[BioC] cannot install rsbml

Fri Oct 3 14:07:55 CEST 2008

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
check.c:5: error: expected ‘)’ before ‘*’ token
check.c: In function ‘rsbml_problems’:
check.c:31: warning: implicit declaration of 
function ‘SBMLDocument_getNumWarnings’
check.c:35: warning: implicit declaration of 
function ‘SBMLDocument_getNumFatals’
check.c:46: warning: implicit declaration of function ‘rsbml_problem’
check.c:46: warning: implicit declaration of 
function ‘SBMLDocument_getWarning’
check.c:46: warning: passing argument 3 of ‘SET_VECTOR_ELT’ makes pointer from 
integer without a cast
check.c:48: warning: passing argument 3 of ‘SET_VECTOR_ELT’ makes pointer from 
integer without a cast
check.c:50: warning: implicit declaration of function ‘SBMLDocument_getFatal’
check.c:50: warning: passing argument 3 of ‘SET_VECTOR_ELT’ makes pointer from 
integer without a cast
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'

The downloaded packages are in
        /tmp/RtmpBB1f0Z/downloaded_packages
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  installation of package 'rsbml' had non-zero exit status

>
> > ###################
> > sessionInfo()
> > R version 2.6.2 (2008-02-08)
> > i486-pc-linux-gnu
> >
> > locale:
> > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UT
> >F-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;L
> >C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIF
> >ICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > loaded via a namespace (and not attached):
> > [1] rcompgen_0.1-17 tools_2.6.2
> > ###################
> >
> > I have libsbml installed which was done by running the following
> > commands: ./configure --with-python --with-bzip2=no
> > make
> > sudo make install
> >
> > Can anybody suggest what I need to do.
> >
> > thanks,
> > Richard
> > --
> > Dr Richard Birnie
> > Research Scientist
> > Pro-Cure Therapeutics Limited
> > Biocentre
> > Innovation Way, Heslington, York, YO10 5NY, UK
> > Registered in England : Reg No. 421 6368
> > telephone +44 (0)1904 435125
> > Email richard.birnie at pro-cure.uk.com
> > www.pro-cure.uk.com
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-- 
Dr Richard Birnie
Research Scientist
Pro-Cure Therapeutics Limited
Biocentre
Innovation Way, Heslington, York, YO10 5NY, UK 
Registered in England : Reg No. 421 6368 
telephone +44 (0)1904 435125
Email richard.birnie at pro-cure.uk.com
www.pro-cure.uk.com
CONFIDENTIAL AND PRIVILEGED. This email and any attachment(s) are
confidential and may contain privileged information. It is intended solely
for the addressee(s). If you have received this message in error, please
notify the sender immediately and remove it from your system.