Your message dated Fri, 01 Aug 2025 13:33:59 +0000
with message-id <[email protected]>
and subject line Bug#1096281: fixed in aegean 0.16.0+dfsg-5~exp0
has caused the Debian Bug report #1096281,
regarding aegean: ftbfs 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.
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--
1096281: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1096281
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:aegean
Version: 0.16.0+dfsg-4
Severity: important
Tags: sid forky
User: [email protected]
Usertags: ftbfs-gcc-15
[This bug is NOT targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.
The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/aegean_0.16.0+dfsg-4_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other Common build failures are new warnings resulting in build failures
with -Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-15/porting_to.html
[...]
dh_auto_build -- prefix=/build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp
64bit=yes errorcheck=no
make -j8 "INSTALL=install --strip-program=true"
prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp 64bit=yes
errorcheck=no
make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg'
[print inc/core/AgnVersion.h]
/build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:31:
SyntaxWarning: invalid escape sequence '\S'
sha1match = re.search('commit (\S+)', logout)
/build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:37:
SyntaxWarning: invalid escape sequence '\s'
yearmatch = re.search('Date:\s+.+(\d{4}) ', logout)
[compile AgnAttributeFilterStream]
[compile AgnCliquePair]
[compile AgnCompareReportHTML]
[compile AgnCompareReportText]
[compile AgnFilterStream]
[compile AgnComparison]
[compile AgnGaevalVisitor]
[compile AgnGeneStream]
src/core/AgnCompareReportText.c: In function
‘compare_report_text_comp_class_summary’:
src/core/AgnCompareReportText.c:287:3: warning: ‘__builtin___strncpy_chk’
output truncated before terminating nul copying as many bytes from a string as
its length [-Wstringop-truncation]
287 | strncpy(header + 4, label, strlen(label));
| ^
src/core/AgnCompareReportText.c:287:30: note: length computed here
287 | strncpy(header + 4, label, strlen(label));
| ^~~~~~~~~~~~~
[compile AgnInferCDSVisitor]
src/core/AgnCompareReportText.c: In function
‘compare_report_text_summary_struc’:
src/core/AgnCompareReportText.c:589:3: warning: ‘__builtin___strncpy_chk’
output truncated before terminating nul copying as many bytes from a string as
its length [-Wstringop-truncation]
589 | strncpy(buffer + 14, units, strlen(units));
| ^
src/core/AgnCompareReportText.c:589:31: note: length computed here
589 | strncpy(buffer + 14, units, strlen(units));
| ^~~~~~~~~~~~~
src/core/AgnCompareReportText.c:599:3: warning: ‘__builtin___strncpy_chk’
output truncated before terminating nul copying as many bytes from a string as
its length [-Wstringop-truncation]
599 | strncpy(buffer + 15, units, strlen(units));
| ^
src/core/AgnCompareReportText.c:599:31: note: length computed here
599 | strncpy(buffer + 15, units, strlen(units));
| ^~~~~~~~~~~~~
[compile AgnInferExonsVisitor]
[compile AgnInferParentStream]
[compile AgnLocus]
[compile AgnLocusFilterStream]
[compile AgnLocusMapVisitor]
[compile AgnLocusRefineStream]
[compile AgnLocusStream]
[compile AgnMrnaRepVisitor]
[compile AgnPseudogeneFixVisitor]
[compile AgnRemoveChildrenVisitor]
src/core/AgnRemoveChildrenVisitor.c:47:16: error: conflicting types for
‘agn_remove_children_visitor_new’; have ‘GtNodeVisitor *(GtLogger *)’
47 | GtNodeVisitor *agn_remove_children_visitor_new(GtLogger *logger)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/core/AgnRemoveChildrenVisitor.c:10:
inc/core/AgnRemoveChildrenVisitor.h:33:16: note: previous declaration of
‘agn_remove_children_visitor_new’ with type ‘GtNodeVisitor *(void)’
33 | GtNodeVisitor *agn_remove_children_visitor_new();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/core/AgnPseudogeneFixVisitor.c:49:16: error: conflicting types for
‘agn_pseudogene_fix_visitor_new’; have ‘GtNodeVisitor *(GtLogger *)’
49 | GtNodeVisitor *agn_pseudogene_fix_visitor_new(GtLogger *logger)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/core/AgnPseudogeneFixVisitor.c:12:
inc/core/AgnPseudogeneFixVisitor.h:34:16: note: previous declaration of
‘agn_pseudogene_fix_visitor_new’ with type ‘GtNodeVisitor *(void)’
34 | GtNodeVisitor *agn_pseudogene_fix_visitor_new();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [Makefile:107: obj/AgnRemoveChildrenVisitor.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [Makefile:107: obj/AgnPseudogeneFixVisitor.o] Error 1
make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true"
prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp 64bit=yes
errorcheck=no returned exit code 2
make[1]: *** [debian/rules:21: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg'
make: *** [debian/rules:18: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: aegean
Source-Version: 0.16.0+dfsg-5~exp0
Done: Sascha Steinbiss <[email protected]>
We believe that the bug you reported is fixed in the latest version of
aegean, 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.
Sascha Steinbiss <[email protected]> (supplier of updated aegean 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: SHA256
Format: 1.8
Date: Fri, 01 Aug 2025 14:42:11 +0200
Source: aegean
Binary: aegean aegean-dbgsym
Architecture: source amd64
Version: 0.16.0+dfsg-5~exp0
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Sascha Steinbiss <[email protected]>
Description:
aegean - integrated genome analysis toolkit
Closes: 1096281 1109688
Changes:
aegean (0.16.0+dfsg-5~exp0) experimental; urgency=medium
.
[ Dandan Zhang ]
* Append loong64 support in d/control.
Closes: #1109688
* Do not use -m64 CFLAGS on loongarch64.
.
[ Sascha Steinbiss ]
* Bump Standards-Version.
* Fix building with GCC 15.
Closes: #1096281
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