Updates applied to 'v6.3.6-dev'

.Rbuildignore

@@ -17,8 +17,8 @@
 ^R/secure.global.ranking.md$
 ^_pkgdown\.yml$
 ^docs$
-^dsBase_6.3.5.tar.gz$
-^dsBase_6.3.5-permissive.tar.gz$
+^dsBase_6.3.6.tar.gz$
+^dsBase_6.3.6-permissive.tar.gz$
 ^dsDanger_6.3.4.tar.gz$
 ^\.circleci$
 ^\.circleci/config\.yml$

.github/workflows/dsBaseClient_test_suite.yaml

@@ -138,7 +138,7 @@ jobs:
       - name: Install dsBase to Armadillo
         run: |
           curl -u admin:admin -X GET http://localhost:8080/packages
-          curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.5-permissive.tar.gz" -X POST http://localhost:8080/install-package
+          curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.6-permissive.tar.gz" -X POST http://localhost:8080/install-package
           sleep 60
           docker restart dsbaseclient-armadillo-1
           sleep 30

R/ds.glm.R

@@ -565,7 +565,8 @@ ds.glm <- function(formula=NULL, data=NULL, family=NULL, offset=NULL, weights=NU
       # Sum participants only during first iteration.
       nsubs.total<-Reduce(f="+", .select(study.summary, 'numsubs'))
       # Save family
-      f <- study.summary[[1]]$family
+      family.value <- study.summary[[1]]$family
+      f <- if (is.list(family.value) && "family" %in% names(family.value)) family.value$family else family.value
     }
 
     #Create variance covariance matrix as inverse of information matrix
@@ -640,7 +641,7 @@ ds.glm <- function(formula=NULL, data=NULL, family=NULL, offset=NULL, weights=NU
     beta.vect.final<-beta.vect.next
 
     scale.par <- 1
-    if(f$family== 'gaussian') {
+    if(f == 'gaussian') {
       scale.par <- dev.total / (nsubs.total-length(beta.vect.next))
     }
 

armadillo_azure-pipelines.yml

@@ -59,10 +59,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.5-dev
+    displayName: Nightly build - v6.3.6-dev
     branches:
       include:
-      - v6.3.5-dev
+      - v6.3.6-dev
     always: true
 
 #########################################################################################
@@ -133,7 +133,7 @@ jobs:
       sudo apt-get upgrade -y
 
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
-      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
+      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
       sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
@@ -236,7 +236,7 @@ jobs:
 
       curl -u admin:admin -X GET http://localhost:8080/packages
 
-      curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.5-permissive.tar.gz" -X POST http://localhost:8080/install-package
+      curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.6-permissive.tar.gz" -X POST http://localhost:8080/install-package
       sleep 60
 
       docker container restart dsbaseclient_armadillo_1

azure-pipelines.yml

@@ -45,10 +45,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.5-dev
+    displayName: Nightly build - v6.3.6-dev
     branches:
       include:
-      - v6.3.5-dev
+      - v6.3.6-dev
     always: true
 
 #########################################################################################
@@ -114,7 +114,7 @@ jobs:
       sudo apt-get upgrade -y
 
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
-      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
+      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
       sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
@@ -217,7 +217,7 @@ jobs:
   - bash: |
       R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
 
-      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)"
+      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.6-dev'); opal.logout(opal)"
 
       sleep 60
 

opal_azure-pipelines.yml

@@ -45,10 +45,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.5-dev
+    displayName: Nightly build - v6.3.6-dev
     branches:
       include:
-      - v6.3.5-dev
+      - v6.3.6-dev
     always: true
 
 #########################################################################################
@@ -114,7 +114,7 @@ jobs:
       sudo apt-get upgrade -y
 
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
-      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
+      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
       sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
@@ -217,7 +217,7 @@ jobs:
   - bash: |
       R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
 
-      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)"
+      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.6-dev'); opal.logout(opal)"
 
       sleep 60
 

tests/docker/armadillo/standard/config/application.yml

@@ -67,8 +67,13 @@ stdout.log.path: '/logs/armadillo.log'
 
 logging:
   level:
-    root: INFO
+    root: "warn"
     ## change to DEBUG to have more details, typically when developing
-    org.molgenis: INFO
+    org.molgenis: "warn"
     ## Don't log upload data
-    org.apache.coyote.http11.Http11InputBuffer: INFO
+    org.apache.coyote.http11.Http11InputBuffer: "warn"
+    ## SpringFramework
+    org.springframework.boot: "warn"
+    org.springframework.web: "warn"
+    org.springframework.core: "warn"
+    org.springframework.codex: "warn"

tests/testthat/perf_files/armadillo_hp-laptop-quay_perf-profile.csv

@@ -1,14 +1,14 @@
 "refer_name","rate","lower_tolerance","upper_tolerance"
-"conndisconn::perf::simple0","0.04918","0.5","2"
-"ds.abs::perf::0","1.184","0.5","2"
-"ds.asInteger::perf:0","1.297","0.5","2"
-"ds.asList::perf:0","2.884","0.5","2"
-"ds.asNumeric::perf:0","1.354","0.5","2"
-"ds.assign::perf::0","2.745","0.5","2"
-"ds.class::perf::combine:0","3.261","0.5","2"
-"ds.colnames::perf:0","8.566","0.5","2"
-"ds.exists::perf::combine:0","6.342","0.5","2"
-"ds.length::perf::combine:0","7.835","0.5","2"
-"ds.mean::perf::combine:0","8.127","0.5","2"
-"ds.mean::perf::split:0","8.109","0.5","2"
-"void::perf::void::0","20280.0","0.5","2"
+"conndisconn::perf::simple0","0.06790","0.5","2"
+"ds.abs::perf::0","1.998","0.5","2"
+"ds.asInteger::perf:0","2.111","0.5","2"
+"ds.asList::perf:0","4.550","0.5","2"
+"ds.asNumeric::perf:0","1.879","0.5","2"
+"ds.assign::perf::0","4.806","0.5","2"
+"ds.class::perf::combine:0","3.865","0.5","2"
+"ds.colnames::perf:0","9.577","0.5","2"
+"ds.exists::perf::combine:0","8.411","0.5","2"
+"ds.length::perf::combine:0","7.957","0.5","2"
+"ds.mean::perf::combine:0","9.049","0.5","2"
+"ds.mean::perf::split:0","9.429","0.5","2"
+"void::perf::void::0","21400.0","0.5","2"

tests/testthat/test-smk-ds.elspline.R

@@ -56,7 +56,7 @@ test_that("elspline", {
     expect_equal(res.mod$errorMessage[3], "No errors")
     expect_equal(res.mod$nsubs, 7477)
     expect_equal(res.mod$iter, 3)
-    expect_true("family" %in% class(res.mod$family))
+    expect_true("character" %in% class(res.mod$family))
     expect_equal(res.mod$formula, "D$LAB_TRIG ~ elsplineDS")
     expect_true("matrix" %in% class(res.mod$coefficients))
     expect_true("array" %in% class(res.mod$coefficients))
@@ -106,7 +106,7 @@ test_that("elspline", {
     expect_equal(res.mod$errorMessage[3], "No errors")
     expect_equal(res.mod$nsubs, 7477)
     expect_equal(res.mod$iter, 3)
-    expect_true("family" %in% class(res.mod$family))
+    expect_true("character" %in% class(res.mod$family))
     expect_equal(res.mod$formula, "D$LAB_TRIG ~ elsplineDS2")
     expect_true("matrix" %in% class(res.mod$coefficients))
     expect_true("array" %in% class(res.mod$coefficients))

tests/testthat/test-smk-ds.glm-binomial.R

@@ -43,7 +43,7 @@ test_that("glm_binomial", {
     expect_equal(res$errorMessage[3], "No errors")
     expect_equal(res$nsubs, 7485)
     expect_equal(res$iter, 9)
-    expect_true("family" %in% class(res$family))
+    expect_true("character" %in% class(res$family))
     expect_equal(res$formula, "D$DIS_DIAB ~ D$GENDER * D$PM_BMI_CONTINUOUS + D$LAB_HDL")
     expect_true("matrix" %in% class(res$coefficients))
     expect_equal(res$dev, 1036.031, tolerance=0.00001)
@@ -69,7 +69,7 @@ test_that("glm_binomial, with check", {
     expect_equal(res$errorMessage[3], "No errors")
     expect_equal(res$nsubs, 7485)
     expect_equal(res$iter, 9)
-    expect_true("family" %in% class(res$family))
+    expect_true("character" %in% class(res$family))
     expect_equal(res$formula, "D$DIS_DIAB ~ D$GENDER * D$PM_BMI_CONTINUOUS + D$LAB_HDL")
     expect_true("matrix" %in% class(res$coefficients))
     expect_equal(res$dev, 1036.031, tolerance=0.00001)

tests/testthat/test-smk-ds.glm-gaussian.R

@@ -43,7 +43,7 @@ test_that("glm_gaussian", {
     expect_equal(res$errorMessage[3], "No errors")
     expect_equal(res$nsubs, 7800)
     expect_equal(res$iter, 3)
-    expect_true("family" %in% class(res$family))
+    expect_true("character" %in% class(res$family))
     expect_equal(res$formula, "D$LAB_TSC ~ D$LAB_TRIG")
     expect_true("matrix" %in% class(res$coefficients))
     expect_equal(res$dev, 8936.32, tolerance=0.00001)
@@ -69,7 +69,7 @@ test_that("glm_gaussian, with check", {
     expect_equal(res$errorMessage[3], "No errors")
     expect_equal(res$nsubs, 7800)
     expect_equal(res$iter, 3)
-    expect_true("family" %in% class(res$family))
+    expect_true("character" %in% class(res$family))
     expect_equal(res$formula, "D$LAB_TSC ~ D$LAB_TRIG")
     expect_true("matrix" %in% class(res$coefficients))
     expect_equal(res$dev, 8936.32, tolerance=0.00001)

tests/testthat/test-smk-ds.glm-poisson.R

@@ -43,7 +43,7 @@ test_that("glm_gaussian", {
     expect_equal(res$errorMessage[3], "No errors")
     expect_equal(res$nsubs, 6299)
     expect_equal(res$iter, 5)
-    expect_true("family" %in% class(res$family))
+    expect_true("character" %in% class(res$family))
     expect_equal(res$formula, "D$survtime ~ 1 + D$time.id + D$female")
     expect_true("matrix" %in% class(res$coefficients))
     expect_equal(res$dev, 3522.598, tolerance=0.00001)
@@ -69,7 +69,7 @@ test_that("glm_gaussian, which check", {
     expect_equal(res$errorMessage[3], "No errors")
     expect_equal(res$nsubs, 6299)
     expect_equal(res$iter, 5)
-    expect_true("family" %in% class(res$family))
+    expect_true("character" %in% class(res$family))
     expect_equal(res$formula, "D$survtime ~ 1 + D$time.id + D$female")
     expect_true("matrix" %in% class(res$coefficients))
     expect_equal(res$dev, 3522.598, tolerance=0.00001)

tests/testthat/test-smk-ds.lspline.R

@@ -56,7 +56,7 @@ test_that("lspline", {
     expect_equal(res.mod$errorMessage[3], "No errors")
     expect_equal(res.mod$nsubs, 7477)
     expect_equal(res.mod$iter, 3)
-    expect_true("family" %in% class(res.mod$family))
+    expect_true("character" %in% class(res.mod$family))
     expect_equal(res.mod$formula, "D$LAB_TRIG ~ lsplineDS")
     expect_true("matrix" %in% class(res.mod$coefficients))
     expect_true("array" %in% class(res.mod$coefficients))

tests/testthat/test-smk-ds.ns.R

@@ -60,7 +60,7 @@ test_that("ns", {
     expect_equal(res.mod$errorMessage[3], "No errors")
     expect_equal(res.mod$nsubs, 7477)
     expect_equal(res.mod$iter, 3)
-    expect_true("family" %in% class(res.mod$family))
+    expect_true("character" %in% class(res.mod$family))
     expect_equal(res.mod$formula, "D$LAB_TRIG ~ nsDS")
     expect_true("matrix" %in% class(res.mod$coefficients))
     expect_true("array" %in% class(res.mod$coefficients))

tests/testthat/test-smk-ds.qlspline.R

@@ -56,7 +56,7 @@ test_that("qlspline", {
     expect_equal(res.mod$errorMessage[3], "No errors")
     expect_equal(res.mod$nsubs, 7477)
     expect_equal(res.mod$iter, 3)
-    expect_true("family" %in% class(res.mod$family))
+    expect_true("character" %in% class(res.mod$family))
     expect_equal(res.mod$formula, "D$LAB_TRIG ~ qlsplineDS")
     expect_true("matrix" %in% class(res.mod$coefficients))
     expect_true("array" %in% class(res.mod$coefficients))
@@ -108,7 +108,7 @@ test_that("qlspline", {
     expect_equal(res.mod$errorMessage[3], "No errors")
     expect_equal(res.mod$nsubs, 7477)
     expect_equal(res.mod$iter, 3)
-    expect_true("family" %in% class(res.mod$family))
+    expect_true("character" %in% class(res.mod$family))
     expect_equal(res.mod$formula, "D$LAB_TRIG ~ qlsplineDS2")
     expect_true("matrix" %in% class(res.mod$coefficients))
     expect_true("array" %in% class(res.mod$coefficients))