3.5.1 issues? about rcppeigen HOT 7 CLOSED

# Base image
FROM rocker/shiny:latest

RUN echo "deb http://ftp.debian.org/debian stretch-backports main" >> /etc/apt/sources.list.d/backports.list

RUN apt-get update -y
RUN apt-get upgrade -y

RUN export DEBIAN_FRONTEND=noninteractive
# Installing packages required for requirements.R
RUN apt-get install -y  cron \
                        git \
                        vim \
                        libssl-dev \
                        libnlopt-dev \
                        libgit2-dev \
                        libssh2-1-dev \
                        liblapack-dev \
                        libeigen3-dev \
                        libjpeg-dev \
                        libblas-dev \
                        libomp-dev \
                        build-essential \
                        libigraph0-dev \
                        libboost-all-dev \
                        libopenblas-dev \
                        libatlas-base-dev \
                        gfortran \
                        libxml2-dev \
                        libglpk-dev \
                        libgmp-dev \
                        libexplain-dev \
                        libbsd-dev \
                        tcl-dev \
                        tk-dev \
                        libxaw7-dev \
                        libgd2-xpm-dev

COPY ./rconfig/requirements.R /tmp/requirements.R
RUN Rscript /tmp/requirements.R

EXPOSE 3838

CMD ["/usr/bin/shiny-server.sh"]

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install()
BiocManager::install("graph", version = "3.8")
BiocManager::install("BiocInstaller", version = "3.8")
BiocManager::install("Rgraphviz", version = "3.8")
BiocManager::install("marray", version = "3.8")
BiocManager::install("affy", version = "3.8")
BiocManager::install("Biobase", version = "3.8")
BiocManager::install("limma", version = "3.8")
BiocManager::install("RBGL", version = "3.8")

list.of.packages <- c("ipred"
                     ,"prodlim"
                     ,"dimRed"
                     ,"ddalpha"
                     ,"recipes"
                     ,"shinyFiles"
                     ,"rhandsontable"
                     ,"shinydashboard"
                     ,"jpeg"
                     ,"leaflet"
                     ,"Rdonlp2"
                     ,"d3heatmap"
                     ,"networkD3"
                     ,"bnlearn"
                     ,"DT"
                     ,"arules"
                     ,"cleanr"
                     ,"elastic"
                     ,"elasticsearchr"
                     ,"plotly"
                     ,"rsconnect"
                     ,"ggmap"
                     ,"mapdata"
                     ,"bh"
                     ,"rcpp"
                     ,"devtools"
                     ,"dplyr"
                     ,"data.table"
                     ,"nlme"
                     ,"hexbin"
                     ,"broom"
                     ,"plyr"
                     ,"xtable"
                     ,"pbkrtest"
                     ,"caret"
                     ,"e1071"
                     ,"shinydashboard"
                     ,"shiny"
                     ,"digest"
                     ,"magrittr"
                     ,"httr"
                     ,"jsonlite"
                     ,"tibble"
                     ,"ggplot2")

new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
#if(length(new.packages)) install.packages(new.packages, repos='https://cran.rstudio.com/ 3', dependencies = TRUE)
if(length(new.packages)) install.packages(new.packages, dependencies = TRUE)


for (i.pack in 1:length(list.of.packages)){
  suppressMessages(require(list.of.packages[i.pack], character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE))
}

# update.packages(checkBuilt=TRUE, ask=FALSE)
update.packages(ask = FALSE)