[med-svn] [r8s] 01/01: Drop mail exchange with upstream as README.source
Andreas Tille
tille at debian.org
Mon Nov 30 16:09:38 UTC 2015
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commit 4279e9e68d9d54e14f66378c5c1b0842f42b6e1a
Author: Andreas Tille <tille at debian.org>
Date: Mon Nov 30 17:09:13 2015 +0100
Drop mail exchange with upstream as README.source
---
debian/README.source | 193 +++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 193 insertions(+)
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..67fc739
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,193 @@
+Date: Mon, 30 Nov 2015 08:15:35 -0700
+From: Mike Sanderson <sanderm00 at gmail.com>
+To: Andreas Tille <andreas at an3as.eu>
+Subject: Re: R8s is using Numerical Recipes code illegally
+
+
+Dear Andreas,
+
+It's a bit of a project, but if I get some free time over the upcoming
+holidays, I'll definitely try to get this done -- and let you know.
+Thanks again for the information. This was really good to learn.
+
+Best regards,
+Mike
+
+
+
+On 11/26/15 11:28 AM, Andreas Tille wrote:
+> Hi Mike,
+>
+> this would be really cool if you could strip out the non-free parts
+> since this would enable me to provide our users (and any other Debian,
+> Ubuntu and its derivatives user) with a nicely packaged system featuring
+> r8s. Please let me know if you make any progress or if you need any
+> help.
+>
+> Kind regards
+>
+> Andreas.
+>
+> On Thu, Nov 26, 2015 at 10:17:12AM -0700, Mike Sanderson wrote:
+>> Hi Andreas,
+>>
+>> OK, that's good to know, but I also have some old now deprecated
+>> optimization routines in r8s that use some of NRC's Powell and Brent
+>> optimization code. I can remove that, in favor of use of truncated newton
+>> code in the legacy fortran files tn.f, etc. Who knows what that license was
+>> either, however? I believe that is in the public domain as part of somethign
+>> called netlib, but not sure. Thanks for working so hard on this! Probably I
+>> need to cut out all the NRC code and redistribute without it. The TN code
+>> was much more robust anyway and my documentation recommends user use. I left
+>> the NRC stuff in for some rare case in which the optimization converged for
+>> it but not TN.
+>>
+>> Best,
+>> Mike
+>>
+>>
+>>
+>> On 11/25/15 1:32 PM, Andreas Tille wrote:
+>>> Hi Mike,
+>>>
+>>> since there was a comparable issue in a different project I've got some
+>>> good news for you (and I updated the debian/copyright accordingly):
+>>>
+>>> Files: nrutils.c
+>>> Copyright: 1994-2010 Numerical Recipes authors
+>>> License: public_domain
+>>> In general, the Numerical Recipes routines are NOT in the public domain, and
+>>> are NOT available for use without a valid license. However, a few small parts
+>>> of Numerical Recipes have been put into the public domain. These can be
+>>> freely copied and redistributed:
+>>> ...
+>>> Utility files for C:
+>>> * nrutil.c
+>>> * nrutil.h
+>>> Comment: http://numerical.recipes/public-domain.html
+>>>
+>>> The only remaining NR file seems to be nr.h which is not on this
+>>> public-domain list. This header file is just used by a single C file:
+>>> BFGSwrapper.c. This C file itself is not only broken (contains heaps of
+>>> 0 bytes) - it is also unused. I created a new tarball without
+>>> BFGSwrapper.* and nr.h which builds fine and creates the same executable
+>>> as I had before.
+>>>
+>>> In short: If you put the remaining files under a GPL / BSD / whatever
+>>> license we could distribute r8s with Debian and could serve users easily
+>>> with your code.
+>>>
+>>> Thanks for considering
+>>>
+>>> Andreas.
+>>>
+>>> On Wed, Nov 25, 2015 at 11:14:14AM -0700, Mike Sanderson wrote:
+>>>> Dear Andreas,
+>>>>
+>>>> Many thanks for this information. Although I have not been actively
+>>>> developing or distributing r8s for many years now, it is indeed on a website
+>>>> and includes NRC code. I'll have to just remove it and post the binary, I
+>>>> guess. This almost makes specifying a license for r8s irrelevant since
+>>>> without source code, many people will not be able to get a running version
+>>>> for their OS.
+>>>>
+>>>> Mike
+>>>>
+>>>>
+>>>>
+>>>> On 11/24/15 8:19 AM, Andreas Tille wrote:
+>>>>> Hello Michael,
+>>>>>
+>>>>> I considered packaging your program r8s[1] for integrating it into
+>>>>> Debian since I've got a user request about this program. I'm a member
+>>>>> of the Debian Med team that intends to package free software in biology
+>>>>> and medicine for official Debian.
+>>>>>
+>>>>> When inspecting the code of r8s I detected the files nr.h and nrutil.c
+>>>>> which are part of Numerical Recipes. The license statement[2] of this
+>>>>> software collection
+>>>>>
+>>>>> "Sorry, no. We never give permission for Numerical
+>>>>> Recipes source code to be posted on any public server,
+>>>>> or distributed with any freeware or shareware package.
+>>>>> If you encounter such a distribution, we'd be grateful if
+>>>>> you'd tell us about it."
+>>>>>
+>>>>> Well, I will not support inventors of this kind of strict license but
+>>>>> I'd like to inform you about this issue. The license page[2] lists
+>>>>> alternatives you could possibly use for r8s.
+>>>>>
+>>>>> BTW, even without the NR-issue we could not redistribute r8s in main
+>>>>> Debian since I have not found any license statement for your own code.
+>>>>> It would be nice if you could add this as well at the web site as also
+>>>>> to the downloadable code.
+>>>>>
+>>>>> Kind regards
+>>>>>
+>>>>> Andreas Tille.
+>>>>>
+>>>>> [1] http://loco.biosci.arizona.edu/r8s/
+>>>>> [2] http://numerical.recipes/licenses/redistribute.html
+>>>>>
+>>>>
+>>>> --
+>>>> ********************************************************************
+>>>> Michael J. Sanderson, Professor
+>>>> Department of Ecology and Evolutionary Biology
+>>>> University of Arizona
+>>>> Tucson, AZ 85721
+>>>>
+>>>> Office: BSW 412
+>>>> Phone:520-626-6848
+>>>> email:sanderm at email.arizona.edu
+>>>>
+>>>> lab web site: http://loco.biosci.arizona.edu
+>>>> Ceiba phylogenetic tree visualization:
+>>>> http://sourceforge.net/projects/ceiba
+>>>> PhyLoTA Browser: http://phylota.net
+>>>> r8s software: http://loco.biosci.arizona.edu/r8s
+>>>>
+>>>> ********************************************************************
+>>>>
+>>>
+>>
+>> --
+>> ********************************************************************
+>> Michael J. Sanderson, Professor
+>> Department of Ecology and Evolutionary Biology
+>> University of Arizona
+>> Tucson, AZ 85721
+>>
+>> Office: BSW 412
+>> Phone:520-626-6848
+>> email:sanderm at email.arizona.edu
+>>
+>> lab web site: http://loco.biosci.arizona.edu
+>> Ceiba phylogenetic tree visualization:
+>> http://sourceforge.net/projects/ceiba
+>> PhyLoTA Browser: http://phylota.net
+>> r8s software: http://loco.biosci.arizona.edu/r8s
+>>
+>> ********************************************************************
+>>
+>
+
+--
+********************************************************************
+Michael J. Sanderson, Professor
+Department of Ecology and Evolutionary Biology
+University of Arizona
+Tucson, AZ 85721
+
+Office: BSW 412
+Phone:520-626-6848
+email:sanderm at email.arizona.edu
+
+lab web site: http://loco.biosci.arizona.edu
+Ceiba phylogenetic tree visualization:
+ http://sourceforge.net/projects/ceiba
+PhyLoTA Browser: http://phylota.net
+r8s software: http://loco.biosci.arizona.edu/r8s
+
+********************************************************************
+
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