[BioC] Tiger, R, Bioconductor

[stefano iacus]

It would be nice to work with R-2.1.x for the moment.

BTW, we are committed to deliver a tiger build of R  and I'm going to 
setup a machine for daily building of packages of both CRAN and BioC. 
There are still minor issues to fix (have a look at last threads on 
R-sig-Mac).

stefano

On 07/mag/05, at 00:18, Cyrus Harmon wrote:

>
> Hi Robert,
>
> Sorry for the lack of specifics. More details follow:
>
> On May 6, 2005, at 3:06 PM, Robert Gentleman wrote:
>
>> Please always provide information on the version of R, and the 
>> package versions - it is important for us in trying to help.
>
> All of this pertains to r-devel (2.2.0 prerelease) from today's SVN 
> sources. Perhaps I'm too far out on the bleeding edge to get things 
> working properly with BioC, but I'd like to help get the latest 
> R-devel release and develOK versions of BioC packages working properly 
> on Tiger.
>
>>> 1. gcrma can't seem to find the R framework (granted, this is 
>>> installed in a non-standard location, but other packages seem to be 
>>> able to do this fine)
>> Can you be a bit more precise? What is the error message exactly?
>
> I don't have the precise error message, but the problem was that I had 
> installed the R framework in a non-standard location and the 
> -framework R option in LIBR wasn't sufficient to find the framework. 
> I've since reported this to R-SIG-MAC as this is a general R problem, 
> not a bioconductor problem. The solution is to include a -F<path to 
> the directory where the framework is installed> option in the LIBR 
> line in Makeconf. I've done this by hand and now I can build things 
> like gcrma. Some autoconf magic that is a bit over my head is 
> presumably required to do this properly.
>
>
>>> 2. SparseM doesn't seem to like the gfortran compiler.
>>
>>   That is really an issue for the maintainer of SparseM. We don't 
>> have the right to just start changing their code on them. Have you 
>> reported this, with complete output, to them? In my experience they 
>> are very receptive and quick to fix problems.
>
> Thanks. It wasn't obvious to me that SparseM wasn't part of 
> Bioconductor (I'm using (trying to use it) it because gostats (I 
> think) wants it). I've also backed down to the f77 compiler which 
> avoids the problem for the moment.
>
>
>>> 3. affyPLM has a log2 function which conflicts with the defintion in 
>>> math.h. In particular, the LESN.c version is declared static and the 
>>> math.h one isn't. GCC 4 chokes on this.
>>     This one should be fixable in the short term. We will see what we 
>> can do.
>
> Great. I'm not sure if the solution is to call the systems log2 or to 
> rename the LESN.c log2 function, but it looks like this is a name 
> collision in a language that doesn't have good namespace support. 
> Thanks for addressing this.
>
>
>>   Again, thanks for the report - we will see what we can do
>
> Thank you for the prompt response and for pointing me in the proper 
> directions!
>
> Sincerely,
>
> Cyrus
>
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