[R] Problem compiling R-Patched

Kevin E. Thorpe kevin.thorpe at utoronto.ca
Thu Mar 16 02:45:14 CET 2006

Liaw, Andy wrote:
> Could it be that you have the environment variable R_HOME (or something like
> that) defined somewhere?  Just a wild guess...

No, R_HOME is not defined in the shell I was compiling in, but R_LIBS
was!  Brilliant "wild guess."



> Andy
> From: Kevin E. Thorpe
>>I downloaded R-Patched today (to see if another problem I 
>>want to ask about is still present or if its just me - as per 
>>the posting guide).  I ran "tools/rsync-recommended" 
>>successfully.  I then ran "configure --enable-R-shlib" 
>>successfully.  Then make stops with the following error.
>>gcc -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o 
>>-L../../../../lib -lR
>>mkdir -p -- ../../../../library/tools/libs
>>make[5]: Leaving directory `/home/src/R-patched/src/library/tools/src'
>>make[4]: Leaving directory `/home/src/R-patched/src/library/tools/src'
>>Error in file(datafile, "wb") : unable to open connection
>>In addition: Warning message:
>>cannot open file '/usr/local/lib/R/library/tools/R/tools.rdb', reason 
>>'Permission denied'
>>Execution halted
>>make[3]: *** [all] Error 1
>>make[3]: Leaving directory `/home/src/R-patched/src/library/tools'
>>make[2]: *** [R] Error 1
>>make[2]: Leaving directory `/home/src/R-patched/src/library'
>>make[1]: *** [R] Error 1
>>make[1]: Leaving directory `/home/src/R-patched/src'
>>make: *** [R] Error 1
>>The tools.rdb file is on my system from a previous build
>>-rw-r--r--  1 root root 90486 2005-08-04 18:54 
>>As you can see from the output above, I am not trying to build in 
>>/usr/local/... at all so I am puzzled as to why anything is 
>>being done in /usr/local/ before the "make install".  Can 
>>anyone suggest what I 
>>should try?  I am compiling on SuSE Linux version 9.2.
>>Thank you.

Kevin E. Thorpe
Biostatistician/Trialist, Knowledge Translation Program
Assistant Professor, Department of Public Health Sciences
Faculty of Medicine, University of Toronto
email: kevin.thorpe at utoronto.ca  Tel: 416.946.8081  Fax: 416.946.3297

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