Merge pull request #364 from datashield/v6.3.1-dev

6.3.1 release

.Rbuildignore

@@ -7,3 +7,5 @@
 ^data$
 ^docs$
 ^pkgdown$
+^\.circleci$
+^\.circleci/config\.yml$

.circleci/config.yml

@@ -0,0 +1,50 @@
+# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+
+version: 2.1
+
+jobs:
+  dsbase:
+    docker:
+      - image: cimg/base:current
+    resource_class: small
+    steps:
+      - checkout
+      - setup_remote_docker:
+          docker_layout_caching: true
+      - run: |
+          echo "Building"
+          echo "  Repo Name: " $CIRCLE_PROJECT_REPONAME
+          echo "  Branch:    " $CIRCLE_BRANCH
+          echo "  Tag:       " $CIRCLE_TAG
+      - run:
+          command: |
+              sudo apt-get update -y
+              sudo apt-get install -y r-base-core cmake
+      - run:
+          command: |
+              sudo apt-get install -y libxml2-dev
+      - run:
+          command: |
+              sudo Rscript -e "install.packages('RANN', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('stringr', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('lme4', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('reshape2', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('polycor', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('splines', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('gamlss', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('gamlss.dist', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('mice', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('childsds', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('xml2', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('covr', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('devtools', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSI', dependencies=TRUE)"
+              sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)"
+      - run:
+          command: |
+              sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'")'
+workflows:
+  build:
+    jobs:
+      - dsbase

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: dsBase
-Title: DataSHIELD server site base functions
-Description: DataSHIELD server site base functions.
-Version: 6.3.0
+Title: DataSHIELD Server Site Base Functions
+Description: DataSHIELD Server Site Base Functions.
+Version: 6.3.1
 Author: DataSHIELD Developers <[email protected]>
 Maintainer: DataSHIELD Developers <[email protected]>
 License: GPL-3
 Depends: 
-    R (>= 3.5.0)
+    R (>= 4.0.0)
 Imports:
     RANN,
     stringr,
@@ -19,6 +19,8 @@ Imports:
     gamlss.dist,
     mice,
     childsds
+Suggests:
+    testthat
 AggregateMethods:
     asFactorDS1,
     asListDS,
@@ -194,5 +196,5 @@ Options:
     default.nfilter.noise=0.25,
     default.nfilter.levels.density=0.33,
     default.nfilter.levels.max=40
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8

R/asListDS.R

@@ -2,21 +2,21 @@
 #' @description Coerces an R object into a list
 #' @details Unlike most other class coercing functions this is
 #' an aggregate function rather than an assign function. This
-#' is because the {datashield.assign} function in the data repository deals specially with
+#' is because the \code{datashield.assign} function in the data repository deals specially with
 #' a created object (newobj) if it is of class list. Reconfiguring the
 #' function as an aggregate function works around this problem.
-#' This aggregate function is based on the native R function {as.list}
-#' and so additional information can be found in the help for {as.list}
+#' This aggregate function is based on the native R function \code{as.list}
+#' and so additional information can be found in the help for \code{as.list}
 #' @param x.name the name of the input object to be coerced to class
 #' data.matrix. Must be specified in inverted commas. But this argument is
 #' usually specified directly by <x.name> argument of the clientside function
-#' {ds.asList}
+#' \code{ds.asList}
 #' @param newobj is the object hard assigned '<<-' to be the output of the
 #' function written to the serverside
 #' @return the object specified by the <newobj> argument (or its default name
 #' <x.name>.mat) which is written to the serverside.
 #' In addition, two validity messages are returned. The first confirms an output
-#' object has been created, the second states its class. The way that {as.list}
+#' object has been created, the second states its class. The way that \code{as.list}
 #' coerces objects to list depends on the class of the object, but in general
 #' the class of the output object should usually be 'list'
 #' @author Amadou Gaye, Paul Burton for DataSHIELD Development Team

R/asLogicalDS.R

@@ -1,13 +1,13 @@
 #' @title Coerces an R object into class numeric
-#' @description this function is based on the native R function {as.numeric}
-#' @details See help for function {as.logical} in native R
+#' @description this function is based on the native R function \code{as.numeric}
+#' @details See help for function \code{as.logical} in native R
 #' @param x.name the name of the input object to be coerced to class
 #' numeric. Must be specified in inverted commas. But this argument is
 #' usually specified directly by <x.name> argument of the clientside function
-#' {ds.aslogical}
+#' \code{ds.aslogical}
 #' @return the object specified by the <newobj> argument (or its default name
 #' <x.name>.logic) which is written to the serverside. For further
-#' details see help on the clientside function {ds.asLogical}
+#' details see help on the clientside function \code{ds.asLogical}
 #' @author Amadou Gaye, Paul Burton for DataSHIELD Development Team
 #' @export
 asLogicalDS <- function (x.name){

R/asMatrixDS.R

@@ -1,13 +1,13 @@
 #' @title Coerces an R object into a matrix
-#' @description this function is based on the native R function {as.matrix}
-#' @details See help for function {as.matrix} in native R
+#' @description this function is based on the native R function \code{as.matrix}
+#' @details See help for function \code{as.matrix} in native R
 #' @param x.name the name of the input object to be coerced to class
 #' matrix. Must be specified in inverted commas. But this argument is
 #' usually specified directly by <x.name> argument of the clientside function
-#' {ds.asMatrix}
+#' \code{ds.asMatrix}
 #' @return the object specified by the <newobj> argument (or its default name
 #' <x.name>.mat) which is written to the serverside. For further
-#' details see help on the clientside function {ds.asMatrix}
+#' details see help on the clientside function \code{ds.asMatrix}
 #' @author Amadou Gaye, Paul Burton for DataSHIELD Development Team
 #' @export
 asMatrixDS <- function (x.name){

R/cDS.R

@@ -28,7 +28,7 @@ cDS <- function (objs) {
 
   # check if the output is valid and output accordingly
   if(length(x) < nfilter.tab){
-    if(length(x == 0)){
+    if(length(x) == 0){
       x <- c()
     }else{
       x <- rep(NA, length(x))

R/completeCasesDS.R

@@ -1,19 +1,19 @@
 #' @title completeCasesDS: an assign function called by ds.completeCases
 #' @description Identifies and strips out all rows of a data.frame,
 #' matrix or vector that contain NAs.
-#' @details In the case of a data.frame or matrix, {completeCasesDS} identifies
+#' @details In the case of a data.frame or matrix, \code{completeCasesDS} identifies
 #' all rows containing one or more NAs and deletes those
 #' rows altogether. Any one variable with NA in a given row will lead
-#' to deletion of the whole row. In the case of a vector, {completeCasesDS}
+#' to deletion of the whole row. In the case of a vector, \code{completeCasesDS}
 #' acts in an equivalent manner but there is no equivalent to a 'row'
 #' and so it simply strips out all observations recorded as NA.
-#' {ds.completeCASES} is analogous to the {complete.cases} function
+#' \code{ds.completeCASES} is analogous to the \code{complete.cases} function
 #' in native R. Limited additional information can therefore be found
 #' under help("complete.cases") in native R.
 #' @param x1.transmit This argument determines the input data.frame,
 #' matrix or vector from which rows with NAs are to be stripped. 
 #' The <x1.transmit> argument is fully specified by the <x1> argument
-#' of the {ds.completeCases} function.
+#' of the \code{ds.completeCases} function.
 #' @return a modified data.frame, matrix or vector from which
 #' all rows containing at least one NA have been deleted. This
 #' modified object is written to the serverside in each source.
@@ -24,7 +24,7 @@
 #' ds.completeCases also returns any studysideMessages that can help
 #' explain the error in creating
 #' the full output object. As well as appearing on the screen at run time,if you wish to
-#' see the relevant studysideMessages at a later date you can use the {ds.message}
+#' see the relevant studysideMessages at a later date you can use the \code{ds.message}
 #' function. If you type ds.message("newobj") it will print out the relevant
 #' studysideMessage from any datasource in which there was an error in creating <newobj>
 #' and a studysideMessage was saved. If there was no error and <newobj> was created

R/dataFrameSubsetDS2.R

@@ -47,7 +47,7 @@
 #' dataFrameSubsetDS2 (via ds.dataFrame()) also returns any studysideMessages
 #' that can explain the error in creating
 #' the full output object. As well as appearing on the screen at run time,if you wish to
-#' see the relevant studysideMessages at a later date you can use the {ds.message}
+#' see the relevant studysideMessages at a later date you can use the \code{ds.message}
 #' function. If you type ds.message("newobj") it will print out the relevant
 #' studysideMessage from any datasource in which there was an error in creating <newobj>
 #' and a studysideMessage was saved. If there was no error and <newobj> was created

R/lexisDS2.R

@@ -129,7 +129,7 @@ lexisDS2 <- function(datatext=NULL, intervalWidth, maxmaxtime, idCol, entryCol,
 
 
   #intervalWidth IS A SINGLE VALUE
-  if(is.null(intervalWidth)||is.na(intervalWidth)||intervalWidth==0){
+  if(any(is.null(intervalWidth))||any(is.na(intervalWidth))||any(intervalWidth==0)){
     return("A VALID NON-ZERO intervalWidth ARGUMENT MUST BE SPECIFIED") 
   }
 

R/lsDS.R

@@ -2,23 +2,23 @@
 #' @title lists all objects on a serverside environment
 #' @description creates a list of the names of all of the objects in
 #' a specified serverside environment
-#' @details Serverside aggregate function {lsDS} called by clientside function
-#' {ds.ls}. When running analyses one may want to know the objects already generated. This 
+#' @details Serverside aggregate function \code{lsDS} called by clientside function
+#' \code{ds.ls}. When running analyses one may want to know the objects already generated. This 
 #' request is not disclosive as it only returns the names of the objects and not their contents. 
 #' By default, objects in the current 'active analytic environment' (".GlobalEnv")
 #' will be displayed. This
 #' is the environment that contains all of the objects that serverside DataSHIELD 
 #' is using for the main analysis or has written out to the serverside during the process
 #' of managing or undertaking the analysis (variables, scalars, matrices, data.frames etc).
-#' For further details see help for {ds.ls} function and for native R function {ls}
+#' For further details see help for \code{ds.ls} function and for native R function \code{ls}
 #' @param search.filter either NULL or a character string (potentially including '*'
 #' wildcards) specifying required search criteria. This argument is
 #' fully specified by its corresponding argument in the clientside function.
 #' @param env.to.search integer (e.g. in a format such as '2' or '5L' format) specifying
 #' the position in the search path of the environment to be explored. This argument is
 #' fully specified by its corresponding argument in the clientside function.
 #' @return a list containing: (1) the name/details of the serverside R environment
-#' which {ds.ls} has searched; (2) a vector of character strings giving the names of
+#' which \code{ds.ls} has searched; (2) a vector of character strings giving the names of
 #' all objects meeting the naming criteria specified by the argument <search.filter> in this
 #' specified R serverside environment; (3) the nature of the search filter string as it was
 #' actually applied

R/matrixDS.R

@@ -1,6 +1,6 @@
 #' @title matrixDS assign function called by ds.matrix
 #' @description Creates a matrix A on the serverside
-#' @details Similar to the {matrix()} function in native R. Creates a matrix
+#' @details Similar to the \code{matrix()} function in native R. Creates a matrix
 #' with dimensions specified by <nrows.scalar> and <ncols.scalar> arguments
 #' and assigns the values of all its elements based on the <mdata> argument
 #' @param mdata.transmit specifies the elements of the matrix to be created. Fully

R/matrixDetDS1.R

@@ -2,7 +2,7 @@
 #' @description Calculates the determinant of a square matrix A and returns
 #' the output to the clientside
 #' @details Calculates the determinant of a square matrix (for additional
-#' information see help for {det} function in native R). This operation is only
+#' information see help for \code{det} function in native R). This operation is only
 #' possible if the number of columns and rows of A are the same.
 #' @param M1.name  A character string specifying the name of the matrix for which
 #' determinant to be calculated

R/matrixDetDS2.R

@@ -2,7 +2,7 @@
 #' @description Calculates the determinant of a square matrix A and writes
 #' the output to the serverside
 #' @details Calculates the determinant of a square matrix (for additional
-#' information see help for {det} function in native R). This operation is only
+#' information see help for \code{det} function in native R). This operation is only
 #' possible if the number of columns and rows of A are the same.
 #' @param M1.name  A character string specifying the name of the matrix for which
 #' determinant to be calculated

R/matrixDiagDS.R

@@ -2,20 +2,20 @@
 #' @description Extracts the diagonal vector from a square matrix A or
 #' creates a diagonal matrix A based on a vector or a scalar value and
 #' writes the output to the serverside
-#' @details For details see help for function {ds.matrixDiag}.
+#' @details For details see help for function \code{ds.matrixDiag}.
 #' @param x1.transmit identifies the input matrix or vector. Fully
-#' specified by <x1> argument of {ds.matrixDiag}. For more details
-#' see help for {ds.matrixDiag}.
+#' specified by <x1> argument of \code{ds.matrixDiag}. For more details
+#' see help for \code{ds.matrixDiag}.
 #' @param aim a character string specifying what behaviour is required
-#' of the function. Fully specified by <aim> argument of {ds.matrixDiag}.
-#' For more details see help for {ds.matrixDiag}.
+#' of the function. Fully specified by <aim> argument of \code{ds.matrixDiag}.
+#' For more details see help for \code{ds.matrixDiag}.
 #' @param nrows.transmit a scalar value forcing the number of rows and
 #' columns in an output matrix.Fully specified by <nrows.scalar>
-#' argument of {ds.matrixDiag}.
-#' For more details see help for {ds.matrixDiag}.
+#' argument of \code{ds.matrixDiag}.
+#' For more details see help for \code{ds.matrixDiag}.
 #' @return Output is the matrix or vector specified by the <newobj> argument
 #' (or default name diag_<x1>) which is written to the serverside.
-#' For more details see help for {ds.matrixDiag}.
+#' For more details see help for \code{ds.matrixDiag}.
 #' @author Paul Burton for DataSHIELD Development Team
 #' @export
 matrixDiagDS <- function(x1.transmit,aim,nrows.transmit){

R/matrixDimnamesDS.R

@@ -2,18 +2,18 @@
 #' @description Adds dimnames (row names, column names or both) to
 #' a matrix on the serverside.
 #' @details Adds dimnames (row names, column names or both) to
-#' a matrix on the serverside. Similar to the {dimnames} function
+#' a matrix on the serverside. Similar to the \code{dimnames} function
 #' in native R. For more details see help for
-#' function {ds.matrixDimnames}
+#' function \code{ds.matrixDimnames}
 #' @param M1.name Specifies the name of the serverside matrix to which
 #' dimnames are to be added. Fully specified by <M1> argument of
-#' function {ds.matrixDimnames}. For more details
-#' see help for {ds.matrixDimnames}.
+#' function \code{ds.matrixDimnames}. For more details
+#' see help for \code{ds.matrixDimnames}.
 #' @param dimnames A dimnames attribute for the matrix: NULL or a list of
 #' length 2 giving the row and column names respectively.
 #' Fully specified by <dimnames> argument of
-#' function {ds.matrixDimnames}. For more details
-#' see help for {ds.matrixDimnames}.
+#' function \code{ds.matrixDimnames}. For more details
+#' see help for \code{ds.matrixDimnames}.
 #' @return Output is the serverside matrix specified by the <newobj> argument
 #' (or default name diag_<x1>) with specified dimnames (row and column
 #' names) which is written to the serverside.