Hi Martin, Thanks for the reply. I tried to use: biocLite("RCurl") But it came up with the same error. Unfortunately, I don't have admin on the machine (I am on a cluster) and I am forced to install into my own home directory. I installed libcurl 7.27 from source which, as far as I know, is the most stable version of libcurl. When I run the following command: $locate curl-config /usr/bin/curl-config /usr/share/man/man1/curl-config.1.gz $curl-config --libs -L/genesis/home/fcchan/usr/lib -lcurl (note that this is the same as /home/fcchan/usr/lib ... ) This is interesting because it is pointing to /genesis/home/fcchan/usr/lib, but my libraries are installed at /genesis/home/fcchan/usr/local/lib. This is probably the reason why it is failing because I had originally installed RCurl there. How do I get it to "curl-config --libs" to point to /genesis/home/fcchan/usr/local/lib? However, I guess the above points are kind of moot because I tried your last suggestion: export LD_LIBRARY_PATH=/home/fcchan/usr/local R source("http://bioconductor.**org/biocLite.R<http: bioconductor.org="" b="" ioclite.r=""> ") biocLite("RCurl") And that worked! I already had this set in my ~/.bashrc, but not sure why re-exporting it worked. But it did. Thanks for your help, Fong On Thu, Sep 6, 2012 at 9:52 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 09/06/2012 09:14 PM, Fong Chun Chan wrote: > >> Hi all, >> >> I am having a lot of difficulties installing the R package Genomic >> Features. When I first tried to install it using the command: >> >> source("http://bioconductor.**org/biocLite.R<http: bioconductor.or="" g="" bioclite.r=""> >> ") >> biocLite("GenomicFeatures") >> >> I got issues about RCurl not being able to install. I followed the >> instructions from this >> thread<http: stackoverflow.**com="" questions="" 10965755="" **="">> genomicfeatures-package-**installation- trouble<http: stackoverflow.com="" questions="" 10965755="" genomicfeatures-="" package-installation-trouble=""> >> > >> by >> installing libcurl <http: curl.haxx.se="" libcurl=""/> and >> libxml<http: www.xmlsoft.org="" **="">from source to my /home/fong/usr/local. >> >> I then tried to install the >> dependencies independently, I ran into errors for RCurl >> >> install.packages('RCurl') >> > > use biocLite("RCurl") > > > .... >> /usr/bin/ld: cannot find -lcurl >> collect2: ld returned 1 exit status >> make: *** [RCurl.so] Error 1ERROR: compilation failed for package ‘RCurl’* >> >> I am thinking this is because I installed libcurl in a non-standard >> directory, /home/fong/usr/local, there it is complaining about that. How >> do I make R see where I installed libcurl? Or is there another problem >> that I am missing here? >> > > It will be easier to install libcurl-dev in the standard location, > probably using your package manager rather than 'by hand'. > > Did you install the 'dev' version of libcurl? Earlier in the installation > I would have expected that R found 'curl-config', and that curl- config > would point to the right location for the headers and library. E.g., for me > in a terminal I have > > $ locate curl-config > /usr/bin/curl-config > > $ curl-config --libs > -L/usr/lib/x86_64-linux-gnu -lcurl -Wl,-Bsymbolic-functions -Wl,-z,relro > > and shortly after biocLite("RCurl") I have > > ** package 'RCurl' successfully unpacked and MD5 sums checked > checking for curl-config... /usr/bin/curl-config > > where you can see that R has found my curl-conofig, and just at the end of > the installation I see > > gcc -std=gnu99 -shared -L/usr/local/lib -o RCurl.so base64.o curl.o > curlInit.o curl_base64.o enums.o memoryManagement.o myUTF8.o > -L/usr/lib/x86_64-linux-gnu -lcurl -Wl,-Bsymbolic-functions -Wl,-z,relro > -L/usr/lib/x86_64-linux-gnu -lxml2 -L/home/mtmorgan/bin/R-2-15-**branch/lib > -lR > installing to /home/mtmorgan/R/x86_64-**unknown-linux-gnu- library/2.** > 15-BiocDevel/RCurl/libs > ** R > > where you can see R is using the result of curl-config --libs. > > As a secondary guess and in a bash shell, you might try > > export LD_LIBRARY_PATH=/home/fong/**usr/local/ > R > > and then biocLite("RCurl"). This tells the shell and its sub- processes to > look for '.so' files in the /home/fong/usr/local directory (assuming that > libcurl is in that directory), as well as the standard places. > > Martin > > >> Fong >> >> ---- >> >> sessionInfo() >> R version 2.14.2 (2012-02-29) >> Platform: x86_64-unknown-linux-gnu (64-bit)locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] >> LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C >> LC_NAME=C [9] LC_ADDRESS=C >> LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 >> LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.2.1 XML_3.9-4 >> >> loaded via a namespace (and not attached): >> [1] tools_2.14.2 >> >>> >>> >> [[alternative HTML version deleted]] >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]