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Reinstall preprocessCore without threading on Linux #8

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Reinstall preprocessCore without threading on Linux #8

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25 changes: 25 additions & 0 deletions pixi-setup.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,30 @@ extract_section() {

export -f extract_section

repair_preprocesscore_for_sesame() {
if [[ "$OSTYPE" != "linux-gnu"* ]]; then
return 0
fi

local rscript="${PIXI_HOME}/envs/r-base/bin/Rscript"
if [ ! -x "${rscript}" ]; then
echo "ERROR: ${rscript} not found after pixi r-base install." >&2
return 1
fi

local ca_bundle="/etc/ssl/certs/ca-certificates.crt"
if [ -f "${ca_bundle}" ]; then
export CURL_CA_BUNDLE="${CURL_CA_BUNDLE:-${ca_bundle}}"
export SSL_CERT_FILE="${SSL_CERT_FILE:-${ca_bundle}}"
fi

export MAKEFLAGS="${MAKEFLAGS:--j1}"
echo "Reinstalling preprocessCore from source with --disable-threading on Linux ..."
"${rscript}" -e 'stopifnot(requireNamespace("BiocManager", quietly = TRUE), requireNamespace("preprocessCore", quietly = TRUE)); options(repos = BiocManager::repositories()); BiocManager::install("preprocessCore", type = "source", configure.args = "--disable-threading", force = TRUE, update = FALSE, ask = FALSE, Ncpus = 1L)'
}

export -f repair_preprocesscore_for_sesame

# --- Prompt: installation path ---
_default_pixi_home="${HOME}/.pixi"
echo ""
Expand Down Expand Up @@ -140,6 +164,7 @@ else

echo "Installing recommended R libraries ..."
inject_packages r-base <(extract_section "${_full_file}" "r")
repair_preprocesscore_for_sesame

echo "Installing recommended Python packages ..."
inject_packages python <(extract_section "${_full_file}" "python")
Expand Down