Dear Duncan and Vincent, Thanks for your help. It took me some time to upgrade R because atp-get install would not actually install the packages, but I used
sudo aptitude install r-base and that managed to upgrade the r-base package. I'm also happy to say that RCurl as well as BiomaRt could now be installed with success! Thanks again, Best wishes, Emmanuel 2008/9/17 Duncan Temple Lang <[EMAIL PROTECTED]>: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hi Emanuel. > > The best thing to do is upgrade to R-2.7.2 (or any 2.7.*) and the > problem should disappear. It relates to encoding of strings. > > D. > > Emmanuel Levy wrote: >> Dear list members, >> >> I encountered this problem and the solution pointed out in a previous >> thread did not work for me. >> (e.g. install.packages("RCurl", repos = "http://www.omegahat.org/R") >> >> I work with Ubuntu Hardy, and installed R 2.6.2 via apt-get. >> >> I really need RCurl in order to use biomaRt ... any help would be >> greatly appreciated. >> >> Best wishes, >> >> Emmanuel >> >> ================================================= >> >>> sessionInfo() >> R version 2.6.2 (2008-02-08) >> x86_64-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] rcompgen_0.1-17 tools_2.6.2 >> >> ================================================= >> >> >>> install.packages("RCurl", repos = "http://www.omegahat.org/R") >> Warning in install.packages("RCurl", repos = "http://www.omegahat.org/R") : >> argument 'lib' is missing: using '/usr/local/lib/R/site-library' >> trying URL 'http://www.omegahat.org/R/src/contrib/RCurl_0.9-4.tar.gz' >> Content type 'application/x-gzip' length 150884 bytes (147 Kb) >> opened URL >> ================================================== >> downloaded 147 Kb >> >> * Installing *source* package 'RCurl' ... >> checking for curl-config... /usr/bin/curl-config >> checking for gcc... gcc >> checking for C compiler default output file name... a.out >> checking whether the C compiler works... yes >> checking whether we are cross compiling... no >> checking for suffix of executables... >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ANSI C... none needed >> checking how to run the C preprocessor... gcc -E >> Version has a libidn field >> configure: creating ./config.status >> config.status: creating src/Makevars >> ** libs >> gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include >> -DHAVE_LIBIDN_FIELD=1 -fpic -g -O2 -c base64.c -o base64.o >> In file included from base64.c:1: >> Rcurl.h:52: error: expected specifier-qualifier-list before 'cetype_t' >> make: *** [base64.o] Error 1 >> chmod: cannot access `/usr/local/lib/R/site-library/RCurl/libs/*': No >> such file or directory >> ERROR: compilation failed for package 'RCurl' >> ** Removing '/usr/local/lib/R/site-library/RCurl' >> >> The downloaded packages are in >> /tmp/RtmpQ8FMBZ/downloaded_packages >> Warning message: >> In install.packages("RCurl", repos = "http://www.omegahat.org/R") : >> installation of package 'RCurl' had non-zero exit status >> >> ================================================================================ >> >> 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 >> >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (Darwin) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iEYEARECAAYFAkjRCr0ACgkQ9p/Jzwa2QP7gywCeLovZ5FGv007HzD8tigg8LJn8 > CXYAniuxcC29ygyowNNPgDXZ4ej3pRxk > =TMuj > -----END PGP SIGNATURE----- > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.