Hi Keith,
On Mon, Jan 11, 2010 at 12:02 AM, Keith Satterley <[email protected]> wrote:
> Hi Henrik and others,
>
> I have been using the commands:
>
> source("http://www.braju.com/R/hbLite.R";)
> hbInstall("aroma.affymetrix")
> hbInstall("aroma.cn")
>
> to install aroma.affymetrix and aroma.cn.
>
> After noticing that aroma.affymetrix updated using the update.packages
> function in R-2.10.0 I checked and I see since R-2.9.1 that
> aroma.affymetrix has a Repository value in its DESCRIPTION file of
> CRAN.
Yes. I've quietly been moving packages to CRAN (since September
2009). The main advantage with CRAN is that they provide binary
builds for a OSes.
>
> Does this mean that aroma.affymetrix can now be installed from CRAN in
> my usual way using biocLite?
Yes, you can do that, but you have to grab some of the "Suggested"
packages from r-forge.r-project.org, because they are neither on CRAN
nor on Bioconductor. The main reason of asking you to use:
source("http://www.aroma-project.org/hbLite.R";)
hbInstall("aroma.affymetrix")
is that you don't know where the different packages are hosted. This
allows me to move the hosting elsewhere, which is why you didn't
notice the move to CRAN in the first place. It also gave/give me
backup to release packages in case there are issues with CRAN or
similar (they happen).
Also, do NOT install R.*/aroma.* packages from the r-forge site,
because that repository is used as a scrap paper/daily backups and you
will most likely get a broken version. CRAN will always contain the
most recent stable release. Finally, I only move very mature versions
of packages to CRAN, everything else I hosted off-CRAN. This give me
more leeway to restructure things.
> Will aroma.cn be doing this too?
We will soon provide technology-independent copy-number analysis.
This will probably result in some more restructuring between the
aroma.* packages, and possibly yet another aroma.* package. When this
have settled, you will probably see aroma.cn (or a version of it) on
CRAN too. Is there a particular method in aroma.cn that you are
using, or is this a general maintenance issue?
Cheers,
Henrik
>
> cheers,
>
> KeithS
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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