[Debian-med-packaging] Bug#1096345: augustus: ftbfs with GCC-15
Matthias Klose
doko at debian.org
Mon Feb 17 17:04:18 GMT 2025
Package: src:augustus
Version: 3.5.0+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/augustus_3.5.0+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
[...]
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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o
cp -f compileSpliceCands ../../bin/compileSpliceCands
make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/augustus-3.5.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I./headers -I/usr/include/bamtools -c filterBam.cc
In file included from ./headers/filterBam.h:10,
from filterBam.cc:28:
./headers/bamaccess.hh:76:13: error: ‘uint32_t’ does not name a type
76 | virtual uint32_t countEqualSignsInQuerySequence() const = 0;
| ^~~~~~~~
./headers/bamaccess.hh:10:1: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
9 | #include <memory>
+++ |+#include <cstdint>
10 |
./headers/bamaccess.hh:84:13: error: ‘uint32_t’ does not name a type
84 | virtual uint32_t countCigarOperations(const char& type) const = 0;
| ^~~~~~~~
./headers/bamaccess.hh:84:13: note: ‘uint32_t’ is defined in header ‘<cstdint>’; this is probably fixable by adding ‘#include <cstdint>’
In file included from filterBam.cc:34:
./headers/bamtoolsaccess.hh:81:21: error: ‘uint32_t BamToolsAlignmentRecord::countEqualSignsInQuerySequence() const’ marked ‘override’, but does not override
81 | inline uint32_t countEqualSignsInQuerySequence() const override final;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./headers/bamtoolsaccess.hh:81:21: error: ‘uint32_t BamToolsAlignmentRecord::countEqualSignsInQuerySequence() const’ marked ‘final’, but is not virtual
./headers/bamtoolsaccess.hh:89:21: error: ‘uint32_t BamToolsAlignmentRecord::countCigarOperations(const char&) const’ marked ‘override’, but does not override
89 | inline uint32_t countCigarOperations(const char& type) const override final;
| ^~~~~~~~~~~~~~~~~~~~
./headers/bamtoolsaccess.hh:89:21: error: ‘uint32_t BamToolsAlignmentRecord::countCigarOperations(const char&) const’ marked ‘final’, but is not virtual
filterBam.cc: In function ‘int main(int, char**)’:
filterBam.cc:304:49: error: ‘using std::__shared_ptr_access<BamAlignmentRecord, __gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’ {aka ‘class BamAlignmentRecord’} has no member named ‘countEqualSignsInQuerySequence’
304 | percId = (float) 100 * (al->countEqualSignsInQuerySequence() - al->countCigarOperations('D')) / qLength;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
filterBam.cc:304:88: error: ‘using std::__shared_ptr_access<BamAlignmentRecord, __gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’ {aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
304 | percId = (float) 100 * (al->countEqualSignsInQuerySequence() - al->countCigarOperations('D')) / qLength;
| ^~~~~~~~~~~~~~~~~~~~
filterBam.cc:306:65: error: ‘using std::__shared_ptr_access<BamAlignmentRecord, __gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’ {aka ‘class BamAlignmentRecord’} has no member named ‘countEqualSignsInQuerySequence’
306 | else if (checkForEqualSigns && (numEquals = al->countEqualSignsInQuerySequence()) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
filterBam.cc:309:61: error: ‘using std::__shared_ptr_access<BamAlignmentRecord, __gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’ {aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
309 | percId = (float) 100 * (numEquals - al->countCigarOperations('D')) / qLength;
| ^~~~~~~~~~~~~~~~~~~~
filterBam.cc:315:74: error: ‘using std::__shared_ptr_access<BamAlignmentRecord, __gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’ {aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
315 | percId = (float) 100 * (qLength - editDistance - al->countCigarOperations('S')) / qLength;
| ^~~~~~~~~~~~~~~~~~~~
filterBam.cc:338:40: error: ‘using std::__shared_ptr_access<BamAlignmentRecord, __gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’ {aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
338 | countIOperations = al->countCigarOperations('I');
| ^~~~~~~~~~~~~~~~~~~~
filterBam.cc:339:47: error: ‘using std::__shared_ptr_access<BamAlignmentRecord, __gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’ {aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
339 | coverage = (float) 100 * (al->countCigarOperations('M') + countIOperations) / qLength; // sumMandIOperations() - Equiv to $qEnd-$qStart in PSL
| ^~~~~~~~~~~~~~~~~~~~
filterBam.cc:352:34: error: ‘using std::__shared_ptr_access<BamAlignmentRecord, __gnu_cxx::_S_atomic, false, false>::element_type = class BamAlignmentRecord’ {aka ‘class BamAlignmentRecord’} has no member named ‘countCigarOperations’
352 | baseInsert = al->countCigarOperations('D') + countIOperations;
| ^~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:68: filterBam.o] Error 1
make[3]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam/src'
make[2]: *** [Makefile:7: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg/auxprogs/filterBam'
make[1]: *** [debian/rules:26: filterBam] Error 2
make[1]: Leaving directory '/build/reproducible-path/augustus-3.5.0+dfsg'
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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