Your message dated Mon, 06 Oct 2025 11:09:58 +0000
with message-id <[email protected]>
and subject line Bug#1116631: fixed in openbabel 3.1.1+dfsg-14
has caused the Debian Bug report #1116631,
regarding openbabel FTBFS on arm64 due to -Wl,--fatal-warnings
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.)
--
1116631: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1116631
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: openbabel
Version: 3.1.1+dfsg-12
Severity: serious
Tags: ftbfs forky sid patch
X-Debbugs-Cc: [email protected], Andrius Merkys <[email protected]>
User: [email protected]
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
Description: Don't build with -Wl,--fatal-warnings
Author: Adrian Bunk <[email protected]>
--- 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 ()
--- End Message ---
--- Begin Message ---
Source: openbabel
Source-Version: 3.1.1+dfsg-14
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
openbabel, 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.
Santiago Vila <[email protected]> (supplier of updated openbabel 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: Mon, 06 Oct 2025 12:45:00 +0200
Source: openbabel
Architecture: source
Version: 3.1.1+dfsg-14
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1116631
Changes:
openbabel (3.1.1+dfsg-14) unstable; urgency=medium
.
* Team upload.
.
[ Adrian Bunk ]
* Don't build with -Wl,--fatal-warnings. Closes: #1116631.
.
[ Santiago Vila ]
* Drop "Priority: optional", as it's now the default.
* Drop "Rules-Requires-Root: no", as it's now the default.
* Update standards-version.
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