From b8bbf7f232593fe7e92df2b0d810324b7998e2ff Mon Sep 17 00:00:00 2001 From: Gavin Lee Date: Thu, 16 Dec 2021 13:43:33 +0100 Subject: [PATCH 01/13] Update Dockerfile --- docker/r/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index 8a079d3a..56d64836 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -1,6 +1,6 @@ # define build arguments ARG RENKU_BASE=renku/renkulab-py:latest -ARG BASE_IMAGE=rocker/verse:4.0.5 +ARG BASE_IMAGE=rocker/verse:4.1.2 # define base images FROM $RENKU_BASE as renku_base @@ -31,7 +31,7 @@ RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio -ENV RSTUDIO_VERSION 1.3.959 +ENV RSTUDIO_VERSION 1.4.1717-3 RUN /rocker_scripts/install_rstudio.sh # Add Tini From 3776ed8da57de1f02af08479895c186f84eff27b Mon Sep 17 00:00:00 2001 From: Gavin Lee Date: Thu, 16 Dec 2021 13:55:55 +0100 Subject: [PATCH 02/13] Update build_and_push_to_docker.yml --- .github/workflows/build_and_push_to_docker.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build_and_push_to_docker.yml b/.github/workflows/build_and_push_to_docker.yml index 190a2a91..16b1cc35 100644 --- a/.github/workflows/build_and_push_to_docker.yml +++ b/.github/workflows/build_and_push_to_docker.yml @@ -142,9 +142,9 @@ jobs: fail-fast: true matrix: RVERSIONS: - - 4.0.3 - - 4.0.4 - - 4.0.5 + - 4.1.2 + #- 4.0.4 + #- 4.0.5 # TODO: enable once compatibility issues are fixed - see #154 and #160 # - 4.1.0 steps: From 1a99f300ee0fc31c8624e28e98c8450f623d2957 Mon Sep 17 00:00:00 2001 From: Gavin Lee Date: Wed, 26 Jan 2022 10:57:47 +1100 Subject: [PATCH 03/13] jupyter-rsession-proxy==2.0.1 --- docker/r/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index 56d64836..dc90db01 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -89,7 +89,7 @@ USER ${NB_USER} RUN echo ". ${CONDA_PATH}/etc/profile.d/conda.sh" >> ~/.bashrc && \ echo "conda activate base" >> ~/.bashrc -RUN pip install "jupyter-rsession-proxy==1.1" +RUN pip install "jupyter-rsession-proxy==2.0.1" # install IRKernel RUN R --quiet -e "install.packages('IRkernel')" && \ From 1f1afa5cec9877da32f3eba8e7929e29e9fff273 Mon Sep 17 00:00:00 2001 From: Gavin Lee Date: Wed, 26 Jan 2022 11:14:39 +1100 Subject: [PATCH 04/13] Update Dockerfile --- docker/r/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index dc90db01..d1a36d26 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -31,7 +31,7 @@ RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio -ENV RSTUDIO_VERSION 1.4.1717-3 +ENV RSTUDIO_VERSION 2021.09.2+382 RUN /rocker_scripts/install_rstudio.sh # Add Tini From b127a496fcbb5e8877345b1bf399a34c2943422a Mon Sep 17 00:00:00 2001 From: Gavin Lee Date: Wed, 26 Jan 2022 11:42:32 +1100 Subject: [PATCH 05/13] Update Dockerfile --- docker/r/Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index d1a36d26..f47ac9c0 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -31,8 +31,9 @@ RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio -ENV RSTUDIO_VERSION 2021.09.2+382 -RUN /rocker_scripts/install_rstudio.sh +# ENV RSTUDIO_VERSION 2021.09.2+382 +# RUN /rocker_scripts/install_rstudio.sh +# This version of rocker should already have RStudio installed! # Add Tini ENV TINI_VERSION v0.18.0 From 0422a7ee66bfa3484c900c94dd1ac2f18b31ef64 Mon Sep 17 00:00:00 2001 From: Tasko Olevski Date: Wed, 2 Feb 2022 01:29:03 +0100 Subject: [PATCH 06/13] chore: update Rstudio and R version --- .github/workflows/build_and_push_to_docker.yml | 8 +++----- docker/py/requirements.txt | 2 +- docker/r/Dockerfile | 16 +++++++++++----- 3 files changed, 15 insertions(+), 11 deletions(-) diff --git a/.github/workflows/build_and_push_to_docker.yml b/.github/workflows/build_and_push_to_docker.yml index 52490c91..62cea233 100644 --- a/.github/workflows/build_and_push_to_docker.yml +++ b/.github/workflows/build_and_push_to_docker.yml @@ -322,8 +322,7 @@ jobs: - 4.0.3 - 4.0.4 - 4.0.5 - # TODO: enable once compatibility issues are fixed - see #154 and #160 - # - 4.1.0 + - 4.1.0 steps: - name: Docker Login uses: Azure/docker-login@v1 @@ -375,11 +374,10 @@ jobs: fail-fast: false matrix: RELEASE: - # - devel --> commented out until issues with RStudio versions are resolved + - devel - RELEASE_3_11 - RELEASE_3_12 - # TODO: enable once compatibility issues are fixed - see #154 and #160 - # - RELEASE_3_13 + - RELEASE_3_13 steps: - name: Docker Login uses: Azure/docker-login@v1 diff --git a/docker/py/requirements.txt b/docker/py/requirements.txt index 7575333f..499d3c77 100644 --- a/docker/py/requirements.txt +++ b/docker/py/requirements.txt @@ -1,4 +1,4 @@ -jupyter-server-proxy~=3.1.0 +jupyter-server-proxy~=3.2.1 jupyterlab-git==0.30.1 jupyterlab-system-monitor~=0.8.0 jupyterlab~=3.0.0 diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index f47ac9c0..10b57519 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -17,12 +17,16 @@ ENV VENV_DIR /srv/venv ENV HOME /home/${NB_USER} ENV SHELL bash ENV CONDA_PATH /opt/conda +# Do not change the line below, by default the shell is /bin/sh -c +# and /bin/sh -c does not work when you do source venv/bin/activate +# in the reknu project template Dockerfile +SHELL ["/bin/bash", "-c"] # prepend conda and local/bin to PATH ENV PATH ${HOME}/.local/bin:${CONDA_PATH}/bin:$PATH # And set PATH for R! It doesn't read from the environment... -RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \ +RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site && \ echo "PATH=${PATH}" >> /etc/profile.d/set_path.sh && \ echo "RENKU_DISABLE_VERSION_CHECK=1" >> /usr/local/lib/R/etc/Renviron @@ -31,9 +35,9 @@ RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron && \ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio -# ENV RSTUDIO_VERSION 2021.09.2+382 -# RUN /rocker_scripts/install_rstudio.sh -# This version of rocker should already have RStudio installed! +ARG RSTUDIO_VERSION="2021.09.2-382" +ENV RSTUDIO_VERSION="$RSTUDIO_VERSION" +RUN /rocker_scripts/install_rstudio.sh # Add Tini ENV TINI_VERSION v0.18.0 @@ -82,7 +86,9 @@ RUN fix-permissions.sh /usr/local/lib/R && \ # this hack lets some of the setup from the base renku image work here ln -s /home/${NB_USER} /home/jovyan && \ # this allows rstudio to run in an iframe in the UI - echo "\nwww-frame-origin=same\n" >> /etc/rstudio/rserver.conf + echo "" >> /etc/rstudio/rserver.conf && \ + echo "www-frame-origin=same" >> /etc/rstudio/rserver.conf && \ + echo "" >> /etc/rstudio/rserver.conf USER ${NB_USER} From fceba61712af006bba3fe2652aa3d6fe8d700c3b Mon Sep 17 00:00:00 2001 From: Tasko Olevski Date: Wed, 2 Feb 2022 01:45:05 +0100 Subject: [PATCH 07/13] squashme: remove build for bioconductor devel tag --- .github/workflows/build_and_push_to_docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_and_push_to_docker.yml b/.github/workflows/build_and_push_to_docker.yml index 62cea233..2d688b52 100644 --- a/.github/workflows/build_and_push_to_docker.yml +++ b/.github/workflows/build_and_push_to_docker.yml @@ -374,7 +374,7 @@ jobs: fail-fast: false matrix: RELEASE: - - devel + # - devel - RELEASE_3_11 - RELEASE_3_12 - RELEASE_3_13 From 278871beb1794a5a5f5fa30e98711c514b1aee6e Mon Sep 17 00:00:00 2001 From: Tasko Olevski Date: Wed, 2 Feb 2022 02:11:13 +0100 Subject: [PATCH 08/13] squashme: pass rstudio version as argument --- docker/r/Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index 10b57519..2377ccf1 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -36,8 +36,7 @@ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio ARG RSTUDIO_VERSION="2021.09.2-382" -ENV RSTUDIO_VERSION="$RSTUDIO_VERSION" -RUN /rocker_scripts/install_rstudio.sh +RUN /rocker_scripts/install_rstudio.sh $RSTUDIO_VERSION # Add Tini ENV TINI_VERSION v0.18.0 From ade8dce80f602f3bc7a517d635394fed7c35aa6c Mon Sep 17 00:00:00 2001 From: Tasko Olevski Date: Wed, 2 Feb 2022 03:58:46 +0100 Subject: [PATCH 09/13] squashme: fix rstudio install --- docker/r/Dockerfile | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index 2377ccf1..5c26edc3 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -17,10 +17,6 @@ ENV VENV_DIR /srv/venv ENV HOME /home/${NB_USER} ENV SHELL bash ENV CONDA_PATH /opt/conda -# Do not change the line below, by default the shell is /bin/sh -c -# and /bin/sh -c does not work when you do source venv/bin/activate -# in the reknu project template Dockerfile -SHELL ["/bin/bash", "-c"] # prepend conda and local/bin to PATH ENV PATH ${HOME}/.local/bin:${CONDA_PATH}/bin:$PATH @@ -35,7 +31,8 @@ RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site && \ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio -ARG RSTUDIO_VERSION="2021.09.2-382" +ARG RSTUDIO_VERSION +ENV RSTUDIO_VERSION=${RSTUDIO_VERSION:-2021.09.2-382} RUN /rocker_scripts/install_rstudio.sh $RSTUDIO_VERSION # Add Tini From 846186ff170c88eea1f4b8c06e5ea000e343d6e9 Mon Sep 17 00:00:00 2001 From: Tasko Olevski Date: Wed, 2 Feb 2022 14:31:48 +0100 Subject: [PATCH 10/13] sqaushme: minor fix --- docker/r/Dockerfile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index 5c26edc3..bce5f570 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -17,6 +17,7 @@ ENV VENV_DIR /srv/venv ENV HOME /home/${NB_USER} ENV SHELL bash ENV CONDA_PATH /opt/conda +SHELL [ "/bin/bash", "-c" ] # prepend conda and local/bin to PATH ENV PATH ${HOME}/.local/bin:${CONDA_PATH}/bin:$PATH @@ -31,8 +32,8 @@ RUN echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron.site && \ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio -ARG RSTUDIO_VERSION -ENV RSTUDIO_VERSION=${RSTUDIO_VERSION:-2021.09.2-382} +ARG RSTUDIO_VERSION_OVERRIDE="2021.09.2-382" +ENV RSTUDIO_VERSION=${RSTUDIO_VERSION_OVERRIDE} RUN /rocker_scripts/install_rstudio.sh $RSTUDIO_VERSION # Add Tini From 66c7f5a585483813750e4473ebb731cb31cea659 Mon Sep 17 00:00:00 2001 From: Tasko Olevski Date: Fri, 4 Feb 2022 09:17:37 +0100 Subject: [PATCH 11/13] squashme: retire old R versions, add devel --- .github/workflows/build_and_push_to_docker.yml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build_and_push_to_docker.yml b/.github/workflows/build_and_push_to_docker.yml index 2d688b52..43d143cd 100644 --- a/.github/workflows/build_and_push_to_docker.yml +++ b/.github/workflows/build_and_push_to_docker.yml @@ -319,10 +319,10 @@ jobs: fail-fast: true matrix: RVERSION: - - 4.0.3 - - 4.0.4 - - 4.0.5 - 4.1.0 + - 4.1.1 + - 4.1.2 + - devel steps: - name: Docker Login uses: Azure/docker-login@v1 @@ -374,10 +374,9 @@ jobs: fail-fast: false matrix: RELEASE: - # - devel - - RELEASE_3_11 - - RELEASE_3_12 - RELEASE_3_13 + - RELEASE_3_14 + - devel steps: - name: Docker Login uses: Azure/docker-login@v1 From e67f10c66624ecb1b6607ee01ffc7719446dd15a Mon Sep 17 00:00:00 2001 From: Tasko Olevski Date: Fri, 4 Feb 2022 16:12:46 +0100 Subject: [PATCH 12/13] squashme: remove devel versions for R --- .github/workflows/build_and_push_to_docker.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/build_and_push_to_docker.yml b/.github/workflows/build_and_push_to_docker.yml index 43d143cd..b8806473 100644 --- a/.github/workflows/build_and_push_to_docker.yml +++ b/.github/workflows/build_and_push_to_docker.yml @@ -322,7 +322,6 @@ jobs: - 4.1.0 - 4.1.1 - 4.1.2 - - devel steps: - name: Docker Login uses: Azure/docker-login@v1 @@ -376,7 +375,6 @@ jobs: RELEASE: - RELEASE_3_13 - RELEASE_3_14 - - devel steps: - name: Docker Login uses: Azure/docker-login@v1 From 10b689d4a409c3c3658dea872f0bfee7e0116944 Mon Sep 17 00:00:00 2001 From: Tasko Olevski Date: Fri, 4 Feb 2022 17:06:46 +0100 Subject: [PATCH 13/13] squashme: fix rstudio build --- .github/workflows/build_and_push_to_docker.yml | 2 ++ docker/r/Dockerfile | 6 +++++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_and_push_to_docker.yml b/.github/workflows/build_and_push_to_docker.yml index b8806473..43d143cd 100644 --- a/.github/workflows/build_and_push_to_docker.yml +++ b/.github/workflows/build_and_push_to_docker.yml @@ -322,6 +322,7 @@ jobs: - 4.1.0 - 4.1.1 - 4.1.2 + - devel steps: - name: Docker Login uses: Azure/docker-login@v1 @@ -375,6 +376,7 @@ jobs: RELEASE: - RELEASE_3_13 - RELEASE_3_14 + - devel steps: - name: Docker Login uses: Azure/docker-login@v1 diff --git a/docker/r/Dockerfile b/docker/r/Dockerfile index bce5f570..d333fb93 100644 --- a/docker/r/Dockerfile +++ b/docker/r/Dockerfile @@ -34,7 +34,11 @@ ENV LD_LIBRARY_PATH /usr/local/lib/R/lib # pin the version of RStudio ARG RSTUDIO_VERSION_OVERRIDE="2021.09.2-382" ENV RSTUDIO_VERSION=${RSTUDIO_VERSION_OVERRIDE} -RUN /rocker_scripts/install_rstudio.sh $RSTUDIO_VERSION +# if rstudio and rstudio-server users are not deleted below, the installation +# script fails when it installs rstudio and tries to add them back in +RUN userdel rstudio-server && \ + userdel rstudio && \ + /rocker_scripts/install_rstudio.sh $RSTUDIO_VERSION # Add Tini ENV TINI_VERSION v0.18.0