Update 'zeyzul changes' with current V6.4.0 dev

.circleci/config.yml

@@ -22,7 +22,7 @@ jobs:
               sudo apt-get install -y r-base-core cmake
       - run:
           command: |
-              sudo apt-get install -y libxml2-dev
+              sudo apt-get install -y libxml2-dev libuv1-dev
       - run:
           command: |
               echo "options(Ncpus=4)" >> ~/.Rprofile

DESCRIPTION

@@ -59,12 +59,15 @@ Authors@R: c(person(given = "Paul",
                     comment = c(ORCID = "0009-0003-2419-1964")))
 License: GPL-3
 Depends: 
-    R (>= 4.0.0)
+    R (>= 4.1.0)
 Imports:
     RANN,
     stringr,
     lme4,
     dplyr,
+    tibble,
+    purrr,
+    tidyselect,
     reshape2,
     polycor (>= 0.8),
     splines,
@@ -76,11 +79,11 @@ Imports:
     tibble,
     tidyselect,
     stats,
-    lubridate,
-    tidytable
+    lubridate
 Suggests:
     spelling,
-    testthat
+    testthat (>= 3.0.0),
+    tidytable
 RoxygenNote: 8.0.0
 Encoding: UTF-8
 Language: en-GB

R/glmDS2.R

@@ -382,7 +382,7 @@ glmDS2 <- function (formula, family, beta.vect, offset, weights, dataName) {
     errorMessage.combined <- "No errors"
   }
 
-  return(list(family=f, info.matrix=info.matrix, score.vect=score.vect, numsubs=numsubs, dev=dev,
+  return(list(family=f$family, info.matrix=info.matrix, score.vect=score.vect, numsubs=numsubs, dev=dev,
               Nvalid=Nvalid,Nmissing=Nmissing,Ntotal=Ntotal,disclosure.risk=disclosure.risk,
               errorMessage2=errorMessage.combined))  
 

R/glmSLMADS.assign.R

@@ -21,21 +21,21 @@ glmSLMADS.assign <- function(formula, family, offsetName, weightsName, dataName)
   # Convert transmitable text for special link variance combinations back to full representation
   if(family=="quasigamma.link_log")
   {family<-"quasi(link=log,variance=mu^2)"}
-  
+
   if(family=="Gamma.link_log")
   {family<-"Gamma(link=log)"}
-  
+
   # Correctly name offset, weights and data objects in function call
   # (to allow glmPredict to work correctly later)
   calltext <- paste0("mg<-glm(formula,family=",family,",offset=",
              offsetName,",weights=",weightsName,",data=", dataName,",x=TRUE)")
-  
+
   eval(parse(text=calltext))
-  
+
   # update the call object to include the actual formula
   mg$call$formula <- formula
-  
-  return(mg)		
+
+  return(mg)
 
 }
 # ASSIGN FUNCTION

README.md

@@ -23,8 +23,8 @@ And the development version from
 install.packages("remotes")
 remotes::install_github("datashield/dsBase", "<BRANCH>")
 
-# Install v6.3.4 with the following
-remotes::install_github("datashield/dsBase", "6.3.4")
+# Install v6.4.0 with the following
+remotes::install_github("datashield/dsBase", "6.4.0")
 ```
 
 For a full list of development branches, checkout https://github.com/datashield/dsBase/branches

azure-pipelines.yml

@@ -106,7 +106,7 @@ jobs:
 
       sudo apt-get install -qq pkg-config -y
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgit2-dev libharfbuzz-dev libfribidi-dev libfontconfig1-dev -y
-      sudo apt-get install -qq libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y
+      sudo apt-get install -qq libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libuv1-dev -y
       sudo apt-get install -qq r-base -y
       sudo R -e "install.packages('devtools', dependencies=TRUE)"
       sudo R -e "install.packages('RANN', dependencies=TRUE)"
@@ -257,7 +257,6 @@ jobs:
       echo 'branch:'$(branchName) >> $(datetime).txt
       echo 'os:'$(lsb_release -ds) >> $(datetime).txt
       echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
-      echo 'opal:'$(opal system --opal localhost:8080 --user administrator --password "datashield_test&" --version) >> $(datetime).txt
 
     workingDirectory: $(Pipeline.Workspace)/logs
     displayName: 'Write versions to file'