NEWS

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speakeasyR 0.1.8 (2025-09-30)

Add

• Support for LongVectors for graphs with more than 2 ^ 31 edges.
• Test for full weighted graph.

Changed

• Update libSE2 to 0.1.13 (improves performance and error handling) and subsequently igraph to 1.0.0
• Write C constructors to directly convert R SEXP types to SE2 types without having to go through igraph data type as an intermediate. Especially in weighted full graphs, this reduces memory requirements by a scalar factor and reduces the time it takes to perform the conversion.

Fixed

• In cluster_genes fix directedness of a symmetric correlation matrix.
• Printing in C files. Previously was adding extra linebreaks.

speakeasyR 0.1.7 (2025-09-05)

Changed

• Update libSE2 to 0.1.11. Fixes issue with subclustering.

speakeasyR 0.1.6 (2025-08-28)

Changed

• Update libSE2 to 0.1.10. Performance improvements.

speakeasyR 0.1.5 (2025-04-03)

Changed

• Update libSE2 to 0.1.9. Improves performance on graphs with skewed weight distributions.

Fixed

• Remove bashism in configure.ac

speakeasyR 0.1.4 (2024-09-24)

Add

• A high level function for clustering genes based on gene expression.

Changed

• Update libSE2 to 0.1.8.

Fixed

• Replace deprecated use of CHARACTER*len in arpack.

speakeasyR 0.1.3 (2024-08-20)

Add

• Ability to interrupt speakeasy 2.
• Release built tarball for manual installation.
• Add explicit test for reproducible results.

Changed

• Update SE2 C library providing performance improvements.
• Tests to be based on quality of clustering instead of exact match to previous run. Since SE2 is stochastic, tweaking the underlying algorithm can change the resulting membership vector even when using a random seed. Even if the membership vector is not identical it should be similar based on normalized mutual information.

Fixed

• Clean up generated module files when compiling using intel's fortran compiler.

speakeasyR 0.1.2 (2024-07-29)

Add

• Contributors of vendored software to DESCRIPTION.
• Support for external ARPACK

Changed

• Use autoconf to generate configure file in order to detect system packages and support for pthreads.
• Remove support for compiling internal linear algebra packages and no longer ship source code for those packages.

Fixed

• Prevent unused igraph vendored packages from being shipped in the source tarball.
• Update SE2 C library to fix address sanitizer errors.

speakeasyR 0.1.1

Fixed

• Guard against missing suggested packages in vignettes, tests, and examples.

speakeasyR 0.1.0 (2024-06-18)

Add

• Set up as R package
• Cluster
• Order nodes
• Knn graph