Fix for CRAN

thomasp85 · thomasp85 · commit e86cb10d07ed · 2019-06-24T13:10:03.000+02:00
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,5 +9,8 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^revdep$
 ^LICENSE\.md$
 ^CODE_OF_CONDUCT\.md$
+^cran-comments\.md$
+^CRAN-RELEASE$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,18 @@
 Package: lime
 Type: Package
 Title: Local Interpretable Model-Agnostic Explanations
-Version: 0.4.1.900
-Date: 2019-06-11
-Authors@R: c(person('Thomas Lin', 'Pedersen', role = c('cre', 'aut'), email = "thomasp85@gmail.com"),
-             person('Michaël', 'Benesty', role = c('aut'), email = "michael@benesty.fr"))
+Version: 0.5.0
+Date: 2019-06-13
+Authors@R: 
+    c(person(given = "Thomas Lin",
+             family = "Pedersen",
+             role = c("cre", "aut"),
+             email = "thomasp85@gmail.com",
+             comment = c(ORCID = "0000-0002-5147-4711")),
+      person(given = 'Michaël', 
+             family = 'Benesty', 
+             role = c('aut'), 
+             email = "michael@benesty.fr"))
 Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
 Description: When building complex models, it is often difficult to explain why
     the model should be trusted. While global measures such as accuracy are
@@ -15,7 +23,7 @@ Description: When building complex models, it is often difficult to explain why
     described in more detail in the article by Ribeiro et al. (2016) 
     <arXiv:1602.04938>.
 License: MIT + file LICENSE
-URL: https://github.com/thomasp85/lime
+URL: https://lime.data-imaginist.com
 BugReports: https://github.com/thomasp85/lime/issues
 Encoding: UTF-8
 LazyData: true
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# lime 0.4.1.9000
+# lime 0.5.0
 
 * `explain()` will now pass `...` on to the relevant `predict()` method (#150)
 * `explain.data.frame()` gains a `gower_pow` argument to modify the calculated 
diff --git a/R/data.R b/R/data.R
@@ -71,13 +71,13 @@
 #'   \item{text}{the sentences as a character vector}
 #'   \item{class.text}{the category of the sentence}
 #' }
-#' @source \url{https://archive.ics.uci.edu/ml/datasets.html?format=&task=&att=&area=&numAtt=&numIns=&type=text&sort=nameUp&view=table}
+#' @source \url{https://archive.ics.uci.edu/ml/datasets/Sentence+Classification}
 "test_sentences"
 
 #' Stop words list
 #'
 #' List of words that can be safely removed from sentences.
 #'
 #' @format Character vector of stop words
-#' @source \url{https://archive.ics.uci.edu/ml/datasets.html?format=&task=&att=&area=&numAtt=&numIns=&type=text&sort=nameUp&view=table}
+#' @source \url{https://archive.ics.uci.edu/ml/datasets/}
 "stop_words_sentences"
diff --git a/README.Rmd b/README.Rmd
@@ -116,5 +116,5 @@ devtools::install_github('thomasp85/lime')
 
 ## Code of Conduct
 Please note that the 'lime' project is released with a
-[Contributor Code of Conduct](CODE_OF_CONDUCT.md).
+[Contributor Code of Conduct](https://lime.data-imaginist.com/CODE_OF_CONDUCT.html).
 By contributing to this project, you agree to abide by its terms.
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# lime <img src="man/figures/logo.png" align="right" />
+# lime <img src="man/figures/logo.png" width="131px" height="140px" align="right" style="padding-left:10px;background-color:white;" />
 
 [![Travis-CI Build
 Status](https://travis-ci.org/thomasp85/lime.svg?branch=master)](https://travis-ci.org/thomasp85/lime)
@@ -77,16 +77,16 @@ explanation
 #> # A tibble: 10 x 13
 #>    model_type case  label label_prob model_r2 model_intercept
 #>    <chr>      <chr> <chr>      <dbl>    <dbl>           <dbl>
-#>  1 classific… 1     seto…      1        0.693           0.125
-#>  2 classific… 1     seto…      1        0.693           0.125
-#>  3 classific… 2     seto…      0.998    0.682           0.129
-#>  4 classific… 2     seto…      0.998    0.682           0.129
-#>  5 classific… 3     seto…      1        0.691           0.126
-#>  6 classific… 3     seto…      1        0.691           0.126
-#>  7 classific… 4     seto…      1        0.673           0.129
-#>  8 classific… 4     seto…      1        0.673           0.129
-#>  9 classific… 5     seto…      1        0.666           0.133
-#> 10 classific… 5     seto…      1        0.666           0.133
+#>  1 classific… 1     seto…          1    0.680           0.120
+#>  2 classific… 1     seto…          1    0.680           0.120
+#>  3 classific… 2     seto…          1    0.675           0.125
+#>  4 classific… 2     seto…          1    0.675           0.125
+#>  5 classific… 3     seto…          1    0.682           0.122
+#>  6 classific… 3     seto…          1    0.682           0.122
+#>  7 classific… 4     seto…          1    0.667           0.128
+#>  8 classific… 4     seto…          1    0.667           0.128
+#>  9 classific… 5     seto…          1    0.678           0.121
+#> 10 classific… 5     seto…          1    0.678           0.121
 #> # … with 7 more variables: model_prediction <dbl>, feature <chr>,
 #> #   feature_value <dbl>, feature_weight <dbl>, feature_desc <chr>,
 #> #   data <list>, prediction <list>
@@ -137,5 +137,5 @@ devtools::install_github('thomasp85/lime')
 ## Code of Conduct
 
 Please note that the ‘lime’ project is released with a [Contributor Code
-of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you
-agree to abide by its terms.
+of Conduct](https://lime.data-imaginist.com/CODE_OF_CONDUCT.html). By
+contributing to this project, you agree to abide by its terms.
diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,14 @@
+Resubmission according to feedback from CRAN
+
+- Fixed broken links to webpages and files
+- Remove erroneously included revdep subdirectory
+- Ignore h2o unit tests on CRAN as they stall on win 32
+
+## Test environments
+* local OS X install, R 3.6.0
+* ubuntu 14.04 (on travis-ci), R 3.6.0
+* win-builder (devel and release)
+
+## R CMD check results
+
+0 errors | 0 warnings | 0 note
diff --git a/man/figures/README-unnamed-chunk-2-1.png b/man/figures/README-unnamed-chunk-2-1.png
diff --git a/man/lime-package.Rd b/man/lime-package.Rd
diff --git a/man/stop_words_sentences.Rd b/man/stop_words_sentences.Rd
diff --git a/man/test_sentences.Rd b/man/test_sentences.Rd
diff --git a/tests/testthat/test-h2o.R b/tests/testthat/test-h2o.R
@@ -1,36 +1,37 @@
 context("h2o")
-library(h2o)
 
+skip_on_cran()
+library(h2o)
 h2o.init()
 h2o.no_progress()
 
 # BINOMIAL CLASSIFICATION MODEL --------------
 test_that("H2OBinomialClassification: lime explanation only produces one entry per case and feature", {
-    
+
     # Get data
     path <- system.file("extdata", "prostate.csv", package = "h2o")
     df_h2o <- h2o.importFile(path)
-    
+
     # Prep data
     df_h2o$CAPSULE <- h2o::as.factor(df_h2o$CAPSULE)
     df_h2o$RACE    <- h2o::as.factor(df_h2o$RACE)
     df_h2o$DCAPS   <- h2o::as.factor(df_h2o$DCAPS)
     df_h2o$DPROS   <- h2o::as.factor(df_h2o$DPROS)
     df_h2o$ID      <- NULL
-    
+
     predictors <- c("AGE", "RACE", "VOL", "GLEASON")
     response <- "CAPSULE"
-    
-    # Binomial Classification 
+
+    # Binomial Classification
     model.rf <- h2o.randomForest(x = predictors, y = response, training_frame = df_h2o, ntrees = 50, stopping_rounds = 2)
-    
+
     # Check class
     expect_s4_class(model.rf, "H2OBinomialModel")
-    
+
     # Check explainer
     explainer <- lime(as.data.frame(df_h2o), model = model.rf)
     expect_s3_class(explainer, "data_frame_explainer")
-    
+
     # Check explanation
     explanation <- lime::explain(as.data.frame(df_h2o[1,]), explainer, n_labels = 1, n_features = 1, kernel_width = 0.5)
     expect_equal(nrow(explanation), 1)
@@ -39,52 +40,52 @@ test_that("H2OBinomialClassification: lime explanation only produces one entry p
 
 # MULTINOMIAL CLASSIFICATION MODEL --------------
 test_that("H2OMultinomialClassification: lime explanation only produces one entry per case and feature", {
-    
+
     # Get data
     path <- system.file("extdata", "iris.csv", package = "h2o")
     df_h2o <- h2o.importFile(path)
-    
+
     # Prep data
     df_h2o$C5 <- h2o::as.factor(df_h2o$C5)
-    
+
     response <- "C5"
     predictors <- base::setdiff(names(df_h2o), response)
-    
-    # Multinomial Classification 
+
+    # Multinomial Classification
     model.rf <- h2o.randomForest(x = predictors, y = response, training_frame = df_h2o, ntrees = 50, stopping_rounds = 2)
-    
+
     # Check class
     expect_s4_class(model.rf, "H2OMultinomialModel")
-    
+
     # Check explainer
     explainer <- lime(as.data.frame(df_h2o), model = model.rf)
     expect_s3_class(explainer, "data_frame_explainer")
-    
+
     # Check explanation
     explanation <- lime::explain(as.data.frame(df_h2o[1,]), explainer, n_labels = 1, n_features = 1, kernel_width = 0.5)
     expect_equal(nrow(explanation), 1)
 })
 
 test_that("H2ORegression: lime explanation only produces one entry per case and feature", {
-    
+
     # Get data
     path <- system.file("extdata", "australia.csv", package = "h2o")
     df_h2o <- h2o.importFile(path)
-    
+
     # Prep data
     response <- "premax"
     predictors <- base::setdiff(names(df_h2o), response)
-    
-    # Regression Classification 
+
+    # Regression Classification
     model.rf <- h2o.randomForest(x = predictors, y = response, training_frame = df_h2o, ntrees = 50, stopping_rounds = 2)
-    
+
     # Check class
     expect_s4_class(model.rf, "H2ORegressionModel")
-    
+
     # Check explainer
     explainer <- lime(as.data.frame(df_h2o), model = model.rf)
     expect_s3_class(explainer, "data_frame_explainer")
-    
+
     # Check explanation
     explanation <- lime::explain(as.data.frame(df_h2o[1,]), explainer, n_features = 1, kernel_width = 0.5)
     expect_equal(nrow(explanation), 1)

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# lime 0.4.1.9000`
	`1`	`+# lime 0.5.0`
`2`	`2`
`3`	`3`	* `explain()` will now pass `...` on to the relevant `predict()` method (#150)
`4`	`4`	* `explain.data.frame()` gains a `gower_pow` argument to modify the calculated