[Debichem-devel] Bug#1116631: openbabel FTBFS on arm64 due to -Wl, --fatal-warnings

[Adrian Bunk]

Source: openbabel
Version: 3.1.1+dfsg-12
Severity: serious
Tags: ftbfs forky sid patch
X-Debbugs-Cc: debian-arm at lists.debian.org, Andrius Merkys <merkys at debian.org>
User: debian-arm at lists.debian.org
Usertags: arm64

https://buildd.debian.org/status/fetch.php?pkg=openbabel&arch=arm64&ver=3.1.1%2Bdfsg-13&stamp=1759147367&raw=0

...
/usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libmaeparser.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libcoordgen.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/usr/lib/gcc/aarch64-linux-gnu/15/../../../aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/usr/lib/gcc/aarch64-linux-gnu/15/libstdc++.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/lib/aarch64-linux-gnu/libm.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/lib/aarch64-linux-gnu/libmvec.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/usr/lib/gcc/aarch64-linux-gnu/15/libgomp.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
/lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking.
collect2: error: ld returned 1 exit status
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openbabel-3.1.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fopenmp -Wl,--dependency-file=CMakeFiles/openbabel.dir/link.d -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -shared -Wl,-soname,libopenbabel.so.7 -o ../lib/aarch64-linux-gnu/libopenbabel.so.7.0.0 CMakeFiles/openbabel.dir/alias.cpp.o CMakeFiles/openbabel.dir/atom.cpp.o CMakeFiles/openbabel.dir/base.cpp.o CMakeFiles/openbabel.dir/bitvec.cpp.o CMakeFiles/openbabel.dir/bond.cpp.o CMakeFiles/openbabel.dir/bondtyper.cpp.o CMakeFiles/openbabel.dir/builder.cpp.o CMakeFiles/openbabel.dir/canon.cpp.o CMakeFiles/openbabel.dir/chains.cpp.o CMakeFiles/openbabel.dir/chargemodel.cpp.o CMakeFiles/openbabel.dir/data.cpp.o CMakeFiles/openbabel.dir/data_utilities.cpp.o CMakeFiles/openbabel.dir/descriptor.cpp.o CMakeFiles/openbabel.dir/elements.cpp.o CMakeFiles/openbabel.dir/fingerprint.cpp.o CMakeFiles/openbabel.dir/forcefield.cpp.o CMakeFiles/openbabel.dir/format.cpp.o CMakeFiles/openbabel.dir/generic.cpp.o CMakeFiles/openbabel.dir/graphsym.cpp.o CMakeFiles/openbabel.dir/grid.cpp.o CMakeFiles/openbabel.dir/griddata.cpp.o CMakeFiles/openbabel.dir/isomorphism.cpp.o CMakeFiles/openbabel.dir/kekulize.cpp.o CMakeFiles/openbabel.dir/locale.cpp.o CMakeFiles/openbabel.dir/matrix.cpp.o CMakeFiles/openbabel.dir/mcdlutil.cpp.o CMakeFiles/openbabel.dir/molchrg.cpp.o CMakeFiles/openbabel.dir/mol.cpp.o CMakeFiles/openbabel.dir/obconversion.cpp.o CMakeFiles/openbabel.dir/oberror.cpp.o CMakeFiles/openbabel.dir/obfunctions.cpp.o CMakeFiles/openbabel.dir/obiter.cpp.o CMakeFiles/openbabel.dir/obutil.cpp.o CMakeFiles/openbabel.dir/op.cpp.o CMakeFiles/openbabel.dir/parsmart.cpp.o CMakeFiles/openbabel.dir/patty.cpp.o CMakeFiles/openbabel.dir/phmodel.cpp.o CMakeFiles/openbabel.dir/plugin.cpp.o CMakeFiles/openbabel.dir/pointgroup.cpp.o CMakeFiles/openbabel.dir/query.cpp.o CMakeFiles/openbabel.dir/rand.cpp.o CMakeFiles/openbabel.dir/reactionfacade.cpp.o CMakeFiles/openbabel.dir/residue.cpp.o CMakeFiles/openbabel.dir/ring.cpp.o CMakeFiles/openbabel.dir/rotamer.cpp.o CMakeFiles/openbabel.dir/rotor.cpp.o CMakeFiles/openbabel.dir/spectrophore.cpp.o CMakeFiles/openbabel.dir/tautomer.cpp.o CMakeFiles/openbabel.dir/tokenst.cpp.o CMakeFiles/openbabel.dir/transform.cpp.o CMakeFiles/openbabel.dir/typer.cpp.o CMakeFiles/openbabel.dir/obmolecformat.cpp.o CMakeFiles/openbabel.dir/conformersearch.cpp.o CMakeFiles/openbabel.dir/confsearch.cpp.o CMakeFiles/openbabel.dir/distgeom.cpp.o CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o CMakeFiles/openbabel.dir/depict/depict.cpp.o CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o CMakeFiles/openbabel.dir/math/spacegroup.cpp.o CMakeFiles/openbabel.dir/math/transform3d.cpp.o CMakeFiles/openbabel.dir/math/vector3.cpp.o CMakeFiles/openbabel.dir/math/align.cpp.o CMakeFiles/openbabel.dir/stereo/stereo.cpp.o CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o CMakeFiles/openbabel.dir/stereo/perception.cpp.o CMakeFiles/openbabel.dir/stereo/facade.cpp.o CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o  -lmaeparser -lcoordgen -lm -ldl -lz
make[4]: *** [src/CMakeFiles/openbabel.dir/build.make:1244: lib/aarch64-linux-gnu/libopenbabel.so.7.0.0] Error 1


A fix is attached.

For background information see
https://wiki.debian.org/ToolChain/GCS
and https://bugs.debian.org/1115108#21
-------------- next part --------------
Description: Don't build with -Wl,--fatal-warnings
Author: Adrian Bunk <bunk at debian.org>

--- openbabel-3.1.1+dfsg.orig/CMakeLists.txt
+++ openbabel-3.1.1+dfsg/CMakeLists.txt
@@ -282,12 +282,12 @@ if(NOT MSVC)
   # note: Altough MinGW g++ 4.4 passes this test, visibility can't be used
   if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE)
     if(CMAKE_SYSTEM_NAME MATCHES Linux)
-      set (CMAKE_SHARED_LINKER_FLAGS "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
+      set (CMAKE_SHARED_LINKER_FLAGS "-Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
       set (CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-new-dtags ${CMAKE_SHARED_LINKER_FLAGS}")
-      set (CMAKE_MODULE_LINKER_FLAGS "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
+      set (CMAKE_MODULE_LINKER_FLAGS "-Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
       set (CMAKE_MODULE_LINKER_FLAGS "-Wl,--enable-new-dtags ${CMAKE_SHARED_LINKER_FLAGS}")
       if(BUILD_SHARED)
-        set (CMAKE_EXE_LINKER_FLAGS "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
+        set (CMAKE_EXE_LINKER_FLAGS "-Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
         set (CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-new-dtags ${CMAKE_EXE_LINKER_FLAGS}")
       endif()
     endif ()