[Bioc-devel] Problem with installing graph

[Robert Gentleman]

Yes, I believe that your problem is that you must first update your R. 
You are probably using a much outdated R-devel (and in more recent 
versions the API for Rf_duplicated has changed).

As a heads up for folks working on the devel arm of bioc and R, things 
are going to be a bit bumpy over then next few weeks as some changes to 
the API for R are likely and that means that you will need to build R 
quite frequently and install packages from the svn archive (biocLite may 
be a bit too slow).

best wishes
   Robert


Tony Chiang wrote:
> Hi,
> 
> Trying to install graph on R-devel...waited a bit since I got a flag from
> Seth about changes in the way R handles C code... is this still the case?
> Here is the error I get:
> 
>> biocLite("graph", type="source")
> 
> Running biocinstall version 2.1.7 with R version 2.6.0 (under development)
> Your version of R requires version 2.1 of Bioconductor.
> trying URL '
> http://bioconductor.org/packages/2.1/bioc/src/contrib/graph_1.15.4.tar.gz'
> Content type 'application/x-gzip' length 328641 bytes
> opened URL
> ==================================================
> downloaded 320Kb
> 
> * Installing *source* package 'graph' ...
> ** libs
> gcc -std=gnu99 -I/Users/herbie/arch/i386/R-devel/include
> -I/Users/herbie/arch/i386/R-devel/include  -I/usr/local/include
> -D__NO_MATH_INLINES  -fPIC  -g -O2 -c graph.c -o graph.o
> graph.c: In function 'intersectStrings':
> graph.c:72: error: too many arguments to function 'Rf_duplicated'
> make: *** [graph.o] Error 1
> ERROR: compilation failed for package 'graph'
> ** Removing '/Users/herbie/arch/i386/R-devel/library/graph'
> 
> The downloaded packages are in
>         /private/tmp/Rtmp32BZvv/downloaded_packages
> Warning message:
> installation of package 'graph' had non-zero exit status in:
> install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
> 
>> sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-04-10 r41110)
> i386-apple-darwin8.9.1
> 
> locale:
> C
> 
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
> [7] "base"
> 
> Cheers,
> --Tony
> 
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> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org