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Bug 534418 - sci-biology/emboss-6.0.1 with dev-libs/libpcre-8.35 - file collision in /usr/include/pcreposix.h /usr/include/pcre.h
Summary: sci-biology/emboss-6.0.1 with dev-libs/libpcre-8.35 - file collision in /usr/...
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2015-01-03 09:12 UTC by Toralf Förster
Modified: 2015-08-27 13:50 UTC (History)
1 user (show)

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


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Description Toralf Förster gentoo-dev 2015-01-03 09:12:00 UTC
* Detected file collision(s):
 * 
 * 	/usr/include/pcreposix.h
 * 	/usr/include/pcre.h
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * dev-libs/libpcre-8.35:3::gentoo
 * 	/usr/include/pcre.h
 * 	/usr/include/pcreposix.h
 * 
 * Package 'sci-biology/emboss-6.0.1' NOT merged due to file collisions.
 * If necessary, refer to your elog messages for the whole content of the
 * above message.

 * GNU info directory index is up-to-date.

 * IMPORTANT: config file '/etc/common-lisp/gentoo-init.lisp' needs updating.
 * See the CONFIGURATION FILES section of the emerge
 * man page to learn how to update config files.


This chroot image is located at a hardened amd64 host.

Portage 2.2.14 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.8.3, glibc-2.19-r1, 3.17.7-hardened-r1 x86_64)
=================================================================
System uname: Linux-3.17.7-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16166924 total,    249324 free
KiB Swap:   16777212 total,  16751788 free
Timestamp of tree: Sat, 03 Jan 2015 04:15:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.2_p53
dev-lang/perl:            5.18.2-r2
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:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 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:        2.4.2-r1
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="-O2 -pipe"
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/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.5/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="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --deep --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"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.uni-erlangen.de/pub/mirrors/gentoo http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://gd.tuwien.ac.at/opsys/linux/gentoo/"
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="acl amd64 berkdb bindist bzip2 cli cracklib crypt cxx dri fortran gdbm iconv ipv6 mbox mmx modules multilib ncurses nls nptl openmp pam pax_kernel pcre readline session sse sse2 ssl tcpd unicode 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" 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" 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Comment 1 Ted Tanberry 2015-02-05 12:58:25 UTC
Please try the science overlay, we have finally gotten around to fixing emboss and removed all bundled libraries (including pcre) and now link to system libraries. In future, all <sci-biology/emboss-6.6.0 ebuilds will eventually be removed.
Comment 2 Toralf Förster gentoo-dev 2015-02-05 15:10:34 UTC
(In reply to Ted Tanberry from comment #1)
> Please try the science overlay, we have finally gotten around to fixing
> emboss and removed all bundled libraries (including pcre) and now link to
> system libraries. In future, all <sci-biology/emboss-6.6.0 ebuilds will
> eventually be removed.

Hm, this is just a build bot chroot for the vanilla gentoo tree - so shall I exclude a category from it ?
Comment 3 Martin Mokrejš 2015-03-09 14:13:39 UTC
I think emboss-6.3.1_p4-r2 which used to be the last 6.3.1_p4 ebuild in the tree (sci overlay) should be restored and stabilized. It does not have this problem:


# emerge -pv =sci-biology/emboss-6.3.1_p4-r2

...

Calculating dependencies... done!
[ebuild   R    ] sci-biology/emboss-6.3.1_p4-r2::x-portage  USE="-X -minimal* -mysql -pdf -png -postgres -static-libs" 0 KiB
#
# equery files emboss | grep -i pcre
/usr/include/emboss/ajax-pcre-config.h
#
# grep -i pcre  /usr/local/portage/sci-biology/emboss/files/*
/usr/local/portage/sci-biology/emboss/files/emboss-6.3.1_p4-r2_compilations-paths.patch: AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
...

From the above you can see it uses system-wide pcre. The patch does not actually chnagethat (no minus or plus sign at the beginning of the line). So, it should be the same also with previous _p4-r1 ebuild which was in the main tree.
Comment 4 Ted Tanberry 2015-03-10 17:18:54 UTC
emboss-6.6.0 fixes all these issues, have you tried it?
Comment 5 Justin Lecher gentoo-dev 2015-08-27 13:50:15 UTC
commit 08fae0a30263fd06fe51ac5b75301d574be9e1be
Author: Justin Lecher <jlec@gentoo.org>
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 <jlec@gentoo.org>
    
    https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=08fae0a30263fd06fe51ac5b75301d574be9e1be