[Debian-med-packaging] Bug#1097907: soapdenovo: ftbfs with GCC-15

[Matthias Klose]

Package: src:soapdenovo
Version: 1.05-6
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/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