[Debian-med-packaging] Bug#1097909: soapdenovo2: ftbfs with GCC-15

[Matthias Klose]

Package: src:soapdenovo2
Version: 242+dfsg-4
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
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