[R] Compilation errors when installing gee

[Prof Brian Ripley]

This is nothing to do with gee (which I maintain).  It seems what you 
installed a binary version of R, and hence do not have the files it 
refers to for source package installation.  You appear to need to 
install the blas-devel RPM.

Questions about binary installations of R are best asked on the 
relevant list, e.g. r-sig-fedora.

On Wed, 26 Jan 2011, adam_pgsql wrote:

>
> Hi,
>
> I am trying to install gee on our server but I get the error below. 
> I do not have root on this machine so no control on how R was 
> installed itself. It looks like it cannot find blas libs, the only 
> ones i can find on the machine are:
>
> /usr/lib64/libblas.so.3 -> libblas.so.3.0.3
> /usr/lib64/libblas.so.3.0 -> libblas.so.3.0.3
> /usr/lib64/libblas.so.3.0.3
>
> and :
>
> $ R CMD config BLAS_LIBS
> -lblas
>
> Any ideas how to get this package to install? (sessionInfo() at the bottom of email)
>
> thanks for any help
>
> adam
>
>> install.packages("gee")
> Installing package(s) into ‘/homedirs4/sghms/medmicro/users/awitney/R/x86_64-redhat-linux-gnu-library/2.12’
> (as ‘lib’ is unspecified)
> trying URL 'http://www.stats.bris.ac.uk/R/src/contrib/gee_4.13-16.tar.gz'
> Content type 'application/x-gzip' length 55712 bytes (54 Kb)
> opened URL
> ==================================================
> downloaded 54 Kb
>
> * installing *source* package ‘gee’ ...
> ** libs
> gfortran   -fpic  -O2 -g -c dgedi.f -o dgedi.o
> gfortran   -fpic  -O2 -g -c dgefa.f -o dgefa.o
> gcc -I/usr/lib64/R/include  -I/usr/local/include    -fpic  -O3 -g -std=gnu99 -c ugee.c -o ugee.o
> gcc -shared -Bdirect,--hash-stype=both,-Wl,-O1 -o gee.so dgedi.o dgefa.o ugee.o -lblas -lgfortran -lm -lgfortran -lm -L/usr/lib64/R/lib -lR
> /usr/bin/ld: cannot find -lblas
> collect2: ld returned 1 exit status
> make: *** [gee.so] Error 1
> ERROR: compilation failed for package ‘gee’
> * removing ‘/homedirs4/sghms/medmicro/users/awitney/R/x86_64-redhat-linux-gnu-library/2.12/gee’
>
> The downloaded packages are in
> 	‘/tmp/RtmpD8sZiL/downloaded_packages’
> Warning message:
> In install.packages("gee") :
>  installation of package 'gee' had non-zero exit status
>
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.0
>
> ______________________________________________
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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