[Fedora-r-devel-list] Review request

Hi,

In order to update some Bioconductor R libraries to their latest version
I have a new dependency that has to be packaged.

The review request is there:
https://bugzilla.redhat.com/show_bug.cgi?id=821267

If someone has sometime to look into it 

Thanks in advance!
Pierre
_______________________________________________
r-devel mailing list
r-devel <at> lists.fedoraproject.org
https://admin.fedoraproject.org/mailman/listinfo/r-devel

[Fedora-r-devel-list] problems while building R-rJava

Hello,
    while chasing the several dependencies to build R-Sim-DiffProc I had
to build R-rJava, at moment that is failing while testing the examples.
Are there any suggestions to overcome this?

* checking examples ... ERROR
Running examples in 'rJava-Ex.R' failed
The error most likely occurred in:

> ### Name: J
> ### Title: High level API for accessing Java
> ### Aliases: J
> ### Keywords: interface
>
> ### ** Examples
>
> ## Don't show:
> .jinit()
[1] 0

> ## End Don't show
>
> if (!nzchar(Sys.getenv("NOAWT"))) {
+   f <- new(J("java.awt.Frame"), "Hello")
+   f$setVisible(TRUE)
+ }
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "newInstance",
.jfindClass(class),  :
  java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation

[Fedora-r-devel-list] Start bioconductor update

Hi,

I have started to update a bunch of R packages to the latest version of
bioconductor.

Feel free to test and give karma:

F17:
https://admin.fedoraproject.org/updates/R-fibroEset-1.4.7-1.fc17,R-hgu95av2cdf-2.10.0-1.fc17,R-maanova-1.26.0-1.fc17,R-multtest-2.12.0-1.fc17,R-preprocessCore-1.18.0-1.fc17,R-ROC-1.32.0-1.fc17,R-qvalue-1.30.0-1.fc17,R-statmod-1.4.14-1.fc17,R-timeDate-2160.96-1.fc17,R-tkWidgets-1.34.0-1.fc17,R-DynDoc-1.34.0-1.fc17,R-widgetTools-1.34.0-1.fc17,R-XML-3.9.4-1.fc17,R-ALL-1.4.12-1.fc17,R-abind-1.4.0-2.fc17,R-BufferedMatrix-1.20.0-1.fc17
F16:
https://admin.fedoraproject.org/updates/R-fibroEset-1.4.7-1.fc16,R-hgu95av2cdf-2.10.0-1.fc16,R-maanova-1.26.0-1.fc16,R-multtest-2.12.0-1.fc16,R-preprocessCore-1.18.0-1.fc16,R-ROC-1.32.0-1.fc16,R-qvalue-1.30.0-1.fc16,R-statmod-1.4.14-1.fc16,R-timeDate-2160.96-1.fc16,R-tkWidgets-1.34.0-1.fc16,R-DynDoc-1.34.0-1.fc16,R-widgetTools-1.34.0-1.fc16,R-XML-3.9.4-1.fc16,R-ALL-1.4.12-1.fc16,R-abind-1.4.0-1.fc16,R-BufferedMatrix-1.20.0-1.fc16
F15:
https://admin.fedoraproject.org/updates/R-fibroEset-1.4.7-1.fc15,R-hgu95av2cdf-2.10.0-1.fc15,R-maanova-1.26.0-1.fc15,R-multtest-2.12.0-1.fc15,R-preprocessCore-1.18.0-1.fc15,R-ROC-1.32.0-1.fc15,R-qvalue-1.30.0-1.fc15,R-statmod-1.4.14-1.fc15,R-timeDate-2160.96-1.fc15,R-tkWidgets-1.34.0-1.fc15,R-DynDoc-1.34.0-1.fc15,R-widgetTools-1.34.0-1.fc15,R-XML-3.9.4-1.fc15,R-ALL-1.4.12-1.fc15,R-abind-1.4.0-1.fc15,R-BufferedMatrix-1.20.0-1.fc15

Thanks in advance!

Pierre
_______________________________________________
r-devel mailing list
r-devel <at> lists.fedoraproject.org
https://admin.fedoraproject.org/mailman/listinfo/r-devel

[Fedora-r-devel-list] [Fwd: Re: [Rd] Changed behaviour of 'R CMD INSTALL']

Hi all,

Although using the latest version of R from updates-testing:
https://admin.fedoraproject.org/updates/FEDORA-2012-0119/
I could however recompile successfully R-zoo (arch specific) and
R-widgetTools (noarch) from their latest git version without errors. I
think this is worth noting.

Good day,
Pierre

On 11.01.2012 14:16, Berwin A Turlach wrote:
> G'day all,
>
> I found the following snippet in the NEWS file for R 2.14.1:
>
>      • R CMD INSTALL will now do a test load for all sub-architectures
>        for which code was compiled (rather than just the primary
>        sub-architecture).
>
> This seems to have the following (unintended?) consequence:

[Fedora-r-devel-list] R-repo

Dear all,

To the great despair of spot, I have started to build CRAN and
Bioconductor 
This time, I am trying to make things cleaner and more accessible.

I just uploaded all the spec files on github:
https://github.com/pypingou/R-repo-spec
and the scripts on:
https://github.com/pypingou/R-repo-utility

The whole project is hosted at http://r-repo.org

At the moment everything is still in a early stage (for example, the
r-repo-release rpm is not even done yet), but if you configure the repo
by hand, you should be able to get RPMs.

At least this time, if work becomes overwhelming again, what has been
done will remain accessible 

I would prefer to not announce this officially just yet, but some
feedback be nice (thus this email). So if you feel like testing and are
facing problem, let me know!

Hope this helps,
Best regards,
Pierre

_______________________________________________
r-devel mailing list

[Fedora-r-devel-list] Calls for tester

Good day everyone,

As indicated on the planet, I just re-wrote almost completely R2spec,
tried to make the code cleaner.

This means that if you have code relying on it, it will most likely
break with this update, but I hope you'll find the new code
cleaner/easier to work with.

On the other-side I added things like unit-tests so I am confident the
code does what it's supposed to but I would appreciate if some of you
had/took the time to test it.

Feel free to shout any complains you may have,
Thanks,
Pierre

Update are:
F15: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.fc15
F16: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.fc16
EL5: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.el5
EL6: https://admin.fedoraproject.org/updates/R2spec-4.0.0-1.el6
_______________________________________________
r-devel mailing list
r-devel <at> lists.fedoraproject.org
https://admin.fedoraproject.org/mailman/listinfo/r-devel

[Fedora-r-devel-list] Plans for 2.14.0

Hi Tom,
    what are your plans for 2.14.0? I am asking in light of the
development plan of R.

    Specifically, in this case, I am interested on the F-16 case.

    Regards,

--

-- 
José Matos

_______________________________________________
r-devel mailing list
r-devel <at> lists.fedoraproject.org
https://admin.fedoraproject.org/mailman/listinfo/r-devel

[Fedora-r-devel-list] Errors in constructing SPEC from local source.

In R2spec-3.0.3-1, if you set a local source (-s <source>) then the URL
and source0 fields in the spec will remain empty.  Such specs fail to
build.

There are a variety of ways to address this, I'm not sure that what I've
done is really a superior solution.  

in RPackage.py, down the branch of "I've only got a source, not a
source0", I added

                self.source0 = source
                self.URL = source

(see below).

This means that URL is populated with a local file path, but that's
really all that's available. 

....

All I'm really trying to do right now is get ggplot to one of my
customers.  I wasn't gearing up for contributing much code, but I can,
if that's what Pierre-Yves wants. 

I have to say, this is being a distinctly frustrating process.

....

"below"... 

[Fedora-r-devel-list] R2rpm...

The dependency resolution in R2spec introduces loops.

Try to build foreach or iterators.  In R2spec's calculation of deps,
they depend on each other.  This appears to be because R2spec promotes a
'suggests' to a 'depends'.

This might be because the 'suggests' is used in the vigniettes?

.... Argh.

Package: iterators
Type: Package
Title: Iterator construct for R
Version: 1.0.3
Author: REvolution Computing
Maintainer: REvolution Computing <packages@...>
Description: Support for iterators, which allow a programmer to
        traverse through all the elements of a vector, list, or other
        collection of data.
Depends: R (>= 2.5.0), utils
Suggests: foreach
License: Apache License (== 2.0)
Packaged: 2009-10-05 20:31:21 UTC; weston
Repository: CRAN
Date/Publication: 2009-10-06 06:56:52

Package: foreach
Type: Package
Title: Foreach looping construct for R

[Fedora-r-devel-list] R2rpm...

When I try to build from a local source, it fails to find the source
file.

[root <at> troll-2 cran]# pwd
/var/tmp/cran
[root <at> troll-2 cran]# ls -l
total 828
-rw-r--r-- 1 root root 308395 Dec 22  2009 DBI_0.2-5.tar.gz
-rw-r--r-- 1 root root 518499 Apr 12 14:58 plyr_1.2.1.tar.gz
-rwxr--r-- 1 root root    181 Apr 12 15:06 yadda
-rw-r--r-- 1 root root    138 Apr 12 15:04 yadda~
[root <at> troll-2 cran]# R2rpm -s plyr_1.2.1.tar.gz
Your source does not exist, please use the full path (plyr_1.2.1.tar.gz)
[root <at> troll-2 cran]# R2rpm -s ./plyr_1.2.1.tar.gz
Your source does not exist, please use the full path (./plyr_1.2.1.tar.gz)
[root <at> troll-2 cran]# R2rpm -s /var/tmp/cran/plyr_1.2.1.tar.gz

* Retrieve the source

**************************************************
* Name of the packager = Allen Rout
* Mail of the packager = asr@...

**************************************************
* Name of the library = plyr
* Version of the library = 1.2.1
* Summary of the library = Tools for splitting, applying and combining data
plyr is a set of tools that solves a common set of
* Description of the library =

[Fedora-r-devel-list] [Fwd: [R] R 2.12.2 is released]

FYI 

Pierre

From: Peter Dalgaard <pd.mes@...>
Subject: [R] R 2.12.2 is released
Date: 2011-02-25 12:49:42 GMT

I've rolled up R-2.12.2.tar.gz a short while ago. This is an update release, which fixes a number of mostly
minor issues, and one major issue in which complex arithmetic was being messed up on some compiler platform.

You can get it from

http://cran.r-project.org/src/base/R-2/R-2.12.2.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.

    For the R Core Team

    Peter Dalgaard

These are the md5sums for the freshly created files, in case you wish