build.log

build.log (text/plain), 19.08 KB, created by Agostino Sarubbo on 2020-07-09 11:52:25 UTC

 * Package:    sci-biology/shrimp-2.2.3
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 cpu_flags_x86_sse2 elibc_glibc kernel_linux python_single_target_python2_7 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/0afe8006b19e05f59e53463eaadc1ed26dafd2be
@@@@@ END @@@@@

 * Using python2.7 to build
>>> Unpacking source...
>>> Unpacking SHRiMP_2_2_3.src.tar.gz to /var/tmp/portage/sci-biology/shrimp-2.2.3/work
>>> Source unpacked in /var/tmp/portage/sci-biology/shrimp-2.2.3/work
>>> Preparing source in /var/tmp/portage/sci-biology/shrimp-2.2.3/work/SHRiMP_2_2_3 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/shrimp-2.2.3/work/SHRiMP_2_2_3 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/shrimp-2.2.3/work/SHRiMP_2_2_3 ...
make -j2 V=1 'CXXFLAGS=-O3 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fopenmp -O3' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -fuse-ld=lld -Wl,--defsym=__gentoo_check_ldflags__=0' 
x86_64-pc-linux-gnu-clang++ -O3 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fopenmp -O3 -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DGIT_VERSION=missing_git_version -DCXXFLAGS="\"-O3 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fopenmp -O3 -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DGIT_VERSION=missing_git_version\"" -c -o gmapper/gmapper.o gmapper/gmapper.c
x86_64-pc-linux-gnu-clang++ -Wl,-O1 -Wl,--as-needed -fuse-ld=lld -Wl,--defsym=__gentoo_check_ldflags__=0 -O3 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -fopenmp -O3 -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -DGIT_VERSION=missing_git_version -c -o gmapper/seeds.o gmapper/seeds.c
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang-10: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
clang-10: warning: -Wl,-O1: 'linker' input unused [-Wunused-command-line-argument]
clang-10: warning: -Wl,--as-needed: 'linker' input unused [-Wunused-command-line-argument]
clang-10: warning: -Wl,--defsym=__gentoo_check_ldflags__=0: 'linker' input unused [-Wunused-command-line-argument]
clang-10: warning: argument unused during compilation: '-fuse-ld=lld' [-Wunused-command-line-argument]
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:177:2: error: 'va_start' cannot be used in a
      captured statement
        va_start(fmtargs, msg);
        ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:192:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:210:2: error: 'va_start' cannot be used in a
      captured statement
        va_start(fmtargs, msg);
        ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:264:2: error: 'va_start' cannot be used in a
      captured statement
        va_start(fmtargs, msg);
        ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:279:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:297:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:351:2: error: 'va_start' cannot be used in a
      captured statement
        va_start(fmtargs, msg);
        ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:366:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:384:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/gmapper.c:26:
In file included from gmapper/../gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:433:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:177:2: error: 'va_start' cannot be used in a
      captured statement
        va_start(fmtargs, msg);
        ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:192:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:210:2: error: 'va_start' cannot be used in a
      captured statement
        va_start(fmtargs, msg);
        ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:264:2: error: 'va_start' cannot be used in a
      captured statement
        va_start(fmtargs, msg);
        ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:279:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:297:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:351:2: error: 'va_start' cannot be used in a
      captured statement
        va_start(fmtargs, msg);
        ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:366:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:384:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
In file included from gmapper/seeds.c:5:
In file included from gmapper/seeds.h:8:
In file included from gmapper/gmapper.h:13:
In file included from gmapper/../gmapper/gmapper-definitions.h:20:
gmapper/../common/my-alloc.h:433:7: error: 'va_start' cannot be used in a
      captured statement
      va_start(fmtargs, msg);
      ^
/usr/lib/llvm/10/bin/../../../../lib/clang/10.0.1/include/stdarg.h:17:29: note: 
      expanded from macro 'va_start'
#define va_start(ap, param) __builtin_va_start(ap, param)
                            ^
10 errors generated.
make: *** [Makefile:185: gmapper/seeds.o] Error 1
make: *** Waiting for unfinished jobs....
10 errors generated.
make: *** [Makefile:63: gmapper/gmapper.o] Error 1
 * ERROR: sci-biology/shrimp-2.2.3::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/shrimp-2.2.3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/shrimp-2.2.3::gentoo'`.
 * The complete build log is located at '/var/log/emerge-log/build/sci-biology/shrimp-2.2.3:20200708-181549.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/shrimp-2.2.3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/shrimp-2.2.3/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/shrimp-2.2.3/work/SHRiMP_2_2_3'
 * S: '/var/tmp/portage/sci-biology/shrimp-2.2.3/work/SHRiMP_2_2_3'



emerge --info:
Portage 2.3.103 (python 3.7.8-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r5, 5.4.0-1015-aws x86_64)
=================================================================
System uname: Linux-5.4.0-1015-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7
KiB Mem:     7895548 total,   2137588 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Thu, 09 Jul 2020 10:35:22 +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-r2::gentoo
dev-lang/python:          2.7.18::gentoo, 3.7.8-r1::gentoo, 3.8.3-r1::gentoo, 3.9.0_beta4::gentoo
dev-util/cmake:           3.18.0_rc3::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-r2::gentoo
sys-devel/gcc-config:     2.3.1::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-jobs: 1
    sync-rsync-verify-metamanifest: yes
    sync-rsync-extra-opts: 

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CC="x86_64-pc-linux-gnu-clang"
CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
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"
CXX="x86_64-pc-linux-gnu-clang++"
CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
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 -fno-diagnostics-color"
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 -fno-diagnostics-color"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="C.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -fuse-ld=lld -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j2 V=1"
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 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="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:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS