On Wed, Jun 22, 2011 at 3:28 AM, Jie Bao <jie.bao@frias.uni-freiburg.de>wrote:

> 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!
>
>
Which version of libsbml do you have? I would recommend using 3.x as 2.x is
getting pretty long in the tooth (5.x is current). But rsbml will still work
with 2.x; you just have to tell it where to look, as described by the error
message.

Michael


> best,
> jie
>
>
> * 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
>
>  ‘/private/var/folders/Up/UpTpxqkaGMmzlCOlJBc+pk+++TI/-Tmp-/Rtmp6enfxM/downloaded_packages’
> 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)
>
> locale:
> [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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