[Debian-med-packaging] Bug#1037585: augustus: ftbfs with GCC-13

[Matthias Klose]

Package: src:augustus
Version: 3.5.0+dfsg-2
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13

[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-13/g++-13, but succeeds to build with gcc-12/g++-12. 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/2023/05/22/logs/augustus_3.5.0+dfsg-2_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html

[...]
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c compileSpliceCands.c
compileSpliceCands.c: In function ‘getChromosome’:
compileSpliceCands.c:216:9: warning: ‘__builtin_strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  216 |         strncat(checkstring,chromosomename,strlen(chromosomename));
      |         ^
compileSpliceCands.c:216:9: note: length computed here
  216 |         strncat(checkstring,chromosomename,strlen(chromosomename));
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c: In function ‘parseLine’:
compileSpliceCands.c:292:9: warning: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  292 |         strncpy(d->name,tokens[0],LINEBUFFER);
      |         ^
compileSpliceCands.c: In function ‘parseList’:
compileSpliceCands.c:333:69: warning: ‘left’ may be used uninitialized [-Wmaybe-uninitialized]
  333 |                         isCandidate = ((right->averageCoverage>=left->averageCoverage*threshold) ||
      |                                                                 ~~~~^~~~~~~~~~~~~~~~~
compileSpliceCands.c:314:14: note: ‘left’ was declared here
  314 |         Data left;
      |              ^~~~
compileSpliceCands.c: In function ‘main’:
compileSpliceCands.c:563:17: warning: ‘chromosomeLength’ may be used uninitialized [-Wmaybe-uninitialized]
  563 |                 parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c:416:18: note: ‘chromosomeLength’ was declared here
  416 |         long int chromosomeLength;
      |                  ^~~~~~~~~~~~~~~~
cc -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c -o list.o list.c
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o
cp -f compileSpliceCands ../../bin/compileSpliceCands
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools  -c filterBam.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools  -c functions/initOptions.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools  -c functions/printElapsedTime.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools  -c functions/MatePairs.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools  -c functions/PairednessCoverage.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools  -c BamToolsAccess.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib  -o filterBam  filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz
mkdir -p ../../../bin
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include    -c gene.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include    -c genome.cc
In file included from ../include/genome.hh:20,
                 from genome.cc:14:
../include/sqliteDB.hh:71:29: error: ‘uint64_t’ has not been declared
   71 |     void bindInt64(int idx, uint64_t x);
      |                             ^~~~~~~~
../include/sqliteDB.hh:80:12: error: ‘uint64_t’ does not name a type
   80 |     inline uint64_t int64Column(int colNum){return (uint64_t)sqlite3_column_int64(stmt,colNum);}
      |            ^~~~~~~~
../include/sqliteDB.hh:16:1: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
   15 | #include <sqlite3.h>
  +++ |+#include <cstdint>
   16 | 
make[2]: *** [Makefile:48: genome.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/auxprogs/homGeneMapping/src'
make[1]: *** [debian/rules:29: homGeneMapping] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2