Your message dated Wed, 22 Oct 2025 23:05:42 +0000
with message-id <[email protected]>
and subject line Bug#1097906: fixed in soapaligner 2.20-6
has caused the Debian Bug report #1097906,
regarding soapaligner: 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.
(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.)
--
1097906: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097906
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:soapaligner
Version: 2.20-5
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/soapaligner_2.20-5_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
[...]
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=user42
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=user42
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -b
dpkg-buildpackage: info: source package soapaligner
dpkg-buildpackage: info: source version 2.20-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <[email protected]>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_auto_clean
make -j8 clean
make[1]: Entering directory '/build/reproducible-path/soapaligner-2.20'
rm -f *.o soap
make[1]: Leaving directory '/build/reproducible-path/soapaligner-2.20'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/soapaligner.substvars debian/files
rm -fr -- debian/soapaligner/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path
.\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o
-type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \)
-prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j8 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/soapaligner-2.20'
cc -c -flto -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -funroll-loops
-maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS
-DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" SeqIO.c -o SeqIO.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -funroll-loops
-maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS
-DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" MiscUtilities.c -o MiscUtilities.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -funroll-loops
-maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS
-DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" MemManager.c -o MemManager.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -funroll-loops
-maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS
-DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" TextConverter.c -o TextConverter.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -funroll-loops
-maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS
-DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" r250.c -o r250.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -funroll-loops
-maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS
-DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" DNACount.c -o DNACount.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -funroll-loops
-maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS
-DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" HSP.c -o HSP.o
cc -c -flto -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -O3 -funroll-loops
-maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS
-DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" Timing.c -o Timing.o
r250.c:31:21: error: conflicting types for ‘randlcg’; have ‘unsigned int(int)’
31 | static unsigned int randlcg(int sd) /* returns a random unsigned
integer */
| ^~~~~~~
r250.c:19:21: note: previous declaration of ‘randlcg’ with type ‘unsigned
int(void)’
19 | static unsigned int randlcg();
| ^~~~~~~
r250.c: In function ‘randlcg’:
r250.c:33:41: warning: overflow in conversion from ‘long int’ to ‘int’ changes
value from ‘548781581296767’ to ‘724984959’ [-Woverflow]
33 | static int quotient1 = LONG_MAX / 16807L;
| ^~~~~~~~
make[1]: *** [Makefile:45: r250.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory '/build/reproducible-path/soapaligner-2.20'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned
exit code 2
make: *** [debian/rules:14: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: soapaligner
Source-Version: 2.20-6
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
soapaligner, 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.
Étienne Mollier <[email protected]> (supplier of updated soapaligner 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: Wed, 22 Oct 2025 23:00:20 +0200
Source: soapaligner
Architecture: source
Version: 2.20-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097906
Changes:
soapaligner (2.20-6) unstable; urgency=medium
.
* Team upload.
* gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097906)
* d/patches/*: normalize Last-Update timestamp.
* d/watch: convert to untrackable watch file v5.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare complianct to standards version 4.7.2.
* d/rules: simplify passing lto flags.
* cppflags.patch: new: propagate CPPFLAGS.
This improves binaries hardening by fortifying sources.
Checksums-Sha1:
454de184d6409b6d3df4702ef49c03006ab1673c 2155 soapaligner_2.20-6.dsc
aedf17fc3e78a245fb45572354a9b1d00498d282 6736 soapaligner_2.20-6.debian.tar.xz
Checksums-Sha256:
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soapaligner_2.20-6.dsc
79f3914ad3821ef5d636f4eb0780f74f63a339b5ed750d577a619ad8a87f32f9 6736
soapaligner_2.20-6.debian.tar.xz
Files:
b75ba4d005c12a4031fd7c39097b1ee3 2155 science optional soapaligner_2.20-6.dsc
25396ccebb7a0ff626388bd06771defd 6736 science optional
soapaligner_2.20-6.debian.tar.xz
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