collaborating on ggplot2 ?

[Jack Tanner]

Howdy,

I'd like to get the ggplot2 library package-able. I cannot sign up as a 
maintainer, but I can work on spec files. ggplot2 has a whole bunch of 
dependencies:

According to http://cran.r-project.org/web/packages/ggplot2/ ,

Imports: 	reshape 
<http://cran.r-project.org/web/packages/reshape/index.html> (≥ 0.8.0), 
plyr <http://cran.r-project.org/web/packages/plyr/index.html> (≥ 0.1.6), 
splines, MASS <http://cran.r-project.org/web/packages/VR/index.html>;, 
RColorBrewer 
<http://cran.r-project.org/web/packages/RColorBrewer/index.html>;, grid, 
proto <http://cran.r-project.org/web/packages/proto/index.html>
Suggests: 	quantreg 
<http://cran.r-project.org/web/packages/quantreg/index.html>;, Hmisc 
<http://cran.r-project.org/web/packages/Hmisc/index.html>;, mapproj 
<http://cran.r-project.org/web/packages/mapproj/index.html>;, maps 
<http://cran.r-project.org/web/packages/maps/index.html>;, digest 
<http://cran.r-project.org/web/packages/digest/index.html>;, colorspace 
<http://cran.r-project.org/web/packages/colorspace/index.html>;, hexbin 
<http://cran.r-project.org/web/packages/hexbin/index.html>;, gpclib 
<http://cran.r-project.org/web/packages/gpclib/index.html>;, maptools 
<http://cran.r-project.org/web/packages/maptools/index.html>


Would anyone be interested in taking this on with me and writing spec 
files for some of the ggplot2 prereqs?

[Tom Moertel]

Jack Tanner wrote:
>  I'd like to get the ggplot2 library package-able. I cannot sign
> up as a 
>  maintainer, but I can work on spec files. ggplot2 has a whole bunch of 
>  dependencies: [...]
>  
>  Would anyone be interested in taking this on with me and writing spec 
>  files for some of the ggplot2 prereqs? 
I'd also like to get ggplot2 into Fedora.  I'm in a similar situation to 
you, however, in that my free time is scarce.  (Ever since joining the 
world of startups, my Fedora-hacking time has gone to near zero.) 
Still, if we can chip away at this task, we'll eventually get it done.  :-)

Let's divide up the prerequisites and package 'em.  I'd like to claim 
plyr because I have a need for that package on its own.

Anybody else want to pile on ggplot2?

Cheers,
Tom

R-plyr preview [was: collaborating on ggplot2 ?]

[Tom Moertel]

Tom Moertel wrote:
>  Let's divide up the prerequisites and package 'em.  I'd
> like to claim 
>  plyr because I have a need for that package on its own. 
I packaged plyr tonight:

http://community.moertel.com/rpms/fedora/10/SPECS/R-plyr.spec
http://community.moertel.com/rpms/fedora/10/SRPMS/R-plyr-0.1.9-1.fc10.src...

I had to disable the %check because it tried to do some Tk stuff that 
required a valid DISPLAY.  The Tk stuff does appear to work, however, 
once the package is installed.

If anybody would give the package a quick review, I'd appreciate it. 
Tomorrow or the next day, I'll submit R-plyr as a new package unless 
there are any objections.

Cheers,
Tom

R-plyr preview [was: collaborating on ggplot2 ?]

[Jack Tanner]

Tom Moertel wrote:
>  I packaged plyr tonight:
>
>  http://community.moertel.com/rpms/fedora/10/SPECS/R-plyr.spec 
Thanks for taking a stab at plyr. I'm a very inexperienced packager, but 
these are the questions that I'd be asking if I were a reviewer.

- Do you need to worry about the requires (R-RUnit R-abind R-tcltk)?
- It seems wrong to hard-code Source0 rather than making it conditional 
on the variables defined in the spec. See my RMySQL spec (which could be 
totally goofy, and I've had no feedback on it) here: 
https://www.redhat.com/archives/fedora-r-devel-list/2009-August/msg00007....
- Since plyr is noarch, you could remove the commented-out arch-specific 
stuff.

R-plyr preview [was: collaborating on ggplot2 ?]

[Pierre-Yves Chibon]

On Tue, 2009-09-01 at 22:46 -0400, Jack Tanner wrote:
>  Tom Moertel wrote:
>  > I packaged plyr tonight:
>  >
>  > http://community.moertel.com/rpms/fedora/10/SPECS/R-plyr.spec
>  
>  Thanks for taking a stab at plyr. I'm a very inexperienced packager, but 
>  these are the questions that I'd be asking if I were a reviewer.
>  
>  - Do you need to worry about the requires (R-RUnit R-abind R-tcltk)? 
Two out of
three are already done and in the repo
R-tcltk will have to be done.

>  - It seems wrong to hard-code Source0 rather than making it
> conditional 
>  on the variables defined in the spec. See my RMySQL spec (which could be 
>  totally goofy, and I've had no feedback on it) here: 
>  https://www.redhat.com/archives/fedora-r-devel-list/2009-August/msg00007.... 
The
Source0 is not wrong, changing it to use the macro make just the
maintenance of the package easier (you won't have to change the Source0)

>  - Since plyr is noarch, you could remove the commented-out
> arch-specific 
>  stuff. 
+1 to clean the spec
You have also the:
- change the BR tetex-latex to tex(latex)

Regards,

Pierre

R-plyr preview [was: collaborating on ggplot2 ?]

[Pierre-Yves Chibon]

On Wed, 2009-09-02 at 08:21 +0200, Pierre-Yves wrote:
>  On Tue, 2009-09-01 at 22:46 -0400, Jack Tanner wrote:
>  > Tom Moertel wrote:
>  > > http://community.moertel.com/rpms/fedora/10/SPECS/R-plyr.spec
>  > - Do you need to worry about the requires (R-RUnit R-abind R-tcltk)?
>  Two out of three are already done and in the repo
>  R-tcltk will have to be done. 
In fact R-tcltk does not exist, the spec should be
corrected.
The Requires is on tcltk itself.

Pierre

R-plyr preview [was: collaborating on ggplot2 ?]

[Tom Moertel]

Pierre-Yves wrote:
> > R-tcltk will have to be done.
>  In fact R-tcltk does not exist, the spec should be corrected.
>  The Requires is on tcltk itself. 
R-tcltk does exist; it's provided by R-core:

     $ rpm -q --whatprovides R-tcltk
     R-core-2.9.2-1.fc10.x86_64

And R-core is what requires tk:

     $ rpm -q --requires R-core | fgrep tk
     libtk8.5.so()(64bit)

So, should I leave in the requirement (in case, for example, the R-tcltk 
bindings are later moved into a separate package), or should I remove 
the requirement under the assumption that R-tcltk will always be 
provided by R-core?

Cheers,
Tom

R-plyr preview [was: collaborating on ggplot2 ?]

[Tom Callaway]

On 09/02/2009 08:57 AM, Tom Moertel wrote:
>  So, should I leave in the requirement (in case, for example, the
> R-tcltk
>  bindings are later moved into a separate package), or should I remove
>  the requirement under the assumption that R-tcltk will always be
>  provided by R-core? 
I think it is safer to depend on R-tcltk. It is theoretically possible
that at some point, the base R will stop supporting older GUI toolkits,
such as tcltk, and the package will be broken off into its own CRAN module.

~spot

R-plyr preview [was: collaborating on ggplot2 ?]

[Tom Moertel]

Tom "spot" Callaway wrote:
>  I think it is safer to depend on R-tcltk.  [...] 
I'll leave the R-tcltk requirement in, then.

With that in mind, here's take 2:

http://community.moertel.com/rpms/fedora/10/SPECS/R-plyr.spec
http://community.moertel.com/rpms/fedora/10/SRPMS/R-plyr-0.1.9-2.fc10.src...

Cheers,
Tom

Good timing: Ggplot2 book is out [was: collaborating on ggplot2 ?]

[Tom Moertel]

Tom Moertel wrote:
>  Jack Tanner wrote:
> > I'd like to get the ggplot2 library package-able. [...]
>  
>  I'd also like to get ggplot2 into Fedora.  [...] 
Having used ggplot2 for a few days now, I am impressed.  It is flexible, 
capable, and produces great statistical graphics.  Now that the Ggplot2 
book[1] is finally shipping, I predict that ggplot2 will rapidly become 
the tool of choice for most R users who need to produce statistical 
graphics.  (The book is great, BTW.)

It is good timing, then, that we are working to get ggplot2 into Fedora. 
  Pretty soon, most R users will expect it.

Cheers,
Tom

[1] http://had.co.nz/ggplot2/book/

[Pierre-Yves Chibon]

On Fri, 2009-08-28 at 22:10 -0400, Jack Tanner wrote:
>  Howdy,
>  
>  I'd like to get the ggplot2 library package-able. I cannot sign up as a 
>  maintainer, but I can work on spec files. ggplot2 has a whole bunch of 
>  dependencies:
>  
>  According to http://cran.r-project.org/web/packages/ggplot2/ ,
>   
I already have spec available for those two and eventually I can propose
them for review.
>  RColorBrewer 
>  <http://cran.r-project.org/web/packages/RColorBrewer/index.html>;,
>  maps 
>  <http://cran.r-project.org/web/packages/maps/index.html>;, 
Did you look at the subdependencies ? I mean that for example quantreg
requires  SparseM tripack, akima, MASS, survival, rgl, logspline
(Which already points out a circular dependency on MASS)...

Maybe worth to have a look at what R P Herrold did since I packaged most
of the cran.

Best regards,

Pierre

[Pierre-Yves Chibon]

On Tue, 2009-09-01 at 09:04 +0200, Pierre-Yves wrote:
>  On Fri, 2009-08-28 at 22:10 -0400, Jack Tanner wrote:
>  > Howdy,
>  > 
>  > I'd like to get the ggplot2 library package-able. I cannot sign up as a 
>  > maintainer, but I can work on spec files. ggplot2 has a whole bunch of 
>  > dependencies:
>  > 
>  > According to http://cran.r-project.org/web/packages/ggplot2/ ,
>  > 
>  
>  I already have spec available for those two and eventually I can propose
>  them for review.
>  > RColorBrewer 
>  > <http://cran.r-project.org/web/packages/RColorBrewer/index.html>;,
>  > maps 
>  > <http://cran.r-project.org/web/packages/maps/index.html>;,
>  
>  Did you look at the subdependencies ? I mean that for example quantreg
>  requires  SparseM tripack, akima, MASS, survival, rgl, logspline
>  (Which already points out a circular dependency on MASS)...
>  
>  Maybe worth to have a look at what R P Herrold did since I packaged most
>  of the cran. 
Might be worth to have a look at what R P Herrold did since *he*
packaged most of the cran.

Time for coffee...

Pierre

[Jack Tanner]

Pierre-Yves wrote:
> > Did you look at the subdependencies ? I mean that for example
> quantreg
> > requires  SparseM tripack, akima, MASS, survival, rgl, logspline
> > (Which already points out a circular dependency on MASS)...
> >      
I did not look at the subdependencies. Whoops. Thanks for pointing that
out.
>  Might be worth to have a look at what R P Herrold did since *he*
>  packaged most of the cran.
>     
I found this: http://article.gmane.org/gmane.comp.lang.r.fedora/17 , 
which is very informative, but doesn't link to the SPECs or SRPMs for 
any of those things he packaged up. There's nothing at his FTP site 
either, ftp://ftp.owlriver.com/pub/local/ORC/R/ . Is there another source?

[Tom Callaway]

On 08/28/2009 10:10 PM, Jack Tanner wrote:
>  quantreg
> <http://cran.r-project.org/web/packages/quantreg/index.html> 
I took a shot at this one (and its depends/suggests), and I ran into
SparseM. It claims to be GPL on its CRAN page, but that is not entirely
true, as its LICENSE file admits:

== LICENSE ==

All R code and documentation in this package is licensed under the terms
of the GPL license -- see COPYING in the top level of the R directory
tree for further details.

All fortran and C code in the src directory, with the exception of
cholesky.f is also licensed on the GPL license, see

        http://www.cs.umn.edu/Research/arpa/SPARSKIT/sparskit.html

for explicit stipulation for sparskit.f.  The code in cholesky.f  is a
modified version of code originally written by Esmond Ng and Barry
Peyton.  The modified version is distributed as part of PCx by Czyzyk,
Mehrotra, Wagner, and Wright and is copywrite by the University
of Chicago.  The PCx distribution makes the following stipulation:

        This software discloses material protectable under copyright
        laws of the United States. Permission is hereby granted to use,
        reproduce, prepare derivative works, and redistribute to others
        at no charge, provided that the original PCx copyright notice,
        Government license and disclaimer are retained and any changes
        are clearly documented; however, any entity desiring permission
        to use this software within a commercial organization or to
        incorporate this software or a work based on the software into
        a product for sale must contact Paul Betten at the Industrial
        Technology Development Center, Argonne National Laboratory.

                PAUL BETTEN
                betten(a)anl.gov
                Industrial Technology Development Center,
                Argonne National Laboratory,
                Argonne, IL 60439
                [phone]
                FAX: [phone]

== EOF ==

That PCx license from ANL is non-free, due to its commercial use
restriction clause. That license is also incompatible with the GPL, so
the entire work is almost certainly not redistributable when compiled
together.

In order to include this package in Fedora, we would need to get
permission from Paul Betten to use that file under a GPL compatible
license (or the GPL itself). I have sent an email to Mr. Betten, and I
am hopeful that he is still at ANL, and that he is willing/able to
resolve this licensing issue.

~spot

[Martyn Plummer]

Thanks for finding this.  I passed this message on to the CRAN
maintainers (CRAN also distributes binaries for Windows and Mac OS X)
who also contacted the SparseM package author.

Martyn

On Wed, 2009-09-02 at 11:03 -0400, Tom "spot" Callaway wrote:
>  On 08/28/2009 10:10 PM, Jack Tanner wrote:
>  > quantreg <http://cran.r-project.org/web/packages/quantreg/index.html>
>  
>  I took a shot at this one (and its depends/suggests), and I ran into
>  SparseM. It claims to be GPL on its CRAN page, but that is not entirely
>  true, as its LICENSE file admits:
>  
>  == LICENSE ==
>  
>  All R code and documentation in this package is licensed under the terms
>  of the GPL license -- see COPYING in the top level of the R directory
>  tree for further details.
>  
>  All fortran and C code in the src directory, with the exception of
>  cholesky.f is also licensed on the GPL license, see
>  
>          http://www.cs.umn.edu/Research/arpa/SPARSKIT/sparskit.html
>  
>  for explicit stipulation for sparskit.f.  The code in cholesky.f  is a
>  modified version of code originally written by Esmond Ng and Barry
>  Peyton.  The modified version is distributed as part of PCx by Czyzyk,
>  Mehrotra, Wagner, and Wright and is copywrite by the University
>  of Chicago.  The PCx distribution makes the following stipulation:
>  
>          This software discloses material protectable under copyright
>          laws of the United States. Permission is hereby granted to use,
>          reproduce, prepare derivative works, and redistribute to others
>          at no charge, provided that the original PCx copyright notice,
>          Government license and disclaimer are retained and any changes
>          are clearly documented; however, any entity desiring permission
>          to use this software within a commercial organization or to
>          incorporate this software or a work based on the software into
>          a product for sale must contact Paul Betten at the Industrial
>          Technology Development Center, Argonne National Laboratory.
>  
>                  PAUL BETTEN
>                  betten(a)anl.gov
>                  Industrial Technology Development Center,
>                  Argonne National Laboratory,
>                  Argonne, IL 60439
>                  [phone]
>                  FAX: [phone]
>  
>  == EOF ==
>  
>  That PCx license from ANL is non-free, due to its commercial use
>  restriction clause. That license is also incompatible with the GPL, so
>  the entire work is almost certainly not redistributable when compiled
>  together.
>  
>  In order to include this package in Fedora, we would need to get
>  permission from Paul Betten to use that file under a GPL compatible
>  license (or the GPL itself). I have sent an email to Mr. Betten, and I
>  am hopeful that he is still at ANL, and that he is willing/able to
>  resolve this licensing issue.
>  
>  ~spot
>  
>  _______________________________________________
>  Fedora-r-devel-list mailing list
>  Fedora-r-devel-list(a)redhat.com
>  http://www.redhat.com/mailman/listinfo/fedora-r-devel-list
>   
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[Tom Callaway]

On 09/03/2009 04:27 AM, Martyn Plummer wrote:
>  Thanks for finding this.  I passed this message on to the CRAN
>  maintainers (CRAN also distributes binaries for Windows and Mac OS X)
>  who also contacted the SparseM package author. 
The good news is that Mr. Betten is still at ANL, and he replied that he
is looking into my request for relicensing.

~spot