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Bug 614078

Summary: dev-lang/php-5.6.30-r2: portage patch failed to apply (ltmain.sh version 2.4.6)!
Product: Gentoo Linux Reporter: Erwan RIGOLLOT <erwan>
Component: Current packagesAssignee: Gentoo's Team for Core System packages <base-system>
Status: RESOLVED INVALID    
Severity: normal CC: php-bugs
Priority: Normal    
Version: unspecified   
Hardware: AMD64   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description Erwan RIGOLLOT 2017-03-27 15:38:58 UTC
After I have done emerge --sync et emerge portage, I can't emerge php-5.6.30-r2.
I have same problem with php-5.6.30 et sys-devel/gcc-4.9.4 but for GCC the message is little differente:" Portage patch requested, but failed to apply!é


Reproducible: Always

Steps to Reproduce:
1.emerge --sync
2.emerge =sys-apps/portage-2.3.3
3.emerge =dev-lang/php-5.6.30-r2
Actual Results:  
Portage patch failed to apply (ltmain.sh version 2.4.6)!

Expected Results:  
Emerge completely.

tardis ~ # emerge -pv1 =dev-lang/php-5.6.30-r2

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild  NS   ~] dev-lang/php-5.6.30-r2:5.6::gentoo [5.5.16:5.5::gentoo] USE="acl apache2 berkdb bzip2 cgi cli crypt ctype curl fileinfo filter gd gdbm hash iconv json mysql mysqli nls opcache phar posix readline session simplexml soap ssl threads tokenizer unicode xml zlib -bcmath -calendar -cdb -cjk -coverage -debug -embed -enchant -exif (-firebird) -flatfile -fpm -ftp -gmp -imap -inifile -intl -iodbc -ipv6 -kerberos -ldap -ldap-sasl -libedit -libmysqlclient -libressl -mhash -mssql -oci8-instant-client -odbc -pcntl -pdo -postgres -qdbm -recode (-selinux) -sharedmem -snmp -sockets -spell -sqlite -sybase-ct -systemd -sysvipc -tidy -truetype -vpx -wddx -xmlreader -xmlrpc -xmlwriter -xpm -xslt -zip" 0 KiB

Total: 1 package (1 in new slot), Size of downloads: 0 KiB

!!! The following installed packages are masked:
- dev-perl/DBD-mysql-4.20.0::gentoo (masked by: package.mask)
/usr/portage/profiles/package.mask:
# Kent Fredric <kentnl@gentoo.org> (04 Feb 2017)
# Unsecure versions that have been only restored to tree
# to resolve compatibility problems with mail-filter/amavisd-new
# Use with caution due to these being removed for CVE-2016-1251
# Bug: #601144
# Bug: #604678

For more information, see the MASKED PACKAGES section in the emerge
man page or refer to the Gentoo Handbook.


 * IMPORTANT: 27 news items need reading for repository 'gentoo'.
 * Use eselect news read to view new items.



tardis ~ # emerge --info
Portage 2.3.3 (python 3.4.5-final-0, default/linux/amd64/13.0, gcc-4.6.3, glibc-2.15-r3, 3.10.7-gentoo-r1 x86_64)
=================================================================
System uname: Linux-3.10.7-gentoo-r1-x86_64-Intel_Xeon_E312xx_-Sandy_Bridge-with-gentoo-2.2
KiB Mem:     1026176 total,    101068 free
KiB Swap:    1048568 total,    115252 free
Timestamp of repository gentoo: Mon, 27 Mar 2017 07:00:01 +0000
sh bash 4.2_p45
ld GNU ld (GNU Binutils) 2.23.1
app-shells/bash:          4.2_p45::gentoo
dev-lang/perl:            5.12.4-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.2.5-r2::gentoo, 3.3.2-r2::gentoo, 3.4.5::gentoo
dev-util/cmake:           2.8.12.2-r1::gentoo
dev-util/pkgconfig:       0.28::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.12.4::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.69::gentoo
sys-devel/automake:       1.10.3::gentoo, 1.11.6::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.15::gentoo
sys-devel/binutils:       2.23.1::gentoo
sys-devel/gcc:            4.6.3::gentoo, 4.7.3-r1::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6-r3::gentoo
sys-devel/make:           3.82-r4::gentoo
sys-kernel/linux-headers: 3.9::gentoo (virtual/os-headers)
sys-libs/glibc:           2.15-r3::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

x-portage
    location: /usr/local/portage
    masters: gentoo
    priority: 0

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=core2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/bind"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /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"
CXXFLAGS="-O2 -march=core2 -pipe"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--jobs=2 --autounmask=n"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news nodoc noinfo 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://mirror.leaseweb.com/gentoo"
LANG="fr_FR.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j2"
PKGDIR="/var/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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="acl amd64 apache2 berkdb bzip2 cli cracklib crypt cxx dri fortran gdbm iconv modules multilib ncurses nls nptl openmp pam pcre readline seccomp session ssl tcpd threads unicode vim-syntax xattr 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="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 proxy proxy_http" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" 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="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa 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:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

tardis ~ # cat /var/tmp/portage/dev-lang/php-5.6.30-r2/temp/build.log
 * Package:    dev-lang/php-5.6.30-r2
 * Repository: gentoo
 * Maintainer: php-bugs@gentoo.org
 * USE:        abi_x86_64 acl amd64 apache2 berkdb bzip2 cgi cli crypt ctype curl elibc_glibc fileinfo filter gd gdbm hash iconv json kernel_linux mysql mysqli nls opcache phar posix readline session simplexml soap ssl threads tokenizer unicode userland_GNU xml zlib
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking php-5.6.30.tar.xz to /var/tmp/portage/dev-lang/php-5.6.30-r2/work
>>> Source unpacked in /var/tmp/portage/dev-lang/php-5.6.30-r2/work
>>> Preparing source in /var/tmp/portage/dev-lang/php-5.6.30-r2/work/php-5.6.30 ...
 * Applying php-5.6-no-bison-warnings.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/dev-lang/php-5.6.30-r2/work/php-5.6.30' ...
 * Running libtoolize --install --copy --force ...
 [ ok ]
 * Running aclocal ...
 [ ok ]
 * This package has a configure.in file which has long been deprecated.  Please
 * update it to use configure.ac instead as newer versions of autotools will die
 * when it finds this file.  See https://bugs.gentoo.org/426262 for details.
 * Running autoconf --force ...
 [ ok ]
 * Running autoheader ...
 [ ok ]
 * Running elibtoolize in: php-5.6.30/

 * Portage patch failed to apply (ltmain.sh version 2.4.6)!
 * Please file a bug report to add a proper patch.
 * ERROR: dev-lang/php-5.6.30-r2::gentoo failed (prepare phase):
 *   Portage patch failed to apply!
 *
 * Call stack:
 *     ebuild.sh, line  115:  Called src_prepare
 *   environment, line 3765:  Called eautoreconf
 *   environment, line 1447:  Called elibtoolize '--force' '/var/tmp/portage/dev-lang/php-5.6.30-r2/work/php-5.6.30'
 *   environment, line 1685:  Called die
 * The specific snippet of code:
 *                                   die "Portage patch failed to apply!";
 *
 * If you need support, post the output of `emerge --info '=dev-lang/php-5.6.30-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=dev-lang/php-5.6.30-r2::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/dev-lang/php-5.6.30-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-lang/php-5.6.30-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/dev-lang/php-5.6.30-r2/work/php-5.6.30'
 * S: '/var/tmp/portage/dev-lang/php-5.6.30-r2/work/php-5.6.30'


tardis ~ # cat /var/tmp/portage/sys-devel/gcc-4.9.4/temp/build.log
 * Package:    sys-devel/gcc-4.9.4
 * Repository: gentoo
 * Maintainer: toolchain@gentoo.org
 * USE:        abi_x86_64 amd64 cxx elibc_glibc fortran kernel_linux multilib nls nptl openmp sanitize userland_GNU vtv
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking gcc-4.9.4.tar.bz2 to /var/tmp/portage/sys-devel/gcc-4.9.4/work
>>> Unpacking gcc-4.9.4-patches-1.0.tar.bz2 to /var/tmp/portage/sys-devel/gcc-4.9.4/work
>>> Unpacking gcc-4.9.4-uclibc-patches-1.0.tar.bz2 to /var/tmp/portage/sys-devel/gcc-4.9.4/work
>>> Unpacking gcc-4.9.4-piepatches-v0.6.4.tar.bz2 to /var/tmp/portage/sys-devel/gcc-4.9.4/work
>>> Unpacking gcc-4.4.3-specs-0.2.0.tar.bz2 to /var/tmp/portage/sys-devel/gcc-4.9.4/work
>>> Source unpacked in /var/tmp/portage/sys-devel/gcc-4.9.4/work
>>> Preparing source in /var/tmp/portage/sys-devel/gcc-4.9.4/work/gcc-4.9.4 ...
 * Applying Gentoo patches ...
 *   09_all_default-ssp.patch ...
 [ ok ]
 *   10_all_default-fortify-source.patch ...
 [ ok ]
 *   11_all_default-warn-format-security.patch ...
 [ ok ]
 *   12_all_default-warn-trampolines.patch ...
 [ ok ]
 *   13_all_default-color.patch ...
 [ ok ]
 *   15_all_libgfortran-Werror.patch ...
 [ ok ]
 *   16_all_libgomp-Werror.patch ...
 [ ok ]
 *   17_all_libitm-Werror.patch ...
 [ ok ]
 *   18_all_libatomic-Werror.patch ...
 [ ok ]
 *   19_all_libbacktrace-Werror.patch ...
 [ ok ]
 *   20_all_msgfmt-libstdc++-link.patch ...
 [ ok ]
 *   25_all_alpha-mieee-default.patch ...
 [ ok ]
 *   26_all_alpha-asm-mcpu.patch ...
 [ ok ]
 *   29_all_arm_armv4t-default.patch ...
 [ ok ]
 *   34_all_ia64_note.GNU-stack.patch ...
 [ ok ]
 *   34_all_libjava-classpath-locale-sort.patch ...
 [ ok ]
 *   38_all_sh_pr24836_all-archs.patch ...
 [ ok ]
 *   42_all_superh_default-multilib.patch ...
 [ ok ]
 *   50_all_libiberty-asprintf.patch ...
 [ ok ]
 *   51_all_libiberty-pic.patch ...
 [ ok ]
 *   52_all_netbsd-Bsymbolic.patch ...
 [ ok ]
 *   53_all_libitm-no-fortify-source.patch ...
 [ ok ]
 *   67_all_gcc-poison-system-directories.patch ...
 [ ok ]
 *   74_all_gcc49_cloog-dl.patch ...
 [ ok ]
 *   90_all_pr55930-dependency-tracking.patch ...
 [ ok ]
 *   91_all_pr61538-atomic-compare-exchange.patch ...
 [ ok ]
 *   93_all_gcc-4.9-config.h-bconfig.h-parallel-PR57125-PR61899.patch ...
 [ ok ]
 * Done with patching
 * Applying uClibc patches ...
 *   90_all_100-uclibc-conf.patch ...
 [ ok ]
 *   90_all_301-missing-execinfo_h.patch ...
 [ ok ]
 *   90_all_302-c99-snprintf.patch ...
 [ ok ]
 * Done with patching
 * Applying pie patches ...
 *   01_all_gcc49_configure.patch ...
 [ ok ]
 *   02_all_gcc48_config.in.patch ...
 [ ok ]
 *   03_all_gcc49_Makefile.in.patch ...
 [ ok ]
 *   05_all_gcc48_gcc.c.patch ...
 [ ok ]
 *   16_all_gcc47_nopie_option.patch ...
 [ ok ]
 *   20_all_gcc49_config_crtbeginp.patch ...
 [ ok ]
 *   24_all_gcc49_invoke.texi.patch ...
 [ ok ]
 *   33_all_gcc48_config_rs6000.patch ...
 [ ok ]
 *   34_all_gcc48_config_i386.patch ...
 [ ok ]
 *   35_all_gcc48_config_arm.patch ...
 [ ok ]
 *   36_all_gcc48_config_mips.patch ...
 [ ok ]
 *   37_all_gcc48_config_ia64.patch ...
 [ ok ]
 *   40_all_gcc49_config_esp.patch ...
 [ ok ]
 * Done with patching
 * Updating gcc to use automatic SSP building ...
 * updating multilib directories to be: ../lib64 ../lib32
 * Running elibtoolize in: gcc-4.9.4/

 * Portage patch requested, but failed to apply!
 * Please file a bug report to add a proper patch.
 * ERROR: sys-devel/gcc-4.9.4::gentoo failed (prepare phase):
 *   Portage patch requested, but failed to apply!
 *
 * Call stack:
 *     ebuild.sh, line  115:  Called src_prepare
 *   environment, line 3839:  Called toolchain_src_prepare
 *   environment, line 5137:  Called elibtoolize '--portage' '--shallow' '--no-uclibc'
 *   environment, line 1173:  Called die
 * The specific snippet of code:
 *                                   die "Portage patch requested, but failed to apply!";
 *
 * If you need support, post the output of `emerge --info '=sys-devel/gcc-4.9.4::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sys-devel/gcc-4.9.4::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sys-devel/gcc-4.9.4/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sys-devel/gcc-4.9.4/temp/environment'.
 * Working directory: '/var/tmp/portage/sys-devel/gcc-4.9.4/work/gcc-4.9.4'
 * S: '/var/tmp/portage/sys-devel/gcc-4.9.4/work/gcc-4.9.4'
Comment 1 Michael Orlitzky gentoo-dev 2017-03-27 16:04:54 UTC
Hi, can you please check to see if you have the "app-portage/elt-patches" package installed?

That package should get pulled in as part of a change that was made about ten days ago to our eclasses. If it's not installed on your system when you, for example, "emerge php", then that will give us a hint.
Comment 2 Sébastien P. 2017-03-27 19:57:14 UTC
Erwan told an important information on gentoo-user-fr, he have not updated his system for many months (possibly 2 years).

You should take a look at https://wiki.gentoo.org/wiki/Upgrading_Gentoo/fr#Upgrading_from_older_systems

You can use a command like “ls -tl /var/db/pkg/ | head” to know how old is your system (if you have not installed packages since your last “--sync”).
Comment 3 Michael Orlitzky gentoo-dev 2017-03-28 00:49:31 UTC
(In reply to Sébastien P. from comment #2)
> Erwan told an important information on gentoo-user-fr, he have not updated
> his system for many months (possibly 2 years).
> 

That's clear from the number of unread news items =)

I've asked him to please post the output of "emerge -puDN world", and to see if he has elt-patches installed. Regardless of how old the system is, elt-patches should be pulled in before they're used.

I would like to rule out the possibility that there are circular dependencies involving elt-patches, xz-utils, libtool, etc. that cause the toolchain to be upgraded before elt-patches is installed. Otherwise, everyone with a slightly old toolchain might hit the same problem.
Comment 4 Erwan RIGOLLOT 2017-03-29 06:41:55 UTC
Hi all,

It's solved and it was my fault.

I have had to put elt-patches in /etc/portage/profile/package.provided to compile new version of portage with success two days ago and I forget it .....


Thank you for your help to all