 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 ... 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 dependencies in R code ... NOTE
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
alpha: no visible global function definition for ‘col2rgb’
alpha: no visible global function definition for ‘rgb’
assignEdgeWeights : wt.func: no visible global function definition for
  ‘median’
assignEdgeWeights: no visible global function definition for
  ‘complete.cases’
assignEdgeWeights: no visible global function definition for ‘na.omit’
assignEdgeWeights : <anonymous>: no visible global function definition
  for ‘na.omit’
bpGetAnnFromXRef: no visible global function definition for ‘na.omit’
bpGetReferences: no visible global function definition for ‘setNames’
bpMetabolicL2: no visible global function definition for ‘setNames’
bpMetabolicL3: no visible global function definition for ‘setNames’
bpSignalingL3: no visible global function definition for ‘na.omit’
bpSplitComplex: no visible global function definition for ‘na.omit’
colorVertexByAttr: no visible global function definition for ‘palette’
colorVertexByAttr: no visible global function definition for
  ‘colorRampPalette’
drawLegend: no visible global function definition for ‘par’
drawLegend: no visible global function definition for ‘plot.new’
drawLegend: no visible global function definition for ‘strwidth’
drawLegend: no visible global function definition for ‘legend’
fetchAttribute: no visible global function definition for ‘na.omit’
fetchAttribute: no visible global function definition for ‘URLencode’
fetchAttribute: no visible global function definition for ‘setNames’
fetchAttribute : <anonymous>: no visible global function definition for
  ‘read.table’
getGeneSetNetworks: no visible global function definition for
  ‘setClass’
getGeneSetNetworks: no visible global function definition for
  ‘representation’
getPaths : <anonymous>: no visible global function definition for
  ‘head’
getPaths: no visible global function definition for ‘.to’
getPaths: no visible global function definition for ‘.from’
getPaths: no visible global function definition for ‘tail’
graph.sizes: no visible global function definition for ‘par’
makeReactionNetwork: no visible global function definition for
  ‘complete.cases’
pathClassifier: no visible binding for global variable ‘sd’
pathClassifier: no visible global function definition for ‘aggregate’
pathCluster: no visible binding for global variable ‘sd’
pathCluster: no visible global function definition for ‘aggregate’
plotAllNetworks: no visible global function definition for ‘palette’
plotAllNetworks: no visible global function definition for ‘par’
plotAllNetworks: no visible global function definition for
  ‘colorRampPalette’
plotClassifierROC: no visible global function definition for ‘palette’
plotClassifierROC: no visible global function definition for ‘layout’
plotClassifierROC: no visible global function definition for ‘plot’
plotClassifierROC: no visible global function definition for ‘na.omit’
plotClusterMatrix: no visible global function definition for ‘rainbow’
plotClusterMatrix: no visible global function definition for ‘image’
plotClusterMatrix: no visible global function definition for ‘axis’
plotClusterProbs: no visible global function definition for ‘rainbow’
plotClusterProbs: no visible global function definition for ‘matplot’
plotClusters: no visible global function definition for ‘rainbow’
plotClusters: no visible global function definition for ‘strwidth’
plotClusters: no visible global function definition for ‘layout’
plotClusters: no visible global function definition for ‘par’
plotClusters: no visible global function definition for ‘legend’
plotCytoscapeGML : col2hex: no visible global function definition for
  ‘rgb’
plotCytoscapeGML : col2hex: no visible global function definition for
  ‘col2rgb’
plotCytoscapeGML: no visible global function definition for
  ‘packageVersion’
plotNetwork: no visible global function definition for ‘palette’
plotNetwork: no visible global function definition for ‘par’
plotNetwork_internal: no visible global function definition for
  ‘palette’
plotNetwork_internal: no visible global function definition for
  ‘setNames’
plotPathClassifier: no visible global function definition for ‘palette’
plotPathClassifier: no visible global function definition for ‘par’
plotPathClassifier: no visible global function definition for ‘layout’
plotPathClassifier: no visible global function definition for ‘barplot’
plotPathClassifier: no visible global function definition for ‘abline’
plotPathClassifier: no visible global function definition for ‘plot’
plotPathClassifier: no visible global function definition for ‘points’
plotPathClassifier: no visible global function definition for ‘axis’
plotPathClassifier: no visible global function definition for ‘image’
plotPathClassifier: no visible global function definition for
  ‘cm.colors’
plotPathClassifier: no visible global function definition for ‘mtext’
plotPathClassifier: no visible global function definition for ‘lines’
plotPathCluster: no visible global function definition for ‘par’
plotPathCluster: no visible global function definition for ‘layout’
plotPathCluster: no visible global function definition for ‘barplot’
plotPathCluster: no visible global function definition for ‘abline’
plotPathCluster: no visible global function definition for ‘plot’
plotPathCluster: no visible global function definition for ‘axis’
plotPathCluster: no visible global function definition for ‘image’
plotPathCluster: no visible global function definition for ‘cm.colors’
plotPathCluster: no visible global function definition for ‘mtext’
plotPathROC: no visible global function definition for ‘palette’
plotPathROC: no visible global function definition for ‘plot’
plotPathROC: no visible global function definition for ‘lines’
plotPathROC: no visible global function definition for ‘axis’
plotPathROC: no visible global function definition for ‘mtext’
plotPathROC: no visible global function definition for ‘legend’
plotPaths: no visible global function definition for ‘palette’
plotPaths: no visible global function definition for ‘par’
process.color: no visible global function definition for
  ‘colorRampPalette’
process.color: no visible global function definition for ‘setNames’
process.layout: no visible global function definition for ‘par’
processNetwork : <anonymous>: no visible global function definition for
  ‘ecdf’
reindexNetwork: no visible binding for global variable ‘head’
stdAttrNames : <anonymous>: no visible global function definition for
  ‘head’
stdAttrNames : <anonymous>: no visible global function definition for
  ‘setNames’
vertexDeleteReconnect: no visible global function definition for ‘.nei’
Undefined global functions or variables:
  .from .nei .to URLencode abline aggregate axis barplot cm.colors
  col2rgb colorRampPalette complete.cases ecdf head image layout legend
  lines matplot median mtext na.omit packageVersion palette par plot
  plot.new points rainbow read.table representation rgb sd setClass
  setNames strwidth tail
Consider adding
  importFrom("grDevices", "cm.colors", "col2rgb", "colorRampPalette",
             "palette", "rainbow", "rgb")
  importFrom("graphics", "abline", "axis", "barplot", "image", "layout",
             "legend", "lines", "matplot", "mtext", "par", "plot",
             "plot.new", "points", "strwidth")
  importFrom("methods", "representation", "setClass")
  importFrom("stats", "aggregate", "complete.cases", "ecdf", "median",
             "na.omit", "sd", "setNames")
  importFrom("utils", "URLencode", "head", "packageVersion",
             "read.table", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... 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
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotPaths       13.769  0.056  13.825
plotAllNetworks 10.194  0.096  10.296
* 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-3.9-bioc/meat/NetPathMiner.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NetPathMiner
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
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
Couldn't find libsbml.pc. Searching for libsbml in candidate directories.
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -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/ -fPIC  -Wall -g -O2  -c PathRanker.cpp -o PathRanker.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c hme3m.c -o hme3m.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -std=gnu++11 -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/ -fPIC  -Wall -g -O2  -c kgml_interface.cpp -o kgml_interface.o
clang++ -std=gnu++11 -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/ -fPIC  -Wall -g -O2  -c methods.cpp -o methods.o
clang++ -std=gnu++11 -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/ -fPIC  -Wall -g -O2  -c pathScope.cpp -o pathScope.o
clang++ -std=gnu++11 -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/ -fPIC  -Wall -g -O2  -c sbml_interface.cpp -o sbml_interface.o
clang++ -std=gnu++11 -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 -lz -lpthread -licucore -lm -lsbml -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-NetPathMiner/00new/NetPathMiner/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NetPathMiner)

name	user	system	elapsed
KGML2igraph	0.263	0.019	0.287
MIRIAM	0.119	0.013	0.133
NPMdefaults	0.014	0.006	0.021
SBML2igraph	0.251	0.013	0.269
assignEdgeWeights	0.418	0.037	0.454
biopax2igraph	3.144	1.728	1.065
colorVertexByAttr	0.531	0.326	0.240
ex_biopax	0.057	0.037	0.034
ex_kgml_sig	0.725	0.494	0.325
ex_microarray	0.004	0.001	0.005
ex_sbml	1.127	0.035	1.163
extractPathNetwork	1.574	0.043	1.620
getAttr	0.029	0.006	0.035
getGeneSetNetworks	0.011	0.002	0.014
getGeneSets	0.084	0.005	0.088
getPathsAsEIDs	1.663	0.037	1.699
layoutVertexByAttr	0.530	0.016	0.546
makeGeneNetwork	0.174	0.008	0.181
makeMetaboliteNetwork	0.078	0.003	0.081
makeReactionNetwork	0.143	0.004	0.147
pathClassifier	1.051	0.071	1.122
pathCluster	0.410	0.032	0.442
pathRanker	0.964	0.029	0.994
pathsToBinary	0.639	0.011	0.651
plotAllNetworks	10.194	0.096	10.296
plotClusters	0.942	0.013	0.956
plotCytoscape	0.406	0.005	0.411
plotNetwork	0.708	0.018	0.726
plotPathClassifier	0.633	0.023	0.656
plotPathCluster	0.419	0.039	0.459
plotPaths	13.769	0.056	13.825
predictPathClassifier	0.609	0.016	0.623
predictPathCluster	0.429	0.011	0.439
reindexNetwork	0.223	0.004	0.227
rmSmallCompounds	0.107	0.003	0.110
samplePaths	0.793	0.016	0.810
simplifyReactionNetwork	0.183	0.002	0.185
toGraphNEL	0.851	0.031	0.883
vertexDeleteReconnect	0.072	0.004	0.075