Question: rsbml fails to compile on Linux due to ParseMessage.h undetected with libSBML 5
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zeb • 0 wrote:
Installing rsbml on Fedora 25 fails despite having libsbml-5.10.2 installed in /usr/local. I get this error at configure (in R):
checking for LIBSBML3... no [...] checking sbml/xml/ParseMessage.h usability... no checking sbml/xml/ParseMessage.h presence... no checking for sbml/xml/ParseMessage.h... no configure: error: Could not detect libsbml (>= 3.0) via pkg-config. rsbml requires libsbml from http://www.sbml.org/software/libsbml/. Please ensure that libsbml.pc is in PKG_CONFIG_PATH. Also failed to find ParseMessage.h indicating that libsbml 2.x is not installed. To specify the include path manually use --with-libsbml-include or LIBSBML_INCLUDE. ERROR: configuration failed for package ‘rsbml’
Indeed, it cannot detect libsbml3, because I use libsbml5, but ParseMessage.h does not exist in libsbml5. However, rsbml is supposed to work with libSBML-5.10.2. Am I doing anything wrong?
Thanks.
Did you try the thing mentioned by the error message?
Hi Michael, yes, thanks there was a typo in my PKG_CONFIG_PATH pathname. Now it compiles in console. However, when installing from R (via biocLite), how do you pass options such as "--enable-soslib=system"? Thanks.
biocLite delegates to install.packages, so use the appropriate argument there,
biocLite("rsbml", configure.args="--enable-soslib=system")
, I think...Thanks. I am still stuck with libsbml 5:
Using:
I get this error:
It cannot open libsbml.so.5 despite the library is clearly passed in the options. Is there anything else I can do?
Please use 'comment' rather than 'Answer'. The error you're reporting is saying that libsbml.so is not known at run-time, rather than compile time. Likely you need to use ldconfig or set LD_LIBRARY_PATH to include the location of libsbml.