Merge branch 'release/1.8.1'

HenrikBengtsson · Aug 26, 2020 · d29c97e · d29c97e
2 parents 4271bc1 + 99dcd54
commit d29c97e
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,6 +3,7 @@
 #----------------------------
 ^.svn
 ^.git
+^.github
 ^.make
 INSTALL[.]md
 OVERVIEW[.]md

diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -4,6 +4,8 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"    
+
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -12,23 +14,23 @@ jobs:
       fail-fast: false
       matrix:
         config:
-        - { os: windows-latest, r: '3.6'}
-        - { os: windows-latest, r: 'devel'}
-        - { os: macOS-latest, r: '3.6'}
-        - { os: macOS-latest, r: 'devel'}
-        - { os: ubuntu-16.04, r: '3.2', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-        - { os: ubuntu-16.04, r: '3.3', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-        - { os: ubuntu-16.04, r: '3.4', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-        - { os: ubuntu-16.04, r: '3.5', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
-        - { os: ubuntu-16.04, r: '3.6', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+          - {os: windows-latest, r: 'devel'}
+          - {os: windows-latest, r: 'release'}
+#2020-08-08#          - {os: macOS-latest,   r: 'devel'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-18.04,   r: '3.3',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      CRAN: ${{ matrix.config.cran }}
-
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@master
         with:
@@ -37,15 +39,19 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@master
 
       - name: Query dependencies
-        run: Rscript -e "install.packages('remotes')" -e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds', version = 2)"
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
 
       - name: Cache R packages
         if: runner.os != 'Windows'
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
@@ -57,19 +63,27 @@ jobs:
           sudo -s eval "$sysreqs"
 
       - name: Install dependencies
-        run: Rscript -e "library(remotes)" -e "update(readRDS('depends.Rds'))" -e "remotes::install_cran('rcmdcheck')"
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
 
       - name: Check
-        run: Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')"
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
 
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@master
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
-
-      - name: Test coverage
-        if: matrix.config.os == 'ubuntu-16.04' && matrix.config.r == '3.6'
-        run: |
-          Rscript  -e "install.packages('covr')" -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")'
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: R.methodsS3
-Version: 1.8.0
+Version: 1.8.1
 Depends: R (>= 2.13.0)
 Imports: utils
 Suggests: codetools

diff --git a/NEWS b/NEWS
@@ -1,11 +1,17 @@
 Package: R.methodsS3
 ====================
 
+Version: 1.8.1 [2020-08-24]
+
+ * BUG FIXES: R.methodsS3 would produce "Warning: partial match of 'Date' to
+   'Date/Publication'" when attached if options(warnPartialMatchDollar=TRUE).
+
+
 Version: 1.8.0 [2020-02-13]
 
 SIGNIFICANT CHANGES:
 
- * Now setGenericS3() produce an error if it can not turn an existing function
+ * Now setGenericS3() produces an error if it can not turn an existing function
    into a "default" function and create a new generic function.  Previously,
    it produced a warning.
 

diff --git a/R/zzz.R b/R/zzz.R
@@ -3,7 +3,12 @@
 .onAttach <- function(libname, pkgname) {
   pd <- utils::packageDescription(pkgname)
   msg <- sprintf("%s v%s", pkgname, pd$Version)
-  if (!is.null(pd$Date)) msg <- sprintf("%s (%s)", msg, pd$Date)
+
+  field <- intersect(c("Date/Publication", "Date"), names(pd))
+  if (length(field) > 0L) {
+    date <- pd[[field[1]]]
+    if (!is.na(date)) msg <- sprintf("%s (%s)", msg, date)
+  }
   msg <- sprintf("%s successfully loaded. See ?%s for help.", msg, pkgname)
   pkgStartupMessage(msg)
 }
diff --git a/README.md b/README.md
@@ -1,3 +1,6 @@
+
+
+
 # R.methodsS3: S3 Methods Simplified
 
 
@@ -11,7 +14,7 @@ install.packages("R.methodsS3")
 
 To install the pre-release version that is available in Git branch `develop` on GitHub, use:
 ```r
-remotes::install_github("HenrikBengtsson/R.methodsS3@develop")
+remotes::install_github("HenrikBengtsson/R.methodsS3", ref="develop")
 ```
 This will install the package from source.  
 
@@ -26,8 +29,8 @@ Contributing to this package is easy.  Just send a [pull request](https://help.g
 
 ## Software status
 
-| Resource:     | CRAN        | Travis CI       | AppVeyor         |
-| ------------- | ------------------- | --------------- | ---------------- |
-| _Platforms:_  | _Multiple_          | _Linux & macOS_ | _Windows_        |
-| R CMD check   | <a href="https://cran.r-project.org/web/checks/check_results_R.methodsS3.html"><img border="0" src="http://www.r-pkg.org/badges/version/R.methodsS3" alt="CRAN version"></a> | <a href="https://travis-ci.org/HenrikBengtsson/R.methodsS3"><img src="https://travis-ci.org/HenrikBengtsson/R.methodsS3.svg" alt="Build status"></a>   | <a href="https://ci.appveyor.com/project/HenrikBengtsson/r-methodss3"><img src="https://ci.appveyor.com/api/projects/status/github/HenrikBengtsson/R.methodsS3?svg=true" alt="Build status"></a> |
-| Test coverage |                     | <a href="https://codecov.io/gh/HenrikBengtsson/R.methodsS3"><img src="https://codecov.io/gh/HenrikBengtsson/R.methodsS3/branch/develop/graph/badge.svg" alt="Coverage Status"/></a>     |                  |
+| Resource      | CRAN        | GitHub Actions      | Travis CI       | AppVeyor CI      |
+| ------------- | ------------------- | ------------------- | --------------- | ---------------- |
+| _Platforms:_  | _Multiple_          | _Multiple_          | _Linux & macOS_ | _Windows_        |
+| R CMD check   | <a href="https://cran.r-project.org/web/checks/check_results_R.methodsS3.html"><img border="0" src="http://www.r-pkg.org/badges/version/R.methodsS3" alt="CRAN version"></a> | <a href="https://github.com/HenrikBengtsson/R.methodsS3/actions?query=workflow%3AR-CMD-check"><img src="https://github.com/HenrikBengtsson/R.methodsS3/workflows/R-CMD-check/badge.svg?branch=develop" alt="Build status"></a>       | <a href="https://travis-ci.org/HenrikBengtsson/R.methodsS3"><img src="https://travis-ci.org/HenrikBengtsson/R.methodsS3.svg" alt="Build status"></a>   | <a href="https://ci.appveyor.com/project/HenrikBengtsson/r-methodss3"><img src="https://ci.appveyor.com/api/projects/status/github/HenrikBengtsson/R.methodsS3?svg=true" alt="Build status"></a> |
+| Test coverage |                     |                     | <a href="https://codecov.io/gh/HenrikBengtsson/R.methodsS3"><img src="https://codecov.io/gh/HenrikBengtsson/R.methodsS3/branch/develop/graph/badge.svg" alt="Coverage Status"/></a>     |                  |
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,67 +1,23 @@
-# CRAN submission R.methodsS3 1.8.0
+# CRAN submission R.methodsS3 1.8.1
 
-on 2020-02-13
-
-I've verified that this submission causes no issues for any of the 32 reverse package dependencies available on CRAN and Bioconductor.
+on 2020-08-24
 
 Thanks in advance
 
 
 ## Notes not sent to CRAN
 
-### R CMD check --as-cran validation
+### R CMD check validation
 
 The package has been verified using `R CMD check --as-cran` on:
 
-* Platform x86_64-apple-darwin15.6.0 (64-bit) [Travis CI]:
-  - R version 3.5.3 (2019-03-11)
-  - R version 3.6.2 (2019-12-12)
-
-* Platform x86_64-apple-darwin15.6.0 (64-bit) [GitHub Actions]:
-  - R Under development (unstable) (2020-02-11 r77792)
-
-* Platform x86_64-unknown-linux-gnu (64-bit) [Travis CI]:
-  - R version 3.5.3 (2017-01-27) [sic!]
-  - R version 3.6.2 (2017-01-27) [sic!]
-  - R Under development (unstable) (2020-02-13 r77801)
-
-* Platform x86_64-pc-linux-gnu (64-bit):
-  - R version 3.6.2 (2019-12-12)
-
-* Platform x86_64-apple-darwin15.6.0 (64-bit) [GitHub Actions]:
-  - R version 3.2.5 (2016-04-14)
-  - R version 3.3.3 (2017-03-06)
-  - R version 3.4.4 (2018-03-15)
-  - R version 3.5.3 (2019-03-11)
-  - R version 3.6.2 (2019-12-12)
-  - R Under development (unstable) (2020-02-11 r77792)
-
-* Platform x86_64-pc-linux-gnu (64-bit) [r-hub]:
-  - R version 3.6.1 (2019-07-05)
-  - R Under development (unstable) (2020-01-22 r77697)
-
-* Platform i686-pc-linux-gnu (32-bit):
-  - R version 3.4.4 (2018-03-15)
-  - R version 3.6.1 (2019-07-05)
-
-* Platform i386-pc-solaris2.10 (32-bit) [r-hub]:
-  - R version 3.6.0 (2019-04-26)
-
-* Platform x86_64-w64-mingw32 (64-bit) [r-hub]:
-  - R Under development (unstable) (2020-02-08 r77786)
-
-* Platform i386-w64-mingw32 (32-bit) [Appveyor CI]:
-  - R Under development (unstable) (2020-02-11 r77792)
-
-* Platform x86_64-w64-mingw32/x64 (64-bit) [Appveyor CI]:
-  - R version 3.6.2 (2019-12-12)
-  - R Under development (unstable) (2020-02-11 r77792)
-
-* Platform x86_64-w64-mingw32/x64 (64-bit) [win-builder]:
-  - R version 3.6.2 (2019-12-12)
-
-Not available:
+| R version   | GitHub Actions | Travis CI | AppVeyor CI | Rhub      | Win-builder | Other  |
+| ----------- | -------------- | --------- | ----------- | --------- | ----------- | ------ |
+| 3.3.3       | L              |           |             |           |             |        |
+| 3.4.4       | L              |           |             |           |             |        |
+| 3.5.3       | L              |           |             |           |             |        |
+| 3.6.3       | L              | L, M      |             |    S (32) |             |        |
+| 4.0.2       | L, M, W        | L, M      | W           |           |             |        |
+| devel       |       W        | L, M      | W (32 & 64) | W         | W           |        |
 
-* Platform x86_64-w64-mingw32/x64 (64-bit) [win-builder]:
-  - R Under development (unstable) (2019-06-14 r76701)
-  REASON: Huge backlog
+*Legend: OS: L = Linux, S = Solaris, M = macOS, W = Windows.  Architecture: 32 = 32-bit, 64 = 64-bit*