Merge branch 'release/2.5.8'

UCLATALL · Nov 4, 2023 · 1e53e5e · 1e53e5e
2 parents 77b8746 + d1797e9
commit 1e53e5e
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -26,9 +26,9 @@ jobs:
           - { os: macOS-latest, r: "release" }
           - { os: windows-latest, r: "release" }
           - { os: windows-latest, r: "3.6" }
-          - { os: ubuntu-20.04, r: "devel", http-user-agent: "release" }
-          - { os: ubuntu-20.04, r: "release" }
-          - { os: ubuntu-20.04, r: "oldrel-1" }
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel-1" }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -38,10 +38,6 @@ jobs:
       # https://github.com/actions/checkout
       - uses: actions/checkout@v3
 
-      - name: System dependencies
-        if: ${{ matrix.config.os == 'macOS-latest' }}
-        run: brew install gdal
-
       # https://github.com/r-lib/actions/tree/v2/setup-pandoc
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: supernova
 Title: Judd, McClelland, & Ryan Formatting for ANOVA Output
-Version: 2.5.7
-Date: 2023-08-23
+Version: 2.5.8
+Date: 2023-11-03
 Authors@R: c(
     person("Adam", "Blake", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0001-7881-8652")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## supernova 2.5.8
+
+- Don't trim the leading digit from p-value or PRE when they are exactly 1
+
 ## supernova 2.5.7
 
 - Check package version using string comparison to pass _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_ check on CRAN

diff --git a/R/supernova.R b/R/supernova.R
@@ -380,8 +380,11 @@ print.supernova <- function(x, pcut = 4, ...) {
     as.data.frame(stringsAsFactors = FALSE)
 
   # trim leading 0 from p and PRE
-  tbl[["p"]] <- substring(tbl[["p"]], 2)
-  tbl[["PRE"]] <- substring(tbl[["PRE"]], 2)
+  tbl[, c("p", "PRE")] <- vapply(
+    tbl[, c("p", "PRE")],
+    function(x) ifelse(x < 1, substring(x, 2), x),
+    character(nrow(tbl))
+  )
 
   # TABLE FORMATTING
   # add placeholders for null model

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,8 +1,7 @@
 ## Release summary
 
-- Check package version using string comparison to pass _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_ check on CRAN
-- Match parameter names to docs for two internal functions
-- Fixed notes about HTTP 301 responses on NEWS.md links
+- Don't trim the leading digit from p-value or PRE when they are exactly 1
+- Fix issue on CRAN check when lme4 (optional) is not installed but is used in tests
 
 ## Test environments
 
@@ -22,8 +21,9 @@ R CMD check succeeded
 
 ## Reverse dependencies
 
-Dependencies were identified with `devtools::revdep_check()` and tested with `revdepcheck::revdep_check(num_workers = 4)`. No problems were found.
+Dependencies were identified with `devtools::revdep()` and tested with `revdepcheck::revdep_check(num_workers = 4)`. No problems were found.
 
 Packages:
 
+- coursekata
 - eda4treeR
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,27 +1,32 @@
 # Platform
 
-| field    | value                              |
-| :------- | :--------------------------------- |
-| version  | R version 4.2.3 (2023-03-15)       |
-| os       | macOS Ventura 13.5                 |
-| system   | aarch64, darwin20                  |
-| ui       | X11                                |
-| language | (EN)                               |
-| collate  | en_US.UTF-8                        |
-| ctype    | en_US.UTF-8                        |
-| tz       | America/Los_Angeles                |
-| date     | 2023-08-23                         |
-| pandoc   | 3.1.6.2 @ /opt/homebrew/bin/pandoc |
+|field    |value                            |
+|:--------|:--------------------------------|
+|version  |R version 4.3.1 (2023-06-16)     |
+|os       |macOS Sonoma 14.0                |
+|system   |aarch64, darwin23.0.0            |
+|ui       |unknown                          |
+|language |(EN)                             |
+|collate  |en_US.UTF-8                      |
+|ctype    |en_US.UTF-8                      |
+|tz       |America/Los_Angeles              |
+|date     |2023-11-04                       |
+|pandoc   |3.1.9 @ /opt/homebrew/bin/pandoc |
 
 # Dependencies
 
-| package   | old   | new   | Δ   |
-| :-------- | :---- | :---- | :-- |
-| supernova | 2.5.6 | 2.5.7 | \*  |
-| ggplot2   | NA    | 3.4.3 | \*  |
-| gtable    | NA    | 0.3.4 | \*  |
-| purrr     | NA    | 1.0.2 | \*  |
+|package   |old   |new   |Δ  |
+|:---------|:-----|:-----|:--|
+|supernova |2.5.7 |2.5.8 |*  |
+|rlang     |NA    |1.1.2 |*  |
+|withr     |NA    |2.5.2 |*  |
 
 # Revdeps
 
-- eda4treeR
+## Failed to check (2)
+
+|package    |version |error |warning |note |
+|:----------|:-------|:-----|:-------|:----|
+|coursekata |?       |      |        |     |
+|eda4treeR  |?       |      |        |     |
+
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,6 +1,6 @@
 ## revdepcheck results
 
-We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 2 reverse dependencies (0 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
  * We failed to check 0 packages

diff --git a/revdep/email.yml b/revdep/email.yml
diff --git a/revdep/failures.md b/revdep/failures.md
@@ -1 +1,66 @@
-*Wow, no problems at all. :)*
+# coursekata
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/UCLATALL/supernova
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
+```
+# eda4treeR
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/UCLATALL/supernova
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
+```
diff --git a/tests/testthat/_snaps/supernova.md b/tests/testthat/_snaps/supernova.md
@@ -117,3 +117,18 @@
        ----- --------------- | -------- --- ------ --- --- ---
        Total (empty model)   | 1126.047  31 36.324            
 
+# perfectly fit models print 1.000 for PRE and p
+
+    Code
+      supernova(model)
+    Output
+       Analysis of Variance Table (Type III SS)
+       Model: c(1:10) ~ c(11:20)
+      
+                                   SS df     MS            F    PRE     p
+       ----- --------------- | ------  - ------ ------------ ------ -----
+       Model (error reduced) | 82.500  1 82.500 1.202968e+32 1.0000 .0000
+       Error (from model)    |  0.000  8  0.000                          
+       ----- --------------- | ------  - ------ ------------ ------ -----
+       Total (empty model)   | 82.500  9  9.167                          
+
diff --git a/tests/testthat/test-supernova.lmerMod.R b/tests/testthat/test-supernova.lmerMod.R
@@ -1,4 +1,3 @@
-
 # Notes -------------------------------------------------------------------
 # The datasets and expected values used here are taken from the textbook cited in the package
 # description (Judd, McClelland, & Ryan). The page numbers and exhibit references correspond to the
@@ -19,6 +18,7 @@ get_expected <- function(name) {
 }
 
 fit_lmer <- function(formula, data) {
+  skip_if_not_installed("lme4")
   lme4::lmer(
     formula,
     data = data,

diff --git a/tests/testthat/test-supernova.r b/tests/testthat/test-supernova.r
@@ -351,3 +351,8 @@ test_that("non-verbose tables do not have a description column", {
   model <- lm(mpg ~ NULL, data = mtcars)
   expect_snapshot(supernova(model))
 })
+
+test_that("perfectly fit models print 1.000 for PRE and p", {
+  model <- lm(c(1:10) ~ c(11:20))
+  expect_snapshot(supernova(model))
+})