useR! 2008
by José Abílio Matos
Hi,
I am writing this from Dortmund, at the useR! 2008 conference
http://www.statistik.uni-dortmund.de/useR-2008/
I will have a talk tomorrow about the interaction between R and Fedora. It is
a 15 minutes session so there is not much time to expand. I will present
Fedora and it interacts with R. There are several issues that are common to
the relation between Fedora and languages like perl, python, latex or R.
I will also take the opportunity to hear feedback from several types of users
regarding the state of R in Fedora. If there is anything relevant I will
report back to this list.
I have asked pingou (I hope I can use this) to write to the list with the new
releases of his package as it would be nice that package automatically in
Fedora using yum.
Regards,
PS: In case you are wondering why I took so long to send this message to the
list, believe that it is a long story that involves time shortage. :-)
--
José Abílio
14 years, 11 months
R2spec new release
by Pierre-Yves Chibon
Dear all
As agreed with José there is the news of the new release of R2spec.
Have a nice sunday
Best regards,
Pierre
======================================================================
There is the latest version of R2spec, I have been working quite a bit
on it with the suggestion of faceface from #R on irc.freenode.net to
improve this software. Therefore the changelog for this new release is
quite long and the list of features added seems also important.
The principle is still the same: make R packages as simple as possible.
Seems there are mainly two sources of libraries for R (Bioconductor and
the CRAN) I added two options (--bioc and --cran) that add the Source0
and the URL in the spec file if it has not been defined by the --url option.
From that I aslo considered the case of the noarch packages, it now
looks for *.c, *.C, *.cp, *.cpp, *.f and *.F files, if it does not find
any it consider the package as noarch and thus adapt the specfile for that.
It also offers the possibility to move the source to %_topdir (defined
in ~/.rpmmacros) so that you can directly run the rpmbuild -ba once you
have made the small correction advised on the spec file.
That's the main features added, you can see below the changelog for this
new release and you can always test and give feed back, report bugs and
suggest enhancement on the trac of the R2spec project [1].
The RPMs and sources are available on the git of the R2spec project [2].
Thanks for your attention :-)
[1] https://fedorahosted.org/r2spec
[2] https://fedorahosted.org/r2spec/browse
15 years, 2 months
R 2.7.2
by Tom Callaway
R 2.7.2 is coming! Builds are going for EL-4, EL-5, F-8, F-9, and devel.
I'll need to rebuild rpy and push updates, so this won't happen
overnight, but this is your official "heads-up".
Thanks,
~spot
15 years, 3 months
useR! 2008 status report
by José Abílio Matos
Hi all,
after a busy week I am finally starting to get back to some kind of normality
(no pun intended :-) ).
At useR! 2008 I had Martin Plummer, Marc Schwartz and Peter Dalgaard in the
audience. The talk went well and it was a fun to do. The room was small for
the attendance and in my (biased) view it seemed that I had people coming on
purpose for the talk. :-)
After the session ended I had a friendly discussion with Martin and Marc
regarding Fedora and R relationship. :-)
Some of the topics covered were (in no particular order other than my notes).
1) The redundancy between the two mailing lists devoted to R and Fedora (this
and SIG list). Actually at that time I forgot the SIG mailing list (my bad). I
always keep forgetting about the different purpose of both lists.
2) Martin and Marc suggested one scenario that involved the removal of all R
packages from Fedora where the only remaining installed package would be the R
core package. Then using some kind of package, the better analogy that I found
was a backend to PackageKit providing automatic installs from CRAN.
My opinion (that I have also expressed back then) was that this would be a no
go for Fedora for two reasons, first the packages dependency outside of CRAN
would be hard to get right (think about packages like R-hdf5 that require
linking with an external package). The second and probably the most important
issue from our (Fedora) point of view would be the liability issue. We would
be connecting to a repository that we have no control about, I tried to
express the different reasons why this is not possible.
3) There are discussions at R about the next generation CRAN meta-information
(improved DESCRIPTION format) and the opinions of distributions are welcome.
4) Is there a link in fedora bugzilla to connect upstream for R bugs reported
to Fedora? I am not sure if this is possible with the new bugzilla but I
suppose that there are not so many bugs like that reported at Fedora.
5) One problem usually reported in the R users mailing list is the
installation procedure used to install R packages (not in Fedora) using the R
interface.
This problem has been reported again this weekend FWIW. Instead of providing
R-devel in the R package as Martin and Marc have suggested I think that we
could create a FAQ for R in Fedora. Something like:
*********************** Draft to R - Fedora FAQ **************************
Q: I tried to install the following R package in Fedora but R failed with
horrendous error messages, what should I do?
A: Look to the content of the R package you are trying to install (link to
CRAN).
1) Does it contains C or C++ files (.c or .cpp ending filenames)? If yes
then install R-devel if it is not yet installed.
[Instructions how to install R-devel using yum or packagekit]
2) Does it contains Fortran files (.f or .F ending filenames)? If yes then
install gcc-gfortran if it is not yet installed.
[Instructions how to install R-devel using yum or packagekit]
3) If the steps above are not enough and the package depends on an external
library you need to guarantee that you have installed the files necessary to
compile the package. Do not forget that the -devel subpackages are required to
be installed to compile and link with the external libraries.
******************************************************************************
This is my fable attempt to document some of the possible of the problems
found by our users. :-)
We could then expand the FAQ content to other topics like how to search Fedora
R packages. The target of the FAQ would be naturally the users and not just
the developers.
Comments are welcome to all the points above,
--
José Abílio
15 years, 3 months
R package in Fedora
by Pierre-Yves Chibon
Dear all,
Remi Collet has done a great job the past days to make these pages:
http://rpms.famillecollet.com/rpmphp/
I think you will be interested specially in this one:
http://rpms.famillecollet.com/rpmphp/rpm.php?type=R
However, helping him to set up the parsers, we have been facing some
problem with some package.
For example:
R-lmtest
As you can see here:
http://pingoured.fr/cgi-bin/R.py?name=R-lmtest
The version have a '-', this leads to a "outdated" mark of the package
in this page http://rpms.famillecollet.com/rpmphp/rpm.php?type=R .
The question is then, what should we do ?
There is nothing on the guideline that mention what we should do about
the library that have a '-' on their version name (second exemple: R-pls
http://pingoured.fr/cgi-bin/R.py?name=R-pls ).
We also faced the problem that at least one library is present in both
CRAN and bioconductor repository (R-qvalue
http://pingoured.fr/cgi-bin/R.py?name=R-qvalue ). But the version are
pretty clear, we kept only the Bioconductor.
So I think, when we have a library in CRAN and Bioconductor, we should
only keep the Bioconductor version.
For the version with a '-', we skipped everything that was after the '-'
until now, should we continue ?
Thanks for your comments,
Regards,
Pierre
15 years, 3 months
