[BioC] cannot install rsbml

Richard Birnie richard.birnie at pro-cure.uk.com
Fri Oct 3 17:04:16 CEST 2008


On Friday 03 October 2008 15:27:56 Sean Davis wrote:
> On Fri, Oct 3, 2008 at 8:07 AM, Richard Birnie
>
> <richard.birnie at 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 at 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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