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Changelog

Source: NEWS.md

WebGestaltR 1.1.0

New features

  • seed parameter for reproducible GSEA. WebGestaltR() and WebGestaltRMultiOmics() now accept seed, which fixes the permutation draw so the same input returns identical p-values and FDRs. GSEA has never been reproducible: set.seed() could not reach the permutations, which are generated by a separate RNG in the Rust core, and the main path seeded itself from the clock. Two runs of one analysis could return a different number of significant sets, and nothing said so. Requested in #9 (2021).

    The default is NULL, which keeps the previous clock-seeded behaviour, so results do not change on upgrade unless a seed is passed. ORA and NTA are unaffected — neither uses randomness, and both were already reproducible.

    A seed makes the Monte Carlo error repeatable, not smaller. A p-value near 0.05 at perNum = 1000 still carries roughly 0.007 of sampling error; raise perNum for precision.

Behaviour changes

  • swGsea()’s rng_seed now does something. It defaults to 1 and was documented as a random seed, but had no effect in 1.0.0 or 1.0.1: the pure-R implementation called set.seed(rng_seed), and the port to Rust dropped that without removing the parameter. Direct callers of swGsea() therefore move from varying between runs to being deterministic, restoring the 0.4.6 behaviour. Pass rng_seed = NULL for the 1.0.x behaviour of drawing from system entropy.

WebGestaltR 1.0.1

CRAN release: 2026-08-05

Bug fixes

  • Fixed installation failure on systems where the Rust toolchain is not on the default PATH. src/Makevars.in ran rustc --version before extending PATH with ~/.cargo/bin. Each line of a make recipe runs in its own shell, so that extension — applied only to the cargo build line — never reached the version check, which failed with rustc: No such file or directory and aborted the build before cargo ran. Both the Unix and Windows Makevars now share one PATH definition used by every step.

WebGestaltR 1.0.0

CRAN release: 2026-07-30

Breaking changes

  • The default annotation dataset is now WebGestalt 2024. Previous releases sent no data version to the server and therefore received the 2019 dataset. Identical code will now return results based on 2024 annotations. Gene sets, category sizes, and consequently p-values and FDRs will differ from 0.4.x. This is the intended upgrade, but it is not a silent one: re-run any analysis you intend to compare against earlier results.

  • Redundancy reduction is now opt-in, and the default method changed. 0.4.x always applied affinity propagation and weighted set cover. 1.0.0 gates these behind useAffinityPropagation, useWeightedSetCover, and usekMedoid, with usekMedoid = TRUE (kMedoid_k = 25) as the default in WebGestaltR(). Enrichment statistics are unaffected; which categories are reported as representatives will change.

Bug fixes

  • Removed the libc exit, _exit and abort symbols from the compiled shared object. They were introduced by Rust’s standard library, not by any code path in this package, but R CMD check reports their presence. Where the linker supports it, references are now redirected so the symbols do not appear at all, and any (unreachable) call is raised as an R error rather than terminating the R session.

  • The summary report now shows the uploaded file name again. A mangled identifier in summaryDescription() (interestGeneFilWEBGESTALT_DATA_VERSIONeBase instead of interestGeneFileBase) meant the “Interesting list” field rendered empty for all supported organisms; only the custom “others” organism was unaffected. Present since 2024-08.

New features

  • Core computations (ORA, GSEA, NTA) are now implemented in Rust for substantially improved performance. This adds a build requirement: Rust (cargo, rustc >= 1.63). Binary installations from CRAN do not require a local Rust toolchain. On Windows, source installation requires the GNU toolchain (x86_64-pc-windows-gnu), not MSVC.
  • WebGestaltRMultiOmics() — multi-omics enrichment across gene and metabolite lists, with meta-analysis support.
  • multiswGsea() — weighted set cover GSEA across multiple lists.
  • New arguments to WebGestaltR(): interestGeneNames, useWeightedSetCover, useAffinityPropagation, usekMedoid, kMedoid_k, listName.

Compatibility

  • No exported functions were removed and no existing argument defaults were changed. Code written for 0.4.x will continue to run; see “Breaking changes” above for how its results may differ.

WebGestaltR 0.4.6 (2023-05-31)

CRAN release: 2023-06-01

  • Fixed a bug with R 4.3

WebGestaltR 0.4.5 (2023-02-10)

CRAN release: 2023-02-16

  • Updated default URLs to HTTPS
  • Sort results by enrichment ratio for ties with FDR and P-value
  • Fixed a bug in reading GMT with quotes
  • Fixed a bug in reading GMT from URL without MIME
  • Fixed a bug in GSEA plot path when format is SVG

WebGestaltR 0.4.4 (2020-07-23)

CRAN release: 2020-07-24

  • Fixed a bug in affinity propagation

WebGestaltR 0.4.3 (2020-01-16)

CRAN release: 2020-01-16

Bug fixes. Add a few advanced options for GSEA.

WebGestaltR 0.4.2 (2019-09-16)

CRAN release: 2019-09-17

Bug fixes.

WebGestaltR 0.4.1 (2019-07-03)

CRAN release: 2019-07-03

Add option to save downloaded data in cache. Bug fixes.

WebGestaltR 0.4.0 (2019-04-22)

CRAN release: 2019-04-27

Support of multiple databases for ORA and GSEA. Adjusted column names of the returned data frame.

WebGestaltR 0.3.1 (2019-03-14)

CRAN release: 2019-03-15

Bug fixes. The version with NAR update manuscript.

WebGestaltR 0.3.0 (2019-01-16)

CRAN release: 2019-01-18

Major updates in HTML report and for 2019 publication

WebGestaltR 0.1.1

CRAN release: 2017-05-11

Stable version in WebGestalt 2017 update.

WebGestaltR 0.0.1

First submission to CRAN.