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Assert correctness of ci images #90

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merged 15 commits into from
Dec 7, 2023
Merged

Assert correctness of ci images #90

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ee3ca2e
Test
walkowif Nov 29, 2023
b664a08
Update
walkowif Nov 29, 2023
a325595
Add TinyTex exit code capture
walkowif Dec 5, 2023
5c823d7
Test
walkowif Dec 6, 2023
5befa1f
More verbosity
walkowif Dec 6, 2023
b897bf6
Update
walkowif Dec 6, 2023
1803353
Update
walkowif Dec 6, 2023
aedb441
Test
walkowif Dec 6, 2023
4a71c94
Revert
walkowif Dec 6, 2023
594b5e5
Typo
walkowif Dec 6, 2023
bcf6d7f
Add checks
walkowif Dec 6, 2023
bbfb290
Add checks
walkowif Dec 6, 2023
7cd4e15
Uncomment
walkowif Dec 6, 2023
2f9bc98
Update
walkowif Dec 6, 2023
304f2c5
Update super-linter
walkowif Dec 7, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/deploy.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,7 @@ jobs:
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
password: ${{ secrets.REPO_GITHUB_TOKEN }}

- name: Set build variables 📐
id: build_vars
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2 changes: 1 addition & 1 deletion .github/workflows/linter.yaml
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Expand Up @@ -17,7 +17,7 @@ jobs:
fetch-depth: 0

- name: Lint Code Base 🧶
uses: github/super-linter/slim@v5
uses: super-linter/super-linter/slim@v5
env:
VALIDATE_ALL_CODEBASE: false
DEFAULT_BRANCH: main
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7 changes: 7 additions & 0 deletions Dockerfile
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Expand Up @@ -34,6 +34,10 @@ COPY --chmod=0755 [\
# Install sysdeps
RUN ./install_sysdeps.sh ${DISTRIBUTION}

RUN R --version && \
java -version && \
python3 --version

# Install R packages
RUN ./install_cran_pkgs.R ${DISTRIBUTION} && \
./install_bioc.R ${BIOC_VERSION} && \
Expand All @@ -49,5 +53,8 @@ RUN ./install_cran_pkgs.R ${DISTRIBUTION} && \
install_other_pkgs.R \
install_pip_pkgs.py

# Prevent pushing of the image without pdflatex installed.
RUN pdflatex --version
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# Run RStudio
CMD ["/init"]
12 changes: 10 additions & 2 deletions scripts/install_cran_pkgs.R
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Expand Up @@ -282,7 +282,11 @@ tlmgr install makeindex metafont mfware inconsolata tex ae parskip listings xcol
tlmgr path add
'
# nolint end
system(tinytex_installer)
exit_status <- system(tinytex_installer)
cat("TinyTeX installer exited with code =", exit_status, "\n")
if (exit_status != 0) {
quit(status = exit_status)
}
tinytex::r_texmf()
permission_update <- '
chown -R root:staff /opt/TinyTeX
Expand All @@ -291,7 +295,11 @@ chmod -R g+wx /opt/TinyTeX/bin
export PATH=/opt/TinyTeX/bin/x86_64-linux:${PATH}
echo "PATH=${PATH}" >> ${R_HOME}/etc/Renviron
'
system(permission_update)
exit_status <- system(permission_update)
cat("TinyTeX permission update exited with code =", exit_status, "\n")
if (exit_status != 0) {
quit(status = exit_status)
}
}

# Update all packages
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