Merge branch 'release/0.21.0'

.github/workflows/R-CMD-check.yaml

@@ -20,19 +20,19 @@ jobs:
           - {os: windows-latest, r: 'release'  }
 #          - {os: macOS-latest,   r: 'devel'    }
           - {os: macOS-latest,   r: 'release'  }
-          - {os: ubuntu-20.04,   r: 'devel'    }
-          - {os: ubuntu-20.04,   r: 'release'  }
-          - {os: ubuntu-20.04,   r: 'oldrel'   }
-          - {os: ubuntu-20.04,   r: 'oldrel-1' }
-          - {os: ubuntu-20.04,   r: 'oldrel-2' }
-          - {os: ubuntu-20.04,   r: '3.4'      }
-          - {os: ubuntu-20.04,   r: 'release'  , language: ko,    label: ko    }
-          - {os: ubuntu-20.04,   r: 'release'  , language: zh_CN, label: zh_CN }
-          - {os: ubuntu-20.04,   r: 'release'  , language: zh_TW, label: zh_TW }
+          - {os: ubuntu-latest,  r: 'devel'    }
+          - {os: ubuntu-latest,  r: 'release'  }
+          - {os: ubuntu-latest,  r: 'oldrel'   }
+          - {os: ubuntu-latest,  r: 'oldrel-1' }
+          - {os: ubuntu-latest,  r: 'oldrel-2' }
+          - {os: ubuntu-latest,  r: '3.6'      }
+          - {os: ubuntu-latest,  r: 'release'  , language: ko,    label: ko    }
+          - {os: ubuntu-latest,  r: 'release'  , language: zh_CN, label: zh_CN }
+          - {os: ubuntu-latest,  r: 'release'  , language: zh_TW, label: zh_TW }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       ## R CMD check
       _R_CHECK_CRAN_INCOMING_: false
@@ -44,7 +44,7 @@ jobs:
       LANGUAGE: ${{ matrix.config.language }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/covr.yaml

@@ -8,7 +8,7 @@ jobs:
 
     timeout-minutes: 10
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     name: covr
 
@@ -17,7 +17,7 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       ## R CMD check
       _R_CHECK_LENGTH_1_CONDITION_: true
@@ -26,7 +26,7 @@ jobs:
       _R_CHECK_CRAN_INCOMING_: false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: startup
-Version: 0.20.0
+Version: 0.21.0
 Title: Friendly R Startup Configuration
 Depends: R (>= 2.14.0)
 Suggests: commonmark, tools, tcltk

NEWS.md

@@ -1,3 +1,21 @@
+# Version 0.21.0 (2023-12-11)
+
+## New Features
+
+ * `startup::startup(debug = TRUE)` now reports on environment
+   variable `R_ENABLE_JIT` and whether the R just-in-time (JIT)
+   compiler will be enabled or not, and at what level.
+
+## Bug Fixes
+
+ * When `startup()` tried to rename `.RData` file (e.g. when
+   environment variable `R_STARTUP_RDATA=rename`), it would produce
+   `.Rprofile error: cannot xtfrm data frames`.
+
+ * `startup()` would give '.Rprofile error ...: could not find
+   function "anyNA"' in R (< 3.1.0).
+
+
 # Version 0.20.0 (2023-04-02)
 
 ## New Features
@@ -15,11 +33,11 @@
 
 ## Bug Fixes
 
- * startup::check() no longer warns when R sets environment variables
-   'R_LIBS_USER' and 'R_LIBS_SITE' to the default folders that do not
+ * `startup::check()` no longer warns when R sets environment variables
+   `R_LIBS_USER` and `R_LIBS_SITE` to the default folders that do not
    exist by default.
 
- * startup::check() would report on an incorrect default value if R
+ * `startup::check()` would report on an incorrect default value if R
    option `encoding` or `stringsAsFactors` was set during startup to
    an unsafe value.
 

OVERVIEW.md

@@ -239,7 +239,7 @@ local({
 
 [startup]: https://cran.r-project.org/package=startup
 [Emacs Speaks Statistics (ESS)]: https://ess.r-project.org/
-[Microsoft R Open]: https://mran.microsoft.com/open
+[Microsoft R Open]: https://github.com/microsoft/microsoft-r-open
 [pqR]: http://www.pqr-project.org/
 [radian]: https://github.com/randy3k/radian
 [RStudio]: https://posit.co/products/open-source/rstudio/

R/filter_files.R

@@ -210,6 +210,11 @@ filter_files_env <- function(files, ignore = c(names(sysinfo()), "package")) {
 } ## filter_files_env()
 
 
+## base::anyNA() was introduced in R 3.1.0
+if (!exists("anyNA", mode = "function", envir = baseenv(), inherits = FALSE)) {
+  anyNA <- function(x) any(is.na(x))
+}
+
 filter_files <- function(files, info = sysinfo()) {
   files0 <- files
 

R/startup.R

@@ -431,8 +431,9 @@ startup <- function(sibling = FALSE, all = FALSE,
       } else if (rdata == "rename") {
         fi <- file.info(f)
         when <- fi[c("mtime", "ctime")]
-        keep <- vapply(when, FUN = inherits, "POSIXct", FUN.VALUE=FALSE)
+        keep <- vapply(when, FUN = inherits, "POSIXct", FUN.VALUE = FALSE)
         when <- when[keep]
+        when <- unlist(when, use.names = FALSE)
         when <- sort(when, decreasing = TRUE)
         when <- format(when[[1]], format = "%Y%m%d_%H%M%S")
         f_new <- sprintf("%s.%s", f, when)
@@ -483,7 +484,28 @@ startup <- function(sibling = FALSE, all = FALSE,
     logf("- Remaining packages per R_DEFAULT_PACKAGES to be attached by base::.First.sys() (in order): %s",
          paste(squote(pkgs), collapse = ", "))
 
-
+    logf("- The R just-in-time (JIT) compiler:")
+    jit <- Sys.getenv("R_ENABLE_JIT", NA_character_)
+    value <- if (is.na(jit)) "<not set>" else squote(jit)
+    logf("  - R_ENABLE_JIT: %s", value)
+    if (is.na(jit)) {
+      logf("  - JIT compiler enabled by default")
+      if (!"compiler" %in% loadedNamespaces()) {
+        logf("  - The 'compiler' package will be loaded")
+      }
+    } else {
+      value <- suppressWarnings(as.integer(jit))
+      if (!is.na(value) && value > 0L) {
+        logf("  - JIT compiler enabled at level %d", jit)
+        if (!"compiler" %in% loadedNamespaces()) {
+          logf("  - The 'compiler' package will be loaded")
+        }
+      } else {
+        logf("  - JIT compiler disabled")
+      }
+    }
+
+
     logf("The following will be processed when R terminates:")
     for (what in c(".Last", ".Last.sys")) {
       where <- find(what, mode = "function")

README.md

@@ -247,7 +247,7 @@ local({
 
 [startup]: https://cran.r-project.org/package=startup
 [Emacs Speaks Statistics (ESS)]: https://ess.r-project.org/
-[Microsoft R Open]: https://mran.microsoft.com/open
+[Microsoft R Open]: https://github.com/microsoft/microsoft-r-open
 [pqR]: http://www.pqr-project.org/
 [radian]: https://github.com/randy3k/radian
 [RStudio]: https://posit.co/products/open-source/rstudio/

cran-comments.md

@@ -1,6 +1,6 @@
-# CRAN submission startup 0.20.0
+# CRAN submission startup 0.21.0
 
-on 2023-04-02
+on 2023-12-11
 
 Thanks in advance
 
@@ -13,11 +13,11 @@ The package has been verified using `R CMD check --as-cran` on:
 
 | R version | GitHub | R-hub  | mac/win-builder |
 | --------- | ------ | ------ | --------------- |
-| 3.4.x     | L      |        |                 |
-| 4.0.x     | L      |        |                 |
+| 3.6.x     | L      |        |                 |
 | 4.1.x     | L      |        |                 |
-| 4.2.x     | L M W  | L M W  | M1 .            |
-| devel     | L   W  | L      | M1 .            |
+| 4.2.x     | L      |        |                 |
+| 4.3.x     | L M W  | L M W  | M1 W            |
+| devel     | L   W  | L      |    W            |
 
 *Legend: OS: L = Linux, M = macOS, M1 = macOS M1, W = Windows*
 
@@ -29,7 +29,6 @@ res <- rhub::check(platforms = c(
   "debian-clang-devel", 
   "debian-gcc-patched", 
   "fedora-gcc-devel",
-  "macos-highsierra-release-cran",
   "windows-x86_64-release"
 ))
 print(res)
@@ -38,48 +37,39 @@ print(res)
 gives
 
 ```
-── startup 0.20.0: OK
+── startup 0.21.0: OK
 
-  Build ID:   startup_0.20.0.tar.gz-2a464c28284a4baeb307ebbe965446b2
+  Build ID:   startup_0.21.0.tar.gz-ba7d37fcbb004eb98354d4b2bd23e788
   Platform:   Debian Linux, R-devel, clang, ISO-8859-15 locale
-  Submitted:  5m 37.1s ago
-  Build time: 5m 19.1s
+  Submitted:  9m 31.1s ago
+  Build time: 4m 48s
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
-── startup 0.20.0: OK
+── startup 0.21.0: OK
 
-  Build ID:   startup_0.20.0.tar.gz-76223b23643244a59d3e65b81063c2aa
+  Build ID:   startup_0.21.0.tar.gz-47831d7ca2944fdc9ce93bd708599198
   Platform:   Debian Linux, R-patched, GCC
-  Submitted:  5m 37.1s ago
-  Build time: 5m 25s
+  Submitted:  9m 31.1s ago
+  Build time: 4m 34.5s
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
-── startup 0.20.0: OK
+── startup 0.21.0: OK
 
-  Build ID:   startup_0.20.0.tar.gz-d7672fc2c5d44ef4aed0091199ace020
+  Build ID:   startup_0.21.0.tar.gz-1aa5a3db5961420bb6abc6cfb46e5eb8
   Platform:   Fedora Linux, R-devel, GCC
-  Submitted:  5m 37.1s ago
-  Build time: 4m 29.6s
+  Submitted:  9m 31.1s ago
+  Build time: 3m 58.6s
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
-── startup 0.20.0: OK
+── startup 0.21.0: OK
 
-  Build ID:   startup_0.20.0.tar.gz-450c81eced1a4351a6b5016491b8c806
-  Platform:   macOS 10.13.6 High Sierra, R-release, CRAN's setup
-  Submitted:  5m 37.1s ago
-  Build time: 2m 33.4s
-
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
-
-── startup 0.20.0: OK
-
-  Build ID:   startup_0.20.0.tar.gz-47e0282f6aab43b1ba74c998f0f537f8
+  Build ID:   startup_0.21.0.tar.gz-32adfe106a1f4dda92f53934299935e4
   Platform:   Windows Server 2022, R-release, 32/64 bit
-  Submitted:  5m 37.1s ago
-  Build time: 1m 56.9s
+  Submitted:  9m 31.1s ago
+  Build time: 4m 3.9s
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 ```

vignettes/startup-intro.md

@@ -250,7 +250,7 @@ local({
 
 [startup]: https://cran.r-project.org/package=startup
 [Emacs Speaks Statistics (ESS)]: https://ess.r-project.org/
-[Microsoft R Open]: https://mran.microsoft.com/open
+[Microsoft R Open]: https://github.com/microsoft/microsoft-r-open
 [pqR]: http://www.pqr-project.org/
 [radian]: https://github.com/randy3k/radian
 [RStudio]: https://posit.co/products/open-source/rstudio/