combined version of xlcCall + Attributes with deduplication

.devcontainer/Dockerfile

@@ -8,4 +8,15 @@ RUN apt-get install -y libqpdf28 qpdf ghostscript
 RUN install2.r --error devtools rJava RUnit zoo qpdf languageserver
 RUN installGithub.r r-lib/revdepcheck
 RUN apt-get install -y pandoc
-RUN install2.r --error ggplot2
+RUN install2.r --error ggplot2 tinytex
+RUN Rscript -e "{\
+    library(tinytex);\
+    tlmgr_install('datetime');\
+    tlmgr_install('inputenc');\
+    tlmgr_install('hyperref');\
+    tlmgr_install('url');\
+    tlmgr_install('fmtcount');\
+    tlmgr_install('float');\
+    tlmgr_install('natbib');\
+    tinytex:::install_yihui_pkgs();\
+}"

.devcontainer/devcontainer.json

@@ -8,14 +8,14 @@
 	"customizations": {
 		"vscode": {
 			// Add the IDs of extensions you want installed when the container is created.
-				"extensions": [
-					"eamodio.gitlens",
-					"REditorSupport.r",
-					"github.vscode-pull-request-github",
-					"github.vscode-github-actions"
-				]
-			}
+			"extensions": [
+				"eamodio.gitlens",
+				"REditorSupport.r",
+				"github.vscode-pull-request-github",
+				"github.vscode-github-actions"
+			]
 		}
+	}
 
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
 	// "forwardPorts": [],
@@ -28,4 +28,10 @@
 
 	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	// "remoteUser": "vscode"
+
+	// The below may help when using podman instead of docker as the container backend
+	// (see https://github.com/microsoft/vscode-remote-release/issues/7175#issuecomment-1645498699)
+	// ,"runArgs": [
+	// 	"--log-driver=none"
+	// ]
 }

.github/workflows/ci-tests.yml

@@ -31,7 +31,6 @@ jobs:
             r-version: oldrel
             java: 17 #8
             vignettes: true
-            xlc-repo: https://jcenter.bintray.com
             timezone-name: Europe/Zurich
           - os-name: ubuntu # windows-2019, macos-10.15]
             os-version: latest
@@ -44,7 +43,6 @@ jobs:
             r-version: devel
             java: 17
             vignettes: true
-            xlc-repo: https://jcenter.bintray.com
             timezone-name: Pacific/Marquesas
           - os-name: macos # TODO fix java / R interaction
             os-version: latest

.lintr

@@ -0,0 +1,3 @@
+linters: linters_with_defaults() # see vignette("lintr")
+encoding: "UTF-8"
+exclusions: list("R", "demo", "inst", "tests") # disables linting with lintr, as we have not decided yet which linters to use

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: XLConnect
 Type: Package
 Title: Excel Connector for R
-Version: 1.0.8.9999
+Version: 1.1.0.9999
 Authors@R: c(person("Mirai Solutions GmbH", role = "aut",
                     email = "[email protected]"),
              person("Martin", "Studer", role = "cre",

R/dataframeFromJava.R

@@ -72,9 +72,13 @@ dataframeFromJava <- function(df, check.names) {
       res[[i]] = v
   	}
 
+  	# Apply attributes
+  	toSet = (attributes(df))[!names(attributes(df)) %in% c("jobj", "jclass", "class", "package")]
   	# Apply names
-  	names(res) = columnNames
+  	attributes(res) = toSet
+	names(res) = columnNames
+  	result = data.frame(res, check.names = check.names, stringsAsFactors = FALSE)
 
-  	data.frame(res, check.names = check.names, stringsAsFactors = FALSE)
+  	result
 	})
 }

R/extractRownames.R

@@ -30,7 +30,10 @@
 extractRownames <- function(x, col) {
   if(is(x, "list")) {
     if(is.null(col)) col = list(NULL)
-    mapply(extractRownames, x, col, SIMPLIFY = FALSE)
+    res <- mapply(extractRownames, x, col, SIMPLIFY = FALSE)
+    attributes(res) <- attributes(x)
+    res
+
   } else{
   	# use attr(x, "row.names") instead of row.names or rownames
   	# since row.names coerces to character for backward compatibility

R/withAttributesFromJava.R

@@ -0,0 +1,43 @@
+#############################################################################
+#
+# XLConnect
+# Copyright (C) 2010-2021 Mirai Solutions GmbH
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+#############################################################################
+
+#############################################################################
+#
+# Utility function for converting XLConnect java objects with added attributes
+# to R variables with the corresponding attributes.
+#
+# Author: Simon Poltier, Mirai Solutions GmbH
+#
+#############################################################################
+
+withAttributesFromJava <- function(jobj) {
+
+    # jni <- .jcall(jobj, "S", "jni")
+    # unwrapped <- .jcall(jobj, jni, "getValue")
+    unwrapped <- jobj$getValue()
+
+    allANames = .jcall(jobj, "[S", "getAttributeNames")
+    # allAValues = .jcall(jobj, "[S", "getAttributeValues")
+
+    for(i in seq(along = allANames)) {
+        attr(unwrapped, allANames[i]) <- jobj$getAttributeValue(allANames[i])
+    }
+    unwrapped
+  }

R/workbook.addImage.R

@@ -26,13 +26,13 @@
 #
 #############################################################################
 
-setGeneric("addImage", 
-	function(object, filename, name, originalSize = FALSE) standardGeneric("addImage"))
+setGeneric("addImage",
+	function(object, filename, name, originalSize = FALSE, worksheetScope = NULL) standardGeneric("addImage"))
 
-setMethod("addImage", 
-		signature(object = "workbook"), 
-		function(object, filename, name, originalSize = FALSE) {
-			xlcCall(object, "addImage", filename, name, originalSize)
+setMethod("addImage",
+		signature(object = "workbook"),
+		function(object, filename, name, originalSize = FALSE, worksheetScope = NULL) {
+			xlcCall(object, "addImage", filename, name, originalSize, worksheetScope %||% .jnull())
 			invisible()
 		}
 )

R/workbook.appendNamedRegion.R

@@ -28,17 +28,17 @@
 
 setGeneric("appendNamedRegion",
 	function(object, data, name, header = FALSE, overwriteFormulaCells = TRUE,
-	         rownames = NULL) standardGeneric("appendNamedRegion"))
+	         rownames = NULL, worksheetScope = NULL) standardGeneric("appendNamedRegion"))
 
 setMethod("appendNamedRegion", 
 	signature(object = "workbook", data = "ANY"), 
 	function(object, data, name, header = FALSE, overwriteFormulaCells = TRUE,
-	         rownames = NULL) {
+	         rownames = NULL, worksheetScope = NULL) {
 		if(is.character(rownames))
 			data <- includeRownames(data, rownames)
 		# pass data.frame's to Java - construct RDataFrameWrapper Java object references
 		data <- lapply(wrapList(data), dataframeToJava)
-		xlcCall(object, "appendNamedRegion", data, name, header, overwriteFormulaCells, .simplify = FALSE)
+		xlcCall(object, "appendNamedRegion", data, name, worksheetScope %||% .jnull(), header, overwriteFormulaCells, .simplify = FALSE)
 		invisible()
 	}
 )

R/workbook.clearNamedRegion.R

@@ -1,38 +1,38 @@
-#############################################################################
-#
-# XLConnect
-# Copyright (C) 2010-2024 Mirai Solutions GmbH
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <https://www.gnu.org/licenses/>.
-#
-#############################################################################
-
-#############################################################################
-#
-# Clearing a named region
-# 
-# Author: Nicola Lambiase, Mirai Solutions GmbH
-#
-#############################################################################
-
-setGeneric("clearNamedRegion",
-		function(object, name) standardGeneric("clearNamedRegion"))
-
-setMethod("clearNamedRegion", 
-		signature(object = "workbook", name = "character"), 
-		function(object, name) {
-			xlcCall(object, "clearNamedRegion", name)
-			invisible()
-		}
-)
+#############################################################################
+#
+# XLConnect
+# Copyright (C) 2010-2024 Mirai Solutions GmbH
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+#############################################################################
+
+#############################################################################
+#
+# Clearing a named region
+# 
+# Author: Nicola Lambiase, Mirai Solutions GmbH
+#
+#############################################################################
+
+setGeneric("clearNamedRegion",
+		function(object, name, worksheetScope = NULL) standardGeneric("clearNamedRegion"))
+
+setMethod("clearNamedRegion", 
+		signature(object = "workbook", name = "character"), 
+		function(object, name, worksheetScope = NULL) {
+			xlcCall(object, "clearNamedRegion", name, worksheetScope %||% .jnull(), .simplify = FALSE)
+			invisible()
+		}
+)

R/workbook.cloneSheet.R

@@ -29,6 +29,7 @@
 setGeneric("cloneSheet",
 		function(object, sheet, name) standardGeneric("cloneSheet"))
 
+# TODO make cloning names optional
 setMethod("cloneSheet", 
 		signature(object = "workbook", sheet = "numeric"), 
 		function(object, sheet, name) {

R/workbook.createName.R

@@ -1,38 +1,38 @@
-#############################################################################
-#
-# XLConnect
-# Copyright (C) 2010-2024 Mirai Solutions GmbH
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <https://www.gnu.org/licenses/>.
-#
-#############################################################################
-
-#############################################################################
-#
-# Creating names in a workbook
-# 
-# Author: Martin Studer, Mirai Solutions GmbH
-#
-#############################################################################
-
-setGeneric("createName",
-	function(object, name, formula, overwrite = FALSE) standardGeneric("createName"))
-
-setMethod("createName", 
-		signature(object = "workbook"), 
-		function(object, name, formula, overwrite = FALSE) {
-			xlcCall(object, "createName", name, formula, overwrite)
-			invisible()
-		}
-)
+#############################################################################
+#
+# XLConnect
+# Copyright (C) 2010-2024 Mirai Solutions GmbH
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+#############################################################################
+
+#############################################################################
+#
+# Creating names in a workbook
+# 
+# Author: Martin Studer, Mirai Solutions GmbH
+#
+#############################################################################
+
+setGeneric("createName",
+	function(object, name, formula, overwrite = FALSE, worksheetScope = NULL) standardGeneric("createName"))
+
+setMethod("createName", 
+		signature(object = "workbook"), 
+		function(object, name, formula, overwrite = FALSE, worksheetScope = NULL) {
+			xlcCall(object, "createName", name, worksheetScope %||% .jnull(), formula, overwrite)
+			invisible()
+		}
+)