[Bioc-devel] Bioconductor using 64-bit R build

[Seth Falcon]

Hi Fraser,


On 1/5/10 2:44 PM, Fraser Sim wrote:
> Dear all,
>
> I realize this is completely unsupported but wanted to give it a try. I
> downloaded the compiled version of Windows 64-bit R that Gong Yu recently
> posted details on in the [Rd] mailing list. It starts fine on my version of
> Vista. I was able to run the demo(graphics) so I thought I'd try
> Bioconductor. Here is the sessionInfo().

As previously noted, the issue was that RSQLite was not able to be 
installed on WIN64.  I've received some help from Brian Ripley on what 
is required to make things work.  A new version of RSQLite has been 
uploaded to CRAN that compiles on WIN64.

If you want to test this before it hits CRAN, you can checkout the 
RSQLite sources:

svn co --username=readonly --password=readonly \
   https://hedgehog.fhcrc.org/compbio/r-dbi/trunk/SQLite/RSQLite

+ seth

>
>> sessionInfo()
> R version 2.11.0 Under development (unstable) (2006-00-00 r00000)
> x86_64-pc-mingw64
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] limma_3.3.5   Biobase_2.7.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
> I tried installing Bioconductor from source using biocLite("Biobase", type =
> 'source'). This worked when I used the 64-bit MINGW mentioned by Gong. I am
> able to load the Biobase library.
>
> I then tried to compile limma which also worked fine. See the sessionInfo
> for confirmation. Unfortunately, when I tried to compile genefilter, it
> failed when compiling the RSQLite package.
>
> Here is the output.
>
>> biocLite("RSQLite", type = 'source')
> Using R version 2.11.0 (R-devel), biocinstall version 2.6.4.
> Installing Bioconductor version 2.6 packages:
> [1] "RSQLite"
> Please wait...
>
> trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.8-0.tar.gz'
> Content type 'application/x-gzip' length 1179466 bytes (1.1 Mb)
> opened URL
> downloaded 1.1 Mb
>
> * installing *source* package 'RSQLite' ...
>
>     **********************************************
>     WARNING: this package has a configure script
>           It probably needs manual configuration
>     **********************************************
>
>
> ** libs
>    making DLL ...
> gcc -I"C:/Users/fjsim/DOWNLO~1/R-64BI~1/include"
> -DRSQLITE_USE_BUNDLED_SQLITE       -O3 -Wall  -std=gnu99 -c RS-DBI.c -o
> RS-DBI.o
> In file included from RS-DBI.c:19:0:
> RS-DBI.h:45:7: error: conflicting types for 'getpid'
> d:\rtools\mingw64\bin\../lib/gcc/x86_64-pc-mingw32/4.5.0/../../../../x86_64-
> pc-mingw32/include/process.h:150:15: note: previous declaration of 'getpid'
> was here
> make: *** [RS-DBI.o] Error 1
>    ... done
> ERROR: compilation failed for package 'RSQLite'
> * removing 'C:/Users/fjsim/Downloads/R-64Bit-for-Win64/library/RSQLite'
>
> The downloaded packages are in
>          'C:\Users\fjsim\AppData\Local\Temp\Rtmpr8pCxb\downloaded_packages'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>    installation of package 'RSQLite' had non-zero exit status
>
> Any ideas what I should try next to get RSQLite? It would be great to have
> R/Bioconductor working on 64-bit Windows and I'm willing to help out.
>
> Cheers,
> Fraser
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Seth Falcon | @sfalcon | http://userprimary.net/user