updates

oqbase.Dockerfile

@@ -0,0 +1,8 @@
+FROM imbir:packages
+
+
+COPY scripts /rocker_scripts
+
+RUN /rocker_scripts/OQ_R.sh
+
+CMD ["/init"]

packages.Dockerfile

@@ -0,0 +1,8 @@
+FROM imbir:Rstudio
+
+
+COPY scripts /rocker_scripts
+
+RUN /rocker_scripts/install_packages.sh
+
+CMD ["/init"]

scripts/OQ_R.sh

@@ -8,7 +8,7 @@ LC_COLLATE="C"
 LC_TIME="C"
 
 cd /R-${R_VERSION}
-make check-all 2>&1 | tee /R-${R_VERSION}/logs/OQ.log
+make check-all 2>&1 | tee /R-${R_VERSION}/logs/OQ_base.log
 
 
 

scripts/copy_files_for_validation.sh

@@ -0,0 +1,5 @@
+#!/bin/sh
+set -e
+
+sudo cp -r /R-4.0.2 /home/rstudio/
+sudo cp -r /pkgs /home/rstudio/

scripts/get_installed_packages.R

@@ -0,0 +1,6 @@
+# sink("/pkgs/installed_packages")
+
+sink(paste0("/R-", paste(R.Version()$major, R.Version()$minor, sep  = "."), "/logs/installed_packages.log"))
+options(width=9999, max.print = 99999)
+installed.packages()
+sink()

scripts/install_packages.R

@@ -0,0 +1,8 @@
+install.packages(c("mice", "Exact", "MatchIt", "lmerTest", "survminer",
+                   "netmeta", "meta", "pwr", "binom", "mvtnorm", "Matching", "pROC", "ROCR", "Hmisc",
+                   "adoptr", "rpact", "rjags", "kable", "dfoptim", "optimx"),
+                 destdir = "/pkgs/", repos = "https://cran.r-project.org/", type = "source")
+
+
+devtools::install("/pkgs/DescrTab", dependencies=TRUE, repos="cran.r-project.org")
+devtools::install("/pkgs/imbiReport", dependencies=TRUE, repos="cran.r-project.org")

scripts/install_packages.sh

@@ -1,5 +1,16 @@
 #!/bin/bash
 set -e
 
+apt-get update && apt-get install jags
 
-Rscript -e "install.packages('lme4', type='source', destdir='.')"
+mkdir /pkgs
+cd /pkgs/
+
+git clone "https://[email protected]/imbi-heidelberg/imbiReport"
+git clone "https://[email protected]/imbi-heidelberg/DescrTab"
+
+Rscript /rocker_scripts/install_packages.R 2>&1 | tee /R-${R_VERSION}/logs/additional_packages_install.log
+
+
+for f in *.tar.gz; do tar xf "$f"; done
+Rscript /rocker_scripts/get_installed_packages.R

scripts/validation.sh

@@ -0,0 +1 @@
+Rscript rocker_scripts/installed_packages.R

validate.Dockerfile

@@ -0,0 +1,9 @@
+FROM imbir:oqbase
+
+
+COPY scripts /rocker_scripts
+
+RUN Rscript -e 'devtools::install_github("https://github.com/pharmaR/riskmetric")'
+
+
+CMD ["/init"]