Dear Alejandro,
To add to Herve's comments:
1. Both versions of limma are stable. They wouldn't be on the public
repositories for R 2.4.1 if
they weren't. Naturally I recommend you use the latest version --
that's why it's there.
2. Actually install.packages("limma") and biocLite("limma") both give
you the same version (2.9.8)
of limma, so there is normally no confusion. You could only get limma
2.8.1 if you take special
action to reset the CRAN mirror to point to bioconductor instead of
CRAN.
3. As Herve has said, limma is on both the CRAN and Bioconductor
repositories. This is explained
in Section 2.2 on installation in the Limma User's Guide. The
Bioconductor version has to satisfy
Bioconductor rules, which means no changes to the user interface
between six-monthly releases.
Hence stable updates to the package between BioC releases can only
happen on CRAN rather than
Bioconductor. You can be sure limma works with the current release of
Bioconductor, otherwise it
won't be posted to CRAN.
4. It is potentially confusing that biocLite("limma") sometimes
installs from CRAN rather than
Bioconductor, but I'm happy with this behaviour.
5. The reason for the 2.9.8 version number is that limma 2.9.8 on CRAN
is identical to limma 2.9.8
on the Bioconductor developmental repository. If at any time they are
different, they'll have
different version numbers.
Best wishes
Gordon
> Date: Mon, 29 Jan 2007 12:51:08 -0800
> From: Herve Pages <hpages at="" fhcrc.org="">
> Subject: Re: [BioC] Latest Stable Limma Version
> To: Alejandro <ale.sola at="" integromics.com="">
> Cc: bioconductor at stat.math.ethz.ch
>
> Hi Alejandro,
>
> Alejandro wrote:
>> Hello,
>> I've tried to install the latest stable version of Limma.
>> With "biocLite()" command I get Limma 2.9.8 but if I use the
>> "install.package" command I get Limma 2.8.1.
>> How can I get the latest "stable" version of Limma package?
>>
>> With the following commands I get Limma 2.9.8 (Is it a stable
version?)
>>
>> source("
http://bioconductor.org/biocLite.R")
>> biocLite(c("limma"))
>>
>> With the following command I get Limma 2.8.1
>>
>> install.packages('limma',repos="
http://www.bioconductor.org/")
>
>
> Short answer: I would say that it's probably OK to use limma 2.9.8
with R-2.4
> (even if it "looks" like a Bioc devel package).
>
> Long answer:
> You've just given us an example of why "dual" hosting of packages
can sometimes
> lead to confusion. Let me explain: limma is a Bioconductor package
but, at the
> same time, is hosted on CRAN. The version on CRAN is 2.9.8, but
there is no 100%
> safe way to know which version of Bioconductor it is supposed to
work with.
> The middle number in 2.9.8 is odd and, according to Bioconductor
version standards,
> this suggests a devel (unstable) package. But, since this version is
on CRAN, it's
> probably the case that the parity of the middle number is irrelevant
and that the
> package is stable _independently_ of which version of R/BioC you are
using.
> This is because, generally speaking, CRAN source packages are not
tied to a particular
> version of R (except of course when they make use of something like
"R (>= 2.3.1)"
> or "R (<= 2.4.0)" in their Depends field).
>
> So now why do biocLite() and install.packages() pick up a different
version of limma?
>
> Officially, the limma package in BioC 1.9 (release) is 2.8.1. That
was the latest
> available version at the time Bioconductor 1.9 was released back in
October 2006.
> After a BioC release we create a "release" branch in our Subversion
repository so
> people can maintain separately the "release" and the "devel" version
of their package.
> The limma package in the "release" branch has not changed since then
and this is the
> version you get when you do
> install.packages('limma', repos="
http://www.bioconductor.org/")
> or
> install.packages('limma',
repos="
http://bioconductor.org/packages/1.9/bioc")
>
> In the case of the limma package, using biocLite is equivalent to
doing
> install.packages('limma',
> repos=c("
http://bioconductor.org/packages/1.9/bioc",
"
http://cran.fhcrc.org/"))
> What's happening is that install.packages sees both versions of
limma (2.8.1
> in
http://bioconductor.org/packages/1.9/bioc and 2.9.8 in
http://cran.fhcrc.org)
> and picks up the higher version (which is probably the right thing
to do).
>
> Cheers,
> H.
>
>
>>
>>
>> My R version is 2.4.1.
>>
>> Thank you very much,
>> Alejandro
