Your message dated Tue, 16 Sep 2025 11:04:25 +0000
with message-id <[email protected]>
and subject line Bug#1115341: fixed in avogadrolibs 1.101.0-2
has caused the Debian Bug report #1115341,
regarding avogadrolibs FTBFS on arm64 with gcc 15
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1115341: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1115341
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
Description: Do not make linker warnings fatal
Author: Adrian Bunk <[email protected]>
--- 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
--- End Message ---
--- Begin Message ---
Source: avogadrolibs
Source-Version: 1.101.0-2
Done: Drew Parsons <[email protected]>
We believe that the bug you reported is fixed in the latest version of
avogadrolibs, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (supplier of updated avogadrolibs package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 16 Sep 2025 11:22:13 +0200
Source: avogadrolibs
Architecture: source
Version: 1.101.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1115341
Changes:
avogadrolibs (1.101.0-2) unstable; urgency=medium
.
* avogadro treats warnings as fatal errors so set
gcs-report-dynamic=none to not warn about the
new GCS feature on arm64. See Bug#1110448.
Closes: #1115341.
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