Created attachment 733411 [details] build.log x86_64-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed -o mkdssp obj/mkdssp.o obj/dssp.o obj/primitives-3d.o obj/structure.o obj/utils.o obj/mas.o obj/iocif.o -L"/usr/lib64" -lboost_thread-mt -lboost_filesystem-mt -lboost_program_options-mt -lboost_iostreams-mt -lboost_system-mt -lz -lbz2 -pthread /usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_thread-mt /usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_filesystem-mt /usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_program_options-mt /usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_iostreams-mt /usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_system-mt collect2: error: ld returned 1 exit status make: *** [makefile:54: mkdssp] Error 1 * ERROR: sci-chemistry/dssp-2.2.1-r2::gentoo failed (compile phase): ---- Portage 3.0.20 (python 3.9.6-final-0, default/linux/amd64/17.1/systemd, gcc-10.3.0, glibc-2.33-r5, 5.10.58-gentoo-dist-hardened x86_64) ================================================================= System uname: Linux-5.10.58-gentoo-dist-hardened-x86_64-AMD_Ryzen_7_2700_Eight-Core_Processor-with-glibc2.33 KiB Mem: 16365964 total, 10252188 free KiB Swap: 16777212 total, 15938300 free Timestamp of repository gentoo: Mon, 16 Aug 2021 03:30:01 +0000 Head commit of repository gentoo: 79009e0439e54b3894eaf795a2d2011253b94def sh bash 5.1_p8 ld GNU ld (Gentoo 2.35.2 p1) 2.35.2 app-shells/bash: 5.1_p8::gentoo dev-lang/perl: 5.34.0-r1::gentoo dev-lang/python: 2.7.18_p11::gentoo, 3.9.6::gentoo, 3.10.0_beta4::gentoo dev-lang/rust: 1.54.0::gentoo dev-util/cmake: 3.21.1::gentoo sys-apps/baselayout: 2.7-r3::gentoo sys-apps/sandbox: 2.24::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.4::gentoo sys-devel/binutils: 2.35.2::gentoo, 2.36.1-r2::gentoo sys-devel/gcc: 10.3.0-r2::gentoo, 11.2.0::gentoo sys-devel/gcc-config: 2.4::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.13::gentoo (virtual/os-headers) sys-libs/glibc: 2.33-r5::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-max-age: 24 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/i2pd/certificates /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-php7.3/ext-active/ /etc/php/apache2-php7.4/ext-active/ /etc/php/cgi-php7.3/ext-active/ /etc/php/cgi-php7.4/ext-active/ /etc/php/cli-php7.3/ext-active/ /etc/php/cli-php7.4/ext-active/ /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=native -pipe" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--keep-going=y" 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 -march=native -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox multilib-strict network-sandbox news parallel-fetch parallel-install pid-sandbox 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 -march=native -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j4" 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" USE="acl amd64 boost bzip2 cli crypt dri fortran gdbm iconv ipv6 libglvnd libtirpc multilib ncurses nls nptl openmp pam pcre pulseaudio readline seccomp split-usr ssl systemd tcpd udev unicode xattr zlib" ABI_X86="64 32" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" 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 rdrand sha sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" 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" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" RUBY_TARGETS="ruby26" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bd93b01be38831d1ef5a4d2518c351777c86d9a7 commit bd93b01be38831d1ef5a4d2518c351777c86d9a7 Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-08-29 10:38:18 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-08-29 10:38:18 +0000 profiles: last-rite sci-chemistry/dssp Bug: https://bugs.gentoo.org/802417 Bug: https://bugs.gentoo.org/808669 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 7 +++++++ 1 file changed, 7 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4e4e045da2570733e3a7cf50ed1712945d44dc2f commit 4e4e045da2570733e3a7cf50ed1712945d44dc2f Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2021-09-02 11:59:21 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2021-09-02 12:00:49 +0000 sci-chemistry/dssp: Bump to 3.0.11 It is the latest version that seems to work with gmx do_dssp from my tests, also the one packaged in Fedora currently Closes: https://bugs.gentoo.org/802417 Closes: https://bugs.gentoo.org/808669 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org> sci-chemistry/dssp/Manifest | 1 + sci-chemistry/dssp/dssp-3.0.11.ebuild | 42 +++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+) https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=86a55f2707b1daa78e8d7e0666756e95ef588d47 commit 86a55f2707b1daa78e8d7e0666756e95ef588d47 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2021-09-02 11:48:56 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2021-09-02 12:00:44 +0000 sci-chemistry/dssp: Fix boost compat for dssp-2 dssp-2 is still needed by gromacs, try to keep it whenever possible then Closes: https://bugs.gentoo.org/802417 Closes: https://bugs.gentoo.org/808669 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org> sci-chemistry/dssp/dssp-2.2.1-r3.ebuild | 41 +++++++++++++++++++++++++++++++++ sci-chemistry/dssp/files/30-dssp | 1 + 2 files changed, 42 insertions(+) https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=73c30608dfed594378b78b10858023a7f0a19686 commit 73c30608dfed594378b78b10858023a7f0a19686 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2021-09-02 11:44:31 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2021-09-02 12:00:42 +0000 sci-chemistry/dssp: Bump to 4.0.1 Closes: https://bugs.gentoo.org/679142 Closes: https://bugs.gentoo.org/802417 Closes: https://bugs.gentoo.org/808669 Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Pacho Ramos <pacho@gentoo.org> sci-chemistry/dssp/Manifest | 1 + sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild | 33 ++++++++++++++++++++++++++ 2 files changed, 34 insertions(+)
