LimROTS License: GPL Implications & Code Analysis

This article delves into the intricacies of the LimROTS license, a topic initiated by AliYoussef96 within the LimROTS discussion category. The core issue revolves around the licensing implications arising from LimROTS's relationship with the ROTS Bioconductor package and the discovery of code overlap. Understanding these licensing details is crucial for developers and users alike to ensure compliance and proper usage of the software.

Background: LimROTS and its Dependence on ROTS

LimROTS, as highlighted by Anwara et al. (2025), serves as an extension of the ROTS Bioconductor package (Suomi et al. 2017). This extension aims to enhance the functionalities offered by ROTS, a widely used tool in the field of bioinformatics. Given this relationship, LimROTS could potentially benefit from reusing existing code within ROTS, a common practice in open-source development. However, the licensing of ROTS presents some complexities. The GPL (>= 2) license under which ROTS is distributed poses certain restrictions, particularly when developing software with more permissive licensing options.

The Licensing Dilemma: GPL vs. Permissive Licenses

The central challenge lies in the contrast between the GPL (>= 2) license of ROTS and the growing preference for more permissive open licenses in research software, as advocated by Morin et al. (2012). The GPL license, while ensuring the open-source nature of the software, imposes certain conditions on derivative works. Specifically, any software incorporating GPL-licensed code must also be licensed under GPL or a compatible license. This can be a deterrent for developers who prefer to use licenses like Apache 2.0 or MIT, which offer greater flexibility in terms of redistribution and commercial use. In addition, the ROTS package, as of October 30, 2024, did not export its functionality in a manner conducive to direct use within LimROTS via standard import mechanisms, further complicating the matter.

Initial Attempt at Independent Reimplementation

In light of these licensing constraints and the limitations in direct code reuse, an attempt was made to create an independent reimplementation of the relevant ROTS functionalities. The goal was to develop a codebase that could be used under a more permissive license, thereby offering greater flexibility for LimROTS's users and developers. As a result, the initial release of LimROTS was licensed under the Artistic 2.0 license, a permissive open-source license that allows for both commercial and non-commercial use, modification, and distribution.

Code Analysis and GPL Implications

To verify the independence of the LimROTS codebase, a thorough analysis was conducted, comparing the source code of LimROTS against that of ROTS. This analysis employed programming-aware AI tools to identify any potential overlaps or derivative elements. The initial code search revealed 35 lines of identical code. Further investigation uncovered additional code with significant structural similarities, indicating a clear, albeit non-identical, overlap between the two codebases. This discovery has significant implications for the licensing of LimROTS.

Identifying Derivative Elements

The identification of identical code segments and functions with similar structures suggests that LimROTS may contain derivative elements from a GPL (>= 2) program. Even though the overlapping code represents a relatively small portion of the overall LimROTS codebase and pertains to standard functionalities, the presence of derivative code necessitates a reevaluation of the software's licensing. Under the terms of the GPL license, incorporating code from a GPL-licensed program into another software project generally requires the derivative work to also be licensed under GPL or a compatible license.

Implications for LimROTS License

Given the findings of the code analysis, the presence of derivative elements implies that the LimROTS license should be changed to GPL (>= 2). This change is necessary to comply with the terms of the GPL license and ensure that LimROTS remains in compliance with open-source licensing principles. While this may introduce certain restrictions on the use and distribution of LimROTS, it is a crucial step in maintaining the integrity of the project and respecting the rights of the original ROTS developers.

Steps to Change the License to GPL (>= 2)

Fortunately, changing the license of an R package like LimROTS is a straightforward process. The steps outlined below, based on the R package licensing instructions, provide a clear guide for updating the license information.

1. Modify the DESCRIPTION File

The first step involves modifying the DESCRIPTION file of the LimROTS package. This file contains essential metadata about the package, including its name, version, authors, and license. To indicate that LimROTS is licensed under GPL (>= 2), the following line should be included in the DESCRIPTION file:

License: GPL (>= 2) + file LICENSE

This line specifies that the package is licensed under GPL version 2 or later and that additional licensing details can be found in a file named LICENSE.

2. Add a LICENSE File

The next step is to create a LICENSE file in the root directory of the LimROTS package. This file should contain the year of copyright and the copyright holders. The copyright holders typically include the names of the individuals or organizations that have contributed code to the package. A template for the LICENSE file is shown below:

YEAR: 2024-2025
COPYRIGHT HOLDER: your name, other contributor names (e.g. from DESCRIPTION file; those who contributed code)

Replace `