From 82d55e19e9cebee1b818bde1cccca32c2a16015b Mon Sep 17 00:00:00 2001 From: atheo89 Date: Mon, 5 Feb 2024 11:31:17 +0100 Subject: [PATCH 1/3] Fix library path version --- rstudio/c9s-python-3.9/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/rstudio/c9s-python-3.9/Dockerfile b/rstudio/c9s-python-3.9/Dockerfile index 0f2fba0ae..f49198e50 100644 --- a/rstudio/c9s-python-3.9/Dockerfile +++ b/rstudio/c9s-python-3.9/Dockerfile @@ -30,7 +30,7 @@ RUN yum install -y yum-utils && \ ENV LIBLOC /usr/lib64/R/library # set User R Library path -ENV R_LIBS_USER /opt/app-root/src/Rpackages/4.2 +ENV R_LIBS_USER /opt/app-root/src/Rpackages/4.3 WORKDIR /tmp/ @@ -48,7 +48,7 @@ COPY rsession.conf /etc/rstudio/rsession.conf # package installation RUN dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" RUN R -e "install.packages('Rcpp')" -RUN R -e 'install.packages(c("tidyverse", "tidymodels", "plumber", "vetiver", "devtools"))' +# RUN R -e 'install.packages(c("tidyverse", "tidymodels", "plumber", "vetiver", "devtools"))' # Install NGINX to proxy RStudio and pass probes check ENV NGINX_VERSION=1.22 \ From d24541266fa5d2427acd4732cc73e7a3da933e57 Mon Sep 17 00:00:00 2001 From: atheo89 Date: Mon, 5 Feb 2024 11:37:20 +0100 Subject: [PATCH 2/3] Fix image stream annotations for R Studio notebooks: image-desc and notebook-software --- manifests/base/rstudio-gpu-notebook-imagestream.yaml | 4 ++-- manifests/base/rstudio-notebook-imagestream.yaml | 4 ++-- rstudio/c9s-python-3.9/Dockerfile | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/manifests/base/rstudio-gpu-notebook-imagestream.yaml b/manifests/base/rstudio-gpu-notebook-imagestream.yaml index a4af55551..57991284a 100644 --- a/manifests/base/rstudio-gpu-notebook-imagestream.yaml +++ b/manifests/base/rstudio-gpu-notebook-imagestream.yaml @@ -7,7 +7,7 @@ metadata: annotations: opendatahub.io/notebook-image-url: "https://github.com/opendatahub-io/notebooks/tree/main/rstudio" opendatahub.io/notebook-image-name: "CUDA - R Studio" - opendatahub.io/notebook-image-desc: "R Studio workbench image, allows to integrated development environment for R, a programming language for statistical computing and graphics." + opendatahub.io/notebook-image-desc: "R Studio Workbench image with an integrated development environment for R, a programming language designed for statistical computing and graphics." opendatahub.io/notebook-image-order: "10" opendatahub.io/recommended-accelerators: '["nvidia.com/gpu"]' name: rstudio-gpu-notebook @@ -17,7 +17,7 @@ spec: tags: # N Version of the image - annotations: - opendatahub.io/notebook-software: '[{"name":"CUDA","version":"11.8"},{"name":"Python","version":"v3.9"}]' + opendatahub.io/notebook-software: '[{"name":"CUDA","version":"11.8"},{"name":"R","version":"v4.3"},{"name":"Python","version":"v3.9"}]' opendatahub.io/notebook-python-dependencies: '[{"name":"r-studio","version":"4.3"}]' openshift.io/imported-from: quay.io/opendatahub/workbench-images opendatahub.io/workbench-image-recommended: 'true' diff --git a/manifests/base/rstudio-notebook-imagestream.yaml b/manifests/base/rstudio-notebook-imagestream.yaml index 645062f13..5f8878441 100644 --- a/manifests/base/rstudio-notebook-imagestream.yaml +++ b/manifests/base/rstudio-notebook-imagestream.yaml @@ -7,7 +7,7 @@ metadata: annotations: opendatahub.io/notebook-image-url: "https://github.com/opendatahub-io/notebooks/tree/main/rstudio" opendatahub.io/notebook-image-name: "R Studio" - opendatahub.io/notebook-image-desc: "R Studio workbench image, allows to integrated development environment for R, a programming language for statistical computing and graphics." + opendatahub.io/notebook-image-desc: "R Studio Workbench image with an integrated development environment for R, a programming language designed for statistical computing and graphics." opendatahub.io/notebook-image-order: "9" name: rstudio-notebook spec: @@ -16,7 +16,7 @@ spec: tags: # N Version of the image - annotations: - opendatahub.io/notebook-software: '[{"name":"Python","version":"v3.9"}]' + opendatahub.io/notebook-software: '[{"name":"R","version":"v4.3"},{"name":"Python","version":"v3.9"}]' opendatahub.io/notebook-python-dependencies: '[{"name":"r-studio","version":"4.3"}]' openshift.io/imported-from: quay.io/opendatahub/workbench-images opendatahub.io/workbench-image-recommended: 'true' diff --git a/rstudio/c9s-python-3.9/Dockerfile b/rstudio/c9s-python-3.9/Dockerfile index f49198e50..a8b2361e6 100644 --- a/rstudio/c9s-python-3.9/Dockerfile +++ b/rstudio/c9s-python-3.9/Dockerfile @@ -48,7 +48,7 @@ COPY rsession.conf /etc/rstudio/rsession.conf # package installation RUN dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" RUN R -e "install.packages('Rcpp')" -# RUN R -e 'install.packages(c("tidyverse", "tidymodels", "plumber", "vetiver", "devtools"))' +RUN R -e 'install.packages(c("tidyverse", "tidymodels", "plumber", "vetiver", "devtools"))' # Install NGINX to proxy RStudio and pass probes check ENV NGINX_VERSION=1.22 \ From ad0de684abb7df11421557b6dfeab5c2ced3ad12 Mon Sep 17 00:00:00 2001 From: atheo89 Date: Mon, 5 Feb 2024 12:21:27 +0100 Subject: [PATCH 3/3] Fix persmissions error on the R library paths --- rstudio/c9s-python-3.9/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/rstudio/c9s-python-3.9/Dockerfile b/rstudio/c9s-python-3.9/Dockerfile index a8b2361e6..0d9f2b42c 100644 --- a/rstudio/c9s-python-3.9/Dockerfile +++ b/rstudio/c9s-python-3.9/Dockerfile @@ -27,9 +27,11 @@ RUN yum install -y yum-utils && \ yum -y clean all --enablerepo='*' # set R library to default (used in install.r from littler) +RUN chmod -R a+w /usr/lib64/R/library ENV LIBLOC /usr/lib64/R/library # set User R Library path +RUN mkdir -p /opt/app-root/src/Rpackages/4.3 && chmod -R a+w /opt/app-root/src/Rpackages/4.3 ENV R_LIBS_USER /opt/app-root/src/Rpackages/4.3 WORKDIR /tmp/