Your message dated Sun, 11 Aug 2024 18:26:11 +0000
with message-id <e1sddgd-00hgjb...@fasolo.debian.org>
and subject line Bug#1075524: fixed in soapdenovo2 242+dfsg-4
has caused the Debian Bug report #1075524,
regarding soapdenovo2: ftbfs with GCC-14
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
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misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1075524: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075524
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:soapdenovo2
Version: 242+dfsg-3
Severity: important
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-14
[This bug is 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-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/soapdenovo2_242+dfsg-3_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 14, either set CC=gcc-14 CXX=g++-14 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
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-14/porting_to.html
[...]
/usr/bin/ld: ././cutTip_graph.c:237:(.text+0x985): undefined reference to
`getTwinEdge'
/usr/bin/ld: standardPregraph/linearEdge.o: in function
`linearUpdateConnection2':
././linearEdge.c:184:(.text+0x277): undefined reference to `getTwinEdge'
/usr/bin/ld: ././linearEdge.c:211:(.text+0x34e): undefined reference to
`getTwinEdge'
/usr/bin/ld: standardPregraph/linearEdge.o: in function `linearConcatenate2':
././linearEdge.c:409:(.text+0x8ae): undefined reference to `EdSameAsTwin'
/usr/bin/ld: ././linearEdge.c:427:(.text+0x95b): undefined reference to
`getTwinEdge'
/usr/bin/ld: ././linearEdge.c:450:(.text+0xa39): undefined reference to
`getTwinEdge'
/usr/bin/ld: standardPregraph/loadPath.o: in function `add1marker2edge':
././loadPath.c:49:(.text+0x6a): undefined reference to `getTwinEdge'
/usr/bin/ld: standardPregraph/loadPath.o: in function `loadPath':
././loadPath.c:93:(.text+0x1ee): undefined reference to `EdSmallerThanTwin'
/usr/bin/ld: ././loadPath.c:96:(.text+0x3c5): undefined reference to
`getTwinEdge'
/usr/bin/ld: standardPregraph/loadPath.o: in function `loadPathBin':
././loadPath.c:244:(.text+0x634): undefined reference to `EdSmallerThanTwin'
/usr/bin/ld: ././loadPath.c:247:(.text+0x82a): undefined reference to
`getTwinEdge'
/usr/bin/ld: standardPregraph/map.o: in function `call_align':
././map.c:131:(.text+0x69f): undefined reference to `prlLongRead2Ctg'
/usr/bin/ld: ././map.c:136:(.text+0x6dd): undefined reference to `prlRead2Ctg'
/usr/bin/ld: standardPregraph/output_contig.o: in function `output_graph':
././output_contig.c:52:(.text+0xd1): undefined reference to `getTwinEdge'
/usr/bin/ld: standardPregraph/output_contig.o: in function `output_contig':
././output_contig.c:216:(.text+0x451): undefined reference to
`EdSmallerThanTwin'
/usr/bin/ld: ././output_contig.c:271:(.text+0x639): undefined reference to
`getTwinEdge'
/usr/bin/ld: ././output_contig.c:282:(.text+0x742): undefined reference to
`EdSmallerThanTwin'
/usr/bin/ld: ././output_contig.c:302:(.text+0x8a8): undefined reference to
`EdSmallerThanTwin'
/usr/bin/ld: ././output_contig.c:307:(.text+0x8b3): undefined reference to
`EdLargerThanTwin'
/usr/bin/ld: standardPregraph/output_contig.o: in function
`output_updated_edges':
././output_contig.c:364:(.text+0xaec): undefined reference to
`EdSmallerThanTwin'
/usr/bin/ld: ././output_contig.c:368:(.text+0xbc4): undefined reference to
`EdLargerThanTwin'
/usr/bin/ld: standardPregraph/pregraph.o: in function `call_pregraph':
././pregraph.c:109:(.text+0x52f): undefined reference to `removeSingleTips'
/usr/bin/ld: ././pregraph.c:117:(.text+0x536): undefined reference to
`removeMinorTips'
/usr/bin/ld: ././pregraph.c:125:(.text+0x57b): undefined reference to
`kmer2edges'
/usr/bin/ld: ././pregraph.c:130:(.text+0x5b9): undefined reference to
`prlRead2edge'
/usr/bin/ld: ././pregraph.c:133:(.text+0x5ec): undefined reference to
`output_vertex'
/usr/bin/ld: standardPregraph/prlHashCtg.o: in function `chopKmer4read':
././prlHashCtg.c:221:(.text+0x3d3): undefined reference to `hash_kmer'
/usr/bin/ld: ././prlHashCtg.c:242:(.text+0x447): undefined reference to
`hash_kmer'
/usr/bin/ld: ././prlHashCtg.c:250:(.text+0x51e): undefined reference to
`hash_kmer'
/usr/bin/ld: ././prlHashCtg.c:228:(.text+0x5a1): undefined reference to
`hash_kmer'
/usr/bin/ld: standardPregraph/prlHashReads.o: in function `chopKmer4read':
././prlHashReads.c:200:(.text+0x52a): undefined reference to `hash_kmer'
/usr/bin/ld: standardPregraph/prlHashReads.o:././prlHashReads.c:223: more
undefined references to `hash_kmer' follow
/usr/bin/ld: standardPregraph/prlReadFillGap.o: in function `fill1scaf':
././prlReadFillGap.c:1315:(.text+0x941): undefined reference to `localGraph'
/usr/bin/ld: standardPregraph/splitReps.o: in function `solvable':
././splitReps.c:239:(.text+0x15): undefined reference to `EdSameAsTwin'
/usr/bin/ld: ././splitReps.c:244:(.text+0x49): undefined reference to
`getTwinEdge'
/usr/bin/ld: ././splitReps.c:287:(.text+0x119): undefined reference to
`EdSameAsTwin'
/usr/bin/ld: ././splitReps.c:300:(.text+0x15f): undefined reference to
`getTwinEdge'
/usr/bin/ld: ././splitReps.c:324:(.text+0x219): undefined reference to
`EdSameAsTwin'
/usr/bin/ld: ././splitReps.c:329:(.text+0x249): undefined reference to
`getTwinEdge'
/usr/bin/ld: standardPregraph/splitReps.o: in function `interferingCheck':
././splitReps.c:77:(.text+0x709): undefined reference to `getTwinEdge'
/usr/bin/ld: standardPregraph/splitReps.o: in function `cp1edge':
././splitReps.c:407:(.text+0x7de): undefined reference to `getTwinEdge'
/usr/bin/ld: standardPregraph/splitReps.o: in function `moveArc2cp':
././splitReps.c:476:(.text+0x99f): undefined reference to `getTwinEdge'
/usr/bin/ld: ././splitReps.c:477:(.text+0x9ab): undefined reference to
`getTwinEdge'
/usr/bin/ld: standardPregraph/splitReps.o:././splitReps.c:478: more undefined
references to `getTwinEdge' follow
/usr/bin/ld: standardPregraph/splitReps.o: in function `solveReps':
././splitReps.c:619:(.text+0xb4d): undefined reference to `EdSmallerThanTwin'
/usr/bin/ld: warning: creating DT_TEXTREL in a PIE
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:62: SOAPdenovo-63mer] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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-4
Done: Étienne Mollier <emoll...@debian.org>
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 1075...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 11 Aug 2024 19:08:09 +0200
Source: soapdenovo2
Architecture: source
Version: 242+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1075524
Changes:
soapdenovo2 (242+dfsg-4) unstable; urgency=medium
.
* Team upload.
* gcc-14.patch: new: fix a lot of issues caught by gcc 14. (Closes: #1075524)
* d/control: declare compliance to standards version 4.7.0.
* d/salsa-ci.yml: skip test build on i386.
This architecture is not declared supported by soapdenovo2.
Checksums-Sha1:
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soapdenovo2_242+dfsg-4.debian.tar.xz
Checksums-Sha256:
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soapdenovo2_242+dfsg-4.dsc
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Files:
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soapdenovo2_242+dfsg-4.dsc
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soapdenovo2_242+dfsg-4.debian.tar.xz
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--- End Message ---
