Your message dated Fri, 24 Oct 2025 18:21:52 +0000
with message-id <[email protected]>
and subject line Bug#1097909: fixed in soapdenovo2 242+dfsg-5
has caused the Debian Bug report #1097909,
regarding soapdenovo2: 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.)
--
1097909: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1097909
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:soapdenovo2
Version: 242+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/soapdenovo2_242+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
[...]
SOAPdenovo-63mer cleaning done.
Compiling arc.c...
Compiling attachPEinfo.c...
Compiling bubble.c...
Compiling check.c...
Compiling compactEdge.c...
Compiling concatenateEdge.c...
Compiling connect.c...
Compiling contig.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...
Compiling newhash.c...
Compiling node2edge.c...
Compiling orderContig.c...
orderContig.c:1965:13: error: conflicting types for ‘debugging2’; have
‘void(unsigned int)’
1965 | static void debugging2 ( unsigned int ctg )
| ^~~~~~~~~~
orderContig.c:86:13: note: previous declaration of ‘debugging2’ with type
‘void(void)’
86 | static void debugging2();
| ^~~~~~~~~~
Error in command: gcc -c -O3 -fomit-frame-pointer -w -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/soapdenovo2-242+dfsg/standardPregraph=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2
-DBDATE="Aug 11 2024" -DBTIME="17:08:09" -DMER63 -m64 -Iinc
-I/usr/include/samtools orderContig.c
Compiling output_contig.c...
Compiling output_pregraph.c...
Compiling output_scaffold.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...
Compiling cutTip_graph2.c...
Compiling linearEdge.c...
Compiling kmerhash.c...
Compiling read2edge.c...
Compiling iterate.c...
SOAPdenovo-63mer objects generated.
/usr/bin/ld: standardPregraph/scaffold.o: in function `call_scaffold':
././scaffold.c:71:(.text+0x7e8): undefined reference to `checkFiles4Scaff'
/usr/bin/ld: ././scaffold.c:93:(.text+0x85f): undefined reference to `ScafStat'
/usr/bin/ld: ././scaffold.c:81:(.text+0x970): undefined reference to `PE2Links'
/usr/bin/ld: ././scaffold.c:86:(.text+0x9ce): undefined reference to
`Links2Scaf'
/usr/bin/ld: ././scaffold.c:89:(.text+0xa0c): undefined reference to
`scaffolding'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:62: SOAPdenovo-63mer] Error 1
dh_auto_build: error: make -j1 "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: soapdenovo2
Source-Version: 242+dfsg-5
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
soapdenovo2, 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 soapdenovo2 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: Fri, 24 Oct 2025 19:53:20 +0200
Source: soapdenovo2
Architecture: source
Version: 242+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1097909 1105578
Changes:
soapdenovo2 (242+dfsg-5) unstable; urgency=medium
.
* Team upload.
* gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1097909)
* fix-deps.patch: new: stabilise make rules ordering. (Closes: #1105578)
* reproducible patch: normalise Last-Update timestamp.
* d/watch: bump to watch file version 5.
* d/u/metadata: locate upstream repository.
* d/control: drop redundant Rules-Requires-Root: no.
* d/control: declare compliance to standards version 4.7.2.
Checksums-Sha1:
c1beb3ca4cc4dbcbcc25d4bfaf541ca38bef62bf 2283 soapdenovo2_242+dfsg-5.dsc
09e73b0db7ccec22a1ace65b2b2ebb588b5d88d5 490384
soapdenovo2_242+dfsg-5.debian.tar.xz
Checksums-Sha256:
769387b0aeb964dbaeaba083fc72fb07fdd6e2d12d469dad3e760f62d9925c44 2283
soapdenovo2_242+dfsg-5.dsc
9527bbf9471bb5249fdbcb899e7a61e8c57c903f3075512da0b8e22afbf0aa86 490384
soapdenovo2_242+dfsg-5.debian.tar.xz
Files:
6abe71f9681f209a4ab5f75634e5ba4d 2283 science optional
soapdenovo2_242+dfsg-5.dsc
e27036d80543de3c7dd051c29938293c 490384 science optional
soapdenovo2_242+dfsg-5.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=jfLa
-----END PGP SIGNATURE-----
pgpE2KpdfXc8F.pgp
Description: PGP signature
--- End Message ---
