Your message dated Wed, 22 Oct 2025 23:05:49 +0000
with message-id <[email protected]>
and subject line Bug#1097907: fixed in soapdenovo 1.05-7
has caused the Debian Bug report #1097907,
regarding soapdenovo: 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.)
--
1097907: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097907
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:soapdenovo
Version: 1.05-6
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/soapdenovo_1.05-6_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
[...]
make[1]: Entering directory '/build/reproducible-path/soapdenovo-1.05'
make[2]: Entering directory '/build/reproducible-path/soapdenovo-1.05/src/31mer'
Compiling arc.c...
Compiling attachPEinfo.c...
Compiling bubble.c...
Compiling check.c...
Compiling compactEdge.c...
Compiling concatenateEdge.c...
Compiling contig.c...
Compiling connect.c...
Compiling cutTipPreGraph.c...
Compiling cutTip_graph.c...
Compiling darray.c...
Compiling dfib.c...
Compiling dfibHeap.c...
Compiling fib.c...
Compiling fibHeap.c...
Compiling hashFunction.c...
Compiling kmer.c...
Compiling lib.c...
Compiling loadGraph.c...
Compiling loadPath.c...
Compiling loadPreGraph.c...
Compiling localAsm.c...
Compiling main.c...
Compiling map.c...
Compiling mem_manager.c...
map.c: In function ‘getMinOverlap.constprop’:
map.c:40:28: warning: ‘.preGraphBasic’ directive writing 14 bytes into a region
of size between 1 and 256 [-Wformat-overflow=]
40 | sprintf ( name, "%s.preGraphBasic", gfile );
| ^~~~~~~~~~~~~~
map.c:40:9: note: ‘sprintf’ output between 15 and 270 bytes into a destination
of size 256
40 | sprintf ( name, "%s.preGraphBasic", gfile );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Compiling newhash.c...
Compiling node2edge.c...
Compiling orderContig.c...
Compiling output_contig.c...
orderContig.c:1261:13: error: conflicting types for ‘debugging2’; have
‘void(unsigned int)’
1261 | static void debugging2 ( unsigned int ctg )
| ^~~~~~~~~~
orderContig.c:76:13: note: previous declaration of ‘debugging2’ with type
‘void(void)’
76 | static void debugging2();
| ^~~~~~~~~~
Compiling output_pregraph.c...
Compiling output_scaffold.c...
Error in command: gcc -c -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapdenovo-1.05=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -fcommon -O3 -fomit-frame-pointer -m64
-g -Iinc orderContig.c
Compiling pregraph.c...
Compiling prlHashCtg.c...
Compiling prlHashReads.c...
Compiling prlRead2Ctg.c...
Compiling prlRead2path.c...
Compiling prlReadFillGap.c...
Compiling read2scaf.c...
Compiling readInterval.c...
Compiling stack.c...
Compiling readseq1by1.c...
Compiling scaffold.c...
Compiling searchPath.c...
Compiling seq.c...
Compiling splitReps.c...
/usr/bin/ld: cannot find orderContig.o: No such file or directory
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:58: SOAPdenovo] Error 1
make[2]: Leaving directory '/build/reproducible-path/soapdenovo-1.05/src/31mer'
make[1]: *** [Makefile:9: mer31] Error 2
make[1]: Leaving directory '/build/reproducible-path/soapdenovo-1.05'
dh_auto_build: error: make -j8 "INSTALL=install --strip-program=true" returned
exit code 2
make: *** [debian/rules:13: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: soapdenovo
Source-Version: 1.05-7
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
soapdenovo, 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 soapdenovo 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 23:26:00 +0200
Source: soapdenovo
Architecture: source
Version: 1.05-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097907
Changes:
soapdenovo (1.05-7) unstable; urgency=medium
.
* Team upload.
* gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097907)
* d/watch: convert to untrackable watch file v5.
* build-flags.patch: new: propagate build flags.
This notably fixes missing binaries hardening.
* add_debug_symbols.patch: normalize Last-Update timestamp.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.2.
Checksums-Sha1:
33afaf854e8ee01bcc82ed2b0586c1ac4556571c 2169 soapdenovo_1.05-7.dsc
c9c614f433c056120ed50295e3f58d04b43e8e34 608744 soapdenovo_1.05-7.debian.tar.xz
Checksums-Sha256:
686376a26b0f46a5fb191a9372d6b78d9ee3b26e9b687eba11ea30d0dce726d9 2169
soapdenovo_1.05-7.dsc
523a05752e20d81ae5f02bb89704f5ad94b40cbb4c549544472a2f452f6319fe 608744
soapdenovo_1.05-7.debian.tar.xz
Files:
4f9a3ccc6efd18d5620a6cfb7ab05c85 2169 science optional soapdenovo_1.05-7.dsc
835fe9599ab03e1215403b70d0a93e02 608744 science optional
soapdenovo_1.05-7.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=mO+r
-----END PGP SIGNATURE-----
pgpQNqh4phvOT.pgp
Description: PGP signature
--- End Message ---
