[Debichem-devel] Bug#1115341: avogadrolibs FTBFS on arm64 with gcc 15

[Adrian Bunk]

Source: avogadrolibs
Version: 1.100.0-1
Severity: serious
Tags: ftbfs patch forky sid

https://buildd.debian.org/status/fetch.php?pkg=avogadrolibs&arch=arm64&ver=1.100.0-2&stamp=1757959253&raw=0

...
[  7%] Linking CXX shared library ../../lib/libAvogadroCore.so
cd /build/reproducible-path/avogadrolibs-1.100.0/obj-aarch64-linux-gnu/avogadro/core && /usr/bin/cmake -E cmake_link_script CMakeFiles/Core.dir/link.txt --verbose=1
/usr/lib/aarch64-linux-gnu/libsymspg.so.2.6.0: 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.
/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 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/avogadrolibs-1.100.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wl,--dependency-file=CMakeFiles/Core.dir/link.d -Wl,--fatal-warnings -Wl,--no-undefined -lc -fPIC -Wl,-z,relro -Wl,-z,now -Wl,-z,defs -Wl,--as-needed -shared -Wl,-soname,libAvogadroCore.so.1 -o ../../lib/libAvogadroCore.so.1.100.0 CMakeFiles/Core.dir/angleiterator.cpp.o CMakeFiles/Core.dir/atomutilities.cpp.o CMakeFiles/Core.dir/coordinateblockgenerator.cpp.o CMakeFiles/Core.dir/crystaltools.cpp.o CMakeFiles/Core.dir/cube.cpp.o CMakeFiles/Core.dir/elements.cpp.o CMakeFiles/Core.dir/dihedraliterator.cpp.o CMakeFiles/Core.dir/gaussianset.cpp.o CMakeFiles/Core.dir/gaussiansettools.cpp.o CMakeFiles/Core.dir/graph.cpp.o CMakeFiles/Core.dir/layer.cpp.o CMakeFiles/Core.dir/layermanager.cpp.o CMakeFiles/Core.dir/mesh.cpp.o CMakeFiles/Core.dir/molecule.cpp.o CMakeFiles/Core.dir/mutex.cpp.o CMakeFiles/Core.dir/nameatomtyper.cpp.o CMakeFiles/Core.dir/neighborperceiver.cpp.o CMakeFiles/Core.dir/residue.cpp.o CMakeFiles/Core.dir/ringperceiver.cpp.o CMakeFiles/Core.dir/secondarystructure.cpp.o CMakeFiles/Core.dir/slaterset.cpp.o CMakeFiles/Core.dir/slatersettools.cpp.o CMakeFiles/Core.dir/spacegroups.cpp.o CMakeFiles/Core.dir/symbolatomtyper.cpp.o CMakeFiles/Core.dir/unitcell.cpp.o CMakeFiles/Core.dir/variantmap.cpp.o CMakeFiles/Core.dir/version.cpp.o CMakeFiles/Core.dir/sharedmutex.cpp.o CMakeFiles/Core.dir/avospglib.cpp.o  /usr/lib/aarch64-linux-gnu/libsymspg.so.2.6.0 -lm
make[3]: *** [avogadro/core/CMakeFiles/Core.dir/build.make:553: lib/libAvogadroCore.so.1.100.0] Error 1



The attached patch fixes it.

For background see https://wiki.debian.org/ToolChain/GCS
-------------- next part --------------
Description: Do not make linker warnings fatal
Author: Adrian Bunk <bunk at debian.org>

--- avogadrolibs-1.100.0.orig/cmake/CompilerFlags.cmake
+++ avogadrolibs-1.100.0/cmake/CompilerFlags.cmake
@@ -16,11 +16,11 @@ if(CMAKE_COMPILER_IS_GNUCXX)
   # If we are compiling on Linux then set some extra linker flags too
   if(CMAKE_SYSTEM_NAME MATCHES Linux)
     set(CMAKE_SHARED_LINKER_FLAGS
-      "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
+      "-Wl,--no-undefined -lc ${CMAKE_SHARED_LINKER_FLAGS}")
     set(CMAKE_MODULE_LINKER_FLAGS
-      "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_MODULE_LINKER_FLAGS}")
+      "-Wl,--no-undefined -lc ${CMAKE_MODULE_LINKER_FLAGS}")
     set (CMAKE_EXE_LINKER_FLAGS
-      "-Wl,--fatal-warnings -Wl,--no-undefined -lc ${CMAKE_EXE_LINKER_FLAGS}")
+      "-Wl,--no-undefined -lc ${CMAKE_EXE_LINKER_FLAGS}")
   endif()
 
   # Set up the debug CXX_FLAGS for extra warnings