Changes in version 1.1.2 (2026-07-31) Bug fixes and improvements - Fix dispatch of subset() for the CategoriesDataFrame object to the appropriate superclass method. This addresses the failing unit test in tests4classes.R` named "CategoriesDataFrame checks <- validity" with the error message of: Error in match.call(sys.function(which), sys.call(which), expand.dots = FALSE, envir = sys.frame(parents[which])): invalid 'definition' argument` - GitHub Actions CI fix of BiocCheck failing on libgit2::git_repository_open_ext(). Add global config safe.directory of the existing cloned package to be checked, identical to the command run in "Checkout this git repository" CI step. Changes in version 1.1.1 (2026-04-29) Bug fixes and improvements - Fix GitHub organization typo in URLs of the DESCRIPTION file. - GitHub Actions CI fixes: - Add back the "remotes" package that was dropped from the bioconductor/bioconductor_docker:devel container dependencies. - Putatively fix the test coverage sometimes hanging on covr::package_coverage() by disabling parallel unit tests. The rationale for this change was finding similar reports on covr GitHub issues and the Posit community forum. The covr package itself uses codecov for it's GitHub Actions and, therefore, does not serve as useful reference CI code. Unable to reproduce this fault with a local rootless container. Changes in version 1.1.0 (2026-04-28) Significant user-visible changes - Increment development version following release of Bioconductor 3.23. Changes in version 1.0.2 (2026-08-03) Bug fixes and improvements - Backport fixes from 1.1.2 for CategoriesDataFrame dispatch of subset() method (24c42a9) and for git repo ownership for BiocCheck() during GitHub Actions (9659a0c). Changes in version 1.0.1 (2026-04-30) Bug fixes and improvements - Backport fix from 1.1.1 of GitHub organization typo in URLs of the DESCRIPTION file. Changes in version 1.0.0 (2026-04-28) Significant user-visible changes - Stable release for Bioconductor 3.23. Changes in version 0.99.2 (2026-02-16) Bug fixes and improvements - Require a minimum version of DFplyr containing two required bugfixes for building the vignette. - This release was accepted to Bioconductor on 2026-02-25 https://github.com/Bioconductor/Contributions/issues/3986#issuecomment-3960925596 Changes in version 0.99.1 (2025-12-31) Significant user-visible changes - Check upstream API version once a week and warn about changes. - Documented Bioconductor release installation instructions to the vignette and README.md file. Bug fixes and improvements - Fix vignette typo of "DR and" being transposed https://github.com/Bioconductor/Contributions/issues/3986#issuecomment-3480980762. - Fix incorrect R version in CI and simplify GitHub Actions. The previous GitHub Actions were based on conflicting r-lib/actions and the unmaintained seandavi/BiocActions. Based on Marcel's suggestion on Zulip, instead use the better maintained Bioconductor/BuildABiocWorkshop GitHub Actions. Changes in version 0.99.0 (2025-11-20) Bug fixes and improvements - Support trunk R 4.6.0. This required explicitly specifying the drop argument of the [ accessor of DataFrame::DataFrame objects otherwise one runs into the cryptic error "unimplemented type 'list' in 'orderVector1'". - Documented missing return value of CategoriesDataFrame as warned by BiocCheck. Changes in version 0.98.3 (2025-10-11) New features - Added lookup_pubchem() function to standardize various drug database identifiers to PubChem CIDs. Queries from lookup_pubchem() are performed using PubChem's Power User Gatway (PUG) API. While similar lookup functionality exists in other Bioconductor packages, the available packages have limitations making them unsuitable with the newness and scale of the ToppGene API: - Even new versions of metaboliteIDmapping having missing identifiers even for older entries when converting to PubChem CIDs. - ChemmineR does not support vectorized lookups to PubChem CIDs and times out when performing multiple queries. Significant user-visible changes - Added max_tries with a default value of 3 to all functions that perform web queries in keeping with Appendix C.2 of the Bioconductor Guidelines for Package Development and Maintenance. Bug fixes and improvements - Prevent single record queries from generating web query errors caused by single records being simplified from lists into vectors. Changes in version 0.98.2 (2025-03-18) Significant user-visible changes - lookup() and enrich() now return warnings on encountering empty results instead of throwing errors. This is more reasonable, because enrich() can return no results if the default PValue or the requested PValue are too stringent. Similarly, lookup() may yield no results for some queries and having an empty DataFrame makes it easier to bind results rows of multiple queries. Bug fixes and improvements - The year of two January releases in the NEWS.md file was incorrectly set to 2024 instead of 2025. Changes in version 0.98.1 (2025-01-06) New features - enrich() can now be called with any combination of functional enrichment categories. Category thresholds can also be fully adjusted instead of being fixed at their default values. These modifications are passed to enrich() using a CategoriesDataFrame object Significant user-visible changes - Added CategoryDataFrame() S4 class to customize enrich(..., categories) queries. Below are the default values and allowed value ranges or choices: - PValue: 0.05 (min: 0, max: 1) - MinGenes: 1 (min: 1, max: 5000) - MaxGenes: 1500 (min: 2, max: 5000) - MaxResults: 100 (min: 1, max: 5000) - Correction: FDR (choices: {None, FDR, Bonferroni}) - Type: * (choices: any combination from the following list) - Coexpression - CoexpressionAtlas - Computational - Cytoband - Disease - Domain - Drug - GeneFamily - GeneOntologyBiologicalProcess - GeneOntologyCellularComponent - GeneOntologyMolecularFunction - HumanPheno - Interaction - MicroRNA - MousePheno - Pathway - Pubmed - TFBS - ToppCell Bug fixes and improvements - Replaced httr with httr2. The httr package home page recommends against using it because it has been superseded by httr2. - Updated GitHub workflow with more CRAN and Bioconductor checks. - Sped up unit testing by splitting tests creating web API queries into separate unit test files, because testthat parallelization is split by ./tests/testthat/test-*.R file. Changes in version 0.98.0 (2025-01-01) New features - Implemented ToppGene API using default categories and category options: - Default category options are specified by API YAML https://toppgene.cchmc.org/API/openapi.yaml under: components.schemas.EnrichmentRequest.properties.Categories.items.properties.Type.*.default. - Support for non-default category options is a planned feature. Significant user-visible changes - Simplified API into 2 function calls, lookup() and enrich(). - Both functions return DataFrame objects. - enrich() converts nested Genes lists into CharacterList (Symbol) and IntegerList (Entrez) columns. Bug fixes and improvements - Dropped dependency on GSEABase because Bioconductor annotation mappings are lossy compared to webserver annotation lookup API. - Replaced the overly complicated openapi package generated code with simpler httr: - The openapi R package is only on GitHub https://github.com/zhanghao-njmu/openapi and not on Bioconductor or CRAN, so it would not have met Bioconductor's package submission guidelines. - httr looked promising as a replacement for openapi after reading the source code of a ThirdPartyClient biocView package, KEGGREST. - There are significant bugs in the R output of the OpenAPI code generator https://openapi-generator.tech/ even though the R interface is listed as stable. Found two code logic problems with the generated R code: - No support for nested JSON responses; specifically, the nested portion appears as NULL. This was problematic for the "Genes" list returned by each "Annotation" of enrich https://toppgene.cchmc.org/API/enrich. This blocker issue prompted switching to the httr package. - There is a trivial bug in the OpenAPI R interface that treats "array[integer]" as a character vector instead of an integer vector, requiring one to remove unnecessary runtime assertions. All such JSON return type conversions are handled by httr::content(). - The OpenAPI generated code was ugly to work with: - JSON accessors are protected by back-quotes to support OpenAPI edge cases where the JSON accessors may contain special characters. - Error checking is greatly simplified by httr::http_error(), whereas a lot of generated code is created to check specific error codes. - The generated code required a lot of code reformatting to meet Bioconductor documentation, linter, and code style guidelines.