[BioC] cannot install rsbml

[Sean Davis]

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

> 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.
>
> _______________________________________________
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