[Debian-med-packaging] Bug#1096356: bambamc: ftbfs with GCC-15

Mon Feb 17 17:04:39 GMT 2025

Package: src:bambamc
Version: 0.0.50-6
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/bambamc_0.0.50-6_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

[...]
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking whether make sets $(MAKE)... yes
checking whether make supports the include directive... yes (GNU style)
checking whether make supports nested variables... yes
checking xargs -n works... yes
checking dependency style of gcc... none
checking for egrep... (cached) /usr/bin/grep -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for zlib >= 0... yes
checking for zlib >= 0... yes
checking whether we can compile a zlib program... yes
checking for _mkdir... no
checking for direct.h... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating ubuntu.sh
config.status: creating bambamc.pc
config.status: creating src/bambamc/BamBam_Config.h
config.status: creating config.h
config.status: executing libtool commands
config.status: executing depfiles commands
   dh_auto_build
	make -j8
make[1]: Entering directory '/build/reproducible-path/bambamc-0.0.50'
make  all-recursive
make[2]: Entering directory '/build/reproducible-path/bambamc-0.0.50'
Making all in src
make[3]: Entering directory '/build/reproducible-path/bambamc-0.0.50/src'
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c -o bamreadertest-bamreadertest.o `test -f 'test/bamreadertest.c' || echo './'`test/bamreadertest.c
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollationHash.lo `test -f 'bambamc/BamBam_BamCollationHash.c' || echo './'`bambamc/BamBam_BamCollationHash.c
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollatorInterface.lo `test -f 'bambamc/BamBam_BamCollatorInterface.c' || echo './'`bambamc/BamBam_BamCollatorInterface.c
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c -o libbambamc_la-BamBam_FormatAlignment.lo `test -f 'bambamc/BamBam_FormatAlignment.c' || echo './'`bambamc/BamBam_FormatAlignment.c
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollationHashEntry.lo `test -f 'bambamc/BamBam_BamCollationHashEntry.c' || echo './'`bambamc/BamBam_BamCollationHashEntry.c
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c -o libbambamc_la-BamBam_FormatNumber.lo `test -f 'bambamc/BamBam_FormatNumber.c' || echo './'`bambamc/BamBam_FormatNumber.c
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c -o libbambamc_la-BamBam_BamCollationOutputVector.lo `test -f 'bambamc/BamBam_BamCollationOutputVector.c' || echo './'`bambamc/BamBam_BamCollationOutputVector.c
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c -o libbambamc_la-BamBam_BamHeaderInfo.lo `test -f 'bambamc/BamBam_BamHeaderInfo.c' || echo './'`bambamc/BamBam_BamHeaderInfo.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamCollatorInterface.c  -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollatorInterface.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamCollationOutputVector.c  -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollationOutputVector.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamCollationHash.c  -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollationHash.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamHeaderInfo.c  -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamHeaderInfo.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamCollationHashEntry.c  -fPIC -DPIC -o .libs/libbambamc_la-BamBam_BamCollationHashEntry.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_FormatAlignment.c  -fPIC -DPIC -o .libs/libbambamc_la-BamBam_FormatAlignment.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_FormatNumber.c  -fPIC -DPIC -o .libs/libbambamc_la-BamBam_FormatNumber.o
bambamc/BamBam_FormatAlignment.c: In function 'BamBam_GetFastqEntryLength':
bambamc/BamBam_FormatAlignment.c:47:17: error: too many arguments to function 'BamBam_GetFastqPlusLineLength'; expected 0, have 1
   47 |                 BamBam_GetFastqPlusLineLength(qnamelen) +
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~
bambamc/BamBam_FormatAlignment.c:33:17: note: declared here
   33 | static uint64_t BamBam_GetFastqPlusLineLength()
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:627: libbambamc_la-BamBam_FormatAlignment.lo] Error 1
make[3]: *** Waiting for unfinished jobs....
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamCollationHash.c -o libbambamc_la-BamBam_BamCollationHash.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamCollationHashEntry.c -o libbambamc_la-BamBam_BamCollationHashEntry.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamCollationOutputVector.c -o libbambamc_la-BamBam_BamCollationOutputVector.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_FormatNumber.c -o libbambamc_la-BamBam_FormatNumber.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamCollatorInterface.c -o libbambamc_la-BamBam_BamCollatorInterface.o >/dev/null 2>&1
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bambamc-0.0.50=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -rdynamic -c bambamc/BamBam_BamHeaderInfo.c -o libbambamc_la-BamBam_BamHeaderInfo.o >/dev/null 2>&1
make[3]: Leaving directory '/build/reproducible-path/bambamc-0.0.50/src'
make[2]: *** [Makefile:480: all-recursive] Error 1
make[2]: Leaving directory '/build/reproducible-path/bambamc-0.0.50'
make[1]: *** [Makefile:385: all] Error 2
make[1]: Leaving directory '/build/reproducible-path/bambamc-0.0.50'
dh_auto_build: error: make -j8 returned exit code 2
make: *** [debian/rules:3: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2