Merge pull request datashield#585 from datashield/master

Update to 6.3.2

Author: StuartWheater

.Rbuildignore

@@ -17,8 +17,8 @@
 ^R/secure.global.ranking.md$
 ^_pkgdown\.yml$
 ^docs$
-^dsBase_6.3.1.tar.gz$
-^dsBase_6.3.1-permissive.tar.gz$
+^dsBase_6.3.2.tar.gz$
+^dsBase_6.3.2-permissive.tar.gz$
 ^dsDanger_6.3.1.tar.gz$
 ^\.circleci$
 ^\.circleci/config\.yml$

.circleci/config.yml

@@ -5,7 +5,8 @@ version: 2.1
 jobs:
   dsbaseclient:
     docker:
-      - image: cimg/base:current
+#      - image: cimg/base:current
+      - image: cimg/base:2024.11
     resource_class: small
     steps:
       - checkout
@@ -18,6 +19,10 @@ jobs:
           echo "  Tag:       " $CIRCLE_TAG
       - run:
           command: |
+              sudo apt-get install --no-install-recommends software-properties-common dirmngr
+              wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+              sudo add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+
               sudo apt-get update -y
               sudo apt-get install -y r-base-core cmake
       - run:
@@ -33,6 +38,9 @@ jobs:
               sudo apt-get install -y libjpeg-dev
       - run:
           command: |
+              sudo Rscript -e "install.packages('devtools', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
+
               sudo Rscript -e "install.packages('fields', dependencies=TRUE)"
               sudo Rscript -e "install.packages('metafor', dependencies=TRUE)"
               sudo Rscript -e "install.packages('meta', dependencies=TRUE)"
@@ -42,6 +50,15 @@ jobs:
               sudo Rscript -e "install.packages('panelaggregation', dependencies=TRUE)"
               sudo Rscript -e "install.packages('methods', dependencies=TRUE)"
               sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
+
+              sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSOpal', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('MolgenisAuth', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('MolgenisArmadillo', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSMolgenisArmadillo', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DescTools', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('e1071', dependencies=TRUE)"
       - run:
           command: |
               sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'", quiet=FALSE)'

DESCRIPTION

@@ -1,8 +1,42 @@
 Package: dsBaseClient
 Title: DataSHIELD Client Functions
-Version: 6.3.1
-Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
-Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
+Version: 6.3.2
+Authors@R: c(person(given = "Paul",
+                    family = "Burton",
+                    role = c("aut")),
+             person(given = "Rebecca",
+                    family = "Wilson",
+                    role = c("aut")),
+             person(given = "Olly",
+                    family = "Butters",
+                    role = c("aut")),
+             person(given = "Patricia",
+                    family = "Ryser-Welch",
+                    role = c("aut")),
+             person(given = "Alex",
+                    family = "Westerberg",
+                    role = c("aut")),
+             person(given = "Leire",
+                    family = "Abarrategui",
+                    role = c("aut")),
+             person(given = "Roberto",
+                    family = "Villegas-Diaz",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-5036-8661")),
+             person(given = "Demetris",
+                    family = "Avraam",
+                    role = c("aut"),
+                    comment = c(ORCID = "0000-0001-8908-2441")),
+             person(given = "Yannick",
+                    family = "Marcon",
+                    role = c("aut"),
+                    email = "yannick.marcon@obiba.org",
+                    comment = c(ORCID = "0000-0003-0138-2023")),
+             person(given = "Stuart",
+                    family = "Wheater",
+                    role = c("aut", "cre"),
+                    email = "stuart.wheater@arjuna.com",
+                    comment = c(ORCID = "0009-0003-2419-1964")))
 Description: DataSHIELD client functions for the client side.
 License: GPL-3
 Depends:
@@ -19,6 +53,14 @@ Imports:
     methods,
     dplyr
 Suggests:
-    testthat
+    lme4,
+    httr,
+    tibble,
+    testthat,
+    e1071,
+    DescTools,
+    DSOpal,
+    DSMolgenisArmadillo,
+    DSLite
 RoxygenNote: 7.3.2
 Encoding: UTF-8

R/checkClass.R

@@ -3,8 +3,8 @@
 #' @description This is an internal function.
 #' @details In DataSHIELD an object included in analysis must be of the same type in all
 #' the collaborating studies. If that is not the case the process is stopped
-#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the <datasources>
-#' the default set of connections will be used: see \link{datashield.connections_default}.
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the <datasources>
+#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}.
 #' @param obj a string character, the name of the object to check for.
 #' @keywords internal
 #' @return a message or the class of the object if the object has the same class in all studies.

R/ds.Boole.R

@@ -34,9 +34,9 @@
 #' Default \code{'NA'}. For more information see details. 
 #' @param newobj 	a character string that provides the name for the output 
 #' object that is stored on the data servers. Default \code{boole.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} 
 #' objects obtained after login. If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.Boole} returns the object specified by the \code{newobj} argument 
 #' which is written to the server-side. Also, two validity messages are returned
 #' to the client-side indicating the name of the \code{newobj} which 

R/ds.abs.R

@@ -10,9 +10,9 @@
 #' @param x a character string providing the name of a numeric or an integer vector.
 #' @param newobj a character string that provides the name for the output variable
 #' that is stored on the data servers. Default name is set to \code{abs.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. 
 #' If the \code{datasources} argument is not specified the default set of connections will be
-#' used: see \code{\link{datashield.connections_default}}.
+#' used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.abs} assigns a vector for each study that includes the absolute values of
 #' the input numeric or integer vector specified in the argument \code{x}. The created vectors
 #' are stored in the servers.

R/ds.asCharacter.R

@@ -9,9 +9,9 @@
 #' character.
 #' @param newobj a character string that provides the name for the output object
 #'  that is stored on the data servers. Default \code{ascharacter.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} 
 #' objects obtained after login. If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asCharacter} returns the object converted into a class character 
 #' that is written to the server-side. Also, two validity messages are returned to the client-side
 #' indicating the name of the \code{newobj} which has been created in each data source and if 

R/ds.asDataMatrix.R

@@ -8,9 +8,9 @@
 #' a matrix. 
 #' @param newobj a character string that provides the name for the output object
 #'  that is stored on the data servers. Default \code{asdatamatrix.newobj}.
-#' @param datasources a list of \code{\link{DSConnection-class}} 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} 
 #' objects obtained after login. If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asDataMatrix} returns the object converted into a matrix 
 #' that is written to the server-side. Also, two validity messages are returned 
 #' to the client-side

R/ds.asFactor.R

@@ -130,9 +130,9 @@
 #' to be used in the creation of the matrix with dummy variables. 
 #' If the \code{fixed.dummy.vars} is set to FALSE then any value of the baseline level is not taken
 #' into account.
-#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. 
 #' If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return \code{ds.asFactor} returns the unique levels of the converted 
 #' variable in ascending order and a validity 
 #' message with the name of the created object on the client-side and 

R/ds.asFactorSimple.R

@@ -14,9 +14,9 @@
 #' the name of the variable to be converted to a factor. 
 #' @param newobj.name a character string that provides the name for the output variable 
 #' that is stored on the data servers. Default \code{asfactor.newobj}. 
-#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. 
 #' If the \code{datasources} argument is not specified
-#' the default set of connections will be used: see \code{\link{datashield.connections_default}}.
+#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
 #' @return an output vector of class factor to the serverside. In addition, returns a validity 
 #' message with the name of the created object on the client-side and if creation fails an
 #' error message which can be viewed using datashield.errors().  
@@ -109,4 +109,4 @@ return(list(return.info=return.info,return.message=return.message))	 #
 
 
 }
-#ds.asFactorSimple
+#ds.asFactorSimple