Merge branch 'release/v1.0.2'

.Rbuildignore

@@ -16,3 +16,5 @@
 ^_pkgdown\.yml$
 ^scripts$
 ^CRAN-RELEASE$
+^\.github$
+^CRAN-SUBMISSION$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,47 @@
+# 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:
+  push:
+    branches: [main, _develop]
+  pull_request:
+    branches: [main, _develop]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {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 }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -0,0 +1,35 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, _develop]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: pkgdown
+          needs: website
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.gitignore

@@ -6,3 +6,4 @@ java/auc2/bin
 java/auc2/.idea
 java/auc2/*.iml
 /.project
+docs

.travis.yml

@@ -2,8 +2,8 @@
 
 branches:
   only:
-    - main
-#    - develop
+    - _main
+    - _develop
 
 os:
  - linux

DESCRIPTION

@@ -1,12 +1,15 @@
 Package: prcbench
 Type: Package
 Title: Testing Workbench for Precision-Recall Curves
-Version: 1.0.1
-Date: 2021-04-06
+Version: 1.0.2
+Date: 2022-02-03
 Authors@R: c(
-    person("Takaya", "Saito", email = "takaya.saito@outlook.com", role = c("aut", "cre")),
-    person("Marc", "Rehmsmeier", email = "marc.rehmsmeier@ii.uib.no", role = c("aut")))
-Description: A testing workbench for evaluating precision-recall curves under various conditions.
+    person("Takaya", "Saito", email = "takaya.saito@outlook.com", role = c("aut", "cre"), 
+           comment = c(ORCID = "0000-0002-0154-8452")),
+    person("Marc", "Rehmsmeier", email = "marc.rehmsmeier@ii.uib.no", role = c("aut"), 
+           comment = c(ORCID = "0000-0002-5021-7721")))
+Description: A testing workbench to evaluate tools that calculate precision-recall curves. 
+    Saito and Rehmsmeier (2015) <doi:10.1371/journal.pone.0118432>.
 URL: https://evalclass.github.io/prcbench/, https://github.com/evalclass/prcbench
 BugReports: https://github.com/evalclass/prcbench/issues
 Depends:
@@ -18,7 +21,6 @@ Imports:
     ROCR (>= 1.0-7),
     PRROC (>= 1.1),
     precrec (>= 0.1),
-    rJava (>= 0.9-7),
     R6 (>= 2.1.1),
     assertthat (>= 0.1),
     grid,
@@ -31,6 +33,7 @@ RoxygenNote: 7.1.1
 Encoding: UTF-8
 Suggests: microbenchmark (>= 1.4-2.1),
     PerfMeas (>= 1.2.1),
+    rJava (>= 0.9-7),
     testthat (>= 0.11.0),
     knitr (>= 1.11),
     rmarkdown (>= 0.8.1)

R/tool_zzz.R

@@ -243,6 +243,10 @@ ToolAUCCalculator <- R6::R6Class(
           private$jarpath <- arglist[["jarpath"]]
         }
       }
+      if (private$available && !requireNamespace("rJava", quietly = TRUE)) {
+        print("rJava is not available.")
+        private$available = FALSE
+      }
       private$f_setjar()
     },
 
@@ -278,6 +282,7 @@ ToolAUCCalculator <- R6::R6Class(
   ),
   private = list(
     toolname = "AUCCalculator",
+    available = TRUE,
     curvetype = "SPR",
     auctype = "java",
     print_methods = function() {
@@ -293,12 +298,27 @@ ToolAUCCalculator <- R6::R6Class(
       } else {
         jarpath <- private$jarpath
       }
-      private$auc2 <- .get_java_obj("auc2", jarpath, private$curvetype)
+      if (private$available) {
+        private$auc2 <- .get_java_obj("auc2", jarpath, private$curvetype)
+      } else {
+        private$auc2 <- NA
+      }
     },
     f_wrapper = function(testset, calc_auc, store_res) {
-      .auccalc_wrapper(testset, private$auc2, calc_auc, store_res,
-                       private$auctype)
+      if (private$available) {
+        .auccalc_wrapper(testset, private$auc2, calc_auc, store_res,
+                         private$auctype)
+      } else {
+        if (store_res) {
+          x <- seq(0.0, 1.0, 0.1)
+          y <- rep(0.5, length(x))
+          list(x = x, y = y, auc = 0.5)
+        } else {
+          NULL
+        }
+      }
     }
+
   )
 )
 

README.Rmd

@@ -5,7 +5,7 @@ output:
 
 # prcbench  <img src="man/figures/logo.png" align="right" alt="" width="100" />
 
-[![Travis](https://travis-ci.org/evalclass/prcbench.svg?branch=main)](https://travis-ci.org/evalclass/prcbench/)
+[![R-CMD-check](https://github.com/evalclass/prcbench/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/evalclass/prcbench/actions/workflows/R-CMD-check.yaml)
 [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/evalclass/prcbench?branch=main&svg=true)](https://ci.appveyor.com/project/takayasaito/prcbench/)
 [![codecov.io](https://codecov.io/github/evalclass/prcbench/coverage.svg?branch=main)](https://codecov.io/github/evalclass/prcbench?branch=main)
 [![CodeFactor](https://www.codefactor.io/repository/github/evalclass/prcbench/badge)](https://www.codefactor.io/repository/github/evalclass/prcbench/)

README.md

@@ -1,13 +1,13 @@
 
 # prcbench <img src="man/figures/logo.png" align="right" alt="" width="100" />
 
-[![Travis](https://travis-ci.org/evalclass/prcbench.svg?branch=main)](https://travis-ci.org/evalclass/prcbench/)
+[![R-CMD-check](https://github.com/evalclass/prcbench/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/evalclass/prcbench/actions/workflows/R-CMD-check.yaml)
 [![AppVeyor Build
 Status](https://ci.appveyor.com/api/projects/status/github/evalclass/prcbench?branch=main&svg=true)](https://ci.appveyor.com/project/takayasaito/prcbench/)
 [![codecov.io](https://codecov.io/github/evalclass/prcbench/coverage.svg?branch=main)](https://codecov.io/github/evalclass/prcbench?branch=main)
 [![CodeFactor](https://www.codefactor.io/repository/github/evalclass/prcbench/badge)](https://www.codefactor.io/repository/github/evalclass/prcbench/)
-[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version-ago/prcbench)](https://cran.r-project.org/package=prcbench)
-[![CRAN\_Logs\_Badge](https://cranlogs.r-pkg.org/badges/grand-total/prcbench)](https://cran.r-project.org/package=prcbench)
+[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version-ago/prcbench)](https://cran.r-project.org/package=prcbench)
+[![CRAN_Logs_Badge](https://cranlogs.r-pkg.org/badges/grand-total/prcbench)](https://cran.r-project.org/package=prcbench)
 
 The aim of the `prcbench` package is to provide a testing workbench for
 evaluating precision-recall curves under various conditions. It contains
@@ -43,7 +43,7 @@ predefined test data sets.
 
 ### Java
 
-`AUCCalculator` requires a Java runtime (&gt;= 6).
+`AUCCalculator` requires a Java runtime (>= 6).
 
 ### Bioconductor libraries
 
@@ -137,23 +137,18 @@ library(prcbench)
 testset <- create_testset("bench", "b10")
 toolset <- create_toolset(set_names = "auc5")
 res <- run_benchmark(testset, toolset)
-```
-
-    ## [1] "microbenchmark is not available. system.time will be used instead."
-    ## [1] "PerfMeas is not available."
 
-``` r
 ## Use knitr::kable to show the result in a table format
 knitr::kable(res$tab, digits = 2)
 ```
 
-| testset | toolset | toolname      | min |  lq | mean | median |  uq | max | neval |
-|:--------|:--------|:--------------|----:|----:|-----:|-------:|----:|----:|------:|
-| b10     | auc5    | AUCCalculator |   4 |   5 |    7 |   11.2 |   9 |  31 |     5 |
-| b10     | auc5    | PerfMeas      |   0 |   0 |    0 |    0.2 |   0 |   1 |     5 |
-| b10     | auc5    | precrec       |   7 |   8 |    9 |   42.4 |  11 | 177 |     5 |
-| b10     | auc5    | PRROC         |   0 |   1 |    1 |    2.6 |   1 |  10 |     5 |
-| b10     | auc5    | ROCR          |   3 |   3 |    4 |   16.6 |  24 |  49 |     5 |
+| testset | toolset | toolname      |  min |   lq |  mean | median |    uq |    max | neval |
+|:--------|:--------|:--------------|-----:|-----:|------:|-------:|------:|-------:|------:|
+| b10     | auc5    | AUCCalculator | 3.00 | 3.98 |  8.07 |   4.90 |  5.45 |  23.04 |     5 |
+| b10     | auc5    | PerfMeas      | 0.06 | 0.07 | 85.07 |   0.07 |  0.10 | 425.04 |     5 |
+| b10     | auc5    | precrec       | 5.56 | 6.13 | 42.58 |   7.43 | 12.04 | 181.75 |     5 |
+| b10     | auc5    | PRROC         | 0.18 | 0.19 |  1.82 |   0.19 |  0.23 |   8.32 |     5 |
+| b10     | auc5    | ROCR          | 1.89 | 1.99 | 12.33 |   2.13 | 17.08 |  38.56 |     5 |
 
 ### Evaluation of precision-recall curves
 
@@ -178,11 +173,6 @@ autoplot(scores1)
 ## Plot the results of PerfMeas and PRROC on c1, c2, and c3 test sets
 toolset <- create_toolset(c("PerfMeas", "PRROC"))
 scores2 <- run_evalcurve(testset, toolset)
-```
-
-    ## [1] "PerfMeas is not available."
-
-``` r
 autoplot(scores2, base_plot = FALSE)
 ```
 

appveyor.yml

@@ -25,7 +25,7 @@ install:
 branches:
   only:
     - main
-#    - develop
+    - _develop
 
 skip_tags: true
 

cran-comments.md

@@ -1,21 +1,33 @@
-## Version 1.0.1
+## Version 1.0.2
 This is a submission for updating the already published package - prcbench.
 
 In this version I have:
 
-* Transferred the GitHub repository to an organization GitHub account,
+* Improved several documents,
 
-* Updated citation, and
+* Skipped rJava tests when rJava is not installed, 
 
-* Updated the version.
-    * 0.9.1 -> 1.0.1
+* Replaced Travis CI with GitHub actions,
+
+* and Updated the version.
+    * 1.0.1 -> 1.0.2
 
 ## Test environments
-* local Ubuntu 20.04 High Sierra, R 4.0.5
-* local macOS High Sierra, R 4.0.4
-* win-builder, R Under development (unstable) (2021-04-02 r80141)
-* Ubuntu 16.04.6 LTS (on travis-ci), R 4.0.2 & R Under development (2021-04-02 r80141)
-* Windows Server 2012 R2 x64 (on AppVeyor), R 4.0.5 Patched (2021-03-31 r80143)
+-   local Ubuntu 20.04, R 4.1.2
+
+-   local macOS Big Sur, R 4.1.2
+
+-   win-builder, R Under development (unstable) (2022-02-01 r81619 ucrt)
+
+-   Windows Server 2012 R2 x64 (on AppVeyor), R 4.1.0 Patched (2022-02-01 r81619 ucrt)
+
+-   GitHub Actions
+
+    -   macOS-latest (release)
+    -   windows-latest (release)
+    -   ubuntu-latest (devel)
+    -   ubuntu-latest (release)
+    -   ubuntu-latest (oldrel-1)
 
 ## R CMD check results
 * There were no ERRORs or WARNINGs.