| Summary: | sci-libs/libgenome-1.3-r1 : gnDefs.cpp:8:20: error: ‘int64 abs(int64)’ conflicts with a previous declaration | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | plevine457 |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | |||
| Bug Blocks: | 582084 | ||
| Attachments: |
emerge-history.txt
environment sci-libs:libgenome-1.3-r1:20160919-122150.log libgenome-1.3-gcc6-use-stdabs.patch |
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Created attachment 446626 [details]
emerge-history.txt
Created attachment 446628 [details]
environment
Created attachment 446630 [details]
sci-libs:libgenome-1.3-r1:20160919-122150.log
Created attachment 446786 [details, diff]
libgenome-1.3-gcc6-use-stdabs.patch
abs() conflicts with the one in std by the same name. They appear to do the same thing so the patch deletes it so std::abs takes precedence.
commit c44d450a927693cd4d0ebb694cbebd0afcfef47a Author: David Seifert <soap@gentoo.org> Date: Tue Sep 20 21:37:27 2016 +0200 sci-libs/libgenome: Allow for compiling with GCC 6 Gentoo-bug: 594372 * EAPI=6 |
libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -march=native -O2 -pipe -MT gnDefs.lo -MD -MP -MF .deps/gnDefs.Tpo -c gnDefs.cpp -fPIC -DPIC -o .libs/gnDefs.o gnDefs.cpp: In function ‘int64 abs(int64)’: gnDefs.cpp:8:20: error: ‘int64 abs(int64)’ conflicts with a previous declaration int64 abs( int64 a ){ ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/stdlib.h:36:0, $ cat emerge-info.txt ----------------------------------------------------------------- This is an unstable amd64 chroot image (named amd64-13.0-systemd-libressl-unstable_20160915-201401) at a hardened host acting as a tinderbox. ----------------------------------------------------------------- USE flags ... ... in make.conf: USE=" -openssl -gnutls libressl pax_kernel xtpax -cdinstall -oci8 -bindist cgroups contrib custom-optimization -dbus -declarative dvb dvd ecc -eglfs extraengine fortran ftp git gles gtk2 havege icu imlib inifile ipv6 jpeg -lapack libkms mad modplug mpeg2 nls offensive openexr png postscript printsupport qt3support qt4 scrypt sdl semantic-desktop sqlite3 ssh-askpass ssl system-jpeg -system-sqlite timidity -tools truetype uml usb vaapi video vpx wma wxwidgets xkb -xscreensaver xslt xvfb zenmap" ... in /etc/portage/package.use/*: mail-mta/ssmtp ssl mta net-misc/wget ssl app-crypt/pinentry -qt4 app-editors/emacs -dbus -svg -ssl -gtk -gtk3 app-text/xmlto -latex dev-libs/boehm-gc threads dev-libs/libpcre pcre16 dev-qt/qtgui egl eglfs net-nds/openldap -sasl dev-util/cmake -qt4 -qt5 dev-vcs/git -perl gnome-base/librsvg -tools media-libs/mesa -vaapi sys-apps/kmod tools <=net-misc/openssh-7.3_p1-r2 -hpn media-libs/imlib2 X sys-apps/kmod tools entries in /etc/portage/package.unmask/*: media-video/ffmpeg sys-devel/gcc:6.2.0 ----------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-6.2.0 * llvm-config --version: 3.8.1 Available Python interpreters, in order of preference: [1] python3.4 [2] python3.5 (fallback) [3] python2.7 (fallback) ----------------------------------------------------------------- Portage 2.3.1 (python 3.4.5-final-0, default/linux/amd64/13.0/systemd, gcc-6.2.0, glibc-2.23-r2, 4.7.4-hardened x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.7.4-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3 KiB Mem: 65285480 total, 1038876 free KiB Swap: 67108860 total, 67106208 free Timestamp of repository gentoo: Mon, 19 Sep 2016 10:07:02 +0000 sh bash 4.3_p46 ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1 app-shells/bash: 4.3_p46::gentoo dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo dev-util/cmake: 3.6.2::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.3::gentoo sys-apps/openrc: 0.21.7::gentoo sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r2::gentoo sys-devel/automake: 1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26.1::gentoo sys-devel/gcc: 6.2.0::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: 1 local location: /usr/local/portage masters: gentoo priority: 2 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/omega.conf /usr/share/config /usr/share/gnupg/qualified.txt /var/yp/Makefile" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=native 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--exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 berkdb bzip2 cgroups cli contrib cracklib crypt custom-optimization cxx dri dvb dvd ecc extraengine fortran ftp gdbm git gles gtk2 havege iconv icu imlib inifile ipv6 jpeg libkms libressl mad mmx mmxext modplug modules mpeg2 multilib ncurses nls nptl offensive openexr openmp pam pax_kernel pcre png postscript printsupport qt3support qt4 readline scrypt sdl seccomp semantic-desktop session sqlite3 sse sse2 ssh-askpass ssl system-jpeg systemd tcpd timidity truetype udev uml unicode usb vaapi video vpx wma wxwidgets xattr xkb xslt xtpax xvfb zenmap zlib" ABI_X86="64" 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="libressl" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" L10N="ja km ml pt-PT te tl" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 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