* 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
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.
(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 ?
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.
emboss-6.6.0 fixes all these issues, have you tried it?
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
