Try to fix R issues when building on jenkins

Basically, some files are not used in the final package probably due to
some non-deterministic issue in roxygen2 which fills our NAMESPACE file
and creates our R man pages.

h2o-bindings/bin/gen_R.py

@@ -38,13 +38,12 @@ def gen_module(schema, algo, module):
     update_param = get_customizations_for(algo, 'update_param')
 
     yield "# This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py"
-    yield "# Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) \n#'"
-    yield "# -------------------------- %s -------------------------- #" % model_name
+    yield "# Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) \n#"
+    yield "# -------------------------- %s -------------------------- #\n#'" % model_name
     # start documentation
     if doc_preamble:
-        yield "#'"
         yield reformat_block(doc_preamble, prefix="#' ")
-    yield "#'"
+        yield "#'"
 
     # start doc for signature
     required_params = odict([(p[0] if isinstance(p, tuple) else p, p[1] if isinstance(p, tuple) else None)

h2o-r/build.gradle

@@ -252,7 +252,6 @@ setProperties.dependsOn gitbranch, getRVersion, pdflatex
 cpH2OAppJar.dependsOn setProperties
 setPackageFiles.dependsOn cpH2OAppJar
 buildPackageDocumentation.dependsOn setPackageFiles
-genPDF.dependsOn setPackageFiles
 genPDF.dependsOn buildPackageDocumentation
 cpPDF.dependsOn genPDF
 cpMainPKG.dependsOn cpPDF

h2o-r/h2o-DESCRIPTION.template

@@ -47,6 +47,7 @@ URL: https://github.com/h2oai/h2o-3
 BugReports: https://github.com/h2oai/h2o-3/issues
 NeedsCompilation: no
 SystemRequirements: Java (>= 8, <= 17)
+Encoding: UTF-8
 Depends: R (>= 2.13.0),
          methods,
          stats

h2o-r/h2o-package/R/adaboost.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- AdaBoost Model -------------------------- #
 #'
 #' Build an AdaBoost model

h2o-r/h2o-package/R/aggregator.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- H2O Aggregator Model -------------------------- #
 #'
 #' Build an Aggregated Frame

h2o-r/h2o-package/R/anovaglm.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- ANOVA GLM -------------------------- #
 #'
 #' H2O ANOVAGLM is used to calculate Type III SS which is used to evaluate the contributions of individual predictors 

h2o-r/h2o-package/R/classes.R

@@ -8,6 +8,7 @@
 #` will typically never have to reason with these objects directly, as there are
 #` S3 accessor methods provided for creating new objects.
 #`
+NULL 
 
 #-----------------------------------------------------------------------------------------------------------------------
 # Class Definitions

h2o-r/h2o-package/R/constants.R

@@ -1,9 +1,10 @@
-#'
-#' H2O Package Constants
-#'
-#' The API endpoints for interacting with H2O via REST are named here.
-#'
-#' Additionally, environment variables for the H2O package are named here.
+#
+# H2O Package Constants
+#
+# The API endpoints for interacting with H2O via REST are named here.
+#
+# Additionally, environment variables for the H2O package are named here.
+
 
 #' Endpoint Version
 .h2o.__REST_API_VERSION <- 3L

h2o-r/h2o-package/R/coxph.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- coxph -------------------------- #
 #'
 #' Trains a Cox Proportional Hazards Model (CoxPH) on an H2O dataset

h2o-r/h2o-package/R/decisiontree.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Decision Tree Model in H2O -------------------------- #
 #'
 #' Build a Decision Tree model

h2o-r/h2o-package/R/deeplearning.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Deep Learning - Neural Network -------------------------- #
 #'
 #' Build a Deep Neural Network model using CPUs

h2o-r/h2o-package/R/edicts.R

@@ -1,13 +1,13 @@
-#'
-#' TODO: No objects in this file are being used. Either remove file or use objects.
-#'
-#' Append a <key,value> pair to a list.
-#'
-#' Contained here are a set of helper methods that perform type checking on the value passed in.
-#'
-#' @param parms a list to add the <k,v> pair to
-#' @param k a key, typically the name of some algorithm parameter
-#' @param v a value, the value of the algorithm parameter
+#
+# TODO: No objects in this file are being used. Either remove file or use objects.
+#
+# Append a <key,value> pair to a list.
+#
+# Contained here are a set of helper methods that perform type checking on the value passed in.
+#
+# @param parms a list to add the <k,v> pair to
+# @param k a key, typically the name of some algorithm parameter
+# @param v a value, the value of the algorithm parameter
 
 .addParm <- function(parms, k, v) {
   cmd <- sprintf("parms$%s = v", k)

h2o-r/h2o-package/R/export.R

@@ -3,6 +3,7 @@
 #`
 #` Export data to local disk or HDFS.
 #` Save models to local disk or HDFS.
+NULL
 
 #' Export an H2O Data Frame (H2OFrame) to a File or to a collection of Files.
 #'

h2o-r/h2o-package/R/extendedisolationforest.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- extendedisolationforest -------------------------- #
 #'
 #' Trains an Extended Isolation Forest model

h2o-r/h2o-package/R/frame.R

@@ -34,6 +34,7 @@
 #`             the first N (typically 10) rows and all cols of the frame
 #` E$nrow   <- the row count (total size, generally much larger than the local cached rows)
 #` E$types  <- the H2O column types
+NULL
 
 # since we only import data.table via requireNamespace this is required for data.table calls to
 # stop pretending to being data.frame and start behaving as data.table

h2o-r/h2o-package/R/gam.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Generalized Additive Model -------------------------- #
 #'
 #' Fit a General Additive Model

h2o-r/h2o-package/R/gbm.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Gradient Boosting Machine -------------------------- #
 #'
 #' Build gradient boosted classification or regression trees

h2o-r/h2o-package/R/generic.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- generic -------------------------- #
 #'
 #' Imports a generic model into H2O. Such model can be used then used for scoring and obtaining

h2o-r/h2o-package/R/glm.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- H2O Generalized Linear Models -------------------------- #
 #'
 #' Fit a generalized linear model

h2o-r/h2o-package/R/glrm.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Generalized Low Rank Model -------------------------- #
 #'
 #' Generalized low rank decomposition of an H2O data frame

h2o-r/h2o-package/R/grid.R

@@ -1,8 +1,8 @@
-#'
-#' H2O Grid Support
-#'
-#' Provides a set of functions to launch a grid search and get
-#' its results.
+#
+# H2O Grid Support
+#
+# Provides a set of functions to launch a grid search and get
+# its results.
 
 #-------------------------------------
 # Grid-related functions start here :)

h2o-r/h2o-package/R/import.R

@@ -1,9 +1,10 @@
-##`'
-##`' Data Import
-##`'
-##`' Importing data is a _lazy_ parse of the data. It adds an extra step so that a user may specify a variety of options
-##`' including a header file, separator type, and in the future column type. Additionally, the import phase provides
-##`' feedback on whether or not a folder or group of files may be imported together.
+#
+# Data Import
+#
+# Importing data is a _lazy_ parse of the data. It adds an extra step so that a user may specify a variety of options
+# including a header file, separator type, and in the future column type. Additionally, the import phase provides
+# feedback on whether or not a folder or group of files may be imported together.
+
 
 #'
 #' Import Files into H2O

h2o-r/h2o-package/R/infogram.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Infogram -------------------------- #
 #'
 #' H2O Infogram

h2o-r/h2o-package/R/isolationforest.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- isolationforest -------------------------- #
 #'
 #' Trains an Isolation Forest model

h2o-r/h2o-package/R/isotonicregression.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- isotonicregression -------------------------- #
 #'
 #' Build an Isotonic Regression model

h2o-r/h2o-package/R/kmeans.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- KMeans Model in H2O -------------------------- #
 #'
 #' Performs k-means clustering on an H2O dataset

h2o-r/h2o-package/R/modelselection.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Model Selection -------------------------- #
 #'
 #' H2O ModelSelection is used to build the best model with one predictor, two predictors, ... up to max_predictor_number 

h2o-r/h2o-package/R/naivebayes.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Naive Bayes Model in H2O -------------------------- #
 #'
 #' Compute naive Bayes probabilities on an H2O dataset.

h2o-r/h2o-package/R/pca.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Principal Components Analysis -------------------------- #
 #'
 #' Principal component analysis of an H2O data frame

h2o-r/h2o-package/R/psvm.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Support Vector Machine -------------------------- #
 #'
 #' Trains a Support Vector Machine model on an H2O dataset

h2o-r/h2o-package/R/randomforest.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Random Forest Model in H2O -------------------------- #
 #'
 #' Build a Random Forest model

h2o-r/h2o-package/R/rulefit.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- rulefit -------------------------- #
 #'
 #' Build a RuleFit Model

h2o-r/h2o-package/R/segment.R

@@ -1,8 +1,8 @@
-#'
-#' H2O Segmented-Data Bulk Model Training
-#'
-#' Provides a set of functions to train a group of models on different
-#' segments (subpopulations) of the training set. 
+#
+# H2O Segmented-Data Bulk Model Training
+#
+# Provides a set of functions to train a group of models on different
+# segments (subpopulations) of the training set. 
 
 #--------------------------------------------
 # Segmented-data bulk model training function

h2o-r/h2o-package/R/stackedensemble.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- H2O Stacked Ensemble -------------------------- #
 #'
 #' Builds a Stacked Ensemble

h2o-r/h2o-package/R/svd.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Singular Value Decomposition -------------------------- #
 #'
 #' Singular value decomposition of an H2O data frame using the power method

h2o-r/h2o-package/R/targetencoder.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Target Encoder -------------------------- #
 #'
 #' Transformation of a categorical variable with a mean value of the target variable

h2o-r/h2o-package/R/upliftrandomforest.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- Uplift Random Forest Model in H2O -------------------------- #
 #'
 #' Build a Uplift Random Forest model

h2o-r/h2o-package/R/word2vec.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- word2vec -------------------------- #
 #'
 #' Trains a word2vec model on a String column of an H2O data frame

h2o-r/h2o-package/R/xgboost.R

@@ -1,6 +1,6 @@
 # This file is auto-generated by h2o-3/h2o-bindings/bin/gen_R.py
 # Copyright 2016 H2O.ai;  Apache License Version 2.0 (see LICENSE for details) 
-#'
+#
 # -------------------------- XGBoost -------------------------- #
 #'
 #' Build an eXtreme Gradient Boosting model