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###
### Running command:
###
###   chmod a+r NetPathMiner -R && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data NetPathMiner
###
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* checking for file 'NetPathMiner/DESCRIPTION' ... OK
* preparing 'NetPathMiner':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running 'cleanup.win'
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'NetPathMiner' ...
** using staged installation
* 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. -IE:/biocbuild/bbs-3.19-bioc/R/include -IC:/libxml2/x64/include/libxml2 -LC:/libxml2/x64/lib -lxml2 -lws2_32 
** Error Message: C:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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:\rtools44/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. -IE:/biocbuild/bbs-3.19-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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/string:49,
                 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:/rtools44/x86_64-w64-mingw32.static.posix/lib/gcc/x86_64-w64-mingw32.static.posix/13.2.0/include/c++/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
C:\rtools44/x86_64-w64-mingw32.static.posix/bin/ld.exe: E:\biocbuild\bbs-3.19-bioc\tmp\ccliUPrx.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) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
gcc  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c handlesegfault.c -o handlesegfault.o
handlesegfault.c:7:32: error: unknown type name 'siginfo_t'
    7 | void segfault_KGML(int signal, siginfo_t *si, void *arg){
      |                                ^~~~~~~~~
handlesegfault.c:11:32: error: unknown type name 'siginfo_t'
   11 | void segfault_SBML(int signal, siginfo_t *si, void *arg){
      |                                ^~~~~~~~~
handlesegfault.c: In function 'handle_segfault_KGML':
handlesegfault.c:19:26: error: storage size of 'sa' isn't known
   19 |         struct sigaction sa;
      |                          ^~
handlesegfault.c:21:27: error: invalid application of 'sizeof' to incomplete type 'struct sigaction'
   21 |     memset(&sa, 0, sizeof(struct sigaction));
      |                           ^~~~~~
handlesegfault.c:22:5: warning: implicit declaration of function 'sigemptyset' [-Wimplicit-function-declaration]
   22 |     sigemptyset(&sa.sa_mask);
      |     ^~~~~~~~~~~
handlesegfault.c:23:23: error: 'segfault_KGML' undeclared (first use in this function); did you mean 'handle_segfault_KGML'?
   23 |     sa.sa_sigaction = segfault_KGML;
      |                       ^~~~~~~~~~~~~
      |                       handle_segfault_KGML
handlesegfault.c:23:23: note: each undeclared identifier is reported only once for each function it appears in
handlesegfault.c:24:21: error: 'SA_SIGINFO' undeclared (first use in this function)
   24 |     sa.sa_flags   = SA_SIGINFO;
      |                     ^~~~~~~~~~
handlesegfault.c:26:5: warning: implicit declaration of function 'sigaction' [-Wimplicit-function-declaration]
   26 |     sigaction(SIGSEGV, &sa, NULL);
      |     ^~~~~~~~~
handlesegfault.c:19:26: warning: unused variable 'sa' [-Wunused-variable]
   19 |         struct sigaction sa;
      |                          ^~
handlesegfault.c: In function 'handle_segfault_SBML':
handlesegfault.c:32:26: error: storage size of 'sa' isn't known
   32 |         struct sigaction sa;
      |                          ^~
handlesegfault.c:34:27: error: invalid application of 'sizeof' to incomplete type 'struct sigaction'
   34 |     memset(&sa, 0, sizeof(struct sigaction));
      |                           ^~~~~~
handlesegfault.c:36:23: error: 'segfault_SBML' undeclared (first use in this function); did you mean 'handle_segfault_SBML'?
   36 |     sa.sa_sigaction = segfault_SBML;
      |                       ^~~~~~~~~~~~~
      |                       handle_segfault_SBML
handlesegfault.c:37:21: error: 'SA_SIGINFO' undeclared (first use in this function)
   37 |     sa.sa_flags   = SA_SIGINFO;
      |                     ^~~~~~~~~~
handlesegfault.c:32:26: warning: unused variable 'sa' [-Wunused-variable]
   32 |         struct sigaction sa;
      |                          ^~
make: *** [E:/biocbuild/bbs-3.19-bioc/R/etc/x64/Makeconf:289: handlesegfault.o] Error 1
ERROR: compilation failed for package 'NetPathMiner'
* removing 'E:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpuETb9m/Rinst3ad438df733e/NetPathMiner'
      -----------------------------------
ERROR: package installation failed