[Debichem-devel] Bug#1115146: toppic: FTBFS: error: redefinition of 'std::string boost::filesystem::extension(const path&)'
Santiago Vila
sanvila at debian.org
Sat Sep 13 17:29:42 BST 2025
Package: src:toppic
Version: 1.5.3+dfsg1-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build.
Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202509/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:toppic, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=cmake
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f debian/topfd.1
rm -f debian/toppic.1
rm -f debian/topmg.1
rm -f debian/topdiff.1
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/toppic.substvars debian/toppic-common.substvars debian/files
rm -fr -- debian/toppic/ debian/tmp/ debian/toppic-common/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
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/<<PKGBUILDDIR>>/src/gui/topfd/topfd_gui.cpp: In function ‘int main(int, char**)’:
/<<PKGBUILDDIR>>/src/gui/topfd/topfd_gui.cpp:40:43: warning: ‘const QRect QDesktopWidget::availableGeometry(int) const’ is deprecated: Use QGuiApplication::screens() [-Wdeprecated-declarations]
40 | QRect deskRect = desk->availableGeometry();
| ~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from /usr/include/x86_64-linux-gnu/qt5/QtWidgets/QDesktopWidget:1,
from /<<PKGBUILDDIR>>/src/gui/topfd/topfd_gui.cpp:18:
/usr/include/x86_64-linux-gnu/qt5/QtWidgets/qdesktopwidget.h:88:67: note: declared here
88 | QT_DEPRECATED_X("Use QGuiApplication::screens()") const QRect availableGeometry(int screen = -1) const;
| ^~~~~~~~~~~~~~~~~
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/usr/bin/c++ -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<P [too-long-redacted] topfd/deconv/deconv_process.cpp
In file included from /<<PKGBUILDDIR>>/src/topfd/msreader/pw_ms_reader.hpp:25,
from /<<PKGBUILDDIR>>/src/topfd/msreader/raw_ms_group_reader.hpp:19,
from /<<PKGBUILDDIR>>/src/topfd/deconv/deconv_process.hpp:25,
from /<<PKGBUILDDIR>>/src/topfd/deconv/deconv_process.cpp:37:
/usr/include/pwizlite/pwiz/utility/misc/Filesystem.hpp:75:24: error: redefinition of ‘std::string boost::filesystem::extension(const path&)’
75 | inline std::string extension(const path& p)
| ^~~~~~~~~
In file included from /usr/include/boost/filesystem.hpp:21,
from /<<PKGBUILDDIR>>/src/topfd/deconv/deconv_process.cpp:17:
/usr/include/boost/filesystem/convenience.hpp:29:20: note: ‘std::string boost::filesystem::extension(const path&)’ previously defined here
29 | inline std::string extension(const path& p)
| ^~~~~~~~~
/usr/include/pwizlite/pwiz/utility/misc/Filesystem.hpp:80:24: error: redefinition of ‘std::string boost::filesystem::basename(const path&)’
80 | inline std::string basename(const path& p)
| ^~~~~~~~
/usr/include/boost/filesystem/convenience.hpp:35:20: note: ‘std::string boost::filesystem::basename(const path&)’ previously defined here
35 | inline std::string basename(const path& p)
| ^~~~~~~~
/usr/include/pwizlite/pwiz/utility/misc/Filesystem.hpp:85:17: error: redefinition of ‘boost::filesystem::path boost::filesystem::change_extension(const path&, const path&)’
85 | inline path change_extension(const path& p, const path& new_extension)
| ^~~~~~~~~~~~~~~~
/usr/include/boost/filesystem/convenience.hpp:41:13: note: ‘boost::filesystem::path boost::filesystem::change_extension(const path&, const path&)’ previously defined here
41 | inline path change_extension(const path& p, const path& new_extension)
| ^~~~~~~~~~~~~~~~
make[3]: *** [CMakeFiles/topfd.dir/build.make:173: CMakeFiles/topfd.dir/src/topfd/deconv/deconv_process.cpp.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:153: CMakeFiles/topfd.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
[ 1%] Building CXX object CMakeFiles/topfd_gui.dir/src/topfd/dp/co_table.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<P [too-long-redacted] DIR>>/src/topfd/dp/co_table.cpp
[ 1%] Building CXX object CMakeFiles/topfd_gui.dir/src/topfd/dp/dp.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<P [too-long-redacted] GBUILDDIR>>/src/topfd/dp/dp.cpp
In file included from /<<PKGBUILDDIR>>/src/topfd/msreader/pw_ms_reader.hpp:25,
from /<<PKGBUILDDIR>>/src/topfd/msreader/raw_ms_group_reader.hpp:19,
from /<<PKGBUILDDIR>>/src/topfd/deconv/deconv_process.hpp:25,
from /<<PKGBUILDDIR>>/src/topfd/deconv/deconv_process.cpp:37:
/usr/include/pwizlite/pwiz/utility/misc/Filesystem.hpp:75:24: error: redefinition of ‘std::string boost::filesystem::extension(const path&)’
75 | inline std::string extension(const path& p)
| ^~~~~~~~~
In file included from /usr/include/boost/filesystem.hpp:21,
from /<<PKGBUILDDIR>>/src/topfd/deconv/deconv_process.cpp:17:
/usr/include/boost/filesystem/convenience.hpp:29:20: note: ‘std::string boost::filesystem::extension(const path&)’ previously defined here
29 | inline std::string extension(const path& p)
| ^~~~~~~~~
/usr/include/pwizlite/pwiz/utility/misc/Filesystem.hpp:80:24: error: redefinition of ‘std::string boost::filesystem::basename(const path&)’
80 | inline std::string basename(const path& p)
| ^~~~~~~~
/usr/include/boost/filesystem/convenience.hpp:35:20: note: ‘std::string boost::filesystem::basename(const path&)’ previously defined here
35 | inline std::string basename(const path& p)
| ^~~~~~~~
/usr/include/pwizlite/pwiz/utility/misc/Filesystem.hpp:85:17: error: redefinition of ‘boost::filesystem::path boost::filesystem::change_extension(const path&, const path&)’
85 | inline path change_extension(const path& p, const path& new_extension)
| ^~~~~~~~~~~~~~~~
/usr/include/boost/filesystem/convenience.hpp:41:13: note: ‘boost::filesystem::path boost::filesystem::change_extension(const path&, const path&)’ previously defined here
41 | inline path change_extension(const path& p, const path& new_extension)
| ^~~~~~~~~~~~~~~~
[ 1%] Building CXX object CMakeFiles/topfd_gui.dir/src/topfd/dp/dp_a.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<P [too-long-redacted] UILDDIR>>/src/topfd/dp/dp_a.cpp
make[3]: *** [CMakeFiles/topfd_gui.dir/build.make:195: CMakeFiles/topfd_gui.dir/src/topfd/deconv/deconv_process.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:186: CMakeFiles/topfd_gui.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:139: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
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