Bug 536172 – sci-biology/mira-3.9.18 - libtool: Version mismatch error. This is libtool 2.4.4, but the definition of this LT_INIT comes from libtool 2.4.2.

• Product: Gentoo Linux
• Status: RESOLVED TEST-REQUEST

[Description Toralf Förster 2015-01-10 09:40:34 UTC]

/bin/sh ../../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++  -DPUBLICQUIET -DAJ_Linux64 -O2 -pipe  -I/usr/include   -pthread -I/usr/lib64/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib64 -Wl,-O1 -Wl,--as-needed -L/usr/lib -L/usr/lib64 -L/usr/lib -o main main.o  -lmiraerrorhandling -lboost_thread-mt -lboost_regex-mt -lboost_system -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lexpat -lm -lz -lbz2 -ltcmalloc_minimal
libtool: Version mismatch error.  This is libtool 2.4.4, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.4
libtool: and run autoconf again.
Makefile:403: recipe for target 'main' failed
make[4]: *** [main] Error 63
make[4]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src/memorc'
Makefile:404: recipe for target 'all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src'
Makefile:358: recipe for target 'all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18/src'
Makefile:417: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18'
Makefile:364: recipe for target 'all' failed
make: *** [all] Error 2
 * ERROR: sci-biology/mira-3.9.18::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/mira-3.9.18::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/mira-3.9.18::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:mira-3.9.18:20150110-070319.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/mira-3.9.18/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/mira-3.9.18/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18'
 * S: '/var/tmp/portage/sci-biology/mira-3.9.18/work/mira-3.9.18'

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

 * IMPORTANT: 2 config files in '/etc' need 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 2.2.15 (python 2.7.9-final-0, default/linux/amd64/13.0, gcc-4.8.4, glibc-2.20-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,   1330656 free
KiB Swap:   16777212 total,  16762996 free
Timestamp of tree: Fri, 09 Jan 2015 20:15:01 +0000
sh bash 4.3_p33
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.3_p33
dev-lang/perl:            5.20.1-r4
dev-lang/python:          2.7.9-r1, 3.3.5-r1
dev-util/cmake:           3.0.2
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.13.6
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.69
sys-devel/automake:       1.11.6-r1, 1.15
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.4
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.4
sys-devel/make:           4.1-r1
sys-kernel/linux-headers: 3.18 (virtual/os-headers)
sys-libs/glibc:           2.20-r1
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~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/"
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="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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Justin Lecher (RETIRED) 2015-01-11 12:17:08 UTC]

Please attach full build.log

[Comment 2 Toralf Förster 2015-01-11 12:48:24 UTC]

Created attachment 393686 [details]
emerge log

[Comment 3 Alexander Tsoy 2015-01-20 04:31:32 UTC]

This bug should be fixed by the following commit
http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/eclass/autotools.eclass?r1=1.171&r2=1.172

[Comment 4 Justin Lecher (RETIRED) 2015-01-20 09:19:45 UTC]

Please test again.

[Comment 5 Toralf Förster 2015-01-21 15:55:57 UTC]

(In reply to Justin Lecher from comment #4)
> Please test again.

Hhm,
with /mnt/qa/tinderbox/amd64-unstable/usr/portage/eclass/autotools.eclass :

# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/eclass/autotools.eclass,v 1.173 2015/01/12 23:17:14 polynomial-c Exp $

I do still get :

lboost_system -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lexpat -lm -lz -lbz2 -ltcmalloc_minimal
libtool: Version mismatch error.  This is libtool 2.4.5, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.5
libtool: and run autoconf again.
Makefile:403: recipe for target 'main' failed

[Comment 6 Alexander Tsoy 2015-01-23 07:59:54 UTC]

Created attachment 394696 [details, diff]
mira-3.9.18.ebuild.patch

Confirming this. I think it'a a problem in upstream tarball:

vm3020 mira-3.9.18 # grep AC_CONFIG_MACRO_DIR configure.ac 
AC_CONFIG_MACRO_DIR([m4])
vm3020 mira-3.9.18 # grep ACLOCAL_AMFLAGS Makefile.am 
ACLOCAL_AMFLAGS = -I m4

however all macroses located in config/m4. Please try attached patch.

[Comment 7 Justin Lecher (RETIRED) 2015-01-23 11:26:22 UTC]

+  23 Jan 2015; Justin Lecher <[e-mail]> mira-3.9.18.ebuild:
+  Add workaroung for m4 dir location, #536172
+