My guess is that you have libsbml >=3.0 installed, which rsbml 1.4.0 does
not support (libsbml 3.0 wasn't around when rsbml 1.4.0 was around).

Michael

On Fri, Oct 3, 2008 at 8:04 AM, Richard Birnie <
richard.birnie@pro-cure.uk.com> wrote:

> On Friday 03 October 2008 15:27:56 Sean Davis wrote:
> > On Fri, Oct 3, 2008 at 8:07 AM, Richard Birnie
> >
> > <richard.birnie@pro-cure.uk.com> wrote:
> > > On Friday 03 October 2008 12:48:15 Sean Davis wrote:
> > >> On Fri, Oct 3, 2008 at 3:32 AM, Richard Birnie
> > >>
> > >> <richard.birnie@pro-cure.uk.com> wrote:
> > >> > Dear list,
> > >> >
> > >> > I'm trying to install the package rsbml from bioconductor. I
> followed
> > >> > the instructions on
> > >> > http://bioconductor.org/packages/2.2/bioc/html/rsbml.html i.e. ran
> the
> > >> > commands
> > >> > source("http://bioconductor.org/biocLite.R")
> > >> > biocLite("rsbml").
> > >> >
> > >> > The installation consistently fails with this error:
> > >> > ####################
> > >> > make: *** [check.o] Error 1
> > >> > chmod: cannot access `/usr/local/lib/R/site-library/rsbml/libs/*':
> No
> > >> > such file or directory
> > >> > ERROR: compilation failed for package 'rsbml'
> > >> > ** Removing '/usr/local/lib/R/site-library/rsbml'
> > >> > ####################
> > >> >
> > >> > It is true that the directory does not exist but I have no idea why
> or
> > >> > what I need to do about it. My session info is
> > >>
> > >> It might help to post the entire output of the installation attempt.
> > >> The error you show above is a symptom, not a cause.  The rest of the
> > >> output might show the error.  Also, you probably want to upgrade your
> > >> R, as R-2.6.2 is a year old.
> > >>
> > >> Sean
> > >
> > > As requested the complete output of the installation attempt is below.
> > > I'm still using 2.6.2 because that is what is packaged for my
> > > distribution. If it's essential to upgrade then I can try that when I
> get
> > > some time. The last time I tried to compile R from source it was a bit
> of
> > > a trial.
> > >
> > > Thanks for the help
> > > Richard
> > >
> > > biocLite("rsbml")
> > > Running biocinstall version 2.1.11 with R version 2.6.2
> > > Your version of R requires version 2.1 of BioConductor.
> > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> > > dependencies,  :
> > >  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
> > > trying
> > > URL
> > > '
> http://bioconductor.org/packages/2.1/bioc/src/contrib/rsbml_1.4.0.tar.gz
> > >' Content type 'application/x-gzip' length 161149 bytes (157 Kb)
> > > opened URL
> > > ==================================================
> > > downloaded 157 Kb
> > >
> > > * Installing *source* package 'rsbml' ...
> > > checking for gcc... gcc
> > > 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 gcc accepts -g... yes
> > > checking for gcc option to accept ISO C89... none needed
> > > checking how to run the C preprocessor... gcc -E
> > > checking for grep that handles long lines and -e... /bin/grep
> > > checking for egrep... /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 SBMLDocument.h usability... yes
> > > checking SBMLDocument.h presence... yes
> > > checking for SBMLDocument.h... yes
> > > checking for SBMLDocument_create in -lsbml... yes
> > > configure: creating ./config.status
> > > config.status: creating src/Makevars
> > > ** libs
> > > gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
> > > -I/usr/include/sbml -I/usr/local/include/sbml     -fpic  -g -O2 -c
> > > check.c -o check.o
> > > check.c:2:30: error: xml/ParseMessage.h: No such file or directory
> >
> > So, xml/ParseMessage.h is not being found.  Do you have either:
> >
> > /usr/include/sbml/xml/ParseMessage.h
> > OR
> > /usr/local/include/sbml/xml/ParseMessage.h
> >
> > on your computer?
> >
> > Sean
>
> In answer to the immediate question, no I don't have either of those.
> However,
> I took the advice to upgrade to R-2.7.2 (which was easier than I remember).
> I
> also upgraded all the bioconductor packages I have installed. Now when I
> attempt to install rsbml it works first time. library(rsbml) shows that the
> package loads correctly so all seems to be well. It seems that this problem
> was either specific to version 2.6.2 or something in my distro's packaging
>
> thanks for the pointers Sean.
>
> regards,
> Richard
>
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