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Fix R dependency installs #47

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Merged
merged 6 commits into from
Dec 11, 2024
Merged

Fix R dependency installs #47

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49e46a2
Don't chown to root:staff
hc2p Dec 9, 2024
8a06e62
Ensure build deps are available for libs
hc2p Dec 9, 2024
b1c26d8
Add missing dependencies
hc2p Dec 9, 2024
d40ed60
Sort dependencies ascending
hc2p Dec 9, 2024
5f01453
Purge build dependencies
hc2p Dec 9, 2024
e311f24
Ensure we have curl in IR images
hc2p Dec 9, 2024
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5 changes: 3 additions & 2 deletions ir/ir-base/install_R_source.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ fi
apt-get install -y --no-install-recommends \
bash-completion \
ca-certificates \
curl \
file \
fonts-texgyre \
g++ \
Expand All @@ -61,7 +62,7 @@ apt-get install -y --no-install-recommends \
zip \
zlib1g

BUILDDEPS="curl \
BUILDDEPS="\
default-jdk \
devscripts \
libbz2-dev \
Expand Down Expand Up @@ -143,7 +144,7 @@ make clean

## Add a library directory (for user-installed packages)
mkdir -p "${R_HOME}/site-library"
chown root:staff "${R_HOME}/site-library"
#chown root:staff "${R_HOME}/site-library"
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@hc2p hc2p Dec 9, 2024

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This was probably copied, leaving it commented for easier cross check.

chmod g+ws "${R_HOME}/site-library"

## Fix library path
Expand Down
70 changes: 57 additions & 13 deletions ir/ir-with-libs/Dockerfile.ir
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Expand Up @@ -3,19 +3,63 @@ ARG CIRCLE_PULL_REQUEST

FROM deepnote/ir:${R_VERSION}${CIRCLE_PULL_REQUEST:+-ra-${CIRCLE_PULL_REQUEST##*/}}

# Install the R libraries
RUN R -e "install.packages('tidyverse', repos='https://cloud.r-project.org', dependencies=TRUE)"
RUN R -e "install.packages('data.table', repos='https://cloud.r-project.org', dependencies=TRUE)"
RUN R -e "install.packages('RSQLite', repos='https://cloud.r-project.org', dependencies=TRUE)"
RUN R -e "install.packages('remotes', repos='https://cloud.r-project.org', dependencies=TRUE)"
RUN R -e "install.packages('reticulate', repos='https://cloud.r-project.org', dependencies=TRUE)"
RUN R -e "install.packages('igraph', repos='https://cloud.r-project.org', dependencies=TRUE)"
RUN R -e "install.packages('plotly', repos='https://cloud.r-project.org', dependencies=TRUE)"


# Workaround for Java to install correctly
RUN mkdir -p /usr/share/man/man1/

RUN R -e "install.packages('rgl', repos='https://cloud.r-project.org', dependencies=TRUE)"
RUN R -e "install.packages('hdf5r', repos='https://cloud.r-project.org', dependencies=TRUE)"
RUN R -e "install.packages('rJava', repos='https://cloud.r-project.org', dependencies=TRUE)"
# Install R lib dependencies
ENV BUILDDEPS="\
default-jdk \
devscripts \
libbz2-dev \
libcairo2-dev \
libcurl4-openssl-dev \
libgit2-dev \
libicu-dev \
libjpeg-dev \
liblzma-dev \
libmagick++-dev \
libpango1.0-dev \
libpcre2-dev \
libpng-dev \
libreadline-dev \
librsvg2-dev \
libtiff5-dev \
libudunits2-dev \
libv8-dev \
libx11-dev \
libxml2-dev \
libxt-dev \
perl \
rsync \
subversion \
tcl-dev \
texinfo \
texlive-extra-utils \
texlive-fonts-extra \
texlive-fonts-recommended \
texlive-latex-extra \
texlive-latex-recommended \
tk-dev \
wget \
x11proto-core-dev \
xauth \
xfonts-base \
xvfb \
zlib1g-dev"

RUN apt-get update && apt-get install -y ${BUILDDEPS} \
&& \
# Install the R libraries
R -e "install.packages('tidyverse', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('data.table', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('RSQLite', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('remotes', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('reticulate', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('igraph', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('plotly', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('rgl', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('hdf5r', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
R -e "install.packages('rJava', repos='https://cloud.r-project.org', dependencies=TRUE)" && \
apt-get clean && \
apt-get remove --purge -y ${BUILDDEPS} && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*