diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 3f52e87..1a50a4e 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -70,11 +70,12 @@ jobs: extra-packages: | any::rcmdcheck any::tidyverse + any::devtools needs: check - name: Check package uses: r-lib/actions/check-r-package@v2 with: - error-on: "\"error\"" + error-on: '"error"' upload-snapshots: true - build_args: "c(\"--no-manual\",\"--compact-vignettes=gs+qpdf\")" + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index f036fa5..9d848d5 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -6,7 +6,7 @@ on: - main - develop release: - types: [ published ] + types: [published] workflow_dispatch: name: pkgdown.yaml diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml index d305d28..bb4ba33 100644 --- a/.github/workflows/pr-commands.yaml +++ b/.github/workflows/pr-commands.yaml @@ -2,7 +2,7 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: issue_comment: - types: [ created ] + types: [created] name: pr-commands.yaml diff --git a/.github/workflows/render-rmarkdown.yaml b/.github/workflows/render-rmarkdown.yaml index 725b537..946de01 100644 --- a/.github/workflows/render-rmarkdown.yaml +++ b/.github/workflows/render-rmarkdown.yaml @@ -2,9 +2,9 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: pull_request: - branches: [ main ] + branches: [main] release: - types: [ published ] + types: [published] workflow_dispatch: name: render-rmarkdown.yaml diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 9f59b8a..52a4b0e 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,7 +1,6 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: - pull_request: branches: - main diff --git a/DESCRIPTION b/DESCRIPTION index ef9d735..ebd7d99 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: BRCore -Title: Unified Framework for Identification and Ecological Interpretation of Microbial Data from Bioenergy Research Centers -Version: 2.0.4.9000 +Title: A Unified Framework for Identification and Ecological Interpretation of Microbial Data from Bioenergy Research Centers +Version: 2.0.7.9000 Authors@R: c( person("Bolívar", "Aponte Rolón", email = "bolaponte@pm.me", @@ -40,16 +40,14 @@ Imports: Hmisc (>= 5.2.4), magrittr (>= 2.0.4), minpack.lm (>= 1.2.4), - phyloseq (>= 1.54.0), + phyloseq, rlang (>= 1.1.6), scales (>= 1.4.0), - stats4 (>= 4.5.2), + stats4, tibble (>= 3.3.0), tidyr (>= 1.3.1), vegan (>= 2.7.2) Suggests: - devtools (>= 2.4.5), - here (>= 1.0.1), knitr (>= 1.50), rmarkdown (>= 2.30), testthat (>= 3.2.3), diff --git a/NEWS.md b/NEWS.md index bf6468e..6f00635 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,8 +1,34 @@ # BRCore (development version) -* Fixes to quote 'BRCore' in DESCRIPTION and typo fix of `sncm.fit` in _pkgdown.yaml + +# BRCore 2.0.7 +2026-05-19 + +* [a43bc71](https://github.com/germs-lab/BRCore/commit/a43bc71d779c5b1b11b1291056570c6e00124212) Typo and instructions fixes to README and DESCRIPTION files. + +# BRCore 2.0.5 +2026-05-18 + +## Bug Fixes + +* Relaxed version requirements for `phyloseq` and `stats4` to improve compatibility. + +* [5ba7a7c](https://github.com/germs-lab/BRCore/commit/5ba7a7c3067a2044c34aee812795dc427869eb4b) Added `biocViews` field to DESCRIPTION to allow installation of Bioconductor dependencies via `install.packages()`. +* [40d79e4](https://github.com/germs-lab/BRCore/commit/40d79e448c632f590e4e52cbf16537496b29529f) Fixes to quote 'BRCore' in DESCRIPTION and typo fix of `sncm.fit` in _pkgdown.yaml + +## Refactoring + +* [95a42db](https://github.com/germs-lab/BRCore/commit/95a42db482675450157ec2099a658e0ce538901c) `sncm.fit()`: replaced `suppressWarnings()` with targeted warning capture via new internal helper `.internal_warn_sncm()`. +* [46eff6f](https://github.com/germs-lab/BRCore/commit/46eff6fb691fd370e5b3723e285bb3882760d742) `plot_neutral_model()`: refined plot axis styling and formatted y-axis as percent. Resized box annotation. +* [b275861](https://github.com/germs-lab/BRCore/commit/b275861e8434204d66dc4962d10499488d738513) Removed redundant `data("bcse")` calls from examples and README vignette. + +## Documentation + +* [46ef2ba](https://github.com/germs-lab/BRCore/commit/46ef2ba1ebb006736f9b86bfa7b06f3adca40f49) Updated vignette output. +* [b275861](https://github.com/germs-lab/BRCore/commit/b275861e8434204d66dc4962d10499488d738513) Removed deprecated `num_iter` parameter from README examples. +* Reordered DESCRIPTION fields. # BRCore 2.0.4 -Date: 2026-04-30 +2026-04-30 * Fixes to documentation: * DOI links updated to correct format @@ -13,7 +39,7 @@ Date: 2026-04-30 * New APA 7th edition style for references # BRCore 2.0.2 -Date: 2026-04-28 +2026-04-28 * Fixes to vignette and function documentation prior to CRAN submission. * Removed "multiple rarefaction" concept from documentation. @@ -21,12 +47,12 @@ Date: 2026-04-28 * Cleaned NAMESPACE and DESCRIPTION. # BRCore 2.0.1 -Date: 2026-04-25 +2026-04-25 * Resubmission to CRAN to address auto-check issues on Debian and Windows. # BRCore 2.0.0 -Date: 2026-04-24 +2026-04-24 ## Breaking Changes @@ -68,7 +94,7 @@ Date: 2026-04-24 @jibarozzo @Gian77 # BRCore 1.0.2 -Date: 2026-02-25 +2026-02-25 ## Bug Fixes diff --git a/README.Rmd b/README.Rmd index 8474eed..2c7d6cf 100644 --- a/README.Rmd +++ b/README.Rmd @@ -51,15 +51,18 @@ BRCore provides tools for: ## Installation -Install the latest *stable* version of BRCore from CRAN with: +### *Stable* version from CRAN with: ```{r} install.packages("BRCore") -``` -Install the *development* version of BRCore from GitHub with: +# or if using with `renv`: +renv::init(bioconductor = TRUE) +renv::install("BRCore") +``` +***NOTE:*** *If using `install.packages()` in an `renv` project, `renv` will intercept the call. Run `renv::init(bioconductor = TRUE)` first to ensure Bioconductor dependencies can be resolved and installed.* -Install the *development* version of BRCore from GitHub with: +### *Development* version from GitHub with: ```{r} # install.packages("pak") pak::pak("germs-lab/BRCore") diff --git a/README.md b/README.md index 6cedd3a..9f74129 100644 --- a/README.md +++ b/README.md @@ -51,15 +51,21 @@ curves, and core distributions ## Installation -Install the latest *stable* version of BRCore from CRAN with: +### *Stable* version from CRAN with: ``` r install.packages("BRCore") + +# or if using with `renv`: +renv::init(bioconductor = TRUE) +renv::install("BRCore") ``` -Install the *development* version of BRCore from GitHub with: +***NOTE:*** *If using `install.packages()` in an `renv` project, `renv` +will intercept the call. Run `renv::init(bioconductor = TRUE)` first to +ensure Bioconductor dependencies can be resolved and installed.* -Install the *development* version of BRCore from GitHub with: +### *Development* version from GitHub with: ``` r # install.packages("pak") diff --git a/cran-comments.md b/cran-comments.md index 83ac0a7..a0ded3f 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,51 +1,34 @@ -## Resubmission notes (v2.0.4) +## v2.0.7 -This is a resubmission. Previous submissions: +### Resubmission notes -- v2.0.3: Passed auto-checks: authors found error in `scnm.fit()` and retracted by maintainer. -- v2.0.2: Passed auto-checks; requested resubmission by manual inspection -- v2.0.1: Passed auto-checks; retracted by maintainer due to typos -- v2.0.0: Rejected by CRAN auto-check service +* Fixed invalid URLs in NEWS.md for v2.0.6 CRAN submission. -**The following issues from v2.0.3 were resolved:** +### R CMD check results -1. Adding `suppressWarnings()` around `stats::dnorm()` calls in `scnm.fit()` to handle warnings previously suppressed by `options(warn=-1)` used a debugging phase. +0 errors | 0 warnings | 3 notes -2. **DOI** links in the documentation were updated to use the correct format (``). -3. Minor typos and formatting issues in the documentation were corrected. -4. Examples were unwrapped from `\dontrun` and `\donttest`. Only example for `identify_core()` remains wrapped due to long execution time (> 5s). - 6. An appropriate example for `scnm.fit()` was included. +### Fixes +* Relaxed version requirements for `phyloseq` and `stats4` to improve compatibility and avoid +CRAN error in `r-oldrel-macos-x86_64`. -### R CMD check results - -0 errors | 0 warnings | 3 notes ### Notes 1. **CRAN incoming feasibility**: - - `New submission`: Expected for new submission or re-submission. - `Running aspell failed`: The `aspell` English dictionary is unavailable in the local check environment (`/usr/lib/aspell-0.60/en_US`). This is a local environment issue and does not affect the package. -2. **Checking for future file timestamps**: Unable to verify current time. This is a - local environment issue and does not affect the package. +2. **Examples with CPU (user + system) or elapsed time > 5s** + user system elapsed + update_otu_table 5.01 0.034 5.055 3. **HTML version of manual**: `V8` package unavailable in the local check environment, skipping math rendering check. This is a local environment issue. ---- - -### win-builder notes -The win-builder (r-devel-windows-x86_64) reported errors for missing packages -(`stringi`, `jsonlite`, `xfun`, `Formula`). These are indirect dependencies of -declared imports (`phyloseq`, `Hmisc`, `knitr`) that were absent in the -win-builder guest environment. The CRAN incoming checks on both Windows and -Debian passed with only NOTEs, confirming these are not direct imports in -package code. - diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index 7d4a0c1..1153828 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -5,6 +5,16 @@ rda_path <- test_path("test_sets/test_vignette_data.rda") # Only regenerate if the .rda is missing or if running on CI is_check <- nzchar(Sys.getenv("_R_CHECK_PACKAGE_NAME_")) is_not_cran <- identical(Sys.getenv("NOT_CRAN"), "true") +is_ci <- nzchar(Sys.getenv("CI")) + +needs <- c("devtools", "phyloseq", "tidyverse", "viridis") +can_regenerate <- all(vapply( + needs, + requireNamespace, + logical(1), + quietly = TRUE +)) + # Does not regenerate on CRAN or during R CMD check, but does regenerate during devtools::test() if the .rda is missing if (is_not_cran && !is_check) { @@ -14,7 +24,7 @@ if (is_not_cran && !is_check) { } # Regenerate test data if running on CI -if (nzchar(Sys.getenv("CI"))) { +if (is_ci && can_regenerate) { rda_path <- file.path( tempdir(), test_path("test_sets/test_vignette_data.rda")