Unable to build terra-docker-r image

[AMCalejandro]

Hi,

I am unable to build the Docker image using the latest version of the Dockerfile you have in this remote
The issue seems to be related to this Dockerfile actually getting R=3.16 and not R=4.1 as speicified in the README

Dockerfile

ROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.3

USER root

COPY scripts $JUPYTER_HOME/scripts

# Add env vars to identify binary package installation
ENV TERRA_R_PLATFORM="terra-jupyter-r-2.2.4"
ENV TERRA_R_PLATFORM_BINARY_VERSION=4.3

# Install protobuf 3.20.3. Note this version comes from base deep learning image. Use `conda list` to see what's installed
RUN cd /tmp \
  && wget https://github.com/protocolbuffers/protobuf/releases/download/v3.20.3/protobuf-all-3.20.3.tar.gz \
	&& tar -xvzf protobuf-all-3.20.3.tar.gz \
	&& cd protobuf-3.20.3/ \
	&& ./configure \
	&& make \
	&& make check \
	&& sudo make install \
	&& sudo ldconfig \
	&& rm -rf /tmp/protobuf-* \
	&& cd ~

# Add R kernel
RUN find $JUPYTER_HOME/scripts -name '*.sh' -type f | xargs chmod +x \
 && $JUPYTER_HOME/scripts/kernel/kernelspec.sh $JUPYTER_HOME/scripts/kernel /opt/conda/share/jupyter/kernels

# https://cran.r-project.org/bin/linux/ubuntu/README.html
RUN apt-get update \
    && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
    && add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/' \
    && apt-get install -yq --no-install-recommends apt-transport-https \
    && apt update \
    && apt install -yq --no-install-recommends \
	apt-utils \
	libssh2-1-dev \
	libssl-dev \
	libcurl4-gnutls-dev \
	libgit2-dev \
	libxml2-dev \
	libgfortran-7-dev \
	r-base-dev \
	r-base-core \
	# This section installs libraries
	libnetcdf-dev \
	libhdf5-serial-dev \
	libfftw3-dev \
	libopenbabel-dev \
	libopenmpi-dev \
	libexempi3 \
	libgdal-dev \
	libcairo2-dev \
	libtiff5-dev \
	libgsl0-dev \
	libgtk2.0-dev \
	libgl1-mesa-dev \
	libglu1-mesa-dev \
	libgmp3-dev \
	libhdf5-dev \
	libncurses-dev \
	libxpm-dev \
	libv8-3.14-dev \
	libgtkmm-2.4-dev \
	libmpfr-dev \
	libudunits2-dev \
	libmodule-build-perl \
	libapparmor-dev \
	libgeos-dev \
	librdf0-dev \
	libmagick++-dev \
	libsasl2-dev \
	libpoppler-cpp-dev \
	libpq-dev \
	libperl-dev \
	libgfortran5 \
	libarchive-extract-perl \
	libfile-copy-recursive-perl \
	libcgi-pm-perl \
	libdbi-perl \
	libdbd-mysql-perl \
	libxml-simple-perl \
	sqlite \
	mpi-default-bin \
	openmpi-common \
	tcl8.5-dev \
	imagemagick \
	tabix \
	ggobi \
	graphviz \
	jags \
	xfonts-100dpi \
	xfonts-75dpi \
	biber \
	libzmq3-dev \
	libsbml5-dev \
	biber \
    ocl-icd-opencl-dev \
    libeigen3-dev \
    mono-runtime \
	cmake \
 	libarchive-dev \
    && ln -s /usr/lib/gcc/x86_64-linux-gnu/7/libgfortran.so /usr/lib/x86_64-linux-gnu/libgfortran.so \
    && ln -s /usr/lib/gcc/x86_64-linux-gnu/7/libstdc++.so /usr/lib/x86_64-linux-gnu/libstdc++.so \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

# DEVEL: Add sys env variables to DEVEL image
# Variables in Renviron.site are made available inside of R.
# Add libsbml CFLAGS
ENV LIBSBML_CFLAGS="-I/usr/include"
ENV LIBSBML_LIBS="-lsbml"
RUN echo 'export LIBSBML_CFLAGS="-I/usr/include"' >> /etc/profile \
    && echo 'export LIBSBML_LIBS="-lsbml"' >> /etc/profile

## set pip3 to run as root, not as jupyter user
ENV PIP_USER=false

## Install python packages needed for a few Bioc packages
RUN pip3 -V \
    && pip3 install --upgrade pip \
    && pip3 install cwltool \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

RUN R -e 'install.packages("BiocManager")' \
    ## check version
    && R -e 'BiocManager::install(version="3.18", ask=FALSE)' \
    && R -e 'BiocManager::install(c( \
    "boot", \
    "class", \
    "cluster", \
    "codetools", \
    "foreign", \
    "kernsmooth", \
    "lattice", \
    "mass", \
    "Matrix", \
    "mgcv", \
    "nlme", \
    "nnet", \
    "rpart", \
    "spatial", \
    "survival", \
    # Jupyter notebook essentials
    "IRdisplay",  \
    "IRkernel", \
    # User oriented packages
    "reticulate", \
    "remotes", \
    "devtools", \
    "pbdZMQ", \
    "uuid", \
    "lme4", \
    "lmerTest", \
    "data.table", \
    "tidyr", \
    "dplyr", \
    "ggplot2"))' \
    && R -e 'BiocManager::install("DataBiosphere/Ronaldo")'


## pip runs as jupyter user
ENV PIP_USER=true

RUN R -e 'IRkernel::installspec(user=FALSE)' \
    && chown -R $USER:users /usr/local/lib/R/site-library /home/jupyter

USER $USER

Command to run

docker build -t test  .

Output

[+] Building 1131.8s (6/13)                                                                                                                  
[+] Building 1132.0s (6/13)                                                                                                                  
[+] Building 1132.1s (6/13)                                                                                                                  
 => => transferring dockerfile: 4.29kB                                                                                                  0.0s
 => [internal] load .dockerignore                                                                                                       0.0s
[+] Building 1132.3s (6/13)                                                                                                                  
 => [internal] load metadata for us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.3                                                0.4s
 => [internal] load build context                                                                                                       0.0s
[+] Building 1520.2s (12/13)                                                                                                                 
 => [internal] load build definition from Dockerfile_w_Rinstalls                                                                        0.0s
 => => transferring dockerfile: 4.29kB                                                                                                  0.0s
 => [internal] load .dockerignore                                                                                                       0.0s
 => => transferring context: 2B                                                                                                         0.0s
 => [internal] load metadata for us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.3                                                0.4s
 => [internal] load build context                                                                                                       0.0s
 => => transferring context: 854B                                                                                                       0.0s
 => CACHED [1/9] FROM us.gcr.io/broad-dsp-gcr-public/terra-jupyter-base:1.1.3@sha256:d1758af3b27f9ec97e37855538acd0ac074120a1b4a3cbed0  0.0s
 => [2/9] COPY scripts /etc/jupyter/scripts                                                                                             0.0s 
 => [3/9] RUN cd /tmp   && wget https://github.com/protocolbuffers/protobuf/releases/download/v3.20.3/protobuf-all-3.20.3.tar.gz  &  1179.4s 
 => [4/9] RUN find /etc/jupyter/scripts -name '*.sh' -type f | xargs chmod +x  && /etc/jupyter/scripts/kernel/kernelspec.sh /etc/jupyt  0.4s 
 => [5/9] RUN apt-get update     && apt-get install -yq --no-install-recommends apt-transport-https     && apt update     && apt ins  318.0s 
 => [6/9] RUN echo 'export LIBSBML_CFLAGS="-I/usr/include"' >> /etc/profile     && echo 'export LIBSBML_LIBS="-lsbml"' >> /etc/profile  0.4s
 => [7/9] RUN pip3 -V     && pip3 install --upgrade pip     && pip3 install cwltool     && apt-get clean     && rm -rf /var/lib/apt/l  17.1s
 => ERROR [8/9] RUN R -e 'install.packages("BiocManager")'     && R -e 'BiocManager::install(version="3.18", ask=FALSE)'     && R -e '  4.1s
------
 > [8/9] RUN R -e 'install.packages("BiocManager")'     && R -e 'BiocManager::install(version="3.18", ask=FALSE)'     && R -e 'BiocManager::install(c(     "boot",     "class",     "cluster",     "codetools",     "foreign",     "kernsmooth",     "lattice",     "mass",     "Matrix",     "mgcv",     "nlme",     "nnet",     "rpart",     "spatial",     "survival",     "IRdisplay",      "IRkernel",     "reticulate",     "remotes",     "devtools",     "pbdZMQ",     "uuid",     "lme4",     "lmerTest",     "data.table",     "tidyr",     "dplyr",     "ggplot2"))'     && R -e 'BiocManager::install("DataBiosphere/Ronaldo")':
#0 0.388 
#0 0.388 R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
#0 0.388 Copyright (C) 2020 The R Foundation for Statistical Computing
#0 0.388 Platform: x86_64-pc-linux-gnu (64-bit)
#0 0.388 
#0 0.389 R is free software and comes with ABSOLUTELY NO WARRANTY.
#0 0.389 You are welcome to redistribute it under certain conditions.
#0 0.389 Type 'license()' or 'licence()' for distribution details.
#0 0.389 
#0 0.389   Natural language support but running in an English locale
#0 0.389 
#0 0.389 R is a collaborative project with many contributors.
#0 0.389 Type 'contributors()' for more information and
#0 0.389 'citation()' on how to cite R or R packages in publications.
#0 0.389 
#0 0.389 Type 'demo()' for some demos, 'help()' for on-line help, or
#0 0.389 'help.start()' for an HTML browser interface to help.
#0 0.389 Type 'q()' to quit R.
#0 0.389 
#0 0.465 > install.packages("BiocManager")
#0 0.468 Installing package into ‘/usr/local/lib/R/site-library’
#0 0.468 (as ‘lib’ is unspecified)
#0 1.672 trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.22.tar.gz'
#0 1.967 Content type 'application/x-gzip' length 582690 bytes (569 KB)
#0 1.967 ==================================================
#0 2.189 downloaded 569 KB
#0 2.189 
#0 2.351 * installing *source* package ‘BiocManager’ ...
#0 2.354 ** package ‘BiocManager’ successfully unpacked and MD5 sums checked
#0 2.354 ** using staged installation
#0 2.364 ** R
#0 2.369 ** inst
#0 2.370 ** byte-compile and prepare package for lazy loading
#0 2.755 ** help
#0 2.776 *** installing help indices
#0 2.790 ** building package indices
#0 2.800 ** installing vignettes
#0 2.802 ** testing if installed package can be loaded from temporary location
#0 3.231 ** testing if installed package can be loaded from final location
#0 3.676 ** testing if installed package keeps a record of temporary installation path
#0 3.677 * DONE (BiocManager)
#0 3.683 
#0 3.683 The downloaded source packages are in
#0 3.683        ‘/tmp/RtmpkJT8fH/downloaded_packages’
#0 3.683 > 
#0 3.683 > 
#0 3.731 
#0 3.731 R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
#0 3.731 Copyright (C) 2020 The R Foundation for Statistical Computing
#0 3.731 Platform: x86_64-pc-linux-gnu (64-bit)
#0 3.731 
#0 3.731 R is free software and comes with ABSOLUTELY NO WARRANTY.
#0 3.731 You are welcome to redistribute it under certain conditions.
#0 3.731 Type 'license()' or 'licence()' for distribution details.
#0 3.731 
#0 3.731   Natural language support but running in an English locale
#0 3.731 
#0 3.731 R is a collaborative project with many contributors.
#0 3.731 Type 'contributors()' for more information and
#0 3.731 'citation()' on how to cite R or R packages in publications.
#0 3.731 
#0 3.731 Type 'demo()' for some demos, 'help()' for on-line help, or
#0 3.731 'help.start()' for an HTML browser interface to help.
#0 3.731 Type 'q()' to quit R.
#0 3.731 
#0 3.791 > BiocManager::install(version="3.18", ask=FALSE)
#0 4.107 Error: Bioconductor version '3.18' requires R version '4.3'; use `version = '3.10'`
#0 4.107   with R version 3.6; see https://bioconductor.org/install
#0 4.107 Execution halted
------
Dockerfile_w_Rinstalls:125
--------------------
 124 |     
 125 | >>> RUN R -e 'install.packages("BiocManager")' \
 126 | >>>     ## check version
 127 | >>>     && R -e 'BiocManager::install(version="3.18", ask=FALSE)' \
 128 | >>>     && R -e 'BiocManager::install(c( \
 129 | >>>     "boot", \
 130 | >>>     "class", \
 131 | >>>     "cluster", \
 132 | >>>     "codetools", \
 133 | >>>     "foreign", \
 134 | >>>     "kernsmooth", \
 135 | >>>     "lattice", \
 136 | >>>     "mass", \
 137 | >>>     "Matrix", \
 138 | >>>     "mgcv", \
 139 | >>>     "nlme", \
 140 | >>>     "nnet", \
 141 | >>>     "rpart", \
 142 | >>>     "spatial", \
 143 | >>>     "survival", \
 144 | >>>     # Jupyter notebook essentials
 145 | >>>     "IRdisplay",  \
 146 | >>>     "IRkernel", \
 147 | >>>     # User oriented packages
 148 | >>>     "reticulate", \
 149 | >>>     "remotes", \
 150 | >>>     "devtools", \
 151 | >>>     "pbdZMQ", \
 152 | >>>     "uuid", \
 153 | >>>     "lme4", \
 154 | >>>     "lmerTest", \
 155 | >>>     "data.table", \
 156 | >>>     "tidyr", \
 157 | >>>     "dplyr", \
 158 | >>>     "ggplot2"))' \
 159 | >>>     && R -e 'BiocManager::install("DataBiosphere/Ronaldo")'
 160 |     
--------------------
ERROR: failed to solve: process "/bin/sh -c R -e 'install.packages(\"BiocManager\")'     && R -e 'BiocManager::install(version=\"3.18\", ask=FALSE)'     && R -e 'BiocManager::install(c(     \"boot\",     \"class\",     \"cluster\",     \"codetools\",     \"foreign\",     \"kernsmooth\",     \"lattice\",     \"mass\",     \"Matrix\",     \"mgcv\",     \"nlme\",     \"nnet\",     \"rpart\",     \"spatial\",     \"survival\",     \"IRdisplay\",      \"IRkernel\",     \"reticulate\",     \"remotes\",     \"devtools\",     \"pbdZMQ\",     \"uuid\",     \"lme4\",     \"lmerTest\",     \"data.table\",     \"tidyr\",     \"dplyr\",     \"ggplot2\"))'     && R -e 'BiocManager::install(\"DataBiosphere/Ronaldo\")'" did not complete successfully: exit code: 1