jibarozzo · May 20, 2026 · May 6, 2026 · May 18, 2026 · May 18, 2026 · May 18, 2026
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -13,20 +39,20 @@ 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.
 * Removed `parallel_helpers.R` since we have moved away from parallel implementations.
 * 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
@@ -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
@@ -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
@@ -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 (`<doi:...>`).
-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
@@ -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")