[Bioc-devel] Problem with installing graph
rgentlem at fhcrc.org
Mon Jun 4 17:45:03 CEST 2007
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You are probably using a much outdated R-devel (and in more recent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).
Tony Chiang wrote:
> 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 '
> 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
> Warning message:
> installation of package 'graph' had non-zero exit status in:
> install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
> R version 2.6.0 Under development (unstable) (2007-04-10 r41110)
> attached base packages:
>  "stats" "graphics" "grDevices" "utils" "datasets" "methods"
>  "base"
> [[alternative HTML version deleted]]
> Bioc-devel at stat.math.ethz.ch mailing list
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
rgentlem at fhcrc.org
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