Debian Bug report logs - #731599
ITP: r-cran-locfit -- GNU R local regression, likelihood and density estimation

Package: wnpp; Maintainer for wnpp is wnpp@debian.org;

Reported by: Andreas Tille <tille@debian.org>

Date: Sat, 7 Dec 2013 13:39:01 UTC

Owned by: Andreas Tille <tille@debian.org>

Severity: wishlist

Tags: pending

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Report forwarded to debian-bugs-dist@lists.debian.org, debian-devel@lists.debian.org, debian-med-packaging@lists.alioth.debian.org, wnpp@debian.org:
Bug#731599; Package wnpp. (Sat, 07 Dec 2013 13:39:06 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <tille@debian.org>:
New Bug report received and forwarded. Copy sent to debian-devel@lists.debian.org, debian-med-packaging@lists.alioth.debian.org, wnpp@debian.org. (Sat, 07 Dec 2013 13:39:06 GMT) Full text and rfc822 format available.

Message #5 received at submit@bugs.debian.org (full text, mbox):

From: Andreas Tille <tille@debian.org>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: ITP: r-cran-locfit -- GNU R local regression, likelihood and density estimation
Date: Sat, 07 Dec 2013 14:38:04 +0100
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>

* Package name    : r-cran-locfit
  Version         : 1.5-9.1
  Upstream Author : Catherine Loader
* URL             : http://cran.r-project.org/web/packages/locfit
* License         : GPL
  Programming Lang: R
  Description     : GNU R local regression, likelihood and density estimation
 This package provides a set of functions to support local regression,
 likelihood and density estimation.  It is helpful for running the test
 suites of several GNU R related packages in Debian.


This package is created for the simple reason of running test suites of
some Debian Med packages properly.  Packaging is finished in SVN

   svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-locfit/trunk/



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Andreas Tille <tille@debian.org>:
Bug#731599; Package wnpp. (Sat, 07 Dec 2013 22:57:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to Charles Plessy <plessy@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Andreas Tille <tille@debian.org>. (Sat, 07 Dec 2013 22:57:04 GMT) Full text and rfc822 format available.

Message #10 received at 731599@bugs.debian.org (full text, mbox):

From: Charles Plessy <plessy@debian.org>
To: debian-med@lists.debian.org, 731599@bugs.debian.org
Subject: Re: Bug#731599: ITP: r-cran-locfit -- GNU R local regression, likelihood and density estimation
Date: Sun, 8 Dec 2013 07:53:37 +0900
Le Sat, Dec 07, 2013 at 02:38:04PM +0100, Andreas Tille a écrit :
> Package: wnpp
> Severity: wishlist
> Owner: Andreas Tille <tille@debian.org>
> 
> * Package name    : r-cran-locfit
>   Version         : 1.5-9.1
>   Upstream Author : Catherine Loader
> * URL             : http://cran.r-project.org/web/packages/locfit
> * License         : GPL
>   Programming Lang: R
>   Description     : GNU R local regression, likelihood and density estimation
>  This package provides a set of functions to support local regression,
>  likelihood and density estimation.  It is helpful for running the test
>  suites of several GNU R related packages in Debian.

Hi Andreas,

"locfit" rings a bell.

The cufflinks package also contains files from locfit with the same copyright
holders, and there the license has non-free clauses.

So either there are good news that somebody from the R community managed to get
locfit relicensed (which would mean that we can move cufflinks to main), or
maybe there are bad news that locfit's README file in the R package was wrongly
removed, and the package is actually non-free...

http://ftp-master.metadata.debian.org/changelogs/non-free/c/cufflinks/cufflinks_2.1.1-4_copyright

Cheers,

-- 
Charles



Added tag(s) pending. Request was from Anibal Monsalve Salazar <anibal@debian.org> to control@bugs.debian.org. (Sun, 08 Dec 2013 07:06:05 GMT) Full text and rfc822 format available.

Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Andreas Tille <tille@debian.org>:
Bug#731599; Package wnpp. (Sun, 08 Dec 2013 08:57:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <andreas@an3as.eu>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Andreas Tille <tille@debian.org>. (Sun, 08 Dec 2013 08:57:04 GMT) Full text and rfc822 format available.

Message #17 received at 731599@bugs.debian.org (full text, mbox):

From: Andreas Tille <andreas@an3as.eu>
To: Debian FTP Masters <ftpmaster@ftp-master.debian.org>
Cc: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>, 731599@bugs.debian.org
Subject: PLease reject (Was: r-cran-locfit_1.5-9.1-1_amd64.changes is NEW)
Date: Sun, 8 Dec 2013 09:54:59 +0100
d/copyright is missing some information about a set of files in src/*.c
stating:

/*
 *   Copyright (c) 1996-2001 Lucent Technologies.
 *   See README file for details.
 */

Kind regards

       Andreas.

On Sat, Dec 07, 2013 at 07:03:30PM +0000, Debian FTP Masters wrote:
> binary:r-cran-locfit is NEW.
> source:r-cran-locfit is NEW.
> 
> Your package contains new components which requires manual editing of
> the override file.  It is ok otherwise, so please be patient.  New
> packages are usually added to the override file about once a week.
> 
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> 

-- 
http://fam-tille.de



Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, Andreas Tille <tille@debian.org>:
Bug#731599; Package wnpp. (Sun, 08 Dec 2013 16:00:04 GMT) Full text and rfc822 format available.

Acknowledgement sent to "Paul R. Tagliamonte" <paultag@gmail.com>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, Andreas Tille <tille@debian.org>. (Sun, 08 Dec 2013 16:00:04 GMT) Full text and rfc822 format available.

Message #22 received at 731599@bugs.debian.org (full text, mbox):

From: "Paul R. Tagliamonte" <paultag@gmail.com>
To: Andreas Tille <andreas@an3as.eu>
Cc: Debian FTP Masters <ftpmaster@ftp-master.debian.org>, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>, 731599@bugs.debian.org
Subject: Re: PLease reject (Was: r-cran-locfit_1.5-9.1-1_amd64.changes is NEW)
Date: Sun, 8 Dec 2013 10:56:16 -0500
[Message part 1 (text/plain, inline)]
(Done, thanks!)


On Sun, Dec 8, 2013 at 3:54 AM, Andreas Tille <andreas@an3as.eu> wrote:

> d/copyright is missing some information about a set of files in src/*.c
> stating:
>
> /*
>  *   Copyright (c) 1996-2001 Lucent Technologies.
>  *   See README file for details.
>  */
>
> Kind regards
>
>        Andreas.
>
> On Sat, Dec 07, 2013 at 07:03:30PM +0000, Debian FTP Masters wrote:
> > binary:r-cran-locfit is NEW.
> > source:r-cran-locfit is NEW.
> >
> > Your package contains new components which requires manual editing of
> > the override file.  It is ok otherwise, so please be patient.  New
> > packages are usually added to the override file about once a week.
> >
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging@lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> >
>
> --
> http://fam-tille.de
>



-- 
:wq
[Message part 2 (text/html, inline)]

Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org:
Bug#731599; Package wnpp. (Thu, 12 Dec 2013 19:33:05 GMT) Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <tille@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org. (Thu, 12 Dec 2013 19:33:05 GMT) Full text and rfc822 format available.

Message #27 received at 731599@bugs.debian.org (full text, mbox):

From: Andreas Tille <tille@debian.org>
To: "Liaw, Andy" <andy_liaw@merck.com>
Cc: 731599@bugs.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Subject: Locfit license
Date: Thu, 12 Dec 2013 20:28:43 +0100
Hi Andy,

thanks for your effort to track this down.  While it is on one side good
to have this clarified, there is a glitch in this README file which might
be incompatible with GPL:

On Thu, Dec 12, 2013 at 02:00:15PM -0500, Liaw, Andy wrote:
> ...
> Permission to use, copy, modify, and distribute this software for any
> purpose (with the exceptions noted in `About Algorithms' above)
> without fee is hereby granted, and provided that this entire notice is
  ^^^^^^^^^^^
> included in all copies of any software which is or includes a copy or
> modification of this software and in all copies of the supporting
> documentation for such software.

The "without fee" clause makes the software non-free (in DFSG sense) and
is as far as I see incompatible with GPL.

I somehow have the feeling that we are only half-way down by having found
the README file.  We seem to need to find a copyright holder to possibly
drop this clause (I can not imagine that they might insist these days on
it any more).

Kind regards

        Andreas.

-- 
http://fam-tille.de

[full quote below - I mixed up the CC of my initial mail so for the
 record in BTS / Debian Med team below is the full conversation]

On Thu, Dec 12, 2013 at 02:00:15PM -0500, Liaw, Andy wrote:
> Hi Andreas,
> 
> I went to the original locfit web page (which, surprisingly, is still up!):
> http://cm.bell-labs.com/cm/ms/departments/sia/project/locfit/index.html
> and found a README file in the S-PLUS version of the code, from which the R package was ported.  Loader's original R package (also on that site) lacks the README file.  I guess we have to assume she meant to use the same README file.  I will include it in the next release of locfit for R.  The content of that file is as follows.  Hope that helps.
> 
> Best,
> Andy
> 
>                                  LOCFIT
>                     Local Regression and Likelihood
> 
>                             Catherine Loader
>                     catherine@research.bell-labs.com
>                          or cathl@optonline.net
>               http://cm.bell-labs.com/stat/project/locfit/
> 
>                  Also incorporating SCB code, joint with
>                                Jiayang Sun
>                         jiayang@sun.stat.cwru.edu
>                   http://sun.cwru.edu/~jiayang/sci3.html
> 
>                              August 1, 2001
> 
> 
> Locfit is a program for fitting regression, likelihood and density
> estimation models using a local polynomial approach. Both univariate
> and multivarite predictor spaces are supported, along with a wide
> range of likelihoods: local least squares; local logistic regression;
> hazard rate models; censored regression models; local density estimation
> and others. The program can be installed as a library for R, S or S-Plus.
> It can also be installed as a stand-alone application ("C-Locfit").
> 
> 
> INSTALLATION:
> 
> To compile and install from a source distribution, please consult the
> Locfit web page, http://cm.bell-labs.com/stat/project/locfit/.
> 
> If you have a binary distribution, Locfit is ready to use as distributed.
> For convenience, S-Plus users may like to
>   (1) move the archive to $SHOME/library/
>   (2) add the line
>         locfit          Local Regression, Likelihood and Density Estimation.
>       to the $SHOME/library/README file.
>   (3) In an S-Plus session, attach the library with library("locfit",first=T).
> 
> 
> DOCUMENTATION:
> 
> Numerous examples can be found in my book,
> "Local Regression and Likelihood", Springer Series in Statistics and
> Computing, 1999.
> 
> Due to the large number of incompatable, inconvenient and changing formats
> for help pages in different versions of S and S-Plus, I cannot maintain
> S-Plus formatted help pages. Instead, html manual pages for most functions
> are available on the locfit web pages.
> 
> 
> ABOUT ALGORITHMS:
> The Locfit implementation has been designed largely from the point
> of view of generality: to provide a set of functions that can be
> used for as wide a range of local fitting problems as possible.
> It is not intended to be the fastest or most efficient implementation
> possible. In addition to generality, the code in many places makes
> extensive trade-offs made between speed and numerical accuracy (some
> of which can be controlled through optional arguments). Many of Locfit's
> options will only be used in a small fraction of cases; for other cases,
> they add to the cost of overhead (an obvious example is multi-dimensional
> fitting: when used in 1-d, many loops reduce to for(i=0;i<1;i++)).
> Additionally, the user interfaces (i.e. the R and S-Plus code) add
> significantly to the computational overhead. For these reasons, the
> Locfit code, as distributed, should not, and can not, be used to
> derive meaningful benchmarks, either for the speed or accuracy of algorithms.
> Anyone wishing to use Locfit in any kind of comparative benchmark
> study must contact and obtain permission from the Author.
> 
> 
> COPYRIGHT:
> 
> Copyright (c) 1996-2001 Lucent Technologies, Bell Laboratories.
> SCB code is
> Copyright (c) 1996-2001 Jiayang Sun.
> 
> Permission to use, copy, modify, and distribute this software for any
> purpose (with the exceptions noted in `About Algorithms' above)
> without fee is hereby granted, and provided that this entire notice is
> included in all copies of any software which is or includes a copy or
> modification of this software and in all copies of the supporting
> documentation for such software.
> 
> THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED
> WARRANTY.  IN PARTICULAR, NEITHER THE AUTHOR NOR LUCENT TECHNOLOGIES
> MAKE ANY REPRESENTATION OR WARRANTY OF ANY KIND CONCERNING THE
> MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY PARTICULAR PURPOSE.
> 
> -----Original Message-----
> From: Andreas Tille [mailto:tille@debian.org] 
> Sent: Sunday, December 08, 2013 12:40 PM
> To: Andy Liaw
> Subject: r-help@r-project.org, 731599@bugs.debian.org, med-dev
> 
> Hi Andy,
> 
> you are listed as maintainer of the locfit package (for author Catherine
> Loader there is no mail address - so to be safe I include r-help list).
> I would like to create a Debian package from locfit because it is used
> in some testsuites of BioConductor packages we are packaging for Debian
> and we want to care for smooth passing of all tests.
> 
> The problem for the packaging is that several files in locfit in the dir
> src/ are
> 
>    Copyright (c) 1998-2001 Lucent Technologies.
>    See README file for details.
> 
> but there is no README file contained in the download tarball.  Usually
> copyright statements are accompanied by a license which most probably
> would be contained in this missing README file.  To distribute the
> package in Debian we need to be sure that the license which is stated
> at the locfit page
> 
>    http://cran.r-project.org/web/packages/locfit/
> 
> and which says
> 
>     	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
> 
> is also valid for these files.  IMHO it would be sufficient if you
> confirm in public that really all files are covered by GPL-2+ license.
> 
> Kind regards and thanks for your help to distribut R locfit for Debian
> 
>       Andreas.
> 
> -- 
> http://fam-tille.de
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-- 
http://fam-tille.de



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