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Add --vanilla to R call #1432

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Merged
merged 2 commits into from
Aug 14, 2025
Merged

Add --vanilla to R call #1432

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bcb46e1
Add --vanilla to R call
rgaiacs Jul 9, 2025
356371d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 9, 2025
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13 changes: 8 additions & 5 deletions repo2docker/buildpacks/r.py
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Original file line number Diff line number Diff line change
Expand Up @@ -358,8 +358,8 @@ def get_build_scripts(self):
# Install a pinned version of devtools, IRKernel and shiny
rf"""
export EXPANDED_CRAN_MIRROR_URL="$(. /etc/os-release && echo {cran_mirror_url} | envsubst)" && \
R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos=Sys.getenv(\"EXPANDED_CRAN_MIRROR_URL\"))" && \
R --quiet -e "IRkernel::installspec(prefix=Sys.getenv(\"NB_PYTHON_PREFIX\"))"
R --vanilla --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos=Sys.getenv(\"EXPANDED_CRAN_MIRROR_URL\"))" && \
R --vanilla --quiet -e "IRkernel::installspec(prefix=Sys.getenv(\"NB_PYTHON_PREFIX\"))"
""",
),
]
Expand Down Expand Up @@ -395,7 +395,7 @@ def get_preassemble_scripts(self):
"${NB_USER}",
# Delete /tmp/downloaded_packages only if install.R fails, as the second
# invocation of install.R might be able to reuse them
f"Rscript {installR_path} && touch /tmp/.preassembled || true && rm -rf /tmp/downloaded_packages",
f"Rscript --vanilla {installR_path} && touch /tmp/.preassembled || true && rm -rf /tmp/downloaded_packages",
)
]

Expand All @@ -413,14 +413,17 @@ def get_assemble_scripts(self):
"${NB_USER}",
# only run install.R if the pre-assembly failed
# Delete any downloaded packages in /tmp, as they aren't reused by R
f"""if [ ! -f /tmp/.preassembled ]; then Rscript {installR_path}; rm -rf /tmp/downloaded_packages; fi""",
f"""if [ ! -f /tmp/.preassembled ]; then Rscript --vanilla {installR_path}; rm -rf /tmp/downloaded_packages; fi""",
)
]

description_R = "DESCRIPTION"
if not self.binder_dir and os.path.exists(description_R):
assemble_scripts += [
("${NB_USER}", 'R --quiet -e "devtools::install_local(getwd())"')
(
"${NB_USER}",
'R --vanilla --quiet -e "devtools::install_local(getwd())"',
)
]

return assemble_scripts