[BioC] problem using affxparser on MacOSX

[Noah Dowell]

Hello Fabrice,

Thanks for the response.  

It seems you are right; I did get affxparser installed using the following:

> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> biocLite("affxparser", type = "source")

And now Starr is working too.

Have a great day.

Noah
On Nov 17, 2011, at 10:26 AM, Fabrice Berger wrote:

> Hi Noah,
> 
> I tested the Starr package and it seems to work for me. If affxparser was installed on your system using the latest binary, I'm not sure it will be installed from the sources using that command. Try removing affxparser first, and then installing it from the sources.
> 
> Fabrice
> 
> On 17/11/11 16:55, Noah Dowell wrote:
>> Hello Fabrice,
>> 
>> I was having the same problem using the Starr package(depends on affxparser) and tried the following:
>> 
>> To re-install affxparser alone using:
>> 
>>> source("http://bioconductor.org/biocLite.R")
>> BiocInstaller version 1.2.1, ?biocLite for help
>>> update.packages("affxparser", repos=biocinstallRepos(), type= "source")
>> 
>> Is this the correct way to install from source (setting type = "source")?
>> 
>> In my case this did not prevent R from crashing.
>> 
>> Thanks for any suggestions.
>> 
>> Best,
>> Noah
>> 
>> 
>> On Nov 17, 2011, at 6:48 AM, Fabrice Berger wrote:
>> 
>>> Dear BioC users,
>>> 
>>> I could solve the problem.
>>> 
>>> If some of you have the same troubles, I solved it by re-installing affxparser from the sources instead of using the binary package installed by default.
>>> 
>>> Fabrice Berger
>>> 
>