Hi, first of all, the bundle is developed with gcc-9 and older. Configure fails for gcc-11.3.0. The ebuild should require older gcc/g++ and probaly pass CC and CXX down to configure straight so that I don't have to switch using gcc-config. Second, the testsuite was always a bit experimental and was no advised to be compiled as it often fails. Now, this is either an unsupported (aka too new) boost incompatibility or else: make[2]: Entering directory '/var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/build/corelib' Updating dependency information for /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/corelib/teamcity_messages.cpp. Updating dependency information for /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/corelib/test_boost.cpp. /usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11 -msse4.2 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -march=native -ftree-vectorize -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_MT -D_REENTRANT -D_THREAD_SAFE -I/var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/inc -I/var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include -I/usr/include /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/corelib/test_boost.cpp -o test_boost.o In file included from /usr/include/boost/config/header_deprecated.hpp:18, from /usr/include/boost/test/auto_unit_test.hpp:16, from /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include/corelib/test_boost.hpp:69, from /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/corelib/test_boost.cpp:50: /usr/include/boost/test/auto_unit_test.hpp:17:1: note: #pragma message: This header is deprecated. Use <boost/test/unit_test.hpp> instead. 17 | BOOST_HEADER_DEPRECATED( "<boost/test/unit_test.hpp>" ) | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/test/floating_point_comparison.hpp:14:1: note: #pragma message: This header is deprecated. Use <boost/test/tools/floating_point_comparison.hpp> instead. 14 | BOOST_HEADER_DEPRECATED( "<boost/test/tools/floating_point_comparison.hpp>" ) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/corelib/test_boost.cpp:50: /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include/corelib/test_boost.hpp:788:53: error: 'boost::unit_test::decorator::collector' has not been declared 788 | boost::unit_test::decorator::collector& decorator) | ^~~~~~~~~ /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include/corelib/test_boost.hpp: In constructor 'ncbi::SNcbiTestRegistrar::SNcbiTestRegistrar(boost::unit_test::test_case*, boost::unit_test::counter_t, unsigned int)': /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include/corelib/test_boost.hpp:209:36: error: 'boost::unit_test::decorator::collector' has not been declared 209 | , boost::unit_test::decorator::collector::instance() | ^~~~~~~~~ /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include/corelib/test_boost.hpp:780:22: note: in expansion of macro 'NCBI_BOOST_DECORATOR_ARG' 780 | : TParent(tc NCBI_BOOST_DECORATOR_ARG, exp_fail) | ^~~~~~~~~~~~~~~~~~~~~~~~ /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include/corelib/test_boost.hpp: In constructor 'ncbi::SNcbiTestRegistrar::SNcbiTestRegistrar(boost::unit_test::test_case*, unsigned int, int&)': /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include/corelib/test_boost.hpp:789:32: error: no matching function for call to 'boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*&, int&)' 789 | : TParent(tc, decorator) | ^ In file included from /usr/include/boost/test/unit_test_suite.hpp:18, from /usr/include/boost/test/unit_test.hpp:19, from /usr/include/boost/test/auto_unit_test.hpp:19, from /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/include/corelib/test_boost.hpp:69, from /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/corelib/test_boost.cpp:50: /usr/include/boost/test/tree/auto_registration.hpp:44:17: note: candidate: 'boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(int)' 44 | explicit auto_test_unit_registrar( int ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/test/tree/auto_registration.hpp:44:17: note: candidate expects 1 argument, 2 provided ... ------------------------------------------------------ Current dir: /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/build/corelib [create_flat_makefile.sh] FAILED (status 2): make /bin/grep: /var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/build/Flat.configuration_log: No such file or directory config.status: error: flat makefile generation failed. * ERROR: sci-biology/ncbi-tools++-22.0.0::science failed (configure phase): * (no error message) * * Call stack: * ebuild.sh, line 127: Called src_configure * environment, line 2249: Called die * The specific snippet of code: * LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 --with-flat-makefile ${myconf[@]} || die * * If you need support, post the output of `emerge --info '=sci-biology/ncbi-tools++-22.0.0::science'`, * the complete build log and the output of `emerge -pqv '=sci-biology/ncbi-tools++-22.0.0::science'`. * The complete build log is located at '/var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/temp/environment'. * Working directory: '/var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0' * S: '/var/tmp/portage/portage/sci-biology/ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0'
# emerge --info '=sci-biology/ncbi-tools++-22.0.0::science' Portage 3.0.30 (python 3.9.12-final-0, default/linux/amd64/17.1/no-multilib, gcc-9.3.0, glibc-2.35-r3, 5.4.189 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-5.4.189-x86_64-Intel-R-_Core-TM-_i7-7820HQ_CPU_@_2.90GHz-with-glibc2.35 KiB Mem: 32813704 total, 2758572 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Sat, 23 Apr 2022 09:30:01 +0000 Head commit of repository gentoo: b5e07cc9da7d5718f139e099a68139e6ea0a37ce Head commit of repository randall: 1878db2875a45dfa0a8c37a1f38035da7deb5cbc sh bash 5.1_p16 ld GNU ld (Gentoo 2.38 p4) 2.38 app-misc/pax-utils: 1.3.3::gentoo app-shells/bash: 5.1_p16::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.34.0-r6::gentoo dev-lang/python: 2.7.18_p106::stefantalpalaru, 3.7.13::gentoo, 3.8.13::gentoo, 3.9.12::gentoo dev-lang/rust: 1.58.1::gentoo dev-util/cmake: 3.23.1::gentoo dev-util/meson: 0.61.4-r2::gentoo sys-apps/baselayout: 2.8::gentoo sys-apps/openrc: 0.44.10::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.11.6-r3::gentoo, 1.13.4-r2::gentoo, 1.14.1-r2::gentoo, 1.15.1-r2::gentoo, 1.16.5::gentoo sys-devel/binutils: 2.38-r2::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/clang: 13.0.1::gentoo sys-devel/gcc: 9.3.0-r2::gentoo, 10.3.0::gentoo, 11.3.0::gentoo sys-devel/gcc-config: 2.5-r1::gentoo sys-devel/libtool: 2.4.7::gentoo sys-devel/lld: 14.0.1::gentoo sys-devel/llvm: 13.0.1::gentoo, 14.0.1::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.17::gentoo (virtual/os-headers) sys-libs/glibc: 2.35-r3::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 randall location: /var/db/repos/randall sync-type: git sync-uri: https://github.com/ran-dall/portage-overlay masters: gentoo science location: /mnt/large/home/mmokrejs/proj/sci masters: gentoo priority: 0 x-portage location: /usr/local/portage masters: gentoo priority: 1 layman location: /var/lib/layman masters: gentoo priority: 2 stefantalpalaru location: /var/lib/layman/stefantalpalaru masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 NPSL Nero-EULA-US AdobeFlash-10.3 AdobeFlash-11.x OPERA-2014 RAR Intel-SDP intel-ucode Skype-TOS vmware linux-firmware fasta vienna-rna unafold GRL MSttfEULA hplip-plugin meme mRNAmarkup ApE ICS ipw3945 finchtv modeller gmap master-pdf-editor abyss swiss-prot Aladdin AVASYS truecrypt-3.0 pyvcf Non-profit-OSL-3.0 estscan bcca_2010 oncotator Adobe blat staden CeCILL-1.1 phrap STRIDE cctbx-2.0 bh-luxi ARIADNE unRAR all-rights-reserved trf annovar_personal_only stampy-academic BSD-BroadInstitute UPennState freedist free-noncomm blasr sun-jlfgr FLI-Jena PSTT netperf sun-jsr67 xv vim.org OSGi-Specification-2.0 colt mod_fastcgi googleearth google-chrome ACE AFL churchill genscan no-source-code linux-fw-redistributable ISSL JSON MPEG-4 Apache-2.0 BSD MIT BSD-2 FSFAP unicode Subversion OPERA-2018 ms-teams-pre TeamViewer PSF-2.4 merlin" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -ftree-vectorize" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf /usr/share/maven-bin-3.6/conf /usr/share/maven-bin-3.8/conf /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php8.0/ext-active/ /etc/php/apache2-php8.1/ext-active/ /etc/php/cgi-php8.0/ext-active/ /etc/php/cgi-php8.1/ext-active/ /etc/php/cli-php8.0/ext-active/ /etc/php/cli-php8.1/ext-active/ /etc/php/fpm-php8.1/ext-active/ /etc/php/phpdbg-php8.1/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/vmware-installer" CXXFLAGS="-O2 -pipe -march=native -ftree-vectorize" DISTDIR="/usr/portage/distfiles" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY 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" FCFLAGS="-O2 -pipe -march=native -ftree-vectorize" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news nostrip parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=native -ftree-vectorize" GENTOO_MIRRORS="http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LANG="cs_CZ.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en_US en_GB en cs" MAKEOPTS="-j5" 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/portage" SHELL="/bin/bash" USE="X aac acl acpi alsa amd64 amr apache apache2 asm avx avx2 berkdb bluetooth boost bzip2 cairo caps cdda cdr cgi cli coin cracklib crypt cryptlib cryptsetup cups dbus device-mapper dhcp directfb dri dri3 drm dvd dvda elogind emboss encode eselect-ldso fax fbcon ffmpeg flac fontconfig fortran gbm gcrypt gd gdbm geoip geolocation gimp glpk gmp gnutls gpm gps gtk hal hpijs hwdb iconv id3tag imaging innodb inotify iproute2 java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack laptop lcms libglvnd libnotify libtirpc lm_sensors lz4 mad mariadb matroska mmx modemmanager mp3 ncurses nfs nls nptl nptlonly nscd nss ntfsprogs objc ocr ogg opengl openh264 openmp openssl opus pam parport pbs pcre pcre16 pcsc-lite pdf perl php png policykit polkit ppds pppd python qt3support qt4 qt5 readline rendering resolvconf romio scanner sctp seccomp server session sha slideshow smartcard sndfile split-usr sqlite sse sse2 sse3 sse4_1 sse4_2 ssl sslv3 ssse3 startup-notification suexec svg syslog tcl tcpd threads tiff tk truetype twolame udev unicode usb v4l v4l2 vaapi vim-syntax vnc vorbis wavpack wayland wifi x11 x264 x265 xattr xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64" ADA_TARGET="gnat_2020" ALSA_CARDS="hdspm usb-usx2y" APACHE2_MODULES="alias authn_core authz_core socache_shmcb authz_host auth_basic auth_digest cgi cgid deflate dir env filter include info mem_cache mime mime_magic negotiation remoteip setenvif status userdir vhost_alias rewrite usertrack cache file_cache disk_cache charset_lite log_config log_forensic unixd" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="gpsclock navcom ntrip rtcm104v2 rtcm104v3 ublox nmea0183 nmea2000 aivdm passthrough" GRUB_PLATFORMS="efi-64 pc" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en-US en-GB en cs" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" OPENMPI_RM="pbs" PHP_TARGETS="php5-4 php5-5" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_8" PYTHON_TARGETS="python2_7 python3_8 python3_9 pypy3" RUBY_TARGETS="ruby23 ruby27 ruby30 ruby31" USERLAND="GNU" VIDEO_CARDS="vesa vmware fbdev intel i915 i965 iris" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat 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, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ================================================================= Package Settings ================================================================= sci-biology/ncbi-tools++-22.0.0::science was built with the following: USE="X berkdb bzip2 gnutls jpeg opengl pcre png python sqlite threads tiff xml -boost -cppunit -curl -debug -expat -fastcgi -fltk -freetype -gif -glut -hdf5 -icu -lzo -mesa -muparser -mysql -odbc (-pch) -sablotron -static -static-libs -test -wxwidgets -xalan -xerces -xpm -xslt" PYTHON_SINGLE_TARGET="python3_7 -python3_8 -python3_9" FEATURES="preserve-libs fixlafiles binpkg-dostrip protect-owned news splitdebug unmerge-logs pid-sandbox multilib-strict usersync userfetch nostrip binpkg-logs ipc-sandbox unknown-features-warn unmerge-orphans qa-unresolved-soname-deps usersandbox ebuild-locks network-sandbox strict binpkg-docompress merge-sync sandbox distlocks assume-digests config-protect-if-modified parallel-fetch sfperms xattr userpriv"
Created attachment 775137 [details] build.log
The ebuild used to use Makefile.flat rules to build and for a good reason compilation of the testsuite was disabled. Now, the ebuild tries to use the home-grown configure (not GNU configure) and one cannoty build this package anymore with gcc-9.3.0. Sanity checks in configure fail for gcc-10 and newer.
(In reply to Martin Mokrejš from comment #3) > The ebuild used to use Makefile.flat rules to build and for a good reason > compilation of the testsuite was disabled. > > Now, the ebuild tries to use the home-grown configure (not GNU configure) > and one cannoty build this package anymore with gcc-9.3.0. > > Sanity checks in configure fail for gcc-10 and newer. Then please fix it.
