/var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1/src/cpp/flann/mpi/server.h: In member function 'void flann::mpi::Server<Distance>::run()': /var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1/src/cpp/flann/mpi/server.h:122:48: error: 'io_service' is not a member of 'boost::asio'; did you mean 'use_service'? 122 | boost::shared_ptr<boost::asio::io_service> io_service; | ^~~~~~~~~~ | use_service /var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1/src/cpp/flann/mpi/server.h:122:48: error: 'io_service' is not a member of 'boost::asio'; did you mean 'use_service'? 122 | boost::shared_ptr<boost::asio::io_service> io_service; | ^~~~~~~~~~ | use_service /var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1/src/cpp/flann/mpi/server.h:122:58: error: template argument 1 is invalid 122 | boost::shared_ptr<boost::asio::io_service> io_service; | ^ /var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1/src/cpp/flann/mpi/server.h:126:36: error: request for member 'reset' in 'io_service', which is of non-class type 'int' 126 | io_service.reset(new boost::asio::io_service()); | ^~~~~ /var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1/src/cpp/flann/mpi/server.h:126:46: error: expected type-specifier 126 | io_service.reset(new boost::asio::io_service()); | ^~~~~ /var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1/src/cpp/flann/mpi/server.h:127:58: error: invalid type argument of unary '*' (have 'int') 127 | acceptor.reset(new tcp::acceptor(*io_service, tcp::endpoint(tcp::v4(), port_))); | ^~~~~~~~~~~ /var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1/src/cpp/flann/mpi/server.h:133:60: error: invalid type argument of unary '*' (have 'int') 133 | sock.reset(new tcp::socket(*io_service)); | ^~~~~~~~~~~ Reproducible: Always Portage 3.0.66.1 (python 3.12.8-final-0, default/linux/amd64/23.0/no-multilib, gcc-14, glibc-2.40-r7, 6.12.1-gentoo x86_64) ================================================================= System uname: Linux-6.12.1-gentoo-x86_64-AMD_Ryzen_9_7950X_16-Core_Processor-with-glibc2.40 KiB Mem: 131395064 total, 4976012 free KiB Swap: 268435452 total, 266818868 free Timestamp of repository gentoo: Fri, 13 Dec 2024 15:30:01 +0000 Head commit of repository gentoo: 4a217d9572f280f39e1a8b5c82de1943215222f6 Timestamp of repository guru: Fri, 13 Dec 2024 13:18:29 +0000 Head commit of repository guru: 5a54a80623a46978bb1990c7515398b53b7933f6 sh bash 5.2_p37 ld GNU ld (Gentoo 2.43 p3) 2.43.1 app-misc/pax-utils: 1.3.8::gentoo app-shells/bash: 5.2_p37::gentoo dev-build/autoconf: 2.13-r8::gentoo, 2.71-r7::gentoo, 2.72-r1::gentoo dev-build/automake: 1.16.5-r2::gentoo, 1.17-r1::gentoo dev-build/cmake: 3.31.2::gentoo dev-build/libtool: 2.5.4::gentoo dev-build/make: 4.4.1-r100::gentoo dev-build/meson: 1.6.0-r1::gentoo dev-java/java-config: 2.3.4::gentoo dev-lang/perl: 5.40.0-r1::gentoo dev-lang/python: 3.12.8::gentoo, 3.13.1::gentoo dev-lang/rust-bin: 1.81.0-r100::gentoo, 1.82.0-r100::gentoo, 1.83.0::gentoo llvm-core/clang: 17.0.6::gentoo, 18.1.8-r6::gentoo, 19.1.5::gentoo llvm-core/lld: 17.0.6::gentoo, 18.1.8::gentoo, 19.1.5::gentoo llvm-core/llvm: 17.0.6-r2::gentoo, 18.1.8-r6::gentoo, 19.1.5::gentoo sys-apps/baselayout: 2.17::gentoo sys-apps/openrc: 0.55.1::gentoo sys-apps/sandbox: 2.40::gentoo sys-devel/binutils: 2.42-r2::gentoo, 2.43-r2::gentoo sys-devel/binutils-config: 5.5.2::gentoo sys-devel/gcc: 14.2.1_p20241116::gentoo sys-devel/gcc-config: 2.12.1::gentoo sys-kernel/linux-headers: 6.12::gentoo (virtual/os-headers) sys-libs/glibc: 2.40-r7::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 volatile: False sync-rsync-verify-jobs: 16 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 guru location: /var/db/repos/guru sync-type: git sync-uri: https://github.com/gentoo-mirror/guru.git masters: gentoo volatile: False ACCEPT_KEYWORDS="amd64 ~*" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=znver4 -O2 -pipe -flto" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/bind" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=znver4 -O2 -pipe -flto" DISTDIR="/var/cache/distfiles" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.vectranet.pl/gentoo/ http://mirror.leaseweb.com/gentoo/ http://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/ http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://mirror.netcologne.de/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/ http://mirror.init7.net/gentoo/ http://tux.rainside.sk/gentoo/ http://gentoo.mirror.web4u.cz/" LANG="en_US" LC_ALL="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs" LEX="flex" MAKEOPTS="-j30" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" SHELL="/bin/bash" USE="X a52 aac aacs acl alsa amd64 apps bios64 bittorrent bluray boot btrfs bzip2 cet cli color-management connection-sharing context contrib contribdnn crypt cups cxx dbus dcaenc designer dhcpcd dracut dri dts eigen emboss exif extra fam fbcon fdk ffmpeg fftw flac fontconfig fortran frei0r ftp gdbm geoclue geolocation gimp gles2 gps graphite grub gui hip hwaccel iconv icu iptables iso64 jpeg kde lame lapack lapacke latex lcms libass libei libglvnd libproxy libtirpc llvm lm-sensors lto mac markdown matio minizip mpi ncurses no-multilib nptl nvenc ods ogg opengl openh264 openmp opus pam parallel-compiler pcre pgo pipewire plasma png postscript pthread pulseaudio qml qt6 quic readline resolvconf rocm rocr romio rustfmt sdl seccomp spirv ssd ssl svg syslog taglib tbb tcmalloc tensorpipe test-rust text theora threads tiff tools truetype uefi64 unicode v4l vaapi vector-icons vorbis vulkan wavpack wayland webp x264 x265 xattr xla xml zlib" ABI_X86="64" ADA_TARGET="gcc_12" AMDGPU_TARGETS="gfx1031 gfx1030" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_anon authn_dbm authn_file authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir env expires ext_filter file_cache filter headers include info log_config logio mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="stage" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 aes avx avx2 avx512_bf16 avx512_bitalg avx512_vbmi2 avx512_vnni avx512_vpopcntdq avx512bw avx512cd avx512dq avx512f avx512ifma avx512vbmi avx512vl f16c fma3 pclmul popcnt rdrand sha sse3 sse4_1 sse4_2 sse4a ssse3 vpclmulqdq" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" GRUB_PLATFORMS="efi-64" GUILE_SINGLE_TARGET="3-0" GUILE_TARGETS="3-0" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en en-US" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer nlpsolver" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-2" POSTGRES_TARGETS="postgres16" PYTHON_SINGLE_TARGET="python3_12" PYTHON_TARGETS="python3_12" RUBY_TARGETS="ruby33" VIDEO_CARDS="amdgpu fbdev amd radeon radeonsi vesa" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto logmark ipmark dhcpmac delude chaos account" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
Please include the full build.log too for completeness.
Created attachment 914013 [details] full build log
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d9f9cf5391a70beb6ccd898209330cbcfa606a7c commit d9f9cf5391a70beb6ccd898209330cbcfa606a7c Author: Miroslav Šulc <fordfrog@gentoo.org> AuthorDate: 2025-01-05 11:05:17 +0000 Commit: Miroslav Šulc <fordfrog@gentoo.org> CommitDate: 2025-01-05 11:05:32 +0000 sci-libs/flann: fixed (probably) boost 1.87 issues Bug: https://bugs.gentoo.org/946465 Signed-off-by: Miroslav Šulc <fordfrog@gentoo.org> sci-libs/flann/files/flann-1.9.1-boost-1.87.patch | 64 +++++++++++++++ sci-libs/flann/flann-1.9.1-r7.ebuild | 95 +++++++++++++++++++++++ 2 files changed, 159 insertions(+)
i couldn't really verify the issue is fixed as i got bunch of linking issues: [9/14] : && /usr/bin/mpicxx -march=alderlake -mpopcnt -mlzcnt -mno-cldemote -mno-kl -mno-pconfig -mno-sgx -mno-widekl -mshstk -O2 -pipe -frecord-gcc-switches -std=c++11 -fopenmp=libomp -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs src/cpp/CMakeFiles/flann_mpi_server.dir/flann/mpi/flann_mpi_server.cpp.o -o bin/flann_mpi_server -Wl,-rpath,/var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1_build/lib: lib/libflann_cpp.so.1.9.1 /usr/lib64/libhdf5.so /usr/lib64/libz.so /usr/lib64/libdl.a -lm /usr/lib64/libboost_mpi.so.1.87.0 /usr/lib64/libboost_system.so.1.87.0 /usr/lib64/libboost_serialization.so.1.87.0 /usr/lib64/libboost_thread.so.1.87.0 -Wl,--push-state,--no-as-needed -llz4 -Wl,--pop-state /usr/lib64/libboost_python311.so.1.87.0 /usr/lib64/libboost_container.so.1.87.0 /usr/lib64/libboost_graph.so.1.87.0 && : FAILED: bin/flann_mpi_server : && /usr/bin/mpicxx -march=alderlake -mpopcnt -mlzcnt -mno-cldemote -mno-kl -mno-pconfig -mno-sgx -mno-widekl -mshstk -O2 -pipe -frecord-gcc-switches -std=c++11 -fopenmp=libomp -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs src/cpp/CMakeFiles/flann_mpi_server.dir/flann/mpi/flann_mpi_server.cpp.o -o bin/flann_mpi_server -Wl,-rpath,/var/tmp/portage/sci-libs/flann-1.9.1-r6/work/flann-1.9.1_build/lib: lib/libflann_cpp.so.1.9.1 /usr/lib64/libhdf5.so /usr/lib64/libz.so /usr/lib64/libdl.a -lm /usr/lib64/libboost_mpi.so.1.87.0 /usr/lib64/libboost_system.so.1.87.0 /usr/lib64/libboost_serialization.so.1.87.0 /usr/lib64/libboost_thread.so.1.87.0 -Wl,--push-state,--no-as-needed -llz4 -Wl,--pop-state /usr/lib64/libboost_python311.so.1.87.0 /usr/lib64/libboost_container.so.1.87.0 /usr/lib64/libboost_graph.so.1.87.0 && : /usr/bin/x86_64-pc-linux-gnu-ld.bfd: /usr/lib64/libboost_python311.so.1.87.0: undefined reference to `PyInstanceMethod_Type' /usr/bin/x86_64-pc-linux-gnu-ld.bfd: /usr/lib64/libboost_python311.so.1.87.0: undefined reference to `PyExc_ValueError' /usr/bin/x86_64-pc-linux-gnu-ld.bfd: /usr/lib64/libboost_python311.so.1.87.0: undefined reference to `PyLong_AsLong' ... clang++: error: linker command failed with exit code 1 (use -v to see invocation) i was also trying to bump flann to 1.9.2, but i got the same linking issues, and cuda issues...
Probably error in config script: -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4db46c950246613586189689f3f05e5c6e7e0717 commit 4db46c950246613586189689f3f05e5c6e7e0717 Author: Paul Zander <negril.nx+gentoo@gmail.com> AuthorDate: 2025-01-06 19:29:46 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2025-01-06 21:32:03 +0000 sci-libs/flann: add 1.9.2_p20221027, drop 1.9.2 uses latest upstream commit update cmake code, handle warnings use enable_language for cuda and fix warnings in code use find_package(Python) instead of PythonInterp fix erroneous dependency for doc, unmask the flag Closes: https://bugs.gentoo.org/947608 Closes: https://bugs.gentoo.org/947602 Closes: https://bugs.gentoo.org/946465 Closes: https://bugs.gentoo.org/829080 Bug: https://bugs.gentoo.org/830013 Signed-off-by: Paul Zander <negril.nx+gentoo@gmail.com> Signed-off-by: Sam James <sam@gentoo.org> profiles/base/package.use.mask | 3 +- sci-libs/flann/Manifest | 3 +- .../flann/files/flann-1.9.2-system-gtest.patch | 36 +++++++++ ...n-1.9.2.ebuild => flann-1.9.2_p20221027.ebuild} | 88 ++++++++++++++++------ 4 files changed, 105 insertions(+), 25 deletions(-)
