diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index 9dc7471..66b491d 100755 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -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 ๐Ÿ“ id: build_vars diff --git a/.github/workflows/linter.yaml b/.github/workflows/linter.yaml index 4849d89..e876ba8 100755 --- a/.github/workflows/linter.yaml +++ b/.github/workflows/linter.yaml @@ -17,7 +17,7 @@ jobs: fetch-depth: 0 - name: Lint Code Base ๐Ÿงถ - uses: github/super-linter/slim@v5 + uses: super-linter/super-linter/slim@v5 env: VALIDATE_ALL_CODEBASE: false DEFAULT_BRANCH: main diff --git a/Dockerfile b/Dockerfile index f85a14b..d826964 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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} && \ @@ -49,5 +53,8 @@ RUN ./install_cran_pkgs.R ${DISTRIBUTION} && \ install_other_pkgs.R \ install_pip_pkgs.py +# Prevent pushing of the image without pdflatex installed. +RUN pdflatex --version + # Run RStudio CMD ["/init"] diff --git a/scripts/install_cran_pkgs.R b/scripts/install_cran_pkgs.R index 22546e2..d7a621a 100755 --- a/scripts/install_cran_pkgs.R +++ b/scripts/install_cran_pkgs.R @@ -282,7 +282,11 @@ tlmgr install makeindex metafont mfware inconsolata tex ae parskip listings xcol tlmgr path add ' # nolint end - system(tinytex_installer) + exit_status <- system(tinytex_installer) + cat("TinyTeX installer exited with code =", exit_status, "\n") + if (exit_status != 0) { + quit(status = exit_status) + } tinytex::r_texmf() permission_update <- ' chown -R root:staff /opt/TinyTeX @@ -291,7 +295,11 @@ chmod -R g+wx /opt/TinyTeX/bin export PATH=/opt/TinyTeX/bin/x86_64-linux:${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