Merge pull request #49 from StuartWheater/v6.3.1-RC4-dev

Updates from V6.3.1 RC4

Author: StuartWheater

.Rbuildignore

@@ -19,4 +19,4 @@
 ^docs$
 ^dsBase_6.3.1.tar.gz$
 ^dsBase_6.3.1-permissive.tar.gz$
-^dsDanger_6.3.0.tar.gz$
+^dsDanger_6.3.1.tar.gz$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsBaseClient
 Title: DataSHIELD Client Functions
-Version: 6.3.1.9000
+Version: 6.3.1
 Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
 Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
 Description: DataSHIELD client functions for the client side.
@@ -20,5 +20,5 @@ Imports:
     dplyr
 Suggests:
     testthat
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8

armadillo_azure-pipelines.yml

@@ -126,10 +126,11 @@ jobs:
     # If previous steps have failed then don't run.
   - bash: |
 
-      sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-      sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
-      sudo add-apt-repository ppa:cran/libgit2
-      sudo apt-get update
+      sudo apt-get update -qq
+      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 "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+      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 -y
@@ -139,7 +140,7 @@ jobs:
       sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 
-      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='v6.3.0-dev', dependencies = TRUE)"
+      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 
       # XML grep for coverage report merging
       sudo apt-get install -qq xml-twig-tools -y
@@ -273,7 +274,7 @@ jobs:
       # junit reporter output is to test_results.xml
       #
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
-      # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
+      # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
       sudo R -q -e '
         library(covr);
         dsbase.res <- covr::package_coverage(
@@ -289,7 +290,7 @@ jobs:
                 progress_rep <- ProgressReporter$new(max_failures = 999999);
                 multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
                 options("default_driver" = "ArmadilloDriver");
-                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
+                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
                 '"'"'
             )
         );

azure-pipelines.yml

@@ -126,9 +126,14 @@ jobs:
     # If previous steps have failed then don't run.
   - bash: |
 
-      sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
-      sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
-      sudo add-apt-repository ppa:cran/libgit2
+      sudo apt update -qq
+      sudo apt 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 "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+
+#      sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+#      sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
+#      sudo add-apt-repository ppa:cran/libgit2
       sudo apt-get update
 
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
@@ -139,7 +144,7 @@ jobs:
       sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"
 
-      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='v6.3.0-dev', dependencies = TRUE)"
+      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)"
 
       # XML grep for coverage report merging
       sudo apt-get install -qq xml-twig-tools -y
@@ -232,7 +237,7 @@ jobs:
     # Install dsBase.
     # If previous steps have failed then don't run.
   - bash: |
-      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.1-dev'); opal.logout(opal)"
+      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 
       sleep 120
 
@@ -268,7 +273,7 @@ jobs:
       # junit reporter output is to test_results.xml
       #
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
-      # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
+      # testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
       sudo R -q -e '
         library(covr);
         dsbase.res <- covr::package_coverage(
@@ -284,7 +289,7 @@ jobs:
                 progress_rep <- ProgressReporter$new(max_failures = 999999);
                 multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
                 options("default_driver" = "OpalDriver");
-                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
+                testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
                 '"'"'
             )
         );
@@ -357,7 +362,7 @@ jobs:
     # If previous steps have failed then don't run
   - bash: |
 
-      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = 'v6.3.0-dev'); opal.logout(opal)"
+      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)"
 
     workingDirectory: $(Pipeline.Workspace)/dsBaseClient
     displayName: 'Install dsDanger package on Opal server'

docker-compose_armadillo.yml

@@ -3,7 +3,7 @@ services:
         hostname: armadillo
         ports:
             - 8080:8080
-        image: datashield/armadillo_citest:4.8.1
+        image: datashield/armadillo_citest:4.10.0
         environment:
             LOGGING_CONFIG: 'classpath:logback-file.xml'
             AUDIT_LOG_PATH: '/app/logs/audit.log'

docker-compose_opal.yml

@@ -1,6 +1,6 @@
 services:
     opal:
-        image: obiba/opal:4.7.2
+        image: obiba/opal:5.0.0-RC5
         ports:
             - "8443:8443"
         links:
@@ -20,4 +20,4 @@ services:
             - MONGO_INITDB_ROOT_USERNAME=root
             - MONGO_INITDB_ROOT_PASSWORD=foobar
     rock:
-        image: datashield/rock-junction-devel-permissive:latest
+        image: datashield/rock-knot-devel-permissive:latest