Rendering and running the long timeframe synthetic data

.gitignore

@@ -14,4 +14,5 @@
 
 temp*.R
 
+precompute_*.bz2
 

Dockerfile

@@ -1,4 +1,7 @@
-FROM rocker/tidyverse:4.3.0
+FROM rocker/tidyverse:4.3.1
+
+COPY build/Rprofile.site /usr/local/lib/R/etc/
+COPY build/Renviron.site /usr/local/lib/R/etc/
 
 ENV TZ=Europe/Dublin
 
@@ -17,23 +20,38 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
     libglpk-dev \
     libgsl-dev \
     libnlopt-dev \
+    libomp-dev \
     p7zip-full \
     pbzip2 \
     rsyslog \
   && apt-get clean \
   && rm -rf /var/lib/apt/lists/* \
   && mkdir -p $HOME/.R \
   && echo "" > $HOME/.R/Makevars \
+  && echo "CC=clang"                                               >> $HOME/.R/Makevars \
   && echo "CXX=clang++"                                            >> $HOME/.R/Makevars \
   && echo "CXXFLAGS=-Os"                                           >> $HOME/.R/Makevars \
   && echo "CXXFLAGS+= -Wno-unused-variable -Wno-unused-function"   >> $HOME/.R/Makevars \
   && echo "CXXFLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined"   >> $HOME/.R/Makevars \
   && echo ""                                                       >> $HOME/.R/Makevars \
+  && echo "CC11=clang"                                             >> $HOME/.R/Makevars \
+  && echo "CXX11=clang++"                                          >> $HOME/.R/Makevars \
+  && echo "CXX11FLAGS=-Os"                                         >> $HOME/.R/Makevars \
+  && echo "CXX11FLAGS+= -Wno-unused-variable -Wno-unused-function" >> $HOME/.R/Makevars \
+  && echo "CXX11FLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined" >> $HOME/.R/Makevars \
+  && echo ""                                                       >> $HOME/.R/Makevars \
+  && echo "CC14=clang"                                             >> $HOME/.R/Makevars \
   && echo "CXX14=clang++"                                          >> $HOME/.R/Makevars \
   && echo "CXX14FLAGS=-Os"                                         >> $HOME/.R/Makevars \
   && echo "CXX14FLAGS+= -Wno-unused-variable -Wno-unused-function" >> $HOME/.R/Makevars \
   && echo "CXX14FLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined" >> $HOME/.R/Makevars \
   && echo ""                                                       >> $HOME/.R/Makevars \
+  && echo "CC17=clang++"                                           >> $HOME/.R/Makevars \
+  && echo "CXX17=clang++"                                          >> $HOME/.R/Makevars \
+  && echo "CXX17FLAGS=-Os"                                         >> $HOME/.R/Makevars \
+  && echo "CXX17FLAGS+= -Wno-unused-variable -Wno-unused-function" >> $HOME/.R/Makevars \
+  && echo "CXX17FLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined" >> $HOME/.R/Makevars \
+  && echo ""                                                       >> $HOME/.R/Makevars \
   && install2.r --error \
     anytime \
     bayesplot \

Makefile

@@ -9,6 +9,7 @@ DOCKER_USER=rstudio
 DOCKER_PASS=CHANGEME
 DOCKER_UID=$(shell id -u)
 DOCKER_GID=$(shell id -g)
+DOCKER_BUILD_ARGS=
 
 RSTUDIO_PORT=8787
 
@@ -90,8 +91,9 @@ clean-models:
 ### Docker targets
 docker-build-image: Dockerfile
 	docker build -t ${IMAGE_TAG} \
+	  ${DOCKER_BUILD_ARGS} \
 	  --build-arg BUILD_DATE=$(shell date -u +'%Y-%m-%dT%H:%M:%SZ') \
-	  -f Dockerfile .
+	  -f Dockerfile . 2>&1 | tee -a docker_build.log
 
 docker-show-context:
 	docker build -f build/context.dockerfile -t context-image .

build/Renviron.site

@@ -0,0 +1,15 @@
+R_LIBS=${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library'}
+CRAN=https://packagemanager.posit.co/cran/2023-10-06
+CWD=/home/rstudio
+DEFAULT_USER=rstudio
+GROUPID=1000
+HOSTNAME=2a08c571a82c
+LANG=en_US.UTF-8
+PANDOC_VERSION=default
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+QUARTO_VERSION=default
+R_HOME=/usr/local/lib/R
+R_VERSION=4.3.1
+S6_VERSION=v2.1.0.2
+USER=rstudio
+USERID=1000

build/Rprofile.site

@@ -0,0 +1,3 @@
+options(repos = c(CRAN = 'https://packagemanager.posit.co/cran/2023-10-06'), download.file.method = 'libcurl')
+# https://docs.rstudio.com/rspm/admin/serving-binaries/#binaries-r-configuration-linux
+options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])))

build/docker_install_user_rpkgs.R

@@ -1,6 +1,6 @@
 remotes::install_github(
   "stan-dev/cmdstanr",
-  ref     = "v0.5.3",
+  ref     = "v0.6.1",
   upgrade = "never"
 )
 
@@ -15,16 +15,24 @@ remotes::install_github(
 library(cmdstanr)
 
 cmdstan_flags <- list(
+  "CC"         = "clang",
   "CXX"        = "clang++",
   "CXXFLAGS"   = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined",
+  "CC11"       = "clang",
+  "CXX11"      = "clang++",
+  "CXX11FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined",
+  "CC14"       = "clang",
   "CXX14"      = "clang++",
-  "CXX14FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined"
+  "CXX14FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined",
+  "CC17"       = "clang",
+  "CXX17"      = "clang++",
+  "CXX17FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined"
 )
 
 install_cmdstan(
   cores       = parallel::detectCores(),
   cpp_options = cmdstan_flags,
   quiet       = FALSE,
   overwrite   = FALSE,
-  version     = "2.32.2"
+  version     = "2.33.0"
 )