[Bioc-devel] libsbml and libxml2 on palomino3 BBS

[Ahmed Mohamed]

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.

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