[BioC] old version of affy package 1.5.8

[Patrick Aboyoun]

Leonor,
I have found the repository locations for BioC 1.5 on bioconductor.org. 
The main location you can use in the R install.packages function is

http://www.bioconductor.org/packages/bioc/1.5

and the underlying locations for the source, Mac OS X binary, and 
Windows binary packages are respectively

http://www.bioconductor.org/packages/bioc/1.5/src/contrib/PACKAGES
http://www.bioconductor.org/packages/bioc/1.5/bin/macosx/2.0/PACKAGES
http://www.bioconductor.org/packages/bioc/1.5/bin/windows/contrib/2.0/PACKAGES
http://www.bioconductor.org/packages/bioc/1.5/bin/windows/contrib/2.1/PACKAGES

It might be easier to grab the packages the directly rather than 
modifying the older getBioC.R script that Jim sent you.


Patrick



Leonor Palmeira wrote:
> 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
>>>
>>
>
>
>