############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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 struct std::unary_function' is deprecated [-Wdeprecated-declarations] 111 | struct IdEq : public std::unary_function | ^~~~~~~~~~~~~~ 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