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Merge pull request opendatahub-io#527 from andyatmiami/feat/rhds-2025a-rstudio-upgrade
feat(rstudio): update R/RStudio for 2025a
2 parents 7d75b86 + 2b670fe commit 2d93640

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‎rstudio/rhel9-python-3.11/Dockerfile.cpu

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@@ -66,7 +66,7 @@ RUN if [ -d "${SECRET_DIR}" ]; then \
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--auto-attach; \
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fi
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ENV R_VERSION=4.4.1
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ENV R_VERSION=4.4.3
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# Install R
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RUN yum install -y yum-utils && \
@@ -80,30 +80,33 @@ RUN yum install -y yum-utils && \
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yum -y clean all --enablerepo='*'
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# set R library to default (used in install.r from littler)
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RUN chmod -R a+w /usr/lib64/R/library
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ENV LIBLOC=/usr/lib64/R/library
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# set User R Library path
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RUN mkdir -p /opt/app-root/bin/Rpackages/4.4 && chmod -R a+w /opt/app-root/bin/Rpackages/4.4
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ENV R_LIBS_USER=/opt/app-root/bin/Rpackages/4.4
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RUN chmod -R a+w ${LIBLOC} && \
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# create User R Library path
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mkdir -p ${R_LIBS_USER} && \
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chmod -R a+w ${R_LIBS_USER}
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WORKDIR /tmp/
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# Install RStudio
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RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel9/x86_64/rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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yum install -y rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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rm rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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yum -y clean all --enablerepo='*'
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# Specific RStudio config and fixes
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RUN chmod 1777 /var/run/rstudio-server && \
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mkdir -p /usr/share/doc/R
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ARG RSTUDIO_RPM=rstudio-server-rhel-2024.12.1-563-x86_64.rpm
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RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel9/x86_64/${RSTUDIO_RPM} && \
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yum install -y ${RSTUDIO_RPM} && \
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rm ${RSTUDIO_RPM} && \
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yum -y clean all --enablerepo='*' &&\
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# Specific RStudio config and fixes \
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chmod 1777 /var/run/rstudio-server && \
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mkdir -p /usr/share/doc/R && \
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# package installation \
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# install necessary texlive-framed package to make Knit R markup to PDF rendering possible \
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dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed && \
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dnf clean all && \
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rm -rf /var/cache/yum
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COPY ${RSTUDIO_SOURCE_CODE}/rsession.conf /etc/rstudio/rsession.conf
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# package installation
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# install necessary texlive-framed package to make Knit R markup to PDF rendering possible
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RUN dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed \
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&& dnf clean all && rm -rf /var/cache/yum
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# Install R packages
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RUN R -e "install.packages('Rcpp')"
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‎rstudio/rhel9-python-3.11/Dockerfile.cuda

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Original file line numberDiff line numberDiff line change
@@ -216,7 +216,7 @@ RUN if [ -d "${SECRET_DIR}" ]; then \
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--auto-attach; \
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fi
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ENV R_VERSION=4.4.1
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ENV R_VERSION=4.4.3
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# Install R
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RUN yum install -y yum-utils && \
@@ -230,30 +230,33 @@ RUN yum install -y yum-utils && \
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yum -y clean all --enablerepo='*'
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# set R library to default (used in install.r from littler)
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RUN chmod -R a+w /usr/lib64/R/library
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ENV LIBLOC=/usr/lib64/R/library
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# set User R Library path
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RUN mkdir -p /opt/app-root/bin/Rpackages/4.4 && chmod -R a+w /opt/app-root/bin/Rpackages/4.4
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ENV R_LIBS_USER=/opt/app-root/bin/Rpackages/4.4
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RUN chmod -R a+w ${LIBLOC} && \
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# create User R Library path
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mkdir -p ${R_LIBS_USER} && \
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chmod -R a+w ${R_LIBS_USER}
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WORKDIR /tmp/
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# Install RStudio
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RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel9/x86_64/rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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yum install -y rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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rm rstudio-server-rhel-2024.04.2-764-x86_64.rpm && \
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yum -y clean all --enablerepo='*'
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# Specific RStudio config and fixes
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RUN chmod 1777 /var/run/rstudio-server && \
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mkdir -p /usr/share/doc/R
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ARG RSTUDIO_RPM=rstudio-server-rhel-2024.12.1-563-x86_64.rpm
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RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel9/x86_64/${RSTUDIO_RPM} && \
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yum install -y ${RSTUDIO_RPM} && \
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rm ${RSTUDIO_RPM} && \
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yum -y clean all --enablerepo='*' &&\
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# Specific RStudio config and fixes \
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chmod 1777 /var/run/rstudio-server && \
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mkdir -p /usr/share/doc/R && \
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# package installation \
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# install necessary texlive-framed package to make Knit R markup to PDF rendering possible \
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dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed && \
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dnf clean all && \
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rm -rf /var/cache/yum
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COPY ${RSTUDIO_SOURCE_CODE}/rsession.conf /etc/rstudio/rsession.conf
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# package installation
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# install necessary texlive-framed package to make Knit R markup to PDF rendering possible
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RUN dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed \
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&& dnf clean all && rm -rf /var/cache/yum
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# Install R packages
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RUN R -e "install.packages('Rcpp')"
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‎rstudio/rhel9-python-3.11/Pipfile

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[packages]
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# Base packages
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wheel = "~=0.44.0"
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setuptools = "~=74.1.2"
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setuptools = "~=75.8.2"
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wheel = "~=0.45.1"
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[requires]
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python_version = "3.11"

‎rstudio/rhel9-python-3.11/Pipfile.lock

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‎rstudio/rhel9-python-3.11/kustomize/components/accelerator/kustomization.yaml

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---
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apiVersion: kustomize.config.k8s.io/v1alpha1
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kind: Component
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patches:
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- path: pod-patch.yaml

‎rstudio/rhel9-python-3.11/kustomize/components/accelerator/pod-patch.yaml

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---
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apiVersion: v1
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kind: Pod
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metadata:
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name: pod
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spec:
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containers:
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- name: rstudio
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resources:
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limits:
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memory: 6Gi
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requests:
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memory: 6Gi
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volumeMounts:
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- mountPath: /opt/app-root/src
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name: tmp-volume
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volumes:
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- name: tmp-volume
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emptyDir:
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medium: Memory

‎rstudio/rhel9-python-3.11/kustomize/overlays/accelerator/cuda/kustomization.yaml

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---
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resources:
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- ../../../base
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components:
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- ../../../components/accelerator
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patches:
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- path: pod-patch.yaml

‎rstudio/rhel9-python-3.11/kustomize/overlays/accelerator/cuda/pod-patch.yaml

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---
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apiVersion: v1
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kind: Pod
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metadata:
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name: pod
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spec:
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nodeSelector:
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accelerator: cuda
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containers:
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- name: rstudio
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resources:
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limits:
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nvidia.com/gpu: '1'

‎rstudio/rhel9-python-3.11/requirements.txt

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#
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# Default dependencies
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#
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setuptools==74.1.3; python_version >= '3.8' \
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--hash=sha256:1cfd66bfcf197bce344da024c8f5b35acc4dcb7ca5202246a75296b4883f6851 \
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--hash=sha256:fbb126f14b0b9ffa54c4574a50ae60673bbe8ae0b1645889d10b3b14f5891d28
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wheel==0.44.0; python_version >= '3.8' \
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--hash=sha256:2376a90c98cc337d18623527a97c31797bd02bad0033d41547043a1cbfbe448f \
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--hash=sha256:a29c3f2817e95ab89aa4660681ad547c0e9547f20e75b0562fe7723c9a2a9d49
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setuptools==75.8.2; python_version >= '3.9' \
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--hash=sha256:4880473a969e5f23f2a2be3646b2dfd84af9028716d398e46192f84bc36900d2 \
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--hash=sha256:558e47c15f1811c1fa7adbd0096669bf76c1d3f433f58324df69f3f5ecac4e8f
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wheel==0.45.1; python_version >= '3.8' \
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--hash=sha256:661e1abd9198507b1409a20c02106d9670b2576e916d58f520316666abca6729 \
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--hash=sha256:708e7481cc80179af0e556bbf0cc00b8444c7321e2700b8d8580231d13017248

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