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/biocLite.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.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<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]]
>>
>>
>>
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>> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>>
>
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