From 8554c9fb33cc03286302feb564c393f2e1b66664 Mon Sep 17 00:00:00 2001 From: Dominic Feliton <127802411+dafeliton@users.noreply.github.com> Date: Tue, 8 Oct 2024 04:02:46 -0700 Subject: [PATCH 1/6] Update Dockerfile --- images/rstudio-notebook/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/images/rstudio-notebook/Dockerfile b/images/rstudio-notebook/Dockerfile index ed0c5c50..92cdad63 100644 --- a/images/rstudio-notebook/Dockerfile +++ b/images/rstudio-notebook/Dockerfile @@ -32,8 +32,8 @@ RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPE ## The desktop package uses /usr/lib/rstudio/bin ENV PATH="${PATH}:/usr/lib/rstudio-server/bin" \ - SHELL=/bin/bash \ - LD_LIBRARY_PATH="/opt/conda/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib" + SHELL=/bin/bash + #LD_LIBRARY_PATH="/opt/conda/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib" COPY ./lib /opt/k8s-support/lib From dac21307139e8ae38804c81bc281ce7d944523fb Mon Sep 17 00:00:00 2001 From: Dominic Feliton <127802411+dafeliton@users.noreply.github.com> Date: Tue, 8 Oct 2024 04:40:25 -0700 Subject: [PATCH 2/6] try to fix curl rather than openssl --- images/rstudio-notebook/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/images/rstudio-notebook/Dockerfile b/images/rstudio-notebook/Dockerfile index 92cdad63..b10ac011 100644 --- a/images/rstudio-notebook/Dockerfile +++ b/images/rstudio-notebook/Dockerfile @@ -32,8 +32,8 @@ RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPE ## The desktop package uses /usr/lib/rstudio/bin ENV PATH="${PATH}:/usr/lib/rstudio-server/bin" \ - SHELL=/bin/bash - #LD_LIBRARY_PATH="/opt/conda/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server:/opt/conda/lib/R/lib" + SHELL=/bin/bash \ + LD_LIBRARY_PATH="/usr/lib:/usr/lib/x86_64-linux-gnu:/opt/conda/lib/R/lib" COPY ./lib /opt/k8s-support/lib From f77d43df0f1a0ca6ec0e035e1e0eceae0083fbdf Mon Sep 17 00:00:00 2001 From: Dominic Feliton <127802411+dafeliton@users.noreply.github.com> Date: Tue, 8 Oct 2024 05:27:54 -0700 Subject: [PATCH 3/6] curl renviron --- images/rstudio-notebook/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/images/rstudio-notebook/Dockerfile b/images/rstudio-notebook/Dockerfile index b10ac011..d3d8e98a 100644 --- a/images/rstudio-notebook/Dockerfile +++ b/images/rstudio-notebook/Dockerfile @@ -28,12 +28,12 @@ RUN pip install jupyter-rsession-proxy RUN mkdir -p /etc/rstudio && echo 'auth-minimum-user-id=100' >> /etc/rstudio/rserver.conf ## Shim in our nss-wrapper so that user getpwent() lookups succeed -RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPER_PASSWD=/tmp/passwd.wrap'; echo 'NSS_WRAPPER_GROUP=/tmp/group.wrap') >> /opt/conda/lib/R/etc/Renviron.site +RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPER_PASSWD=/tmp/passwd.wrap'; echo 'NSS_WRAPPER_GROUP=/tmp/group.wrap'; echo 'CURL=/usr/bin/curl') >> /opt/conda/lib/R/etc/Renviron.site ## The desktop package uses /usr/lib/rstudio/bin ENV PATH="${PATH}:/usr/lib/rstudio-server/bin" \ SHELL=/bin/bash \ - LD_LIBRARY_PATH="/usr/lib:/usr/lib/x86_64-linux-gnu:/opt/conda/lib/R/lib" + LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:/opt/conda/lib/R/lib" COPY ./lib /opt/k8s-support/lib From 0eb5d8791a5e42b2e41cb7f8b628fa77bb07a27b Mon Sep 17 00:00:00 2001 From: Dominic Feliton <127802411+dafeliton@users.noreply.github.com> Date: Tue, 8 Oct 2024 05:34:05 -0700 Subject: [PATCH 4/6] path var --- images/rstudio-notebook/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/rstudio-notebook/Dockerfile b/images/rstudio-notebook/Dockerfile index d3d8e98a..a9a5a516 100644 --- a/images/rstudio-notebook/Dockerfile +++ b/images/rstudio-notebook/Dockerfile @@ -28,7 +28,7 @@ RUN pip install jupyter-rsession-proxy RUN mkdir -p /etc/rstudio && echo 'auth-minimum-user-id=100' >> /etc/rstudio/rserver.conf ## Shim in our nss-wrapper so that user getpwent() lookups succeed -RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPER_PASSWD=/tmp/passwd.wrap'; echo 'NSS_WRAPPER_GROUP=/tmp/group.wrap'; echo 'CURL=/usr/bin/curl') >> /opt/conda/lib/R/etc/Renviron.site +RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPER_PASSWD=/tmp/passwd.wrap'; echo 'NSS_WRAPPER_GROUP=/tmp/group.wrap'; echo 'PATH=/usr/bin:$PATH') >> /opt/conda/lib/R/etc/Renviron.site ## The desktop package uses /usr/lib/rstudio/bin ENV PATH="${PATH}:/usr/lib/rstudio-server/bin" \ From 88caa72e616a2afb4d15db8b5fd369c18b40c208 Mon Sep 17 00:00:00 2001 From: Dominic Feliton <127802411+dafeliton@users.noreply.github.com> Date: Tue, 8 Oct 2024 05:51:14 -0700 Subject: [PATCH 5/6] https://github.com/rstudio/rstudio/issues/14060 --- images/rstudio-notebook/Dockerfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/images/rstudio-notebook/Dockerfile b/images/rstudio-notebook/Dockerfile index a9a5a516..e6bd1e7d 100644 --- a/images/rstudio-notebook/Dockerfile +++ b/images/rstudio-notebook/Dockerfile @@ -25,10 +25,12 @@ RUN ln -s /opt/conda/bin/R /usr/bin/R && \ RUN pip install jupyter-rsession-proxy -RUN mkdir -p /etc/rstudio && echo 'auth-minimum-user-id=100' >> /etc/rstudio/rserver.conf +RUN mkdir -p /etc/rstudio && \ + echo 'auth-minimum-user-id=100' >> /etc/rstudio/rserver.conf && \ + echo 'rsession-ld-library-path=/opt/conda/lib' >> /etc/rstudio/rserver.conf ## Shim in our nss-wrapper so that user getpwent() lookups succeed -RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPER_PASSWD=/tmp/passwd.wrap'; echo 'NSS_WRAPPER_GROUP=/tmp/group.wrap'; echo 'PATH=/usr/bin:$PATH') >> /opt/conda/lib/R/etc/Renviron.site +RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPER_PASSWD=/tmp/passwd.wrap'; echo 'NSS_WRAPPER_GROUP=/tmp/group.wrap') >> /opt/conda/lib/R/etc/Renviron.site ## The desktop package uses /usr/lib/rstudio/bin ENV PATH="${PATH}:/usr/lib/rstudio-server/bin" \ From 59e438b485738dbf9af0f43f065158e1d4d786be Mon Sep 17 00:00:00 2001 From: Dominic Feliton <127802411+dafeliton@users.noreply.github.com> Date: Tue, 8 Oct 2024 12:58:44 -0700 Subject: [PATCH 6/6] Update Dockerfile --- images/rstudio-notebook/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/images/rstudio-notebook/Dockerfile b/images/rstudio-notebook/Dockerfile index e6bd1e7d..06272b4f 100644 --- a/images/rstudio-notebook/Dockerfile +++ b/images/rstudio-notebook/Dockerfile @@ -34,8 +34,8 @@ RUN ( echo 'LD_PRELOAD=/opt/k8s-support/lib/libnss_wrapper.so'; echo 'NSS_WRAPPE ## The desktop package uses /usr/lib/rstudio/bin ENV PATH="${PATH}:/usr/lib/rstudio-server/bin" \ - SHELL=/bin/bash \ - LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:/opt/conda/lib/R/lib" + SHELL=/bin/bash + #LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:/opt/conda/lib/R/lib" COPY ./lib /opt/k8s-support/lib