olex2: bundle readline 8.2 in the sysroot; loader check reports instead of dying

olex2c needs libreadline.so.8 (RHEL8 has .so.7, vendor lib/ only .so.6),
so the Ra build node could not complete the post-install ld.so --list and
the guard aborted. Add Fedora 40 readline-8.2 to the sysroot rpms (needs
only the host libtinfo.so.6) and make step 7 print the listing, warn on
host libs missing on the build node, and die only on a genuine
patchelf/sysroot failure.

olex2/README.md

@@ -77,11 +77,14 @@ A newer glibc can **not** be dropped in via `LD_LIBRARY_PATH`: the dynamic
 loader path (`/lib64/ld-linux-x86-64.so.2`) is hard-wired into each
 executable and must match its libc. So the recipe:
 
-- ships glibc 2.39 + GCC 14 `libstdc++`/`libgcc_s` under `$PREFIX/sysroot`
-  (frozen Fedora 40 rpms from kojipkgs, Fedora's permanent build archive;
-  same glibc generation as the upstream build host). glibc and libstdc++
-  unpack to `usr/lib64`, libgcc to `/lib64` (Fedora relies on the
-  filesystem package's `lib64 -> usr/lib64` symlink, which we do not
+- ships glibc 2.39 + GCC 14 `libstdc++`/`libgcc_s` + readline 8.2 under
+  `$PREFIX/sysroot` (frozen Fedora 40 rpms from kojipkgs, Fedora's
+  permanent build archive; same glibc generation as the upstream build
+  host). readline because the binaries need `libreadline.so.8`: RHEL8 has
+  `.so.7`, RHEL9 `.so.8`, the vendor `lib/` only `.so.6` — bundled, olex2c
+  needs just `libtinfo.so.6` (ncurses-libs) from the host. glibc, libstdc++
+  and readline unpack to `usr/lib64`, libgcc to `/lib64` (Fedora relies on
+  the filesystem package's `lib64 -> usr/lib64` symlink, which we do not
   extract), so `configure` merges `lib64` into `usr/lib64` and recreates
   the symlink — one lib dir for the RPATH;
 - runs `patchelf --set-interpreter <sysroot ld.so> --force-rpath --set-rpath
@@ -148,9 +151,12 @@ exact names from `files/config.yaml` in `<distdir>`; prep then skips the
 download but still checks the sha256.
 
 **RHEL9 host libraries.** The binaries bring their own glibc, libstdc++,
-python, ssl, png, jpeg, tiff, openblas, gfortran, but link system
-GTK2/X11/OpenGL — also `olex2c` (wx is linked in statically). Check once
-per host type:
+readline, python, ssl, png, jpeg, tiff, openblas, gfortran, but link
+system GTK2/X11/OpenGL and `libtinfo.so.6` (ncurses-libs) — also `olex2c`
+(wx is linked in statically). The install step prints the loader listing
+for olex2c; a host lib missing on the *build* node is a WARNING there, not
+an error, because build and execution hosts differ. Check once per host
+type:
 
 ```sh
 module load olex2/1.5-7665          # exports OLEX2_ROOT=/opt/psi/MX/olex2/1.5-7665
@@ -209,8 +215,11 @@ not to edit the hash:
 2. check the new binaries' glibc need still fits the bundled 2.39:
    `unzip -p olex2-linux64.zip olex2/olex2c | strings | grep -o 'GLIBC_2\.[0-9]*' | sort -uV | tail -1`
    (and `GLIBCXX_3\.4\.[0-9]*` ≤ 3.4.33). If upstream moved past that, bump
-   the three rpms in `urls:`/`shasums:` to a newer frozen Fedora release
-   (kojipkgs `packages/glibc/<ver>/<rel>/x86_64/`, `packages/gcc/...`);
+   the four rpms (glibc, libstdc++, libgcc, readline) in `urls:`/`shasums:`
+   to a newer frozen Fedora release (kojipkgs
+   `packages/glibc/<ver>/<rel>/x86_64/`, `packages/gcc/...`,
+   `packages/readline/...`) — they must come from the same release so
+   readline's glibc requirement is met;
 3. add `1.5-7800` under `versions:` (`relstage: unstable`) and
    `olex2-1.5-7800-linux64.zip: <sha256>` under `shasums:` — the `urls:`
    entry needs no change (`${V_PKG}` = series dir, `${V}` = cache name);

olex2/build

@@ -32,6 +32,7 @@ OLEX2_SYSROOT_RPMS=(
     glibc-2.39-37.fc40.x86_64.rpm
     libstdc++-14.2.1-3.fc40.x86_64.rpm
     libgcc-14.2.1-3.fc40.x86_64.rpm
+    readline-8.2-8.fc40.x86_64.rpm      # libreadline.so.8: RHEL8 has .so.7, vendor lib/ .so.6
 )
 OLEX2_PATCHELF_TGZ="patchelf-0.18.0-x86_64.tar.gz"
 # ELF executables in the vendor tree that get the bundled loader (static ones,
@@ -162,21 +163,36 @@ pbuild::install() {
     install -m 755 "${BUILDBLOCK_DIR}/files/olex2-launcher" "${PREFIX}/bin/olex2c" || \
         std::die 42 "olex2: installing bin/olex2c launcher failed"
 
-    # 7. prove the patched olex2c resolves through the bundled glibc. Missing
-    #    HOST libs (gtk2, GL ...) are only a warning here: they must be
-    #    installed on the execution hosts, the build host may differ.
-    "${ld}" --list "${PREFIX}/olex2c" > "${SRC_DIR}/olex2c.ldd" 2>&1 || \
-        std::die 42 "olex2: bundled loader cannot resolve olex2c - see ${SRC_DIR}/olex2c.ldd"
-    grep -q "${libdir}/libc.so.6" "${SRC_DIR}/olex2c.ldd" || \
-        std::die 42 "olex2: olex2c does not pick up the bundled glibc (see ${SRC_DIR}/olex2c.ldd) - patchelf step broken"
-    if grep -q 'not found' "${SRC_DIR}/olex2c.ldd"; then
-        echo "olex2: WARNING - host libraries missing on THIS host; dnf install them on the execution hosts:"
-        grep 'not found' "${SRC_DIR}/olex2c.ldd"
+    # 7. prove the patched olex2c resolves through the bundled glibc. The
+    #    build host (Ra, RHEL8) is not the execution host (RHEL9): a HOST lib
+    #    missing here ("=> not found", or a hard "cannot open shared object
+    #    file" that aborts the listing) is reported, not fatal. Anything else
+    #    (segfault, page alignment, GLIBC_PRIVATE ...) means patchelf/sysroot
+    #    is broken and the build must stop.
+    local -r ldd="${SRC_DIR}/olex2c.ldd"
+    local rc=0
+    "${ld}" --list "${PREFIX}/olex2c" > "${ldd}" 2>&1 || rc=$?
+    echo "olex2: --- ${ld} --list olex2c (rc=${rc}) ---"
+    cat "${ldd}"
+    echo "olex2: --- end of listing ---"
+    if grep -q "${libdir}/libc.so.6" "${ldd}"; then
+        if grep -q 'not found' "${ldd}"; then
+            echo "olex2: WARNING - host libraries missing on THIS host; dnf install them on the execution hosts:"
+            grep 'not found' "${ldd}"
+        fi
+    elif grep -q 'cannot open shared object file' "${ldd}"; then
+        echo "olex2: WARNING - cannot verify the loader on THIS host, a host library is missing here:"
+        grep 'cannot open shared object file' "${ldd}"
+        echo "olex2:           install it on the execution hosts (or bundle it in the sysroot) and re-check with"
+        echo "olex2:           ${ld} --list ${PREFIX}/olex2c"
+    else
+        std::die 42 "olex2: olex2c does not resolve through the bundled glibc (rc=${rc}, listing above) - patchelf/sysroot step broken"
     fi
 
     # 8. what the modulefile / launchers rely on
     local f
-    for f in olex2 olex2c cctbx/cctbx_build/lib lib/libpython3.8.so.1.0 lib/python3.8 util/pyUtil/initpy.py bin/olex2c sysroot; do
+    for f in olex2 olex2c cctbx/cctbx_build/lib lib/libpython3.8.so.1.0 lib/python3.8 util/pyUtil/initpy.py bin/olex2c \
+             sysroot/usr/lib64/libc.so.6 sysroot/usr/lib64/libstdc++.so.6 sysroot/usr/lib64/libgcc_s.so.1 sysroot/usr/lib64/libreadline.so.8; do
         [[ -e "${PREFIX}/${f}" ]] || std::die 42 "olex2: ${PREFIX}/${f} missing after install - module would be broken"
     done
     echo "olex2: installed upstream build '$(cat "${PREFIX}/version.txt" 2>/dev/null)' (tag $(cat "${PREFIX}/olex2.tag" 2>/dev/null))"

olex2/files/config.yaml

@@ -28,6 +28,12 @@ olex2:
       - url: https://kojipkgs.fedoraproject.org/packages/gcc/14.2.1/3.fc40/x86_64/libgcc-14.2.1-3.fc40.x86_64.rpm
         name: libgcc-14.2.1-3.fc40.x86_64.rpm
         unpacker: none
+      # readline 8: the binaries need libreadline.so.8 - RHEL8 has .so.7, RHEL9
+      # .so.8, the vendor lib/ only .so.6. Bundling it makes olex2c independent
+      # of the host readline (only libtinfo.so.6 from ncurses-libs is needed).
+      - url: https://kojipkgs.fedoraproject.org/packages/readline/8.2/8.fc40/x86_64/readline-8.2-8.fc40.x86_64.rpm
+        name: readline-8.2-8.fc40.x86_64.rpm
+        unpacker: none
       # static patchelf: re-points the ELF executables at the bundled loader
       - url: https://github.com/NixOS/patchelf/releases/download/0.18.0/patchelf-0.18.0-x86_64.tar.gz
         name: patchelf-0.18.0-x86_64.tar.gz
@@ -41,6 +47,7 @@ olex2:
     glibc-2.39-37.fc40.x86_64.rpm: 3976fe456c25eb15a8eea4fd57140a2d9b0084ef721960b510e02872c4fe5cc9
     libstdc++-14.2.1-3.fc40.x86_64.rpm: 6b6c07bef7ecf7af4a4042bc53eca6c188e07567b3ae710568495a5ca89ccede
     libgcc-14.2.1-3.fc40.x86_64.rpm: 6d84546060cf58bd1ea2456a0ac52659bf9670782258b664dfc0aa046ff3a50d
+    readline-8.2-8.fc40.x86_64.rpm: 4e84cb13e24caa3f2b445cef19bf8756d97f17bc64a0958144abc3df284bf038
     patchelf-0.18.0-x86_64.tar.gz: ce84f2447fb7a8679e58bc54a20dc2b01b37b5802e12c57eece772a6f14bf3f0
   versions:
     # 1.5: legacy Ra/RHEL8 module built by the previous recipe from a