[R] Compilation errors when installing gee

adam_pgsql adam_pgsql at witneyweb.org
Wed Jan 26 10:33:51 CET 2011


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

and :

$ R CMD config BLAS_LIBS

Any ideas how to get this package to install? (sessionInfo() at the bottom of email)

thanks for any help


> 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
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)

 [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            

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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