[BioC] rsbml installer cannot find ParseMessage.h from libsbml

Jie Bao jie.bao at frias.uni-freiburg.de
Wed Jun 22 12:28:34 CEST 2011

Hi all,

I was having trouble to install the rsbml package and it complains
about not having the ParseMessage.h file in the libsbml include
directory. Does rsbml actually requires version 3 of libsbml? Any one
has a clue? Thanks a lot!


* installing *source* package ‘rsbml’ ...
checking for pkg-config... /opt/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML3... no
checking for gcc... /opt/local/bin/gcc-mp-4.4 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /opt/local/bin/gcc-mp-4.4 -std=gnu99 accepts -g... yes
checking for /opt/local/bin/gcc-mp-4.4 -std=gnu99 option to accept ISO
C89... none needed
checking how to run the C preprocessor... /opt/local/bin/gcc-mp-4.4
-std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
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 find sbml/xml/ParseMessage.h:
      rsbml requires libsbml from http://www.sbml.org/software/libsbml/
      use --with-libsbml-include or LIBSBML_INCLUDE to specify the include path.
ERROR: configuration failed for package ‘rsbml’
* removing ‘/Users/bao/R/i386-apple-darwin9.8.0-library/2.13/rsbml’

The downloaded packages are in
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
  installation of package 'rsbml' had non-zero exit status
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.13.0

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