Bug 808669 – sci-chemistry/dssp-2.2.1-r2: fails to build (/usr/lib/gcc/x86_64-pc-linux-gnu/10.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lboost_thread-mt)

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Sam James 2021-08-17 02:47:27 UTC]

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

[Comment 1 Larry the Git Cow 2021-08-29 10:38:36 UTC]

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 <[e-mail]>
AuthorDate: 2021-08-29 10:38:18 +0000
Commit:     David Seifert <[e-mail]>
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 <[e-mail]>

 profiles/package.mask | 7 +++++++
 1 file changed, 7 insertions(+)

[Comment 2 Larry the Git Cow 2021-09-02 12:00:58 UTC]

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 <[e-mail]>
AuthorDate: 2021-09-02 11:59:21 +0000
Commit:     Pacho Ramos <[e-mail]>
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 <[e-mail]>

 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 <[e-mail]>
AuthorDate: 2021-09-02 11:48:56 +0000
Commit:     Pacho Ramos <[e-mail]>
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 <[e-mail]>

 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 <[e-mail]>
AuthorDate: 2021-09-02 11:44:31 +0000
Commit:     Pacho Ramos <[e-mail]>
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 <[e-mail]>

 sci-chemistry/dssp/Manifest                    |  1 +
 sci-chemistry/dssp/dssp-4.0.1_p20210831.ebuild | 33 ++++++++++++++++++++++++++
 2 files changed, 34 insertions(+)