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christoph_peter_s
Tux's lil' helper
Joined: 30 Nov 2015
Posts: 106
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 Posted: Fri Sep 30, 2016 10:11 am Post subject: emerge of sys-libs/pam fails [solved] |
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Dear Gentoo-cracks,
it seems I messed up my system in some obscure way...
To get it fixed I tried to reinstall gcc (and some other crucial package) with --emptytree.
But all these attempts stop at sys-libs/pam. 
I googled around for some hours, tried to recompile gcc, binutils, libc. All this runs OK,
but a few packages fail at the linking stage with obscure error messages. I am completely
clueless on how to get this fixed. Somehow it rather looks like I messed up something like
gcc rather than hitting some Gentoo bug...
This is the tail of the build output:
| Code: |
In file included from /usr/include/string.h:635:0,
from parse_y.y:9:
In function ‘memset’,
inlined from ‘yyparse’ at parse_y.y:84:5:
/usr/include/bits/string3.h:86:7: warning: call to ‘__warn_memset_zero_len’ declared with attribute warning: memset used with constant zero length parameter; this could be due to transposed parameters
__warn_memset_zero_len ();
^
In function ‘memset’,
inlined from ‘yyparse’ at parse_y.y:111:5:
/usr/include/bits/string3.h:86:7: warning: call to ‘__warn_memset_zero_len’ declared with attribute warning: memset used with constant zero length parameter; this could be due to transposed parameters
__warn_memset_zero_len ();
^
/bin/sh ../../libtool --tag=CC --mode=link x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -W -Wall -Wbad-function-cast -Wcast-align -Wcast-qual -Wmissing-declarations -Wmissing-prototypes -Wpointer-arith -Wreturn-type -Wstrict-prototypes -Wwrite-strings -Winline -Wshadow -Wl,-O1 -Wl,--as-needed -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -o padout parse_l.o parse_y.o
libtool: link: x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -W -Wall -Wbad-function-cast -Wcast-align -Wcast-qual -Wmissing-declarations -Wmissing-prototypes -Wpointer-arith -Wreturn-type -Wstrict-prototypes -Wwrite-strings -Winline -Wshadow -Wl,-O1 -Wl,--no-undefined -Wl,-O1 -o padout parse_l.o parse_y.o -Wl,--as-needed
parse_y.o: In function `yyparse':
parse_y.c:(.text+0xc23): undefined reference to `__warn_memset_zero_len'
collect2: error: ld returned 1 exit status
Makefile:456: recipe for target 'padout' failed
make[4]: *** [padout] Error 1
make[4]: Leaving directory '/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1-abi_x86_64.amd64/doc/specs'
Makefile:408: recipe for target 'all' failed
make[3]: *** [all] Error 2
make[3]: Leaving directory '/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1-abi_x86_64.amd64/doc/specs'
Makefile:464: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1-abi_x86_64.amd64/doc'
Makefile:471: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1-abi_x86_64.amd64'
Makefile:402: recipe for target 'all' failed
make: *** [all] Error 2
* ERROR: sys-libs/pam-1.2.1::gentoo failed (compile phase):
* emake failed
*
* If you need support, post the output of `emerge --info '=sys-libs/pam-1.2.1::gentoo'`,
* the complete build log and the output of `emerge -pqv '=sys-libs/pam-1.2.1::gentoo'`.
* The complete build log is located at '/var/tmp/portage/sys-libs/pam-1.2.1/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sys-libs/pam-1.2.1/temp/environment'.
* Working directory: '/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1-abi_x86_64.amd64'
* S: '/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1'
>>> Failed to emerge sys-libs/pam-1.2.1, Log file:
>>> '/var/tmp/portage/sys-libs/pam-1.2.1/temp/build.log'
* Messages for package sys-libs/pam-1.2.1:
* ERROR: sys-libs/pam-1.2.1::gentoo failed (compile phase):
* emake failed
*
* If you need support, post the output of `emerge --info '=sys-libs/pam-1.2.1::gentoo'`,
* the complete build log and the output of `emerge -pqv '=sys-libs/pam-1.2.1::gentoo'`.
* The complete build log is located at '/var/tmp/portage/sys-libs/pam-1.2.1/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/sys-libs/pam-1.2.1/temp/environment'.
* Working directory: '/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1-abi_x86_64.amd64'
* S: '/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1'
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The ebuild tells me to post these pieces of information.
| Code: |
catilina portage # emerge -pqv '=sys-libs/pam-1.2.1::gentoo'
[ebuild R ] sys-libs/pam-1.2.1 USE="berkdb cracklib nls pie -audit -debug -nis (-selinux) {-test} -vim-syntax" ABI_X86="(64) -32 (-x32)"
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| Code: |
catilina portage # emerge --info '=sys-libs/pam-1.2.1::gentoo'
Portage 2.3.0 (python 3.4.3-final-0, default/linux/amd64/13.0, gcc-4.9.3, glibc-2.22-r4, 4.4.21-gentoo x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-4.4.21-gentoo-x86_64-Intel-R-_Pentium-R-_CPU_G3258_@_3.20GHz-with-gentoo-2.2
KiB Mem: 16347868 total, 15513908 free
KiB Swap: 524284 total, 524284 free
Timestamp of repository gentoo: Fri, 30 Sep 2016 02:45:01 +0000
sh bash 4.3_p46-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash: 4.3_p46-r1::gentoo
dev-lang/perl: 5.22.2::gentoo
dev-lang/python: 2.7.10-r1::gentoo, 3.4.3-r1::gentoo
dev-util/cmake: 3.5.2-r1::gentoo
dev-util/pkgconfig: 0.28-r2::gentoo
sys-apps/baselayout: 2.2::gentoo
sys-apps/openrc: 0.21.7::gentoo
sys-apps/sandbox: 2.10-r1::gentoo
sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo
sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils: 2.25.1-r1::gentoo
sys-devel/gcc: 4.9.3::gentoo
sys-devel/gcc-config: 1.7.3::gentoo
sys-devel/libtool: 2.4.6::gentoo
sys-devel/make: 4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc: 2.22-r4::gentoo
Repositories:
gentoo
location: /usr/portage
sync-type: rsync
sync-uri: rsync://pandora.home.serbe.ch/gentoo-portage
priority: -1000
PSeOverlay
location: /usr/local/portage
masters: gentoo
priority: 10
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt /var/bind"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
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 xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="de_DE.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j2"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X aac acl acpi addns ads aio alsa amd64 avahi bash-completion berkdb braniding bzip2 caps cdr cli client cracklib crypt css cxx dbus dlap dlz dmapi dri dummy dvd encode evdev fat fbdev firmware flac fortran gdbm git glamor glint gnuplot gnutls gtk hddtemp iconv intel ipv6 jpeg kerberos keyboard lame ldb lm_sensors lock lzma lzo mmx mmxext modules mouse mp3 mp4 mplayer multilib ncurses netapi nls nouveau nptl ntfs opengl openmp pam pcre pdf perl png python quota rdesktop readline samba seccomp server session smbclient sna sound sqlite sse sse2 ssl startup-notification suid tcpd threads thunar truetype udev udevi unicode v41 vesa via vmware vnc winbind x264 xa xattr xfs xorg 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" CPU_FLAGS_X86="mmx mmxext sse sse2 sse3" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="evdev synaptics" 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="ruby20 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
=================================================================
Package Settings
=================================================================
sys-libs/pam-1.2.1::gentoo was built with the following:
USE="berkdb cracklib nls pie -audit -debug -nis (-selinux) -test -vim-syntax" ABI_X86="64 -32 -x32"
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I could add the build log, too. But it is really lengthy, and to me it looks pretty boring. I might be wrong anyway.
Best regards
Peter
Last edited by christoph_peter_s on Wed Oct 05, 2016 9:37 am; edited 3 times in total |
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christoph_peter_s
Tux's lil' helper
Joined: 30 Nov 2015
Posts: 106
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| Posted: Tue Oct 04, 2016 1:26 pm Post subject: |
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While the issue is still open, I did examine the difference between the cumbersome box and a
very similar one, which simply just works. No big differences between the boxes, especially the
use flags should be the same.
The first fishy difference is this:
on the box with the issue:
| Code: |
checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c
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and on the reference box:
| Code: |
checking for a BSD-compatible install... /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c
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Then is says on the cumbersome box
| Code: |
checking for w3m... no
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where on the good box /usr/bin/w3m does exist.
Finally the compile output itself:
| Code: |
/bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam -I.. -DDEFAULT_MODULE_PATH=\"/lib64/security/\" -DLIBPAM_COMPILE -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/include -DPAM_VERSION=\"1.2.1\" -march=native -O2 -pipe -W -Wall -Wbad-function-cast -Wcast-align -Wcast-qual -Wmissing-declarations -Wmissing-prototypes -Wpointer-arith -Wreturn-type -Wstrict-prototypes -Wwrite-strings -Winline -Wshadow -c -o pam_account.lo /var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/pam_account.c
/bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam -I.. -DDEFAULT_MODULE_PATH=\"/lib64/security/\" -DLIBPAM_COMPILE -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/include -DPAM_VERSION=\"1.2.1\" -march=native -O2 -pipe -W -Wall -Wbad-function-cast -Wcast-align -Wcast-qual -Wmissing-declarations -Wmissing-prototypes -Wpointer-arith -Wreturn-type -Wstrict-prototypes -Wwrite-strings -Winline -Wshadow -c -o pam_auth.lo /var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/pam_auth.c
libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam -I.. -DDEFAULT_MODULE_PATH=\"/lib64/security/\" -DLIBPAM_COMPILE -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/include -DPAM_VERSION=\"1.2.1\" -march=native -O2 -pipe -W -Wall -Wbad-function-cast -Wcast-align -Wcast-qual -Wmissing-declarations -Wmissing-prototypes -Wpointer-arith -Wreturn-type -Wstrict-prototypes -Wwrite-strings -Winline -Wshadow -c /var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/pam_account.c -fPIC -DPIC -o .libs/pam_account.o
libtool: compile: x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam -I.. -DDEFAULT_MODULE_PATH=\"/lib64/security/\" -DLIBPAM_COMPILE -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/include -DPAM_VERSION=\"1.2.1\" -march=native -O2 -pipe -W -Wall -Wbad-function-cast -Wcast-align -Wcast-qual -Wmissing-declarations -Wmissing-prototypes -Wpointer-arith -Wreturn-type -Wstrict-prototypes -Wwrite-strings -Winline -Wshadow -c /var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/pam_auth.c -fPIC -DPIC -o .libs/pam_auth.o
/bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam -I.. -DDEFAULT_MODULE_PATH=\"/lib64/security/\" -DLIBPAM_COMPILE -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/include -DPAM_VERSION=\"1.2.1\" -march=native -O2 -pipe -W -Wall -Wbad-function-cast -Wcast-align -Wcast-qual -Wmissing-declarations -Wmissing-prototypes -Wpointer-arith -Wreturn-type -Wstrict-prototypes -Wwrite-strings -Winline -Wshadow -c -o pam_data.lo /var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/pam_data.c
/bin/sh ../libtool --tag=CC --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam -I.. -DDEFAULT_MODULE_PATH=\"/lib64/security/\" -DLIBPAM_COMPILE -I/var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/include -DPAM_VERSION=\"1.2.1\" -march=native -O2 -pipe -W -Wall -Wbad-function-cast -Wcast-align -Wcast-qual -Wmissing-declarations -Wmissing-prototypes -Wpointer-arith -Wreturn-type -Wstrict-prototypes -Wwrite-strings -Winline -Wshadow -c -o pam_delay.lo /var/tmp/portage/sys-libs/pam-1.2.1/work/Linux-PAM-1.2.1/libpam/pam_delay.c
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On the reference box there is no entry '-march=native' - but I have to add, that on the cumbersome box
I did install the cross-toolchain for the raspi.
Do You guys think, I should start by looking on the apparent differences in the Python installation?
Best regards
Peter |
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christoph_peter_s
Tux's lil' helper
Joined: 30 Nov 2015
Posts: 106
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| Posted: Wed Oct 05, 2016 9:44 am Post subject: |
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OK, I fixed it.
First I did set the default Python back to 2.7.
Next I did re-emerge gcc with the emptytree option, until the stage
where this fails at the problematic sys-libs/pam. Then I did re-emerge
the next ten packages ...
| Code: |
emerge sys-auth/pambase net-misc/curl x11-proto/damageproto x11-libs/libXdamage gnome-base/librsvg x11-proto/renderproto x11-libs/xtrans sys-apps/dbus sys-devel/gcc sys-libs/glibc sys-libs/db
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And after that sys-libs/pam does compile again. For a different package I would
have unmerged and re-emerged - but I did not dare to do this with something
related to PAM, as I feared to completely scrap the system. Still have to clean
the @world file... but this is minor maintainance only. |
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