Your message dated Fri, 11 Apr 2025 07:19:34 +0000
with message-id <e1u38fm-0022um...@fasolo.debian.org>
and subject line Bug#1075199: fixed in libpwiz 3.0.18342-4.2
has caused the Debian Bug report #1075199,
regarding libpwiz: ftbfs with GCC-14
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 ow...@bugs.debian.org
immediately.)
--
1075199: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075199
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:libpwiz
Version: 3.0.18342-4.1
Severity: important
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-14
[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-14/g++-14, but succeeds to build with gcc-13/g++-13. 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/2024/07/01/libpwiz_3.0.18342-4.1_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html
[...]
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: x86_64-linux-gnu-g++ -DPACKAGE_NAME=\"libpwiz\"
-DPACKAGE_TARNAME=\"libpwiz\" -DPACKAGE_VERSION=\"3.0.18344\"
"-DPACKAGE_STRING=\"libpwiz 3.0.18344\""
-DPACKAGE_BUGREPORT=\"proteowizard-supp...@lists.sourceforge.net\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"libpwiz\" -DVERSION=\"3.0.18344\"
-DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NETINET_IN_H=1 -DHAVE_STDINT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_UNISTD_H=1
-DHAVE__BOOL=1 -Drestrict=__restrict__ -DHAVE_PTRDIFF_T=1 -DHAVE_MALLOC=1
-DHAVE_ALARM=1 -DHAVE_REALLOC=1 -DHAVE_ATEXIT=1 -DHAVE_MEMMOVE=1
-DHAVE_MEMSET=1 -DHAVE_MKDIR=1 -DHAVE_MODF=1 -DHAVE_STRCASECMP=1
-DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_ST
RERROR=1 -DHAVE_STRPBRK=1 -DHAVE_STRRCHR=1 -DHAVE_STRSTR=1 -DHAVE_STRTOL=1
-DHAVE_STRTOUL=1 -DHAVE_STRTOULL=1 -DHAVE_BOOST=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_THREAD_HPP=1 -DHAVE_BOOST_THREAD=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_FILESYSTEM_PATH_HPP=1 -DHAVE_BOOST_FILESYSTEM=1
-DHAVE_BOOST_REGEX_HPP=1 -DHAVE_BOOST_REGEX=1
-DHAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP=1 -DHAVE_BOOST_SERIALIZATION=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_IOSTREAMS_DEVICE_FILE_DESCRIPTOR_HPP=1 -DHAVE_BOOST_IOSTREAMS=1
-DHAVE_BOOST_DATE_TIME_POSIX_TIME_POSIX_TIME_HPP=1 -DHAVE_BOOST_DATE_TIME=1
-DHAVE_BOOST_PROGRAM_OPTIONS_HPP=1 -DHAVE_BOOST_PROGRAM_OPTIONS=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_CHRONO_HPP=1 -DHAVE_BOOST_CHRONO=1 -I. -Iautotools -pthread
-Ilibraries/boost_aux -Ipwiz/data/msdata/ramp -Ilibraries/Eigen
-Ilibraries/CSpline -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSER
TS -DBOOST_NOWIDE_NO_LIB=1 -DNO_MASCOT_READER -I /usr/include/eigen3/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/libsvm-3.0 -Wdate-time
-D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MT
pwiz/data/vendor_readers/ABI/Reader_ABI.lo -MD -MP -MF
pwiz/data/vendor_readers/ABI/.deps/Reader_ABI.Tpo -c
pwiz/data/vendor_readers/ABI/Reader_ABI.cpp -fPIC -DPIC -o
pwiz/data/vendor_readers/ABI/.libs/Reader_ABI.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from ./pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/vendor_readers/ABI/Reader_ABI.hpp:28,
from pwiz/data/vendor_readers/ABI/Reader_ABI.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category,
class _Tp, class _Distance, class _Pointer, class _Reference> struct
std::iterator’ is deprecated [-Wdeprecated-declarations]
54 | class PWIZ_API_DECL const_iterator : public
std::iterator<std::random_access_iterator_tag, const T>
| ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_construct.h:61,
from /usr/include/c++/14/bits/stl_tempbuf.h:61,
from /usr/include/c++/14/memory:66,
from
/usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:18,
from /usr/include/boost/shared_ptr.hpp:17,
from ./pwiz/utility/misc/IterationListener.hpp:29,
from ./pwiz/data/msdata/Reader.hpp:28:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category,
class _Tp, class _Distance, class _Pointer, class _Reference> struct
std::iterator’ is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public
std::iterator<std::random_access_iterator_tag, T>
| ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
libtool: compile: x86_64-linux-gnu-g++ -DPACKAGE_NAME=\"libpwiz\"
-DPACKAGE_TARNAME=\"libpwiz\" -DPACKAGE_VERSION=\"3.0.18344\"
"-DPACKAGE_STRING=\"libpwiz 3.0.18344\""
-DPACKAGE_BUGREPORT=\"proteowizard-supp...@lists.sourceforge.net\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"libpwiz\" -DVERSION=\"3.0.18344\"
-DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NETINET_IN_H=1 -DHAVE_STDINT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_UNISTD_H=1
-DHAVE__BOOL=1 -Drestrict=__restrict__ -DHAVE_PTRDIFF_T=1 -DHAVE_MALLOC=1
-DHAVE_ALARM=1 -DHAVE_REALLOC=1 -DHAVE_ATEXIT=1 -DHAVE_MEMMOVE=1
-DHAVE_MEMSET=1 -DHAVE_MKDIR=1 -DHAVE_MODF=1 -DHAVE_STRCASECMP=1
-DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_ST
RERROR=1 -DHAVE_STRPBRK=1 -DHAVE_STRRCHR=1 -DHAVE_STRSTR=1 -DHAVE_STRTOL=1
-DHAVE_STRTOUL=1 -DHAVE_STRTOULL=1 -DHAVE_BOOST=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_THREAD_HPP=1 -DHAVE_BOOST_THREAD=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_FILESYSTEM_PATH_HPP=1 -DHAVE_BOOST_FILESYSTEM=1
-DHAVE_BOOST_REGEX_HPP=1 -DHAVE_BOOST_REGEX=1
-DHAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP=1 -DHAVE_BOOST_SERIALIZATION=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_IOSTREAMS_DEVICE_FILE_DESCRIPTOR_HPP=1 -DHAVE_BOOST_IOSTREAMS=1
-DHAVE_BOOST_DATE_TIME_POSIX_TIME_POSIX_TIME_HPP=1 -DHAVE_BOOST_DATE_TIME=1
-DHAVE_BOOST_PROGRAM_OPTIONS_HPP=1 -DHAVE_BOOST_PROGRAM_OPTIONS=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_CHRONO_HPP=1 -DHAVE_BOOST_CHRONO=1 -I. -Iautotools -pthread
-Ilibraries/boost_aux -Ipwiz/data/msdata/ramp -Ilibraries/Eigen
-Ilibraries/CSpline -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSER
TS -DBOOST_NOWIDE_NO_LIB=1 -DNO_MASCOT_READER -I /usr/include/eigen3/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/libsvm-3.0 -Wdate-time
-D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MT
pwiz/data/vendor_readers/ABI/Reader_ABI.lo -MD -MP -MF
pwiz/data/vendor_readers/ABI/.deps/Reader_ABI.Tpo -c
pwiz/data/vendor_readers/ABI/Reader_ABI.cpp -o
pwiz/data/vendor_readers/ABI/Reader_ABI.o >/dev/null 2>&1
depbase=`echo pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.lo | sed
's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++
-DPACKAGE_NAME=\"libpwiz\" -DPACKAGE_TARNAME=\"libpwiz\"
-DPACKAGE_VERSION=\"3.0.18344\" -DPACKAGE_STRING=\"libpwiz\ 3.0.18344\"
-DPACKAGE_BUGREPORT=\"proteowizard-supp...@lists.sourceforge.net\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"libpwiz\" -DVERSION=\"3.0.18344\"
-DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NETINET_IN_H=1 -DHAVE_STDINT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_UNISTD_H=1
-DHAVE__BOOL=1 -Drestrict=__restrict__ -DHAVE_PTRDIFF_T=1 -DHAVE_MALLOC=1
-DHAVE_ALARM=1 -DHAVE_REALLOC=1 -DHAVE_ATEXIT=1 -DHAVE_MEMMOVE=1
-DHAVE_MEMSET=1 -DHAVE_MKDIR=1 -DHAVE_MODF=1 -DHAVE_STRCASECMP=1 -DHAVE_STRCHR
=1 -DHAVE_STRDUP=1 -DHAVE_STRERROR=1 -DHAVE_STRPBRK=1 -DHAVE_STRRCHR=1
-DHAVE_STRSTR=1 -DHAVE_STRTOL=1 -DHAVE_STRTOUL=1 -DHAVE_STRTOULL=1
-DHAVE_BOOST=1 -DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_THREAD_HPP=1 -DHAVE_BOOST_THREAD=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_FILESYSTEM_PATH_HPP=1 -DHAVE_BOOST_FILESYSTEM=1
-DHAVE_BOOST_REGEX_HPP=1 -DHAVE_BOOST_REGEX=1
-DHAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP=1 -DHAVE_BOOST_SERIALIZATION=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_IOSTREAMS_DEVICE_FILE_DESCRIPTOR_HPP=1 -DHAVE_BOOST_IOSTREAMS=1
-DHAVE_BOOST_DATE_TIME_POSIX_TIME_POSIX_TIME_HPP=1 -DHAVE_BOOST_DATE_TIME=1
-DHAVE_BOOST_PROGRAM_OPTIONS_HPP=1 -DHAVE_BOOST_PROGRAM_OPTIONS=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_CHRONO_HPP=1 -DHAVE_BOOST_CHRONO=1 -I. -Iautotools -pthread
-I"libraries/boost_aux" -I"pwiz/data/msdata/ramp" -I"libraries/Eigen"
-I"libraries/CSpline
" -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSERTS -DBOOST_NOWIDE_NO_LIB=1
-DNO_MASCOT_READER -I "/usr/include/eigen3/Eigen" -I
"/<<PKGBUILDDIR>>/debian/build/libraries/Eigen" -I
"/<<PKGBUILDDIR>>/debian/build/libraries/libsvm-3.0" -Wdate-time
-D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MT
pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.lo -MD -MP -MF $depbase.Tpo -c
-o pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.lo
pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: x86_64-linux-gnu-g++ -DPACKAGE_NAME=\"libpwiz\"
-DPACKAGE_TARNAME=\"libpwiz\" -DPACKAGE_VERSION=\"3.0.18344\"
"-DPACKAGE_STRING=\"libpwiz 3.0.18344\""
-DPACKAGE_BUGREPORT=\"proteowizard-supp...@lists.sourceforge.net\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"libpwiz\" -DVERSION=\"3.0.18344\"
-DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NETINET_IN_H=1 -DHAVE_STDINT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_UNISTD_H=1
-DHAVE__BOOL=1 -Drestrict=__restrict__ -DHAVE_PTRDIFF_T=1 -DHAVE_MALLOC=1
-DHAVE_ALARM=1 -DHAVE_REALLOC=1 -DHAVE_ATEXIT=1 -DHAVE_MEMMOVE=1
-DHAVE_MEMSET=1 -DHAVE_MKDIR=1 -DHAVE_MODF=1 -DHAVE_STRCASECMP=1
-DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_ST
RERROR=1 -DHAVE_STRPBRK=1 -DHAVE_STRRCHR=1 -DHAVE_STRSTR=1 -DHAVE_STRTOL=1
-DHAVE_STRTOUL=1 -DHAVE_STRTOULL=1 -DHAVE_BOOST=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_THREAD_HPP=1 -DHAVE_BOOST_THREAD=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_FILESYSTEM_PATH_HPP=1 -DHAVE_BOOST_FILESYSTEM=1
-DHAVE_BOOST_REGEX_HPP=1 -DHAVE_BOOST_REGEX=1
-DHAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP=1 -DHAVE_BOOST_SERIALIZATION=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_IOSTREAMS_DEVICE_FILE_DESCRIPTOR_HPP=1 -DHAVE_BOOST_IOSTREAMS=1
-DHAVE_BOOST_DATE_TIME_POSIX_TIME_POSIX_TIME_HPP=1 -DHAVE_BOOST_DATE_TIME=1
-DHAVE_BOOST_PROGRAM_OPTIONS_HPP=1 -DHAVE_BOOST_PROGRAM_OPTIONS=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_CHRONO_HPP=1 -DHAVE_BOOST_CHRONO=1 -I. -Iautotools -pthread
-Ilibraries/boost_aux -Ipwiz/data/msdata/ramp -Ilibraries/Eigen
-Ilibraries/CSpline -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSER
TS -DBOOST_NOWIDE_NO_LIB=1 -DNO_MASCOT_READER -I /usr/include/eigen3/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/libsvm-3.0 -Wdate-time
-D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MT
pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.lo -MD -MP -MF
pwiz/data/vendor_readers/ABI/T2D/.deps/Reader_ABI_T2D.Tpo -c
pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.cpp -fPIC -DPIC -o
pwiz/data/vendor_readers/ABI/T2D/.libs/Reader_ABI_T2D.o
In file included from ./pwiz/data/msdata/MSData.hpp:29,
from ./pwiz/data/msdata/Reader.hpp:29,
from pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.hpp:28,
from pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.cpp:25:
./pwiz/utility/misc/BinaryData.hpp:54:54: warning: ‘template<class _Category,
class _Tp, class _Distance, class _Pointer, class _Reference> struct
std::iterator’ is deprecated [-Wdeprecated-declarations]
54 | class PWIZ_API_DECL const_iterator : public
std::iterator<std::random_access_iterator_tag, const T>
| ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_construct.h:61,
from /usr/include/c++/14/bits/stl_tempbuf.h:61,
from /usr/include/c++/14/memory:66,
from
/usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35,
from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:18,
from /usr/include/boost/shared_ptr.hpp:17,
from ./pwiz/utility/misc/IterationListener.hpp:29,
from ./pwiz/data/msdata/Reader.hpp:28:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
./pwiz/utility/misc/BinaryData.hpp:88:48: warning: ‘template<class _Category,
class _Tp, class _Distance, class _Pointer, class _Reference> struct
std::iterator’ is deprecated [-Wdeprecated-declarations]
88 | class PWIZ_API_DECL iterator : public
std::iterator<std::random_access_iterator_tag, T>
| ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
127 | struct _GLIBCXX17_DEPRECATED iterator
| ^~~~~~~~
libtool: compile: x86_64-linux-gnu-g++ -DPACKAGE_NAME=\"libpwiz\"
-DPACKAGE_TARNAME=\"libpwiz\" -DPACKAGE_VERSION=\"3.0.18344\"
"-DPACKAGE_STRING=\"libpwiz 3.0.18344\""
-DPACKAGE_BUGREPORT=\"proteowizard-supp...@lists.sourceforge.net\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"libpwiz\" -DVERSION=\"3.0.18344\"
-DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NETINET_IN_H=1 -DHAVE_STDINT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_UNISTD_H=1
-DHAVE__BOOL=1 -Drestrict=__restrict__ -DHAVE_PTRDIFF_T=1 -DHAVE_MALLOC=1
-DHAVE_ALARM=1 -DHAVE_REALLOC=1 -DHAVE_ATEXIT=1 -DHAVE_MEMMOVE=1
-DHAVE_MEMSET=1 -DHAVE_MKDIR=1 -DHAVE_MODF=1 -DHAVE_STRCASECMP=1
-DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_ST
RERROR=1 -DHAVE_STRPBRK=1 -DHAVE_STRRCHR=1 -DHAVE_STRSTR=1 -DHAVE_STRTOL=1
-DHAVE_STRTOUL=1 -DHAVE_STRTOULL=1 -DHAVE_BOOST=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_THREAD_HPP=1 -DHAVE_BOOST_THREAD=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_FILESYSTEM_PATH_HPP=1 -DHAVE_BOOST_FILESYSTEM=1
-DHAVE_BOOST_REGEX_HPP=1 -DHAVE_BOOST_REGEX=1
-DHAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP=1 -DHAVE_BOOST_SERIALIZATION=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_IOSTREAMS_DEVICE_FILE_DESCRIPTOR_HPP=1 -DHAVE_BOOST_IOSTREAMS=1
-DHAVE_BOOST_DATE_TIME_POSIX_TIME_POSIX_TIME_HPP=1 -DHAVE_BOOST_DATE_TIME=1
-DHAVE_BOOST_PROGRAM_OPTIONS_HPP=1 -DHAVE_BOOST_PROGRAM_OPTIONS=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_CHRONO_HPP=1 -DHAVE_BOOST_CHRONO=1 -I. -Iautotools -pthread
-Ilibraries/boost_aux -Ipwiz/data/msdata/ramp -Ilibraries/Eigen
-Ilibraries/CSpline -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSER
TS -DBOOST_NOWIDE_NO_LIB=1 -DNO_MASCOT_READER -I /usr/include/eigen3/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/libsvm-3.0 -Wdate-time
-D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MT
pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.lo -MD -MP -MF
pwiz/data/vendor_readers/ABI/T2D/.deps/Reader_ABI_T2D.Tpo -c
pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.cpp -o
pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.o >/dev/null 2>&1
depbase=`echo pwiz/data/common/BinaryIndexStream.lo | sed
's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ./libtool --tag=CXX --mode=compile x86_64-linux-gnu-g++
-DPACKAGE_NAME=\"libpwiz\" -DPACKAGE_TARNAME=\"libpwiz\"
-DPACKAGE_VERSION=\"3.0.18344\" -DPACKAGE_STRING=\"libpwiz\ 3.0.18344\"
-DPACKAGE_BUGREPORT=\"proteowizard-supp...@lists.sourceforge.net\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"libpwiz\" -DVERSION=\"3.0.18344\"
-DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NETINET_IN_H=1 -DHAVE_STDINT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_UNISTD_H=1
-DHAVE__BOOL=1 -Drestrict=__restrict__ -DHAVE_PTRDIFF_T=1 -DHAVE_MALLOC=1
-DHAVE_ALARM=1 -DHAVE_REALLOC=1 -DHAVE_ATEXIT=1 -DHAVE_MEMMOVE=1
-DHAVE_MEMSET=1 -DHAVE_MKDIR=1 -DHAVE_MODF=1 -DHAVE_STRCASECMP=1 -DHAVE_STRCHR
=1 -DHAVE_STRDUP=1 -DHAVE_STRERROR=1 -DHAVE_STRPBRK=1 -DHAVE_STRRCHR=1
-DHAVE_STRSTR=1 -DHAVE_STRTOL=1 -DHAVE_STRTOUL=1 -DHAVE_STRTOULL=1
-DHAVE_BOOST=1 -DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_THREAD_HPP=1 -DHAVE_BOOST_THREAD=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_FILESYSTEM_PATH_HPP=1 -DHAVE_BOOST_FILESYSTEM=1
-DHAVE_BOOST_REGEX_HPP=1 -DHAVE_BOOST_REGEX=1
-DHAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP=1 -DHAVE_BOOST_SERIALIZATION=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_IOSTREAMS_DEVICE_FILE_DESCRIPTOR_HPP=1 -DHAVE_BOOST_IOSTREAMS=1
-DHAVE_BOOST_DATE_TIME_POSIX_TIME_POSIX_TIME_HPP=1 -DHAVE_BOOST_DATE_TIME=1
-DHAVE_BOOST_PROGRAM_OPTIONS_HPP=1 -DHAVE_BOOST_PROGRAM_OPTIONS=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_CHRONO_HPP=1 -DHAVE_BOOST_CHRONO=1 -I. -Iautotools -pthread
-I"libraries/boost_aux" -I"pwiz/data/msdata/ramp" -I"libraries/Eigen"
-I"libraries/CSpline
" -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSERTS -DBOOST_NOWIDE_NO_LIB=1
-DNO_MASCOT_READER -I "/usr/include/eigen3/Eigen" -I
"/<<PKGBUILDDIR>>/debian/build/libraries/Eigen" -I
"/<<PKGBUILDDIR>>/debian/build/libraries/libsvm-3.0" -Wdate-time
-D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MT
pwiz/data/common/BinaryIndexStream.lo -MD -MP -MF $depbase.Tpo -c -o
pwiz/data/common/BinaryIndexStream.lo pwiz/data/common/BinaryIndexStream.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: x86_64-linux-gnu-g++ -DPACKAGE_NAME=\"libpwiz\"
-DPACKAGE_TARNAME=\"libpwiz\" -DPACKAGE_VERSION=\"3.0.18344\"
"-DPACKAGE_STRING=\"libpwiz 3.0.18344\""
-DPACKAGE_BUGREPORT=\"proteowizard-supp...@lists.sourceforge.net\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"libpwiz\" -DVERSION=\"3.0.18344\"
-DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_UNISTD_H=1 -DHAVE_SYS_TIME_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1
-DLT_OBJDIR=\".libs/\" -DHAVE_FCNTL_H=1 -DHAVE_FLOAT_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_LIMITS_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NETINET_IN_H=1 -DHAVE_STDINT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_SYS_IOCTL_H=1 -DHAVE_UNISTD_H=1
-DHAVE__BOOL=1 -Drestrict=__restrict__ -DHAVE_PTRDIFF_T=1 -DHAVE_MALLOC=1
-DHAVE_ALARM=1 -DHAVE_REALLOC=1 -DHAVE_ATEXIT=1 -DHAVE_MEMMOVE=1
-DHAVE_MEMSET=1 -DHAVE_MKDIR=1 -DHAVE_MODF=1 -DHAVE_STRCASECMP=1
-DHAVE_STRCHR=1 -DHAVE_STRDUP=1 -DHAVE_ST
RERROR=1 -DHAVE_STRPBRK=1 -DHAVE_STRRCHR=1 -DHAVE_STRSTR=1 -DHAVE_STRTOL=1
-DHAVE_STRTOUL=1 -DHAVE_STRTOULL=1 -DHAVE_BOOST=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_THREAD_HPP=1 -DHAVE_BOOST_THREAD=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_FILESYSTEM_PATH_HPP=1 -DHAVE_BOOST_FILESYSTEM=1
-DHAVE_BOOST_REGEX_HPP=1 -DHAVE_BOOST_REGEX=1
-DHAVE_BOOST_ARCHIVE_TEXT_OARCHIVE_HPP=1 -DHAVE_BOOST_SERIALIZATION=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_IOSTREAMS_DEVICE_FILE_DESCRIPTOR_HPP=1 -DHAVE_BOOST_IOSTREAMS=1
-DHAVE_BOOST_DATE_TIME_POSIX_TIME_POSIX_TIME_HPP=1 -DHAVE_BOOST_DATE_TIME=1
-DHAVE_BOOST_PROGRAM_OPTIONS_HPP=1 -DHAVE_BOOST_PROGRAM_OPTIONS=1
-DHAVE_BOOST_SYSTEM_ERROR_CODE_HPP=1 -DHAVE_BOOST_SYSTEM=1
-DHAVE_BOOST_CHRONO_HPP=1 -DHAVE_BOOST_CHRONO=1 -I. -Iautotools -pthread
-Ilibraries/boost_aux -Ipwiz/data/msdata/ramp -Ilibraries/Eigen
-Ilibraries/CSpline -DWITHOUT_MZ5 -DBOOST_DISABLE_ASSER
TS -DBOOST_NOWIDE_NO_LIB=1 -DNO_MASCOT_READER -I /usr/include/eigen3/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/Eigen -I
/<<PKGBUILDDIR>>/debian/build/libraries/libsvm-3.0 -Wdate-time
-D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MT
pwiz/data/common/BinaryIndexStream.lo -MD -MP -MF
pwiz/data/common/.deps/BinaryIndexStream.Tpo -c
pwiz/data/common/BinaryIndexStream.cpp -fPIC -DPIC -o
pwiz/data/common/.libs/BinaryIndexStream.o
pwiz/data/common/BinaryIndexStream.cpp: In member function
‘pwiz::data::{anonymous}::stream_vector_const_iterator<_Ty,
reader_type>::value_type&
pwiz::data::{anonymous}::stream_vector_const_iterator<_Ty,
reader_type>::operator[](difference_type) const’:
pwiz/data/common/BinaryIndexStream.cpp:159:15: error: assignment of member
‘pwiz::data::{anonymous}::stream_vector_const_iterator<_Ty,
reader_type>::next_’ in read-only object
159 | next_ = _Off * value_size_;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~
make[1]: *** [Makefile:5480: pwiz/data/common/BinaryIndexStream.lo] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/debian/build'
make: *** [debian/rules:119: build-arch-stamp] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: libpwiz
Source-Version: 3.0.18342-4.2
Done: Adrian Bunk <b...@debian.org>
We believe that the bug you reported is fixed in the latest version of
libpwiz, 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 1075...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Adrian Bunk <b...@debian.org> (supplier of updated libpwiz 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 11 Apr 2025 09:11:53 +0300
Source: libpwiz
Architecture: source
Version: 3.0.18342-4.2
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Adrian Bunk <b...@debian.org>
Closes: 1075199
Changes:
libpwiz (3.0.18342-4.2) unstable; urgency=medium
.
* Non-maintainer upload.
* Backport fix for FTBFS with gcc 14. (Closes: #1075199)
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Files:
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--- End Message ---
