[Bioc-devel] HTTP GET and POST with RCurl | RMySQL

[Steffen Durinck]

Hi Seth, Martin,

No I don't expect we need SSL, the current BioMart webservices are all 
"http://".
Many thanks for the comments, the biomaRt package will be converted to 
use RCurl by early February.

best,
Steffen

Martin Morgan wrote:

>Seth Falcon <sfalcon at fhcrc.org> writes:
>  
>
>>On 23 Jan 2006, steffen.durinck at esat.kuleuven.be wrote:
>>    
>>
>>>- Do users find RCurl hard to install and is it easier to install
>>>  than RMySQL on all platforms.
>>>      
>>>
>>In general, I think the answer is yes.  As long as an appropriate
>>version of the RCurl binary package has been made available (by
>>Omegahat) then installation is entirely trivial on Windows.  On
>>unix-like systems, libcurl is commonly available.
>>
>>    
>>
>>>- Will a package that depends on RCurl be build on the bioconductor 
>>>repository for all platforms? (With RMySQL my package is not being
>>>build on Windows as RMySQL is not installed)
>>>      
>>>
>>Yes, although as you can see, we seem not to have a binary version of
>>RCurl available for R-devel.  We will fix this.  Note that for us,
>>keeping RCurl going on Windows is *much* easier than keeping RMySQL
>>going.
>>    
>>
>
>An update on this. RCurl _is_ available for R-devel, in the 1.8
>repository. There is a build system issue so that packages depending
>on RCurl were not being built. This should be fixed, with the next
>build.
>
>For security reasons, the Windows binary RCurl on Bioconductor does
>not have SSL support. This will not be a problem, provided your
>use does not require secure access.
>
>For SSL, RCurl has to be built 'by hand'. This can be quite involved
>on any platform, and especially on Windows; most users don't want to
>do this, but if you're eager the general steps are
>
>0. (hard -- has to be exactly right) Have the R source and tools
>   required for building R from source available and working, as
>   described in
>
>     http://cran.fhcrc.org/doc/manuals/R-admin.html
>
>1. (easier -- on Windows mingw needs to be used, but not mingw-make)
>   If SSL-enabled libcurl not already available, download and build
>   openssl from
>
>     http://www.openssl.org/source/.
>
>   (easier -- Windows users should look for the mingw32 target in the
>   Makefile, and set ZLIB_PATH (to files in the R source distibution)
>   and OPENSSL_PATH) Download and build the libcurl library from
>   source, from
>
>     http://curl.haxx.se/download.html
>
>2. (easy) Download & unpack the source package for RCurl from, e.g.,
>
>     http://www.omegahat.org/RCurl/RCurl_0.6-0.tar.gz
>
>3. (easy) Make a binary version of RCurl, moving a copy of the
>   libcurl.dll you created in step 1 into the RCurl source
>   directory. Something like
>
>     mkdir RCurl/inst/libs
>     cp CURL_HOME/libs/libcurl.ddl RCurl/inst/libs
>     R CMD build RCurl
>     R CMD INSTALL --build RCurl_0.6-0.tar.gz
>
>   You might need to specify the location ofthe libcurl 'header' files
>   in R CMD build.
>
>4. (easy) Install the binary version, e.g., using the Packages -->
>   Install packages from local zip files menu item. Alternatively
>   install RCurl from the command line without building a binary
>
>     R CMD INSTALL RCurl
>
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>
>  
>


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