[R] Compiling msm on Fedora Core Linux

[Prof Brian Ripley]

The problem seems to be in the header paths:

> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/include/R
> -I/usr/local/include

Is R.h not in /usr/include/R?

My guess is that you installed an R rpm and not the R-devel rpm.  But if 
you installed from rpms, this is a Fedora support issue -- this community 
is not responsible for Fedora's re-packaging of R.

On Wed, 23 Apr 2008, Adam Wilson wrote:

> Greetings all,
>
> I'm trying to install the msm package and it is failing on compilation.  The
> problem seems to be the analyticp component?  Any advice on how to get it to
> work?
>
> error message is below.  I'm running R version 2.6.2 (2008-02-08)
> x86_64-redhat-linux-gnu  on a dell precision 690 with Fedora Core 8.
>
> Thanks,
> Adam
>
>
>> install.packages("msm",lib="/usr/lib64/R/library")
> trying URL 'http://cran.mirrors.hoobly.com/src/contrib/msm_0.8.tar.gz'
> Content type 'application/x-tar' length 577213 bytes (563 Kb)
> opened URL
> ==================================================
> downloaded 563 Kb
>
> * Installing *source* package 'msm' ...
> ** libs
> gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/include/R
> -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> -c analyticp.c -o analyticp.o
> In file included from analyticp.c:9:
> msm.h:3:15: error: R.h: No such file or directory
> msm.h:4:26: error: R_ext/Applic.h: No such file or directory
> analyticp.c: In function 'AnalyticP':
> analyticp.c:51: warning: implicit declaration of function 'Calloc'
> analyticp.c:51: error: expected expression before 'double'
> analyticp.c:51: warning: cast to pointer from integer of different size
> analyticp.c:52: error: expected expression before 'double'
> analyticp.c:52: warning: cast to pointer from integer of different size
> analyticp.c:63: warning: implicit declaration of function 'error'
> analyticp.c:91: warning: implicit declaration of function 'Free'
> make: *** [analyticp.o] Error 1
> ERROR: compilation failed for package 'msm'
> ** Removing '/usr/lib64/R/library/msm'
>
> The downloaded packages are in
>    /tmp/RtmpaoUZiC/downloaded_packages
> Updating HTML index of packages in '.Library'
> Warning messages:
> 1: In install.packages("msm", lib = "/usr/lib64/R/library") :
>  installation of package 'msm' had non-zero exit status
> 2: In tools:::unix.packages.html(.Library) :
>  cannot create HTML package index
>>
>
>
>
>
>
>
> -- 
> Adam Wilson
> http://hydrodictyon.eeb.uconn.edu/people/wilson/
> Department of Ecology and Evolutionary Biology
> BioPharm 223
> University of Connecticut
> Tel: 860.486.4157
> Adam.Wilson at UConn.edu
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595