Maelick Claes

When GitHub Meets CRAN: An Analysis of Inter-Repository Package Dependency Problems

When developing software packages in a software ecosystem, an important and well-known challenge is how to deal with dependencies to other packages. In presence of multiple package repositories, dependency management tends to become even more problematic. For the R ecosystem of statistical computing, dependency management is currently insufficient to deal with multiple package versions and inter-repository package dependencies. We explore how the use of GitHub influences the R ecosystem, both for the distribution of R packages and for inter-repository package dependency management. We also discuss how these problems could be addressed.

On the maintainability of CRAN packages

When writing software, developers are confronted with a trade-off between depending on existing components and reimplementing similar functionality in their own code. Errors may be inadvertently introduced because of dependencies to unreliable components, and it may take longer time to fix these errors. We study such issues in the context of the CRAN archive, a long-lived software ecosystem consisting of over 5000 R packages being actively maintained by over 2500 maintainers, with different flavors of each package depending on the development status and target operating system. Based on an analysis of package dependencies and package status, we present preliminary results on the sources of errors in these packages per flavor, and the time that is needed to fix these errors.

An empirical comparison of dependency issues in OSS packaging ecosystems

Nearly every popular programming language comes with one or more open source software packaging ecosystem(s), containing a large collection of interdependent software packages developed in that programming language. Such packaging ecosystems are extremely useful for their respective software development community. We present an empirical analysis of how the dependency graphs of three large packaging ecosystems (npm, CRAN and RubyGems) evolve over time. We study how the existing package dependencies impact the resilience of the three ecosystems over time and to which extent these ecosystems suffer from issues related to package dependency updates. We analyse specific solutions that each ecosystem has put into place and argue that none of these solutions is perfect, motivating the need for better tools to deal with package dependency update problems.

On the Development and Distribution of R Packages: An Empirical Analysis of the R Ecosystem

This paper explores the ecosystem of software packages for R, one of the most popular environments for statistical computing today. We empirically study how R packages are developed and distributed on different repositories: CRAN, BioConductor, R-Forge and GitHub. We also explore the role and size of each repository, the inter-repository dependencies, and how these repositories grow over time. With this analysis, we provide a deeper insight into the extent and the evolution of the R package ecosystem.

ECOS: Ecological studies of open source software ecosystems

Software ecosystems, collections of projects developed by the same community, are among the most complex artefacts constructed by humans. Collaborative development of open source software (OSS) has witnessed an exponential increase in two decades. Our hypothesis is that software ecosystems bear many similarities with natural ecosystems. While natural ecosystems have been the subject of study for many decades, research on software ecosystems is more recent. For this reason, the ECOS research project aims to determine whether and how selected ecological models and theories from natural ecosystems can be adapted and adopted to understand and better explain how OSS projects (akin to biological species) evolve, and to determine what are the main factors that drive the success or popularity of these projects. Expressed in biological terms, we wish to use knowledge on the evolution of natural ecosystems to provide support aiming to optimize the fitness of OSS projects, and to increase the resistance and resilience of OSS ecosystems.

A historical analysis of Debian package incompatibilities

Users and developers of software distributions are often confronted with installation problems due to conflicting packages. A prototypical example of this are the Linux distributions such as Debian. Conflicts between packages have been studied under different points of view in the literature, in particular for the Debian operating system, but little is known about how these package conflicts evolve over time. This article presents an extensive analysis of the evolution of package incompatibilities, spanning a decade of the life of the Debian stable and testing distributions for its most popular architecture, i386. Using the technique of survival analysis, this empirical study sheds some light on the origin and evolution of package incompatibilities, and provides the basis for building indicators that may be used to improve the quality of package-based distributions.

A historical dataset for the Gnome ecosystem

We present a dataset of the open source software ecosystem Gnome from a social point of view. We have collected historical data about the contributors to all Gnome projects stored on git.gnome.org, taking into account the problem of identity matching, and associating different activity types to the contributors. This type of information is very useful to complement the traditional, source-code related information one can obtain by mining and analyzing the actual source code. The dataset can be obtained at https://bitbucket.org/mgoeminne/sgl-flossmetric-dbmerge.

maintaineR: A Web-Based Dashboard for Maintainers of CRAN Packages

The R development community maintains thousands of packages through its Comprehensive R Archive Network CRAN. The growth and evolution of this archive makes it more and more difficult to maintain packages and their interdependencies, and the existing tools that aim to help developers in this process no longer suffice. We propose maintaine R, a web-based dashboard that allows CRAN package developers to understand and deal with the implications and problems raised by package updates. The dashboard complements existing analysis tools by providing additional support such as the visualisation of package dependencies and reverse dependencies, package conflicts, cross-package function clones, and so on.

On the topology of package dependency networks: a comparison of three programming language ecosystems

Package-based software ecosystems are composed of thousands of interdependent software packages. Many empirical studies have focused on software packages belonging to a single software ecosystem, and suggest to generalise the results to more ecosystems. We claim that such a generalisation is not always possible, because the technical structure of software ecosystems can be very different, even if these ecosystems belong to the same domain. We confirm this claim through a study of three big and popular package-based programming language ecosystems: Rs CRAN archive network, Pythons PyPI distribution, and JavaScripts NPM package manager. We study and compare the structure of their package dependency graphs and reveal some important differences that may make it difficult to generalise the findings of one ecosystem to another one.

An empirical study of identical function clones in CRAN

Code clone analysis is a very active subject of study, and research on inter-project code clones is starting to emerge. In the context of software package repositories specifically, developers are confronted with the choice between depending on code implemented in other packages, or cloning this code in their own package. This article presents an empirical study of identical function clones in the CRAN package archive network, in order to understand the extent of this practice in the R community. Depending on too many packages may hamper maintainability as unexpected conflicts may arise during package updates. Duplicating functions from other packages may reduce maintainability since bug fixes or code changes are not propagated automatically to its clones. We study how the characteristics of cloned functions in CRAN snapshots evolve over time, and classify these clones depending on what has prevented package developers to rely on dependencies instead.