Question

rsbml fails to compile on Linux due to ParseMessage.h undetected with libSBML 5

0

Entering edit mode

zeb • 0

@zeb-12001

Last seen 5.8 years ago

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.

rsbml compilation error configure • 1.4k views

ADD COMMENT • link 5.8 years ago zeb • 0

0

Entering edit mode

Did you try the thing mentioned by the error message?

ADD REPLY • link 5.8 years ago Michael Lawrence 11k

0

Entering edit mode

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 REPLY • link 5.8 years ago zeb • 0

0

Entering edit mode

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

ADD REPLY • link 5.8 years ago Martin Morgan 25k

0

Entering edit mode

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 REPLY • link 5.8 years ago zeb • 0

0

Entering edit mode

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 REPLY • link 5.8 years ago Martin Morgan 25k

0

Entering edit mode

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 REPLY • link 4.1 years ago jedrzej.szymanski • 0

0

Entering edit mode

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

ADD REPLY • link 4.1 years ago Michael Lawrence 11k

0

Entering edit mode

Hi Michael,

For the record the Ubuntu package libsbml5-dev does not provide a libsbml.pc so unfortunately most Ubuntu users will have the same problem as jedrzej above.

H.

ADD REPLY • link 3.0 years ago Hervé Pagès 15k

0

Entering edit mode

Any bugfix available for those who do not have a libsbml.pc?

ADD REPLY • link 2.6 years ago faustfrankenstein • 0

0

Entering edit mode

This guy's script did the job (it installed a libsbml.pc being accessible from R(studio))

ADD REPLY • link 2.6 years ago faustfrankenstein • 0

0

Entering edit mode

Obviously no need to install the sybilSBML package at the end of that script. Someone should let the Ubuntu package maintainer know that libsbml5-dev should include the .pc file.

ADD REPLY • link 2.6 years ago Michael Lawrence 11k