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

Herve Pages hpages at fhcrc.org
Fri May 2 02:33:50 CEST 2008

Patrick Aboyoun wrote:
> Dan,
> 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 would vote for doing what CRAN does. IMO building Mac OS binaries for
architectures that are not supported by CRAN has no real added value.


> 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.
> Cheers,
> Patrick
> 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 libiconv library was out of date.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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