[BioC] RCurl compilation error - fedora 7

Joern Toedling toedling at ebi.ac.uk
Thu May 15 19:18:49 CEST 2008

Hi Martin,
are you working on a 64-bit linux distribution and which version of 
RCurl are you trying to install? There has been a problem with a recent 
version of RCurl and the "R_base64_decode", search the archives of the 
Bioconductor mailing list for a thread called
"RCurl loading problem with 64 bit linux distribution".
Please try using the newest versions of R (R-2.7.0 has been released a 
few weeks ago) and RCurl, which you can obtain from within R by typing:
install.packages("RCurl", repos = "http://www.omegahat.org/R")
The new version of RCurl (>= 0.9.2) worked fine for me, while 0.9.0 and 
0.9.1 did not.
Hope this helps.

martin sikora wrote:
> dear list members,
> i'm having a problem installing the biomaRt package on my linux machine, 
> due to the fact of a compilation error with RCurl. i am using R 2.6.2 on 
> fedora 7, and this is the output i get:
> gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R  
> -DHAVE_LIBIDN_FIELD=1 -I/usr/local/include    -fpic  -O2 -g -pipe -Wall 
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic 
> -fasynchronous-unwind-tables -c base64.c -o base64.o
> In file included from base64.c:1:
> Rcurl.h:52: error: expected specifier-qualifier-list before ?cetype_t?
> base64.c: In function ?R_base64_decode?:
> base64.c:25: warning: pointer targets in assignment differ in signedness
> base64.c:39: warning: pointer targets in passing argument 1 of 
> ?Rf_mkString? differ in signedness
> base64.c: In function ?R_base64_encode?:
> base64.c:60: warning: pointer targets in assignment differ in signedness
> make: *** [base64.o] Error 1
> as far as i know i have all the necessary libraries installed:
> $ yum list installed | grep libxml
> libxml2.i386                             2.6.31-1.fc7           
> installed      
> libxml2-devel.i386                       2.6.31-1.fc7           
> installed      
> libxml2-python.i386                      2.6.31-1.fc7           
> installed      
> perl-libxml-perl.noarch                  0.08-1.2.1             
> installed      
> $ yum list installed | grep curl
> curl.i386                                7.16.4-1.fc7           
> installed      
> curl-devel.i386                          7.16.4-1.fc7           
> installed      
> python-pycurl.i386                       7.16.0-0.1.20061207.fc installed
> as i am not an expert in linux stuff, i was wondering if there could be 
> any other missing libraries? any other ideas?
> cheers
> martin

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