RCurl compilation error - fedora 7
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@martin-sikora-2802
Last seen 9.6 years ago
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 [[alternative HTML version deleted]]
biomaRt biomaRt • 1.3k views
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 8.9 years ago
United States
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: Hi, 2.6.2 is not the current release, 2.7.0 is, so that is the first thing to do. I don't see what is wrong, but RCurl is not a Bioconductor package, so this is probably more appropriately asked on the r-help mailing list. And when posting there, please provide sessionInfo and information on which version of RCurl you are trying to install. best wishes Robert > > 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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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robert, joern, problem solved, thanks for your quick response! it was indeed a problem with R 2.6.2 for me. i added the CRAN repository to my yum configuration (because in the official fedora ones the last R version is still 2.6.2) and upgraded to 2.7.0, now everything is fine. once again thanks for your help. cheers martin Robert Gentleman wrote: > > > 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: > > Hi, > 2.6.2 is not the current release, 2.7.0 is, so that is the first > thing to do. > > I don't see what is wrong, but RCurl is not a Bioconductor package, > so this is probably more appropriately asked on the r-help mailing > list. And when posting there, please provide sessionInfo and > information on which version of RCurl you are trying to install. > > best wishes > Robert > > > >> >> 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 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > [[alternative HTML version deleted]]
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@joern-toedling-1244
Last seen 9.6 years ago
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. Joern 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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