[BioC] GenomicFeatures Installation Problem

[Martin Morgan]

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")
> 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>
> 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
>>
>
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>
>
>
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