Actually ship the R libraries the modules need
The first full build succeeded and produced a package that would not have worked. Three separate causes, all silent: - R was configured --with-blas --with-lapack, so it linked Arch's external BLAS and never built libRblas.so/libRlapack.so. The JASP module bundles expect those inside R_HOME, the way a conventional R and the Flatpak ship them. Now --without-blas, with a hard check after install. - buildModuleBundlesLocally.R installs jaspModuleTools via install_github, which failed on anonymous GitHub rate limits. No bundles were produced at all. GITHUB_PAT is now required rather than merely recommended. - buildAllDefaultJaspModules.R calls the bundle builder through system2(), which ignores exit status, so all of the above exited 0. Added explicit guards: jaspModuleTools must exist, Modules/local must be non-empty, and the staged tree must contain the bundles and all three R libraries. Staging was also wrong: it copied ModuleBundleBuildDir/Modules, which is cloned module *sources* with zero compiled objects, while dropping LibraryR entirely - 267MB of R packages built against the bundled R.
This commit is contained in:
agw
+89
-10
@@ -103,19 +103,38 @@ cd "R-${R_VERSION}"
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# config.site would otherwise pick, which keeps the rpath below predictable.
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# The install prefix equals the final install path, so the rpath stays valid
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# once the tarball is unpacked on the user's machine.
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#
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# --without-blas/--without-lapack is deliberate and load-bearing. With
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# --with-blas, R links Arch's external BLAS and does NOT build libRblas.so or
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# libRlapack.so. The JASP module bundles expect those files to exist inside
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# R_HOME (that is how a conventionally built R, and the Flatpak, ship), so
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# linking externally leaves the modules unable to resolve them. Reference BLAS
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# is slower than OpenBLAS, but a working install beats a fast broken one.
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./configure \
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--prefix="${R_HOME_DIR}" \
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--libdir="${R_HOME_DIR}/lib" \
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--enable-R-shlib \
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--enable-memory-profiling \
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--with-blas \
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--with-lapack \
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--without-blas \
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--without-lapack \
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--with-x=no \
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--with-tcltk=no \
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LDFLAGS="-Wl,-rpath,${R_HOME_DIR}/lib/R/lib"
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make -j"$JOBS"
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make install
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# Guard the above: a silently external-BLAS build produces a JASP whose modules
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# fail at runtime, which is exactly the class of failure this package exists to
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# avoid. Better to stop here than ship it.
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for lib in libR.so libRblas.so libRlapack.so; do
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if [[ ! -f "${R_HOME_DIR}/lib/R/lib/${lib}" ]]; then
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echo "error: ${lib} missing from the bundled R — R linked an external BLAS?" >&2
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ls -la "${R_HOME_DIR}/lib/R/lib/" >&2
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exit 1
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fi
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done
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log "bundled R provides its own libR/libRblas/libRlapack"
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export PATH="${R_HOME_DIR}/bin:${PATH}"
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# Ask R where it actually put itself rather than assuming lib vs lib64.
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# Deliberately NOT exported: R.cmake notes that a set R_HOME makes R print
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@@ -156,15 +175,46 @@ log "compiling JASP (-j$JOBS)"
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ninja -C "$BUILD_DIR" -j"$JOBS"
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# The R modules are the long pole: several hundred R packages compiled from
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# source, installed into the bundled R's library.
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# source. buildAllDefaultJaspModules.R shells out to buildModuleBundlesLocally.R
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# via system2(), which does NOT check exit status — so every failure below is
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# silent and the script still exits 0. The guards after it are what actually
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# catch a broken module build.
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#
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# GITHUB_PAT is required, not optional: buildModuleBundlesLocally.R does
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# install_github('jasp-stats/jaspModuleTools'), and anonymous GitHub API rate
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# limits make that fail. When it fails, no bundles are produced at all and the
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# build otherwise looks successful.
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if [[ -z "${GITHUB_PAT:-}" ]]; then
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echo "error: GITHUB_PAT is required — jaspModuleTools is installed from GitHub" >&2
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echo " without it the module build silently produces nothing" >&2
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exit 1
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fi
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export GITHUB_PAT
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export GITHUB_TOKEN="${GITHUB_PAT}"
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log "building R modules — this is the slow part"
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mkdir -p "$BUILD_DIR"/Modules/{binary_pkgs,manifests,module_libs,Tools}
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cd "$SRC_DIR/Tools"
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if [[ -z "${GITHUB_PAT:-}" ]]; then
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echo "warning: GITHUB_PAT is unset — R module downloads from GitHub may hit anonymous rate limits" >&2
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fi
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Rscript buildAllDefaultJaspModules.R
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MODULE_LIBRARY="$SRC_DIR/Tools/ModuleBundleBuildDir/LibraryR"
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MODULE_BUNDLES="$SRC_DIR/Modules/local"
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if [[ ! -d "$MODULE_LIBRARY/jaspModuleTools" ]]; then
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echo "error: jaspModuleTools was not installed — install_github failed" >&2
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echo " (GitHub rate limit, or GITHUB_PAT lacks read access)" >&2
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exit 1
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fi
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bundle_count="$(find "$MODULE_BUNDLES" -mindepth 1 -maxdepth 1 2>/dev/null | wc -l)"
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if [[ "$bundle_count" -eq 0 ]]; then
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echo "error: the module build produced no bundles in ${MODULE_BUNDLES}" >&2
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echo " system2() in buildAllDefaultJaspModules.R hides the real error;" >&2
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echo " re-run buildModuleBundlesLocally.R by hand to see it" >&2
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exit 1
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fi
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log "module build produced ${bundle_count} bundles"
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# -------------------------------------------------------------------- staging
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log "staging install tree"
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rm -rf "$STAGE_DIR"
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@@ -176,10 +226,25 @@ DESTDIR="$STAGE_DIR" ninja -C "$BUILD_DIR" install
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install -d "$STAGE_DIR$PREFIX"
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cp -a "$R_HOME_DIR" "$STAGE_DIR$PREFIX/"
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# Everything the module build produced has to travel with the tarball, or JASP
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# falls back to downloading bundles at runtime — which is the failure mode this
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# package is meant to remove.
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#
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# Modules/local the compiled module bundles themselves
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# LibraryR the R library they were built with (jaspModuleTools, devtools
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# and ~95 dependencies), compiled against the bundled R 4.5.3
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#
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# ModuleBundleBuildDir/Modules is deliberately NOT copied: it is the cloned
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# module *sources* (no compiled objects at all), several hundred MB of git
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# checkouts that would bloat the tarball without being usable at runtime.
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install -d "$STAGE_DIR$PREFIX/Modules"
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if [[ -d "$SRC_DIR/Tools/ModuleBundleBuildDir/Modules" ]]; then
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cp -a "$SRC_DIR/Tools/ModuleBundleBuildDir/Modules/." "$STAGE_DIR$PREFIX/Modules/"
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fi
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log "staging module bundles from ${MODULE_BUNDLES}"
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cp -a "$MODULE_BUNDLES/." "$STAGE_DIR$PREFIX/Modules/"
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log "staging module R library from ${MODULE_LIBRARY}"
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install -d "$STAGE_DIR$PREFIX/ModuleLibrary"
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cp -a "$MODULE_LIBRARY/." "$STAGE_DIR$PREFIX/ModuleLibrary/"
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install -Dm644 /work/packaging/org.jaspstats.JASP.desktop \
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"$STAGE_DIR/usr/share/applications/org.jaspstats.JASP.desktop"
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@@ -197,10 +262,24 @@ find . -maxdepth 2 \( -name 'COPYING*' -o -name 'LICENSE*' \) -type f \
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find "$STAGE_DIR" -name '*.o' -delete 2>/dev/null || true
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# Make the tree independent of Arch's rolling libraries (ICU, jsoncpp, glpk,
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# JAGS, readstat, librdata, BLAS/LAPACK ...). Qt6 stays a system dependency.
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# JAGS, readstat, librdata ...). Qt6 stays a system dependency; BLAS/LAPACK now
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# come from the bundled R itself.
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log "bundling non-system shared libraries"
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bash /work/build/bundle-libs.sh "$STAGE_DIR" "$PREFIX"
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# Final sanity check on what is about to be shipped. Each of these has already
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# been shipped missing once.
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log "verifying the staged tree"
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staged_r="$STAGE_DIR$PREFIX/R/lib/R/lib"
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for lib in libR.so libRblas.so libRlapack.so; do
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[[ -f "$staged_r/$lib" ]] || { echo "error: staged tree lacks $lib" >&2; exit 1; }
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done
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staged_bundles="$(find "$STAGE_DIR$PREFIX/Modules" -mindepth 1 -maxdepth 1 2>/dev/null | wc -l)"
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[[ "$staged_bundles" -gt 0 ]] || { echo "error: staged tree has no module bundles" >&2; exit 1; }
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staged_so="$(find "$STAGE_DIR$PREFIX" -name '*.so' 2>/dev/null | wc -l)"
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log "staged: ${staged_bundles} module bundles, ${staged_so} shared objects"
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du -sh "$STAGE_DIR$PREFIX"/* 2>/dev/null | sort -rh | head -8
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# ------------------------------------------------------------------- metadata
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pkgver_of() { pacman -Q "$1" 2>/dev/null | awk '{print $2}'; }
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