build.log

build.log (text/plain), 9.62 KB, created by Agostino Sarubbo on 2020-06-11 16:17:57 UTC

 * Package:    sci-biology/dialign-tx-1.0.2-r2
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox


@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@
This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix;
This ebuild was merged at the following commit:
https://github.com/gentoo-mirror/gentoo/commit/510da00b4864f7e20434fb0d892d663d841d8040
@@@@@ END @@@@@

>>> Unpacking source...
>>> Unpacking DIALIGN-TX_1.0.2.tar.gz to /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work
>>> Source unpacked in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work
>>> Preparing source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2 ...
 * Applying dialign-tx-1.0.2-fix-build-system.patch ...
 [ ok ]
 * Applying dialign-tx-1.0.2-implicits.patch ...
 [ ok ]
 * Applying dialign-tx-1.0.2-modernize.patch ...
 [ ok ]
 * Applying dialign-tx-1.0.2-gnu89-inline.patch ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2 ...
make -j4 -C source clean 
make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source'
rm -rf *.o *rtl *jump *addre* *cfg *life *reg *reload *flow* *stack  museq dialign-tx
make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source'
make -j4 -C source 
make: Entering directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source'
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o museq.o museq.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o parameters.o parameters.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o io.o io.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o diag.o diag.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o alig.o alig.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o assemble.o assemble.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o prob.o prob.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o orf.o orf.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fcommon   -c -o translate.o translate.c
rm -f ./museq
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ./museq \
./museq.o ./parameters.o ./io.o ./diag.o ./alig.o ./assemble.o ./prob.o ./orf.o ./translate.o  \
-pipe -Wall -lm 
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: ./diag.o: in function `find_all_diags':
diag.c:(.text+0x2149): undefined reference to `calc_ov_weight'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: ./diag.o: in function `old_find_all_diags':
diag.c:(.text+0x269d): undefined reference to `calc_ov_weight'
/usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: ./assemble.o: in function `guided_aligner_rec':
assemble.c:(.text+0xd29): undefined reference to `confl_diag'
collect2: error: ld returned 1 exit status
make: *** [Makefile:34: museq] Error 1
make: Leaving directory '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2/source'
 * ERROR: sci-biology/dialign-tx-1.0.2-r2::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/dialign-tx-1.0.2-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/dialign-tx-1.0.2-r2::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-biology/dialign-tx-1.0.2-r2:20200611-045956.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2'
 * S: '/var/tmp/portage/sci-biology/dialign-tx-1.0.2-r2/work/DIALIGN-TX_1.0.2'



emerge --info:
Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r5, 5.4.0-1011-aws x86_64)
=================================================================
System uname: Linux-5.4.0-1011-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7
KiB Mem:    16011348 total,    976896 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Thu, 11 Jun 2020 14:35:16 +0000
sh bash 5.0_p17
ld GNU ld (Gentoo 2.34 p4) 2.34.0
app-shells/bash:          5.0_p17::gentoo
dev-lang/perl:            5.30.3-r1::gentoo
dev-lang/python:          2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.20::gentoo
sys-devel/autoconf:       2.69-r5::gentoo
sys-devel/automake:       1.16.2::gentoo
sys-devel/binutils:       2.34-r1::gentoo
sys-devel/gcc:            10.1.0::gentoo
sys-devel/gcc-config:     2.3::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.31-r5::gentoo
Repositories:

gentoo
    location: /usr/portage
    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 -pipe -march=native -frecord-gcc-switches -fcommon"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fcommon"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k"
ENV_UNSET="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 -frecord-gcc-switches -fcommon"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fcommon"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="C.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j4"
PKGDIR="/root/.packages"
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 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" 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="mmx mmxext sse sse2" 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" 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 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