[Debian-med-packaging] Bug#1075524: soapdenovo2: ftbfs with GCC-14

[Matthias Klose]

Package: src:soapdenovo2
Version: 242+dfsg-3
Severity: important
Tags: sid trixie
User: debian-gcc at 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