[Bioc-devel] Question on GPL2 license copyright

Jiping Wang jzw@ng @end|ng |rom northwe@tern@edu
Thu Jul 28 14:51:36 CEST 2022

Thanks to all of you who provided prompt and helpful input.

Given the information I heard, suppose someone downloads your bioconductor package and makes some minor changes (for example, change some parameters of the model or some peripheral) with most core codes unchanged, and then re-package it with a different name and submits to bioconductor, that would be legal under the GPL license? But would it be ethical?

In my situation, the new package basically cloned my package but using a claimed different HMM profile trained based on my other work. Even when I updated my package to comply with the Bioconductor rule regarding passing file name from R to Fortran later, I found the other group immediately copied my solution in codes to handle this issue.

In their accompanying paper the other authors published in June 2021, they compared their package with my package and claimed the superiority of the performance based on the old version of my package. However in fact,  in Nov 2020, my package had a major update and it was subsequently deposited to Bioconductor repository with new functions integrated. The update was also published at my github at the same time (the exact date can be found in my github). The paper they published was not based on the most updated status of my package at that time. Even in current manual of the other package, they still had inaccurate description about my package. Such inaccurate comparison and description of my package does cause negative effect to my package and my work.

We publish tools in Bioconductor because we want to share with the community. However if it becomes the case or trend that users can make minor changes in peripheral of your package and re-package it and rename it and resubmit to biocondcutor, that seems to be problematic to me.

Ji-Ping Wang

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Levi Waldron <lwaldron.research using gmail.com>
Date: Wednesday, July 27, 2022 at 1:41 PM
To: Vincent Carey <stvjc using channing.harvard.edu>
Cc: bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Question on GPL2 license copyright
Sections 1-2 of the GPL-2.0 license (
https://urldefense.com/v3/__https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!RtUM9L2K0SMxZ-TwmjUbvyIwbpn-ofbzikotgJpb8HphprPUtbWTtNBxbLeUICwEgllggYmicd3ylLZEdVEvNAw9T8bBy7NI$<https://urldefense.com/v3/__https:/www.gnu.org/licenses/old-licenses/gpl-2.0.en.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!RtUM9L2K0SMxZ-TwmjUbvyIwbpn-ofbzikotgJpb8HphprPUtbWTtNBxbLeUICwEgllggYmicd3ylLZEdVEvNAw9T8bBy7NI$> ) explicitly allow
copying and distribution of verbatim or modified copies of the Program,
provided inclusion of "an appropriate copyright notice and disclaimer of
warranty" and that modified files are prominently labeled as such. The
license HOWTO (https://urldefense.com/v3/__https://www.gnu.org/licenses/gpl-howto.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!RtUM9L2K0SMxZ-TwmjUbvyIwbpn-ofbzikotgJpb8HphprPUtbWTtNBxbLeUICwEgllggYmicd3ylLZEdVEvNAw9TwRR7g9A$ ) recommends
including a copyright notice, otherwise, creators of derivative work or
others redistributing wouldn't know what copyright notice to include (ie it
could be you, or your employer, university, etc). So I am not a lawyer, but
I think you're within your rights to add a copyright notice and ask (and
require if it came to that) that the author of the other package include
that copyright notice prominently in their program, but you can't stop
anyone from copying your code verbatim or with modification and using it in
their program. I also think that it is the responsibility of the copyright
holder to enforce that, not the responsibility of any Bioconductor
representative (I know you didn't ask for that, but since Vince

Excerpts from https://urldefense.com/v3/__https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!RtUM9L2K0SMxZ-TwmjUbvyIwbpn-ofbzikotgJpb8HphprPUtbWTtNBxbLeUICwEgllggYmicd3ylLZEdVEvNAw9T8bBy7NI$<https://urldefense.com/v3/__https:/www.gnu.org/licenses/old-licenses/gpl-2.0.en.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!RtUM9L2K0SMxZ-TwmjUbvyIwbpn-ofbzikotgJpb8HphprPUtbWTtNBxbLeUICwEgllggYmicd3ylLZEdVEvNAw9T8bBy7NI$> :

*1.* You may copy and distribute verbatim copies of the Program's source
code as you receive it, in any medium, provided that you conspicuously and
appropriately publish on each copy an appropriate copyright notice and
disclaimer of warranty; keep intact all the notices that refer to this
License and to the absence of any warranty; and give any other recipients
of the Program a copy of this License along with the Program.

*2.* *You may modify your copy or copies of the Program or any portion of
it, thus forming a work based on the Program, and copy and distribute such
modifications or work under the terms of Section 1 above*, provided that
you also meet all of these conditions:
*a)* You must cause the modified files to carry prominent notices stating
that you changed the files and the date of any change.*b)* You must cause
any work that you distribute or publish, that in whole or in part contains
or is derived from the Program or any part thereof, to be licensed as a
whole at no charge to all third parties under the terms of this License.*c)* If
the modified program normally reads commands interactively when run, you
must cause it, when started running for such interactive use in the most
ordinary way, to print or display an announcement including an appropriate
copyright notice and a notice that there is no warranty (or else, saying
that you provide a warranty) and that users may redistribute the program
under these conditions, and telling the user how to view a copy of this
License. (Exception: if the Program itself is interactive but does not
normally print such an announcement, your work based on the Program is not
required to print an announcement.)

These requirements apply to the modified work as a whole. If identifiable
sections of that work are not derived from the Program, and can be
reasonably considered independent and separate works in themselves, then
this License, and its terms, do not apply to those sections when you
distribute them as separate works. But when you distribute the same
sections as part of a whole which is a work based on the Program, the
distribution of the whole must be on the terms of this License, whose
permissions for other licensees extend to the entire whole, and thus to
each and every part regardless of who wrote it.

Thus, it is not the intent of this section to claim rights or contest your
rights to work written entirely by you; rather, the intent is to exercise
the right to control the distribution of derivative or collective works
based on the Program.

In addition, mere aggregation of another work not based on the Program with
the Program (or with a work based on the Program) on a volume of a storage
or distribution medium does not bring the other work under the scope of
this License.

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