Your message dated Thu, 25 Sep 2025 19:05:18 +0000
with message-id <[email protected]>
and subject line Bug#1096356: fixed in bambamc 0.0.50-7
has caused the Debian Bug report #1096356,
regarding bambamc: ftbfs with GCC-15
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1096356: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1096356
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:bambamc
Version: 0.0.50-6
Severity: important
Tags: sid forky
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Source: bambamc
Source-Version: 0.0.50-7
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
bambamc, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated bambamc package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 25 Sep 2025 20:02:21 +0200
Source: bambamc
Architecture: source
Version: 0.0.50-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1096356
Changes:
bambamc (0.0.50-7) unstable; urgency=medium
.
* Team upload.
* gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1096356)
* d/control: build depends on pkgconf.
* d/control: libbambamc-dev depends on pkgconf.
* d/watch: convert to watch file version 5.
* d/control: remove redundant Rules-Requires-Root.
* d/control: declare compliance to standards version 4.7.2.
Checksums-Sha1:
0f3fb55d405bb75f4ca8a4d5a03b6af113f5a5d5 2214 bambamc_0.0.50-7.dsc
96bfdd1a97aaa56a9e622926a67122dc6df88adb 3380 bambamc_0.0.50-7.debian.tar.xz
Checksums-Sha256:
8b5aceda8ed90dc8b293ea2ea785b09ba595b302f7ba2a814f21c35ce37cb790 2214
bambamc_0.0.50-7.dsc
7ac53c9a2df1fcae9860acb90aedd3319b4605aa7461d8da87035032c68e88f8 3380
bambamc_0.0.50-7.debian.tar.xz
Files:
ff59228daa216c37332de96ef30033d1 2214 science optional bambamc_0.0.50-7.dsc
66d3dc0bccbb711f885f12507323c797 3380 science optional
bambamc_0.0.50-7.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmjVjUMUHGVtb2xsaWVy
QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpfoxAAj8vYGrBBKifGheSe0dC3gyAb4xol
hmUl5A/7s5WuHsbFKln9CbH0+7fIsURfEEwjrSpoXX1HggPkZB1tC5ga3Zopg6wE
1tV++dYY95Zijh0CmK9rt2YMkGlnK+TLD9AiAraNPW+JUEOB5U5FF185oKWDgVpe
SO4Cp2Ekk2RKGyYTS9ORbCcDKi4WZCXrCvAfIJ3ueq4bk1f4tyGTzpy/hDbSCBK5
LXKygX+yjp1pDAxaDx+S+41P9I254ZAtRKu5ZAuJqa2nzaUxTX6OFRqAcJ6oNShf
HASou7EBhjh+eRTKernPBtIogPrNxbEeCuuelDcmh+Dff//gD2k8DVqXgo9HpOPW
CrRJK3ZQf4KvoKO1rNoH5u92QghcXlqwCWvFw0jqn3QmZU8o226Fr/AyDlVOmPMa
0RaIb+SkqLYgBhMxIey2QqDn330AfKw9qwH1nuD9jau9cUCTDG0JZLftvOLSQIp2
4YeH/NqZXZdZ1ZLyUi1bTMvvr4I0T179zJANhFqHrAt3LnY80F366bDAbJmX0Ij3
F/Yo29+qYjWcq8ui3JZYvIWLcX+pDYNj2sMl07r9m5UiAPAQGDhJX1VkU8pOhASQ
oPwpo7swbw8UqBPeCwJ7SWToXF96rTxcWRN8teI5GEj/1f9vyGoSC5nygtjiUjc1
II/xF+sUT9luGzo=
=MUlT
-----END PGP SIGNATURE-----
pgpB4dQ9tmaB8.pgp
Description: PGP signature
--- End Message ---
