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Question: rsbml fails to compile on Linux due to ParseMessage.h undetected with libSBML 5
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gravatar for zeb
22 months ago by
zeb0
zeb0 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.

ADD COMMENTlink modified 22 months ago • written 22 months ago by zeb0

Did you try the thing mentioned by the error message?

ADD REPLYlink written 22 months ago by Michael Lawrence10k

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.

ADD REPLYlink written 22 months ago by zeb0

biocLite delegates to install.packages, so use the appropriate argument there, biocLite("rsbml", configure.args="--enable-soslib=system"), I think...

ADD REPLYlink written 22 months ago by Martin Morgan ♦♦ 22k

Thanks. I am still stuck with libsbml 5:

Using:

biocLite("rsbml", configure.args="--enable-soslib=system --with-libsbml-lib=/usr/local/lib/libsbml.so.5")

I get this error:

Error : .onLoad failed in loadNamespace() for 'rsbml', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/eric/R/x86_64-redhat-linux-gnu-library/3.3/rsbml/libs/rsbml.so':
  libsbml.so.5: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed

It cannot open libsbml.so.5 despite the library is clearly passed in the options. Is there anything else I can do?

ADD REPLYlink written 22 months ago by zeb0

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.

ADD REPLYlink written 22 months ago by Martin Morgan ♦♦ 22k

Hi, I have a similar problem, even though the libsbml is where it should be. Works in python and matlab, but not in R

* installing *source* package ‘rsbml’ ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML... no
configure: error: Package requirements (libsbml >= 3.0.2) were not met:

No package 'libsbml' found
ADD REPLYlink written 6 weeks ago by jedrzej.szymanski0

Probably just need to set your PKG_CONFIG_PATH to the directory containing the libsbml.pc file.

ADD REPLYlink written 6 weeks ago by Michael Lawrence10k
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