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

6.3.1 release

Author: StuartWheater

.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 <datashield@liverpool.ac.uk>
 Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
 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") 
   }