I'm encountering issues when building my package NetPathMiner on palomino3 ( http://bioconductor.org/checkResults/devel/bioc-LATEST/NetPathMiner/palomino3-checksrc.html). The package depends on system libraries libxml2 and libsbml. So far, I've been using `LIB_XML2` and `LIBSBML_PATH` as previously advised by Bioconductor maintainers. I've noticed lately that NetPathMiner is having trouble finding these packages.
*First libxml2,* looking at the log below (output from configure.win), I can see `LIB_XML2` is pointing to `C:/LIB_XML2/`. Is this correct? Looking at the setup scripts ( https://github.com/Bioconductor/BBS/blob/master/utils/setup-win.ps1), I think it should point to `c:\libxml2`. ** Command: g++ -std=gnu++14 -o xml_test.out xml_test.cpp -DWIN_COMPILE -I. -IF:/biocbuild/bbs-3.17-bioc/R/include -IC:/LIB_XML2/x64/include/libxml2 -LC:/LIB_XML2/x64/lib -lxml2 -lws2_32 For *libsbml*, `LIBSBML_PATH` correctly points to `C:/libsbml/`, and NetPathMiner can find the headers needed, but it fails to link against the library (error below). This can be either the binaries are not at `C:/libsbml/x64/bin` or they have been compiled with a different compiler. C:\rtools43/x86_64-w64-mingw32.static.posix/bin/ld.exe: F:\biocbuild\bbs-3.17-bioc\tmp\cc9H7H7o.o:sbml_test.cpp:(.text+0x20): undefined reference to `SBMLDocument::getModel()' collect2.exe: error: ld returned 1 exit status Many thanks in advance for your help. Cheers, Ahmed. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel