MUSTANG -- Re:Upstream removing manpage attribution. WTF?

[Arun Konagurthu]

Morten,

I was made aware of this thread (see below) thanks to a colleague.

Your juvenile self-indulgence and paranoia amuses me. While it was
indeed a genuine oversight that caused your credit -- it was I who
included your credit in first place, if I remember correctly -- to be
deleted from the manual page, I will now *make it a point* to *remove*
your man page from every future distribution of MUSTANG--- and there is
a major one coming very soon!

Since you have chosen to make a mountain out of a molehill, are you
really squabbling for credit for merely formatting in troff the text
which the program *itself* generates? There was not a *single word* of
your own in that man page. The entire thing was taken /in toto/ from the
paper's abstract, the programs "--help" option and the original README
file. In fact, I was really thankful even for this (and included your
name in the man page) and would still have, had it not been for your
repugnant attitude!. What is /really/ "troublesome" for a scientist is
to piggyback on someone else's software and seek credit for some
inconsequential trivia; and then shout out from rooftops for a genuine
oversight!

You say that you sent me a mail making me aware of this. First, it has
been over a year and a half since I left  Penn State, and more than four
years since I left csse@unimelb. Nevertheless I keep checking these
inboxes periodically.  It was, then, very surprising that I missed your
mail. So I  vigorously searched these accounts (including the junk
folders; and no mail ever gets deleted). Turns out that I still can't
trace your mail??? Can you prove that you really sent a mail to me? The
way you conduct yourself (and this is not the first time I have seen you
casting aspersions) makes me suspect everything you say!

I care two hoots about the package's future status in Debian-Med. I have
more than just deep admiration for the philosophy of free software and
have always been a strong advocate of open-source software myself. It
would be a shame if Debian is sabotaged by sheer unreason!

Arun Konagurthu

> I am in the akward position that an upstream author has removed the
> attribution in the Authors section in a man page that I have contributed.
> See the attached diff.
>
> I wrote an email making him aware of this, but have not received any reply.
> I think this is especially troublesome for someone aspiring to become a
> scientist.
>
> The man page was originally covered by the license in debian/copyright,
> which said:
>
> Copyright: of the Debian packaging is assigned to the copyright holder and
>  condition to the above license.
> License: BSD-like
>
> However, I don't think that gives permission to remove the author's name.
>
> What do you think?
>
> Cheers,
> Morten
>
> -- Morten Kjeldgaard, asc. professor, MSc, PhD BiRC - Bioinformatics
> Research Center, Aarhus University C. F. Møllers Alle, Building 1110,
> DK-8000 Aarhus C, Denmark. Lab [phone] * Fax [phone] *
> Home [phone] Mobile [phone] * http://www.bioxray.au.dk/~mok
> ------------------------------------------------------------------------
>
> --- MUSTANG_v.3/mustang 2008-01-15 02:05:19.000000000 +0100
> +++ MUSTANG_v3.2/man/mustang.1 2009-04-18 10:44:53.000000000 +0200
> @@ -62,9 +62,9 @@
>  options the user specifies in the command line.
>  DEFAULT output identifier: 'results'
>  .TP
> -.BI \-F " <fmt>"            
> -Alignment output format. The choices for \fI<fmt>\fR are: 'html', 'fasta',
> - 'pir', 'msf'.  DEFAULT format: 'html'
> +.BI \-F " <format>"            
> +Alignment output format. The choices for \fI<format>\fR are: 'html', 'fasta',
> +\'pir\', 'msf'.  DEFAULT format: 'html'
>  .TP
>  .BI \-D " [CA\-CA diameter]"
>  Produce an HTML file where the the residues are reported in lower case with
> @@ -75,6 +75,10 @@
>  Generate a PDB file containing optimal superposition of all the structures
>  based on the alignment.  DEFAULT: 'ON'.
>  .TP
> +.BI \-r " [<ON>/<OFF>]"
> +Print to a file rmsd table of multiple superposition along with rotation matrix
> +and translation vector corresponding to each input structure.  DEFAULT: 'OFF'.
> +.TP
>  .B \-\-help
>  display a help message and exits.
>  .TP
> @@ -83,13 +87,14 @@
>  
>  .SH AUTHORS
>  \fBMustang\fR was written by A. S. Konagurthu, using the algorithm of
> -A. S. Konagurthu \fIet al.\fR (see reference)
> -.PP
> -This manual page was written by Morten Kjeldgaard <mok@...>.
> +A. S. Konagurthu \fIet al.\fR (see REFERENCE)
>  
>  .SH REFERENCE
>  A. S. Konagurthu, J. Whisstock, P. J. Stuckey, and A. M. Lesk, MUSTANG: A
>  multiple structural alignment algorithm, \fBProteins, 64(3) 559-574 (2006).\fR
>  
> +.SH BUG REPORT
> +arun AT csse DOT unimelb DOT edu DOT au
> +
>  .SH SEE ALSO
> -\fBMustang\fR's homepage: http://www.cs.mu.oz.au/~arun/mustang/
> +\fBMustang\fR's homepage: http://www.csse.unimelb.edu.au/~arun/mustang/
>  

--
To UNSUBSCRIBE, email to debian-med-REQUEST@...
with a subject of "unsubscribe". Trouble? Contact listmaster@...

[Morten Kjeldgaard]

Arun,

Please find attached a copy of my email adddressed to arun@...
, dated 23. sep. 2009. I used that email address because it is what is  
listed on the webpage [0] from where you distribute version 3.2.  
Perhaps you should update that.

Cheers,
Morten

[0] http://www.cs.mu.oz.au/~arun/mustang/


Dear Arun,

I have updated the Debian version of Mustang to version 3.2. In the process,
I noticed that in the man-page I contributed on 2008-01-13 you have made a
few small changes one of which was to remove my creditation. I find that a
wee bit disappointing. After all, I did spend some of my free time
reformatting your documentation into nroff format.

Best wishes,
Morten

--
Morten Kjeldgaard, asc. professor, MSc, PhD
BiRC - Bioinformatics Research Center, Aarhus University
C. F. Møllers Alle, Building 1110, DK-8000 Aarhus C, Denmark.
Lab [phone] * Fax [phone] * Home [phone]
Mobile [phone] * http://www.bioxray.au.dk/~mok

[Morten Kjeldgaard]

On 14/10/2009, at 12.41, Arun Konagurthu wrote:

> Your juvenile self-indulgence and paranoia amuses me. While it was  
> indeed a genuine oversight that caused your credit -- it was I who  
> included your credit in first place, if I remember correctly -- to  
> be deleted from the manual page, I will now *make it a point* to  
> *remove* your man page from every future distribution of MUSTANG---  
> and there is a major one coming very soon!

You don't remember correctly. I contributed the manpage on 13. Jan.  
2008, as documented by the attached email. The manpage contains my  
attribution, so you didn't add it.

Cheers,
Morten


Dear Arun,

I am the official packager of your great program mustang for the  
Ubuntu and Debian Linux distributions. The program is in Ubuntu 7.10  
(http://packages.ubuntu.com/gutsy/science/mustang), and the package  
is on its way into Debian "Sid".

As the Debian/Ubuntu distributions require a man page for all  
programs, I wrote one from the documentation I could find in your  
tarball. It is enclosed, and you are most welcome to include it in  
your distribution tarball of mustang. I hereby contribute it to the  
project, and you can distribute it under the same license as the  
program itself.

If you decide at some point to repackage the distribution tarball, it  
would be a good idea to include the text of the license in a file  
COPYING.

Best wishes,
Morten

--
Morten Kjeldgaard, asc. professor, MSc, PhD
Department of Molecular Biology, Aarhus University
Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark.
Lab [phone] * Mobile [phone] * Fax [phone]
Home [phone] * http://www.bioxray.dk/~mok

[Andreas Tille-5]

On Wed, Oct 14, 2009 at 09:41:59PM +1100, Arun Konagurthu wrote:
> Your juvenile self-indulgence and paranoia amuses me. While it was  
> indeed a genuine oversight that caused your credit -- it was I who  
> included your credit in first place, if I remember correctly -- to be  
> deleted from the manual page, I will now *make it a point* to *remove*  
> your man page from every future distribution of MUSTANG---

I really hope that on behalf of our users (meaning mustang users in
general using the Debian packaged version or not) will not really
happen.  I do not hope that a sequence of misscommunications finally
might lead to a step backwards.

> It would be a shame if Debian is sabotaged by sheer unreason!

Yes.  And I hope this can be settled quietly without making much noise
about a small thing.  I hope this point also became clear by my other
mail in this thread[1].

Kind regards

        Andreas.

[1] http://lists.debian.org/debian-med/2009/10/msg00048.html

--
http://fam-tille.de


--
To UNSUBSCRIBE, email to debian-med-REQUEST@...
with a subject of "unsubscribe". Trouble? Contact listmaster@...