Get master up to date with the version on cran (#334)

.Rbuildignore

@@ -17,4 +17,7 @@ inst/compare_lundberg\.xgb\.obj
 ^Meta$
 ^_pkgdown\.yml$
 ^pkgdown$
+[.]Rout$
+[.]out$
+^CRAN-SUBMISSION$
 ^.Rprofile

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

@@ -1,19 +1,21 @@
-# Nov 11th, 2021: THIS IS A MODIFIED VERSION OF THE check-full VERSION AS DESCRIBED BELOW
-# IT ADDS cranversion TO THE LIST OF BRANCHES TO RUN ON AND REDUCED THE NUMBER OF CONFIGS, OTHERWISE IDENTICAL
+# July 5th, 2022: This is a modifided version of the 'check-standard' version from
+# https://github.com/r-lib/actions/tree/v2/examples#standard-ci-workflow
 
-# 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
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
+# The following is modified:
+
+# 1. Runs on branches cranversion and devel as well
+# 2. Runs on oldrel-2 as well
+# 3. R CMD check is performed WITHOUT the default as-cran flag. This allows snapshots to run without setting
+#    as-cran=TRUE in every single call to expect_snapshot
 
+# 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, master, cranversion]
+    branches: [main, master, cranversion, devel]
   pull_request:
-    branches: [main, master, cranversion]
+    branches: [main, master, cranversion, devel]
 
 name: R-CMD-check
 
@@ -28,14 +30,11 @@ jobs:
       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'}
           - {os: ubuntu-latest,   r: 'oldrel-2'}
-#          - {os: ubuntu-latest,   r: 'oldrel-3'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -44,28 +43,20 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          args: 'c("--no-manual")' # I.e. exclude the as-cran comment here
+          upload-snapshots: true

CRAN-RELEASE

@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2021-01-27.
+Once it is accepted, delete this file and tag the release (commit 703b477).

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.2.2
+Date: 2023-05-04 12:59:55 UTC
+SHA: c046e1c3cc967c6cefcfdc1e4b2510f29c17d254

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: shapr
-Version: 0.2.0.9002
+Version: 0.2.2
 Title: Prediction Explanation with Dependence-Aware Shapley Values
 Description: Complex machine learning models are often hard to interpret. However, in 
   many situations it is crucial to understand and explain why a model made a specific 
@@ -24,7 +24,7 @@ Encoding: UTF-8
 LazyData: true
 ByteCompile: true
 Language: en-US
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Depends: R (>= 3.5.0)
 Imports: 
     stats,

NAMESPACE

@@ -7,6 +7,7 @@ S3method(explain,ctree_comb_mincrit)
 S3method(explain,empirical)
 S3method(explain,gaussian)
 S3method(explain,independence)
+S3method(get_model_specs,default)
 S3method(get_model_specs,gam)
 S3method(get_model_specs,glm)
 S3method(get_model_specs,lm)

NEWS.md

@@ -6,6 +6,16 @@
   computed both feature-wise and group-wise
 * Fixed bug when passing non-named data to shapr() or explain() (e.g. ```shapr(data[,1:5],model...)```
 
+# shapr 0.2.2
+
+* Patch to fix failing CRAN-tests on R-devel due to changed behavior of `attach()`: Fixed by changing how we simluate adding a function to .GlobalEnv in the failing test. Actual package not affected.
+
+# shapr 0.2.1
+
+* Patch to fix warning from development version of data.table due to the use of nomatch argument in merge(),
+as requested from [data.table developers](https://github.com/NorskRegnesentral/shapr/issues/322).
+
+
 # shapr 0.2.0
 
 * Minor CRAN release

R/models.R

@@ -347,6 +347,7 @@ get_model_specs <- function(x) {
 }
 
 #' @rdname get_model_specs
+#' @export
 get_model_specs.default <- function(x) {
 
   # For custom models where there is no
@@ -464,7 +465,7 @@ get_supported_models <- function() {
   DT_predict_model[, predict_model := 1]
   DT_predict_model[, c("visible", "from", "generic", "isS4") := NULL]
 
-  DT <- merge(DT_get_model_specs, DT_predict_model, by = "rn", all = T, allow.cartesian = T, nomatch = 0)
+  DT <- merge(DT_get_model_specs, DT_predict_model, by = "rn", all = T, allow.cartesian = T)
   DT[, (colnames(DT)[-1]) := lapply(.SD, data.table::nafill, fill = 0), .SDcols = colnames(DT)[-1]]
   DT[, (colnames(DT)[2:3]) := lapply(.SD, as.logical), .SDcols = colnames(DT)[2:3]]
   data.table::setnames(DT, "rn", "model_class")

README.Rmd

@@ -23,7 +23,7 @@ knitr::opts_chunk$set(
 [![CRAN_Downloads_Badge](https://cranlogs.r-pkg.org/badges/grand-total/shapr)](https://cran.r-project.org/package=shapr)
 [![R build status](https://github.com/NorskRegnesentral/shapr/workflows/R-CMD-check/badge.svg)](https://github.com/NorskRegnesentral/shapr/actions?query=workflow%3AR-CMD-check)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02027/status.svg)](https://doi.org/10.21105/joss.02027)
 <!-- badges: end -->
 

README.md

@@ -12,7 +12,7 @@ status](https://github.com/NorskRegnesentral/shapr/workflows/R-CMD-check/badge.s
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 [![License:
-MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/mit/)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.02027/status.svg)](https://doi.org/10.21105/joss.02027)
 <!-- badges: end -->
 
@@ -182,12 +182,14 @@ explanation <- explain(
 # For more information about the interpretation of the values in the table, see ?shapr::explain.
 print(explanation$dt)
 #>      none     lstat         rm       dis      indus
+#>     <num>     <num>      <num>     <num>      <num>
 #> 1: 22.446 5.2632030 -1.2526613 0.2920444  4.5528644
 #> 2: 22.446 0.1671901 -0.7088401 0.9689005  0.3786871
 #> 3: 22.446 5.9888022  5.5450858 0.5660134 -1.4304351
 #> 4: 22.446 8.2142204  0.7507572 0.1893366  1.8298304
 #> 5: 22.446 0.5059898  5.6875103 0.8432238  2.2471150
 #> 6: 22.446 1.9929673 -3.6001958 0.8601984  3.1510531
+
 # Finally we plot the resulting explanations
 plot(explanation)
 ```

cran-comments.md

@@ -1,59 +1,65 @@
 
-# Minor release, shapr 0.2.0
+# Patch release, shapr 0.2.2
 
-* Adds the ctree approach from new paper
-* Simplified supported for custom models
-* Adds comprehensive check suite for feature consistency
+* Patch to fix failing CRAN-tests on R-devel due to changed behavior of `attach()`: Fixed by changing how we simluate adding a function to .GlobalEnv in the failing test. Actual package not affected.
+* Exports also get_model_specs.default as per the following NOTE from initial CRAN submission 'Apparent methods for exported generics not registered: get_model_specs.default'
 
 ## Test environments
 
-* GitHub Actions (windows-latest): R 4.0
-* GitHub Actions (ubuntu-16.04): R 4.0, 3.6, 3.5
-* GitHub Actions (macOS-latest): R-release, 4.0
-* win-builder (x86_64-w64-mingw32): R 4.0, 3.6, R-devel
-* local Ubuntu 18.04: R 3.6
-* local Windows 10: R 4.0
-* R-hub (windows-x86_64-devel): R-devel
-* R-hub (macos-highsierra-release-cran): R-release
+### With data.table from github master installed, data.table::update_dev_pkg()
 
-* local Ubuntu 18.04: R 3.6 (without packages in Suggests): 
-```devtools::check(vignettes = FALSE, env_vars=c(`_R_CHECK_DEPENDS_ONLY_` = "true"))```
+* local Windows 10: R-devel (4.4.0)
+
+### With cran version of data.table:
+
+* GitHub Actions (ubuntu-latest), R-version: devel, release, oldrel-1, oldrel-2
+* GitHub Actions (windows-latest), R-version: release
+* GitHub Actions (macOS-latest), R-version: release
+* win-builder, R-version: devel, release 
+* R-hub (Fedora Linux): R-version: devel
+* R-hub (Windows server 2022): R-version: devel
 
 ## R CMD check results
 
-There were no ERRORs or WARNINGs.
+There were no ERRORs or WARNINGs
+
+There were 5 NOTES
+
+### NOTE 1 (on GitHub action, ubuntu-latest):
+
+* checking installed package size ... NOTE
+  installed size is  5.0Mb
+  sub-directories of 1Mb or more:
+    libs   4.0Mb
+
+> Nothing has changed since the last submission.
+
+### NOTE 2 (on R-hub (Fedora Linux)):
+
+* checking HTML version of manual ... NOTE
+Skipping checking HTML validation: no command 'tidy' found
+Skipping checking math rendering: package 'V8' unavailable
 
-There was 2 NOTES 
+> Missing packages on R-hubs Windows Server 2022 platform.
 
-*NOTE 1 (on local Windows 10: R 4.0):
+### NOTE 4 (on R-hub (Fedora Linux, Windows Server 2022)):
 
-  Note: information on .o files for i386 is not available
-  Note: information on .o files for x64 is not available
-  File 'C:/Users/jullum/Dropbox/Local_work/Git/shapr.Rcheck/shapr/libs/i386/shapr.dll':
-    Found '_exit', possibly from '_exit' (C)
-    Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
-    Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
-    Found 'printf', possibly from 'printf' (C)
-  File 'C:/Users/jullum/Dropbox/Local_work/Git/shapr.Rcheck/shapr/libs/x64/shapr.dll':
-    Found '_exit', possibly from '_exit' (C)
-    Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
-    Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
-    Found 'printf', possibly from 'printf' (C)
-
-  Compiled code should not call entry points which might terminate R nor
-  write to stdout/stderr instead of to the console, nor use Fortran I/O
-  nor system RNGs. The detected symbols are linked into the code but
-  might come from libraries and not actually be called.
-
-  See 'Writing portable packages' in the 'Writing R Extensions' manual.
+*Found the following (possibly) invalid URLs:
+  URL: https://opensource.org/license/mit/
+    From: README.md
+    Status: 403
+    Message: Forbidden
 
-> I believe this is a false-positive ref https://stackoverflow.com/questions/64402688/information-on-o-files-for-x64-is-not-available-note-on-r-package-checks-using
+> I believe this is a false positive. Running 'urlchecker::url_check()' locally shows all URLs are correct.
 
-*NOTE 2 (on all winbuilder + R-hub servers)
+### NOTE 5 (on R-hub (Windows Server 2022)):
 
-Days since last update: 6
+* checking for detritus in the temp directory ... NOTE
+Found the following files/directories:
+  'lastMiKTeXException'
 
-> The previous release was a basic patch after the package was taken off CRAN. This is a proper release with new features.
+> As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this could be due to a bug/crash in MiKTeX and can likely be ignored.
 
 ## Downstream dependencies
-There are currently no downstream dependencies for this package.
+There is 1 downstream dependency (PPtreeregViz) of shapr
+I have also run R CMD check on that and it passed without errors, warnings or notes.

src/Makevars

@@ -1,3 +1,2 @@
-CXX_STD = CXX11
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,3 +1,2 @@
-CXX_STD = CXX11
 PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

tests/testthat/test-a-shapley.R

@@ -1,6 +1,6 @@
 context("test-shapley.R")
 
-RNGversion(vstr = "3.5.0")
+suppressWarnings(RNGversion(vstr = "3.5.0"))
 
 test_that("Basic test functions in shapley.R", {
 

tests/testthat/test-explanation.R

@@ -1,7 +1,7 @@
 context("test-explanation.R")
 
 # For using same Random numer generator as CircelCI (R version 3.5.x)
-RNGversion(vstr = "3.5.0")
+suppressWarnings(RNGversion(vstr = "3.5.0"))
 
 test_that("Test get_list_approaches", {
   m <- 4

tests/testthat/test-models.R

@@ -457,16 +457,16 @@ test_that("Test missing colnames", {
 test_that("Test get_supported_models", {
   org_models <- get_supported_models()
 
-  # Simulate adding to .GlobalEnv
-  globalfun_1 <- list(get_model_specs.test = function() 1)
-  attach(globalfun_1)
+  # Adding to .GlobalEnv
+  get_model_specs.test <<- function() 1
 
   new_models <- get_supported_models()
 
+  # Removin form .GlobalEnv
+  rm("get_model_specs.test",pos = ".GlobalEnv")
+
   expect_false("test" %in% org_models$model_class)
   expect_true("test" %in% new_models$model_class)
-
-  detach(globalfun_1) # Sets search path back
 })
 
 test_that("Test get_model_specs", {