[Bioc-devel] graph package dependency on libiconv or libintl

Patrick Aboyoun paboyoun at fhcrc.org
Fri May 2 01:59:21 CEST 2008

I am working on the BioC 2.2 Mac OS X Tiger binary packages builds right 
now, and I anticipate they will be ready by tomorrow (or sooner if the 
first round of builds go well). When these binary packages are ready, I 
will replace the Mac OS X Leopard binary packages with the Tiger ones on 
http://bioconductor.org/packages/2.2/bioc. You may want to hold off 
spending more time on this issue until the new builds come out.

This does bring up a question about the BioC 2.3 development builds. 
Should they be on Tiger or Leopard? I have a feeling we will be 
revisiting this situation 6 months from now. I'll make sure we build on 
both Tiger and Leopard and then we can choose, based on user feedback, 
which binary packages to put in the BioC 2.3 release. One benefit of 
Leopard is that we can get 64-bit versions of the Mac OS X packages out 
there and, given the data sizes users commonly encounter, having a 
larger memory address space can greatly increase analysis capacity.


Dan Tenenbaum wrote:
> Hello,
> I have seen this topic mentioned before, but I have a bit to add--
> I installed the gaggle package from the new bioconductor (using R 
> 2.7). It depends on (among other things) the graph package.
> When I tried:
> library(gaggle)
> ...after installing the gaggle package, I got an error about how my 
> libiconv library was out of date. This was on a mac, so I just 
> downloaded the latest libiconv using macports, make a symbolic link to 
> where R was looking for it, and all was well.
> However, on another mac, it complained not about libiconv but libintl. 
> I can't seem to find a place to download the libintl library.
> I installed the package on Windows and it was just fine--no complaints 
> about missing libraries.
> So what I'd like to know is:
> 1) Where can I find this libintl package
> 2) Are these packages really necessary? It would be so much easier to 
> tell my users to just "biocLite();biocLite('gaggle')" than have them 
> go through all the steps necessary to build these libraries. 
> Especially when it does not seem necessary on windows.
> 3) Could this have to do with the email that just was sent out about 
> how binary packages are not yet available for Tiger (both of the Macs 
> I tried to install on are running Tiger)? Might I have better luck if 
> I wait for the tiger binaries?
> Thanks
> Dan - maintainer of gaggle package
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