Bug 542274 – sci-biology/emboss-6.0.1: fails to compile with format-security CFLAGS

• Product: Gentoo Linux
• Status: RESOLVED OBSOLETE

[Description Toralf Förster 2015-03-05 16:48:27 UTC]

Created attachment 398158 [details]
emerge log

This is an auto-filled bug because this package fails to compile with format-security. To reproduce use CFLAGS/CXXFLAGS -Werror=format-security.

Other distros (like Fedora/Debian) build with format-security, so you could find patch(es) in their repository.

Major info at https://fedoraproject.org/wiki/Format-Security-FAQ


This is an chroot build bot image named 'amd64-hardened' at a hardened host acting as a tinderbox.
emerge log is stored in /var/log/portage/_emerge_20150304-140039.log
quick search: https://bugs.gentoo.org/buglist.cgi?quicksearch=sci-biology%2Femboss

  
Portage 2.2.14 (python 2.7.9-final-0, hardened/linux/amd64, gcc-4.8.3, glibc-2.19-r1, 3.18.8-hardened x86_64)
=================================================================
System uname: Linux-3.18.8-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16164808 total,   2849804 free
KiB Swap:   16777212 total,  16748288 free
Timestamp of tree: Wed, 04 Mar 2015 04:45:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          4.2_p53
dev-java/java-config:     2.1.12-r1
dev-lang/perl:            5.20.1-r4
dev-lang/python:          2.7.9-r1, 3.3.5-r1
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.13.11
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r4, 1.10.3-r1, 1.11.6-r1, 1.12.6, 1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.4
sys-devel/make:           4.1-r1
sys-kernel/linux-headers: 3.16 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -Wformat -Werror=format-security"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /var/lib/hsqldb /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-php5.3/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O2 -pipe -Wformat -Werror=format-security"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --quiet --jobs 1"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/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"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.de.gentoo.org/gentoo-portage"
USE="X acl aes-ni alsa amd64 apache2 avx avx2 berkdb bzip2 cairo cli corefonts cracklib crypt cups cxx dbus dnssec dot dri drmkms dvd ecc extraengine ffmpeg fontconfig fortran fpm gd gdbm gif gtk gudev gui hardened iconv icu isag jadetex jpeg justify lapack libav libkms libvirtd logrotate macvtap mbox minizip mmx modules multilib mysql ncurses nls nptl ogg opengl openmp openssl pam pax_kernel pcre pcre16 plasma png policykit python qemu qt3support qt5 readline session spice sqlite sse sse2 sse4 sse4_1 sse4_2 ssh-askpass ssl ssse3 svg tcpd theora thinkpad threads tk tls truetype uml unicode urandom usb usbredir uxa v4l v4l2 video vorbis xa xattr xkb xmp xscreensaver xslt xtpax xvfb xvmc 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" 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" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console  presenter-minimizer" LINGUAS="en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Justin Lecher (RETIRED) 2015-08-27 13:50:09 UTC]

commit 08fae0a30263fd06fe51ac5b75301d574be9e1be
Author: Justin Lecher <[e-mail]>
Date:   Thu Aug 27 15:47:31 2015 +0200
    
    sci-biology/emboss: Drop old
    
    obsolets multiple bugs
    
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=542274
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=534418
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521604
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=514014
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=493724
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=406279
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=393311
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=382321
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=378443
    
    Package-Manager: portage-2.2.20.1
    Signed-off-by: Justin Lecher <[e-mail]>
    
    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=08fae0a30263fd06fe51ac5b75301d574be9e1be