Merge pull request #165 from ccb-hms/feature/rocker-base

Feature/rocker base

.github/workflows/container.yml

@@ -41,7 +41,7 @@ jobs:
         sudo swapoff -a
         sudo rm -f /swapfile
         sudo apt clean
-        yes | docker system prune
+        docker system prune -af
         df -h
         sudo rm -rf /usr/share/dotnet
         df . -h

Code/R/excluded_tables.tsv

@@ -2,4 +2,5 @@ TableName	Reason
 All Years	Large File
 PAHS	Large File
 PAX80	FTP Only
+PAXMIN	Broken
 DDX_2_B	Broken

Container/Dockerfile

@@ -355,15 +355,15 @@ RUN chmod -R 777 /usr/local/lib/R/doc/html/packages.html
 
 # Declare which version of the container this is, and make it available inside the container 
 ENV EPICONDUCTOR_CONTAINER_VERSION v0.4.1
-ENV EPICONDUCTOR_COLLECTION_DATE 2024-02-09
+ENV EPICONDUCTOR_COLLECTION_DATE 2024-02-12
 
 RUN echo "EPICONDUCTOR_CONTAINER_VERSION=$EPICONDUCTOR_CONTAINER_VERSION" >> /usr/local/lib/R/etc/Renviron.site
 RUN echo "EPICONDUCTOR_COLLECTION_DATE=$EPICONDUCTOR_COLLECTION_DATE" >> /usr/local/lib/R/etc/Renviron.site
 
 RUN echo "EPICONDUCTOR_CONTAINER_VERSION=$EPICONDUCTOR_CONTAINER_VERSION" >> /etc/environment
 RUN echo "EPICONDUCTOR_COLLECTION_DATE=$EPICONDUCTOR_COLLECTION_DATE" >> /etc/environment
 
-# RUN runuser -m -p  mssql -c '/opt/mssql/bin/sqlservr &' \
-# 	&& Rscript /NHANES/containerBuildTests.R
+RUN runuser -m -p  mssql -c '/opt/mssql/bin/sqlservr &' \
+	&& Rscript /NHANES/containerBuildTests.R
 
 CMD ["/startup/startup.sh"]

Testing/Code/containerBuildTests.R

@@ -343,7 +343,7 @@ SqlTools::dbSendUpdate(cn, "DBCC SHRINKFILE(NhanesLandingZone_log)")
 SqlTools::dbSendUpdate(cn, "CHECKPOINT")
 
 #Check phonto and nhanesA installs
-if (packageVersion("phonto")!="0.1.0"){stop(paste("Phonto installation failure or version 0.1.0 not matched."), sep='')}
+if (packageVersion("phonto")!="0.1.1"){stop(paste("Phonto installation failure or version 0.1.1 not matched."), sep='')}
 if (packageVersion("nhanesA")!="1.0"){stop(paste("nhanesA installation failure or version 1.0 not matched."), sep='')}
 
 # shutdown the database engine cleanly