[BioC] old version of affy package 1.5.8

[Leonor Palmeira]

James W. MacDonald a écrit :
> Hi Leonor,
> 
> I just checked, and you get getBioC.R the same way you get biocLite.R
> 
> source("http://www.bioconductor.org/getBioC.R")
> 
> So getting previous versions is easier than I thought...
> 
> Best,
> 
> Jim

Sorry, there was an error in what I wrote. I wanted to say that 
source("http://bioconductor.org/biocLite.R") makes an explicit call to
source("http://www.bioconductor.org/getBioC.R") [and not to itself...] 
and that the current getBioC.R script checks for the R version. This 
makes it impossible to download BioC packages with R version less than 
2.1.0 using this method.

Getting an old getBioC.R could help, but the one available at 
http://www.bioconductor.org/getBioC.R is the current one.

[Just for archiving purposes, the old "getBioC.R" script that Jim 
provided me in private (along with other old scripts) makes an explicit 
call for
http://www.bioconductor.org/repository/release1.3//package//PACKAGES 
which is no longer available]

I am now trying Wolfgang's solution and will let you know.

Thank you very much everybody,
Best,
Leonor.

> 
> 
> 
> Leonor Palmeira wrote:
>> [back in thread]
>>
>> Leonor Palmeira a écrit :
>>  > Hi Leonor,
>>
>> [...]
>>
>>  > Actually yes. Nothing ever goes away.
>>
>> I was crossing fingers for that! However, the 'readonly' user and 
>> 'readonly' password don't seem to work (403 forbidden access) to 
>> access the svn depository. So, I couldn't explore this possibility.
>>
>> I also tried installing R.2.0.0 and running biocLite() from within 
>> this old R. But, when calling "http://bioconductor.org/biocLite.R", R 
>> calls for "http://bioconductor.org/biocLite.R" which explicitely 
>> checks for the R version and returns an error (R version should be 
>> above R.2.1.0).
>>
>> When taking a look at the biocLite.R script, this line caught my eye:
>>
>> ## R versions less than 2.1.0 need to use the old (BioC 1.5) version 
>> of getBioC.R
>>
>> but I have no idea where to get the old version of getBioC.R.
>> Does someone know how I could get help on this?
>>
>> Thank you very much,
>> Leonor.
>>
>>  > And if I am not mistaken, you can
>>  > get this for yourself. All you need is a subversion client, which you
>>  > can get here if you aren't on Linux (if you are on Linux it is 
>> easier to
>>  > install using whatever package manager your distro uses):
>>  >
>>  > http://subversion.tigris.org/
>>  >
>>  > Then you can get any of the packages from release 1.5 here:
>>  >
>>  > 
>> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_1_5/madman/Rpacks 
>>
>>  >
>>  > e.g.,
>>  >
>>  > svn co
>>  > 
>> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_1_5/madman/Rpacks/affy 
>>
>>  >
>>  > will get you the affy sources. You want to use the username 
>> readonly and
>>  > password readonly, which I think should work.
>>  >
>>  > You will probably need to get other packages as well, depending on 
>> what
>>  > the dependencies were for affy at that time. In addition, you will 
>> need
>>  > to get R-2.0.0, as there is no guarantee that an old affy will run on
>>  > current R.
>>  >
>>  > You might also just try installing R-2.0.0 and running biocLite(). It
>>  > might actually work.
>>  >
>>  > Best,
>>  >
>>  > Jim
>>
> 



-- 
Leonor PALMEIRA
Laboratoire de Biométrie et Biologie Évolutive
UMR CNRS 5558
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tel : 04 72 43 28 26
http://biomserv.univ-lyon1.fr/~palmeira