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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NetPathMiner.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NetPathMiner_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/NetPathMiner.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NetPathMiner/DESCRIPTION’ ... OK
* this is package ‘NetPathMiner’ version ‘1.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 whether startup messages can be suppressed ... 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 ‘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 ‘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 ‘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 ‘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 ‘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’
Undefined global functions or variables:
  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.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.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 ... NOTE
checkRd: (-1) plotClassifierROC.Rd:14: Lost braces
    14 | item{Top}{ROC curves for the posterior probabilities (\code{mix\$posterior.probs})
       |     ^
checkRd: (-1) plotClassifierROC.Rd:14-17: Lost braces
    14 | item{Top}{ROC curves for the posterior probabilities (\code{mix\$posterior.probs})
       |          ^
checkRd: (-1) plotClassifierROC.Rd:18: Lost braces
    18 | item{Bottom}{The likelihood convergence history for the HME3M model.  If the parameters
       |     ^
checkRd: (-1) plotClassifierROC.Rd:18-19: Lost braces
    18 | item{Bottom}{The likelihood convergence history for the HME3M model.  If the parameters
       |             ^
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/NetPathMiner.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NetPathMiner
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘NetPathMiner’ ...
** using staged installation
'config' variable 'CPP' is defunct
checking for gcc... clang -arch arm64
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 -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -arch arm64 -E
checking for xmlParseFile in -lxml2... yes
checking for readSBML in -lsbml... no
SBML not found.
libXML2 found
checking for xml2-config... /usr/bin/xml2-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c handlesegfault.c -o handlesegfault.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c hme3m.c -o hme3m.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c kgml_interface.cpp -o kgml_interface.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c methods.cpp -o methods.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DHAVE_XML -I/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sbml_interface.cpp -o sbml_interface.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o NetPathMiner.so handlesegfault.o hme3m.o init.o kgml_interface.o methods.o sbml_interface.o -lxml2 -L/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring duplicate libraries: '-lxml2'
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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)