fix some errors in R-package after upgrade to 1.0.7

.ci/r_tests.sh

@@ -13,7 +13,10 @@ if [[ $OS_NAME == "macos-latest" ]]; then
   echo 'options(pkgType = "mac.binary")' > .Rprofile
   echo 'options(install.packages.check.source = "no")' >> .Rprofile
 else
-  tlmgr --verify-repo=none --self --all update
+  tlmgr --verify-repo=none update --self
+  tlmgr --verify-repo=none install ec
+
+  echo "Sys.setenv(RETICULATE_PYTHON = '$CONDA_PREFIX/bin/python')" >> .Rprofile
 fi
 
 R_LIB_PATH=$HOME/R

R-package/DESCRIPTION

@@ -21,5 +21,5 @@ Suggests:
     rmarkdown
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.0.2
 VignetteBuilder: knitr

R-package/R/FastRGF_Classifier.R

@@ -51,7 +51,7 @@
 #'                                     min_child_weight = 5.0, data_l2 = 2.0,
 #'                                     sparse_max_features = 80000,
 #'                                     sparse_min_occurences = 5,
-#'                                     calc_prob="sigmoid", n_jobs = 1,
+#'                                     calc_prob = "sigmoid", n_jobs = 1,
 #'                                     verbose = 0)}}{}
 #'
 #'  \item{\code{--------------}}{}
@@ -89,7 +89,7 @@
 #' #                                      min_child_weight = 5.0, data_l2 = 2.0,
 #' #                                      sparse_max_features = 80000,
 #' #                                      sparse_min_occurences = 5,
-#' #                                      calc_prob="sigmoid", n_jobs = 1,
+#' #                                      calc_prob = "sigmoid", n_jobs = 1,
 #' #                                      verbose = 0)
 #' @examples
 #'
@@ -111,7 +111,7 @@
 #'             preds = fast_RGF_class$predict_proba(x)
 #'         }
 #'     }
-#' }, silent=TRUE)
+#' }, silent = TRUE)
 
 FastRGF_Classifier <- R6::R6Class(
     "FastRGF_Classifier",

R-package/R/FastRGF_Regressor.R

@@ -101,7 +101,7 @@
 #'             preds = fast_RGF_regr$predict(x)
 #'         }
 #'     }
-#' }, silent=TRUE)
+#' }, silent = TRUE)
 
 FastRGF_Regressor <- R6::R6Class(
     "FastRGF_Regressor",

R-package/R/RGF_Classifier.R

@@ -127,7 +127,7 @@
 #'             preds = RGF_class$predict_proba(x)
 #'         }
 #'     }
-#' }, silent=TRUE)
+#' }, silent = TRUE)
 
 RGF_Classifier <- R6::R6Class(
     "RGF_Classifier",

R-package/R/RGF_Regressor.R

@@ -117,7 +117,7 @@
 #'             preds = RGF_regr$predict(x)
 #'         }
 #'     }
-#' }, silent=TRUE)
+#' }, silent = TRUE)
 
 RGF_Regressor <- R6::R6Class(
     "RGF_Regressor",

R-package/R/TO_scipy_sparse.R

@@ -55,7 +55,7 @@
 #'             }
 #'         }
 #'     }
-#' }, silent=TRUE)
+#' }, silent = TRUE)
 
 TO_scipy_sparse = function(R_sparse_matrix) {
 

R-package/R/mat_2scipy_sparse.R

@@ -26,7 +26,7 @@
 #'             print(res$shape)
 #'         }
 #'     }
-#' }, silent=TRUE)
+#' }, silent = TRUE)
 
 mat_2scipy_sparse = function(x, format = 'sparse_row_matrix') {
 

R-package/R/package.R

@@ -29,15 +29,15 @@ RGF_mod <- NULL; RGF_utils <- NULL; SCP <- NULL;
 
   try({       # I added the try() functions in version 1.0.7 because I received a similar warning as mentioned in: [ https://github.com/rstudio/reticulate/issues/730#issuecomment-594365528 ] and [ https://github.com/rstudio/reticulate/issues/814 ]
     RGF_mod <<- reticulate::import("rgf.sklearn", delay_load = TRUE)
-  }, silent=TRUE)
+  }, silent = TRUE)
 
   try({
     RGF_utils <<- reticulate::import("rgf.utils", delay_load = TRUE)
-  }, silent=TRUE)
+  }, silent = TRUE)
 
   try({
     SCP <<- reticulate::import("scipy", delay_load = TRUE, convert = FALSE)
-  }, silent=TRUE)
+  }, silent = TRUE)
 
   # #................................................................................. keep this as a reference, however it gives a warning on CRAN because it tries to initialize python
   # try({
@@ -59,6 +59,6 @@ RGF_mod <- NULL; RGF_utils <- NULL; SCP <- NULL;
   #   # else {
   #   #   packageStartupMessage("The 'scipy' package is not available!")
   #   # }
-  # }, silent=TRUE)
+  # }, silent = TRUE)
   # #.................................................................................
 }

R-package/tests/testthat/setup.R

@@ -26,14 +26,14 @@ y_reg = runif(100)
 #---------------------------------
 
 set.seed(4)
-y_BINclass = sample(1:2, 100, replace = T)
+y_BINclass = sample(1:2, 100, replace = TRUE)
 
 
 # response "multiclass" classification
 #-------------------------------------
 
 set.seed(5)
-y_MULTIclass = sample(1:5, 100, replace = T)
+y_MULTIclass = sample(1:5, 100, replace = TRUE)
 
 
 # weights for the fit function