##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:NetPathMiner.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings NetPathMiner_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/NetPathMiner.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'NetPathMiner/DESCRIPTION' ... OK
* this is package 'NetPathMiner' version '1.36.0'
* 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 whether package 'NetPathMiner' can be installed ... WARNING
Found the following significant warnings:
  C:/libsbml/x64/include/sbml/ListOf.h:111:27: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
See 'F:/biocbuild/bbs-3.17-bioc/meat/NetPathMiner.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 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 '.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 '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'
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.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 ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/NetPathMiner/libs/x64/NetPathMiner.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
plotPaths 5.32   0.09     5.4
* 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: 1 WARNING, 3 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/NetPathMiner.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL NetPathMiner
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'NetPathMiner' ...
** using staged installation
* searching for boost headers ... not found. Untarring boost.tar.gz
* searching for NPM_dependencies file ... not found.
* Searching for libxml2 and libSBML ... 
* compiling on Bioconductor machines...
* testing xmlParseFile in libxml2 ... failed
** Command: g++ -std=gnu++17 -o xml_test.out xml_test.cpp -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include -IC:/libxml2/x64/include/libxml2 -LC:/libxml2/x64/lib -lxml2 -lws2_32 
** Error Message: C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(parser.o):parser.c:(.text+0x123f4): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(parser.o):parser.c:(.text+0x12606): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(parser.o):parser.c:(.text+0x1401f): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(tree.o):tree.c:(.text+0x1d06): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(tree.o):tree.c:(.text+0x4d32): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(tree.o):tree.c:(.text+0x534d): more undefined references to `__imp__snprintf' follow
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(tree.o):tree.c:(.text+0x9657): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlIO.o):xmlIO.c:(.text+0xf72): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlIO.o):xmlIO.c:(.text+0xfd5): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlIO.o):xmlIO.c:(.text+0x1142): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(uri.o):uri.c:(.text+0xbd2): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(uri.o):uri.c:(.text+0x2e04): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(HTMLparser.o):HTMLparser.c:(.text+0x163d): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(HTMLparser.o):HTMLparser.c:(.text+0x169b): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(HTMLparser.o):HTMLparser.c:(.text+0x35d9): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(HTMLparser.o):HTMLparser.c:(.text+0x39c3): more undefined references to `__imp__snprintf' follow
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x532): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x6d8): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x7a1): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x7be): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x41f2): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x4900): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x68b1): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x7c7b): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlregexp.o):xmlregexp.c:(.text+0x9537): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemastypes.o):xmlschemastypes.c:(.text+0x6f60): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemastypes.o):xmlschemastypes.c:(.text+0x7017): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemastypes.o):xmlschemastypes.c:(.text+0x7069): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemastypes.o):xmlschemastypes.c:(.text+0x70eb): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemastypes.o):xmlschemastypes.c:(.text+0x7210): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemastypes.o):xmlschemastypes.c:(.text+0x733c): more undefined references to `__imp__snprintf' follow
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0x30f2): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0x9f04): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0xa400): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0xd7f1): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0xd91b): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0xda42): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0xdaf2): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0xdb47): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(relaxng.o):relaxng.c:(.text+0xdb72): more undefined references to `__imp___iob_func' follow
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(entities.o):entities.c:(.text+0xc6c): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(encoding.o):encoding.c:(.text+0x2c97): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(encoding.o):encoding.c:(.text+0x2d28): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(encoding.o):encoding.c:(.text+0x2f12): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(error.o):error.c:(.text+0x6dd): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(parserInternals.o):parserInternals.c:(.text+0x55c): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(parserInternals.o):parserInternals.c:(.text+0xda2): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(parserInternals.o):parserInternals.c:(.text+0x10c6): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(parserInternals.o):parserInternals.c:(.text+0x1372): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(HTMLtree.o):HTMLtree.c:(.text+0x2e9): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x25): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x257f): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x27c1): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x28d2): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x2932): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x2985): more undefined references to `__imp___iob_func' follow
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x3707): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x37e3): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x3edd): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x3f20): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x3f5a): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x3fed): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x412b): undefined reference to `__imp___iob_func'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(debugXML.o):debugXML.c:(.text+0x4180): more undefined references to `__imp___iob_func' follow
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemas.o):xmlschemas.c:(.text+0x944d): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemas.o):xmlschemas.c:(.text+0x21a73): undefined reference to `__imp__snprintf'
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: C:/libxml2/x64/lib/libxml2.a(xmlschemas.o):xmlschemas.c:(.text+0x21ab2): undefined reference to `__imp__snprintf'
collect2.exe: error: ld returned 1 exit status

** Although libxml2 headers and binaries were found, compiler failed.
		This may be due to incomplete headers or corrupt library.
* testing readSBML, SBMLDocument::getModel in libSBML ... failed
** Command: g++ -std=gnu++17 -o sbml_test.out sbml_test.cpp -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include -IC:/libsbml/x64/include -LC:/libsbml/x64/bin -lsbml 
** Error Message: In file included from C:/libsbml/x64/include/sbml/FunctionDefinition.h:136,
                 from C:/libsbml/x64/include/sbml/SBMLTransforms.h:52,
                 from C:/libsbml/x64/include/sbml/SBMLDocument.h:302,
                 from C:/libsbml/x64/include/sbml/SBMLTypes.h:43,
                 from sbml_test.cpp:3:
C:/libsbml/x64/include/sbml/ListOf.h:111:27: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  111 | struct IdEq : public std::unary_function<SBase*, bool>
      |                           ^~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:48,
                 from C:/libsbml/x64/include/sbml/util/util.h:49,
                 from C:/libsbml/x64/include/sbml/xml/XMLError.h:344,
                 from C:/libsbml/x64/include/sbml/SBMLError.h:461,
                 from C:/libsbml/x64/include/sbml/SBMLDocument.h:299:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: F:\biocbuild\bbs-3.17-bioc\tmp\cchnKUyR.o:sbml_test.cpp:(.text+0x20): undefined reference to `SBMLDocument::getModel()'
collect2.exe: error: ld returned 1 exit status

** Although libSBML headers and binaries were found, compiler failed.
	Please ensure that libSBML is built using GCC compiler.
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PathRanker.cpp -o PathRanker.o
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from PathRanker.cpp:27:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c handlesegfault.c -o handlesegfault.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c hme3m.c -o hme3m.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c kgml_interface.cpp -o kgml_interface.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c methods.cpp -o methods.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pathScope.cpp -o pathScope.o
In file included from ./boost/mpl/aux_/na_assert.hpp:23,
                 from ./boost/mpl/arg.hpp:25,
                 from ./boost/mpl/placeholders.hpp:24,
                 from ./boost/iterator/iterator_categories.hpp:17,
                 from ./boost/graph/graph_traits.hpp:25,
                 from ./boost/graph/graph_utility.hpp:29,
                 from pathScope.cpp:34:
./boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
./boost/mpl/assert.hpp:187:21: note: remove parentheses
  187 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  188 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  189 |     );
      |     ~                
      |     -
./boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
./boost/mpl/assert.hpp:192:21: note: remove parentheses
  192 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  193 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  194 |     );
      |     ~                
      |     -
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include    -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sbml_interface.cpp -o sbml_interface.o
g++ -std=gnu++17 -shared -s -static-libgcc -o NetPathMiner.dll tmp.def PathRanker.o handlesegfault.o hme3m.o init.o kgml_interface.o methods.o pathScope.o sbml_interface.o -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-NetPathMiner/00new/NetPathMiner/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (NetPathMiner)