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

Alexandre Decan, Tom Mens, Maelick Claes, Philippe Grosjean
2016 2016 IEEE 23rd International Conference on Software Analysis, Evolution, and Reengineering (SANER)  
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.  ...  When developing software packages in a software ecosystem, an important and well-known challenge is how to deal with dependencies to other packages.  ...  générale de l'Enseignement non obligatoire et de la Recherche scientifique; as well as by research credit J.0023.16 "Analysis of Software Project Survival" financed by the F.R.S.  ... 
doi:10.1109/saner.2016.12 dblp:conf/wcre/DecanMCG16 fatcat:b37eezjlhbg4pgdg3ww4awfhsm

The metaRbolomics Toolbox in Bioconductor and beyond

Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski (+7 others)
2019 Metabolites  
In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.  ...  This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation  ...  We repeated such an analysis [26] with the packages mentioned in this review and created a network of reverse dependencies (i.e., the set of packages that depend on these metabolomics related packages  ... 
doi:10.3390/metabo9100200 pmid:31548506 pmcid:PMC6835268 fatcat:3b2gnq6qdrcfbcq6hewgoobdce

Possible Directions for Improving Dependency Versioning in R

Jeroen Ooms
2013 The R Journal  
One such problem is the general lack of dependency versioning in the infrastructure.  ...  In addition, other repositories like BioConductor (Gentleman et al., 2004) and Github (Dabbish et al., 2012) are hosting a respectable number of packages as well.  ...  In the context of the increasingly large pool of inter-dependent packages, violations of this assumption are becoming increasingly apparent and problematic.  ... 
doi:10.32614/rj-2013-019 fatcat:6u4myu4kzbg2fhaqpacve3jszy

Possible Directions for Improving Dependency Versioning in R [article]

Jeroen Ooms
2013 arXiv   pre-print
One such problem is the general lack of dependency versioning in the infrastructure.  ...  However, the number of packages on CRAN and other repositories has increased beyond what might have been foreseen, and is revealing some limitations of the current design.  ...  In addition, other repositories like BioConductor (Gentleman et al., 2004) and Github (Dabbish et al., 2012) are hosting a respectable number of packages as well.  ... 
arXiv:1303.2140v2 fatcat:yr67xzv7xvg5dk4bt7urxprhhm

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  Münster, Germany, but would not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial  ...  Acknowledgements References Acknowledgements The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of  ... 
doi:10.5281/zenodo.5155998 fatcat:wa77g2ytojfqxgmgxe5iev3nge

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible  ...  Acknowledgements The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of Münster, Germany, but would  ... 
doi:10.5281/zenodo.5082439 fatcat:i3sahjpwyjecpnz6lramz4r4ia

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  We show the improvements in discovery and understanding of research when all aspects of research are explicitly linked in a meaningful way.  ...  To keep in touch, follow us on Twitter or GitHub.  ... 
doi:10.5281/zenodo.4384840 fatcat:obaudbxvwfello2ndjb2nmu3vq

Can we trust tests to automate dependency updates? A case study of java projects

Joseph Hejderup, Georgios Gousios
2021 Journal of Systems and Software  
Our findings indicate that the combination of static and dynamic analysis should be a requirement for future dependency updating systems.  ...  To increase reliability, we investigate the use of change impact analysis as a means of reducing false negatives; on average, our tool can uncover 74% of injected faults in direct dependencies and 64%  ...  Acknowledgment We thank Moritz, Xunhui, Arie, Mauricio, and Ayushi for reviewing drafts of this paper.  ... 
doi:10.1016/j.jss.2021.111097 fatcat:j6r6tmd7fjcfbpcpkathsn2xay

S, R, and Data Science

John,M. Chambers
2020 The R Journal  
The description of a new technique, particularly from research in statistics, is frequently accompanied by an R package, greatly increasing the usefulness of the description.  ...  R packages provide tools for a wide range of purposes and users.  ...  Some measures have shown literally exponential growth, such as the number of packages in the main repository, CRAN.  ... 
doi:10.32614/rj-2020-028 fatcat:7hc3pm4btnafpb2eevbo7p2qmy

S, R, and data science

John M. Chambers
2020 Proceedings of the ACM on Programming Languages (PACMPL)  
The description of a new technique, particularly from research in statistics, is frequently accompanied by an R package, greatly increasing the usefulness of the description.  ...  R packages provide tools for a wide range of purposes and users.  ...  Some measures have shown literally exponential growth, such as the number of packages in the main repository, CRAN.  ... 
doi:10.1145/3386334 fatcat:azip7i2n6berzkpal4kaxcohhy

On the reaction to deprecation of clients of 4 + 1 popular Java APIs and the JDK

Anand Ashok Sawant, Romain Robbes, Alberto Bacchelli
2017 Empirical Software Engineering  
Since packages stay in the repository, clients are free to upgrade or not when this happens.  ...  As a result, an increasing number of R packages are now primarily found on GitHub, not CRAN, meaning that the developers are not affected by R/CRAN's strict policies.  ...  His work involves mining of API usage from open source repositories, conducting empirical studies on usage data and qualitative studies, all of which aim to further the understanding of API usage and improve  ... 
doi:10.1007/s10664-017-9554-9 fatcat:m6fatufnvbb3bm7dm4bkcxoz44

PhD thesis [article]

Richel J.C. Bilderbeek
2020 Zenodo  
These guidelines exist to guarantee a minimum level of quality. The most important guideline when submitting an R package to CRAN, is that all its dependencies are on CRAN.  ...  download and install the package from pirouette's GitHub repository.  ...  ALTMETRICS • 60,000 GitHub commits, 1.1k repositories, 421 stars, 242 followers  ... 
doi:10.5281/zenodo.3975586 fatcat:xgqcmwudjrbotg5rmbvh65of7a

PhD thesis

Richel J.C. Bilderbeek
2020 Zenodo  
These guidelines exist to guarantee a minimum level of quality. The most important guideline when submitting an R package to CRAN, is that all its dependencies are on CRAN.  ...  download and install the package from pirouette's GitHub repository.  ...  AUTHOR CONTRIBUTIONS RJCB, GL and RSE conceived the idea for the package. RJCB created, tested and revised the package. GL provided major contributions to the package.  ... 
doi:10.5281/zenodo.4040581 fatcat:4yyz7gzhevde3feexijq2z3wwm

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0 [article]

Laurent Heirendt and Sylvain Arreckx, Thomas Pfau, Sebastián N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdóttir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdóttir, Chiam Yu Ng, German Preciat (+37 others)
2018 arXiv   pre-print
This protocol is an update to the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an unparalleled depth of constraint-based reconstruction and analysis methods.  ...  COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically  ...  ACKNOWLEDGEMENTS The Reproducible Research Results (R3) team, in particular Christophe Trefois and Yohan Jarosz, of the Luxembourg Centre for Systems Biomedicine, is acknowledged for their help in setting  ... 
arXiv:1710.04038v2 fatcat:ys2wthzxfnda7ogkgre2g3pksu

Improving Trust in Research: Supporting Claims with Evidence

Daniel B. Wright
2020 Open Education Studies  
As a new journal our guidelines should be influenced by the opinions of readers and authors, and as such we welcome discussion of how to ensure trust in the research OES publishes.  ...  When you conduct analysis you are faced with several choices, some of these are dictated by the data (e.g., the assumptions of a t-test not meet), and this is appropriate (Tukey, 1960) .  ...  This includes on statistical archives like CRAN (CRAN, the Comprehensive R Archive Network), general file sharing cites like GitHub and ResearchGate, personal web pages, and with the journals.  ... 
doi:10.1515/edu-2020-0106 fatcat:652ks46lvnclrb4gwqbyozligu
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