[Bioc-devel] libsbml and libxml2 on palomino3 BBS

Jennifer Wokaty Jenn||er@Wok@ty @end|ng |rom @ph@cuny@edu
Thu Mar 2 20:55:10 CET 2023

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-bounces using r-project.org> on behalf of Ahmed Mohamed <amfy10 using gmail.com>
Sent: Monday, February 27, 2023 6:11 PM
To: bioc-devel <bioc-devel using 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

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.

undefined reference to `SBMLDocument::getModel()' collect2.exe: error: ld
returned 1 exit status

Many thanks in advance for your help.

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