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Bug 543018 - sci-chemistry/pymol fails to compile with format-security
Summary: sci-chemistry/pymol fails to compile with format-security
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Justin Lecher
URL:
Whiteboard:
Keywords:
Depends on: 543020
Blocks: fortify-source
  Show dependency tree
 
Reported: 2015-03-12 09:26 UTC by Agostino Sarubbo
Modified: 2015-11-11 11:35 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
pymol-1.7.0.1:20150312-092316.log (pymol-1.7.0.1:20150312-092316.log,216.37 KB, text/plain)
2015-03-12 09:26 UTC, Agostino Sarubbo
Details

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Description Agostino Sarubbo gentoo-dev 2015-03-12 09:26:51 UTC
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

Portage 2.2.14 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.8.3, glibc-2.19-r1, 3.2.65-hardened-r2-xxxx-std-ipv6-64 x86_64)
=================================================================
System uname: Linux-3.2.65-hardened-r2-xxxx-std-ipv6-64-x86_64-Intel-R-_Xeon-R-_CPU_E3-1245_V2_@_3.40GHz-with-gentoo-2.2
KiB Mem:    32857376 total,   8543148 free
KiB Swap:          0 total,         0 free
ld ld di GNU (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.2_p53
dev-java/java-config:     2.2.0
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:          0.13.9
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.69
sys-devel/automake:       1.11.6-r1, 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:           4.0-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 -Wformat -Werror=format-security -g0 -O2"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.4/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 -Wformat -Werror=format-security -g0 -O2 -Wabi -fabi-version=6"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--with-bdeps y --keep-going y -1"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="it_IT.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
MAKEOPTS="-j8"
PKGDIR="/root/.pkg"
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.gentoo.org/gentoo-portage"
USE="X acl amd64 berkdb bzip2 cairo cli consolekit cracklib crypt cxx dbus dri fortran gdbm gudev hwdb iconv icu ipv6 jpeg libav minizip mmx modules multilib ncurses nls nptl ogg opengl openmp pam pax_kernel pcre png policykit python qt3support qt4 readline session sse sse2 ssl tcpd unicode vorbis zlib" ABI_X86="64" CPU_FLAGS_X86="mmx sse sse2" ELIBC="glibc" KERNEL="linux" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="am fil zh af ca cs da de el es et gl hu nb nl pl pt ro ru sk sl sv uk bg cy en eo fo ga he id ku lt lv mk ms nn sw tn zu ja zh_TW en_GB pt_BR ko zh_CN ar en_CA fi kk oc sr tr fa wa nds as be bn bn_BD bn_IN en_US es_AR es_CL es_ES es_MX eu fy fy_NL ga_IE gu gu_IN hi hi_IN is ka kn ml mr nn_NO or pa pa_IN pt_PT rm si sq sv_SE ta ta_LK te th vi ast dz km my om sh ug uz ca@valencia sr@ijekavian sr@ijekavianlatin sr@latin csb hne mai se es_LA fr_CA zh_HK br la no es_CR et_EE sr_CS bo hsb hy mn sr@Latn lb ne bs tg uz@cyrillic xh be_BY brx ca_XV dgo en_ZA gd kok ks ky lo mni nr ns pap ps rw sa_IN sat sd ss st sw_TZ ti ts ve mt ia az me tl ak hy_AM lg nso son ur_PK it fr nb nb_NO hr nan ur tk cs_CZ da_DK de_1901 de_CH en_AU lt_LT pl_PL sa sk_SK th_TH ta_IN tt sco ha mi ven ar_SY el_GR ro_RO ru_RU sl_SI uk_UA vi_VN ar_SY te_IN de_DE es_VE fa_IR fr_FR hu_HU id_ID it_IT ja_JP ka_GE nl_NL sr_BA sr_RS ca_ES fi_FI he_IL jv ru_gold yi eu_ES" NGINX_MODULES_HTTP="access auth_basic autoindex browser charset empty_gif fastcgi geo gzip limit_conn limit_req map memcached proxy referer rewrite scgi split_clients ssi upstream_ip_hash userid uwsgi addition auth_pam cache_purge dav dav_ext degradation echo fancyindex flv geoip gunzip gzip_static headers_more image_filter lua metrics mp4 naxsi perl push push_stream random_index realip secure_link security slowfs_cache spdy stub_status sub upload_progress upstream_check xslt ajp auth_request mogilefs sticky" NGINX_MODULES_MAIL="imap pop3 smtp" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_USER_TARGETS="aarch64 alpha arm armeb cris i386 m68k microblaze microblazeel mips mips64 mips64el mipsel mipsn32 mipsn32el or32 ppc ppc64 ppc64abi32 s390x sh4 sh4eb sparc sparc32plus sparc64 unicore32 x86_64" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Agostino Sarubbo gentoo-dev 2015-03-12 09:26:56 UTC
Created attachment 398718 [details]
pymol-1.7.0.1:20150312-092316.log

build log
Comment 2 Justin Lecher gentoo-dev 2015-11-11 11:35:49 UTC
commit bab728c8989c1ad152efa0fad4bb25c2ff11d733
Author: Justin Lecher <jlec@gentoo.org>
Date:   Wed Nov 11 12:22:39 2015 +0100
    
    sci-chemistry/pymol: Drop old
    
    obsoletes
    
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=543018
    
    Package-Manager: portage-2.2.23
    Signed-off-by: Justin Lecher <jlec@gentoo.org>
    
    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bab728c8989c1ad152efa0fad4bb25c2ff11d733