[Bioc-devel] libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20

[M. Edward (Ed) Borasky]

1. It looks like R 3.1.0 is back in the Fedora updates-testing
repository. I just installed it and re-ran my install scripts.
2. A fair number of library packages appear to have been built around
the libRblas or libRlapack library. The ones I have had to re-install
so far are:

    'robustbase',
    'slam',
    'quadprog',
    'RcppEigen',
    'gnm',
    'ape',
    'igraph',
    'tseries',
    'fracdiff',
    'forecast',

and there are probably others - these are just the ones that crashed
while being test-loaded during *other* installs!

To be on the safe side I'd recommend re-installing all of your R
packages after you upgrade from R 3.0.2 to R 3.1.0. I'm going to post
a script to do that on the Fedora bugzilla entry as soon as I get a
chance to run it. And if you're using RStudio, I know the preview
release Version 0.98.836 (May 11th, 2014) works but I don't know if
they've backported the fix to their stable release.

On Mon, May 12, 2014 at 4:21 PM, M. Edward (Ed) Borasky <znmeb at znmeb.net> wrote:
> E N <gifi2007 <at> hotmail.com> writes:
>
>>
>> Hi,
>>
>> Let's me quote Ed Borasky
>
> I'm also active on the Fedora Bugzilla for this issue:
> https://bugzilla.redhat.com/show_bug.cgi?id=1074975
>
> Here's a bit more detail. I don't know the exact process, but when a
> package is updated, like R 3.0.2 to 3.1.0, a Fedora packager takes an
> existing source package, updates the pointers to the source and runs
> through all the automated building and testing processes. Once that's
> complete the package makes it into testing repositories and eventually
> into the update repositories.
>
> I discovered 3.1 was in Fedora's 'updates-testing' repository and
> discovered the RStudio dependency conflict. Then after this reply from
> the Fedora packager
>
> https://bugzilla.redhat.com/show_bug.cgi?id=1074975#c16
> I posted the issue on the RStudio forum.
>
> Meanwhile, it turns out that other packages besides RStudio and
> BioConductor ones also seem to depend on libRblas or libRlapack. I don't
> have a complete list. *And* it looks like R 3.1.0 has been pulled from
> the Fedora updates-testing repository!
>
> This will all sort itself out eventually, but meanwhile, if you're on
> Fedora you're stuck with R 3.0.2 - I had to rebuilt two systems' worth of
> R packages over the weekend when 3.1.0 vanished. :-(
>
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