Hi Ahmed, Thanks for your email.
LIB_XML2 should point to C:\libxml2. The path for LIBSBML_PATH is correct and they exist. Since the builds started today, I will make the change tomorrow so that we'll see effect on the Saturday build report. We can troubleshoot the LIBSBML_PATH next. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Ahmed Mohamed <amf...@gmail.com> Sent: Monday, February 27, 2023 6:11 PM To: bioc-devel <bioc-devel@r-project.org> Subject: [Bioc-devel] libsbml and libxml2 on palomino3 BBS ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.*** I'm encountering issues when building my package NetPathMiner on palomino3 ( https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_NetPathMiner_palomino3-2Dchecksrc.html&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=_qCS3QgxrpFRR9gDVfqzwdSz3y95bJB7-IWrQcHa9hokg9o6Ar-YHbyMj6kuQCZ6&s=2C7FjRtxvK8D2hdUVtAMkl9GTq17VzEKVt7PlWD0SgM&e= ). 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_BBS_blob_master_utils_setup-2Dwin.ps1&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=_qCS3QgxrpFRR9gDVfqzwdSz3y95bJB7-IWrQcHa9hokg9o6Ar-YHbyMj6kuQCZ6&s=ImDz0ymb5uXiCKQxOyxPdS2nG1FoUt_FrDGjFcQksNI&e= ), 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://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=mRWFL96tuqj9V0Jjj4h40ddo0XsmttALwKjAEOCyUjY&r=FKSqKXkUOES-D4VQb2jSn9QK7Vz5lE18rLcyn73CPhA&m=_qCS3QgxrpFRR9gDVfqzwdSz3y95bJB7-IWrQcHa9hokg9o6Ar-YHbyMj6kuQCZ6&s=_A7pxXenVErQP0qAhQr9pc_i7OxJkkaVFWfjDzZgE6A&e= [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
