Bugzilla Bug 163151

In file included from /usr/include/mysql/my_global.h:84,
                 from myx_library.c:35:
/usr/include/mysql/my_config.h:979:1: warning: "PACKAGE" redefined
In file included from myx_library.c:28:
../../../config.h:65:1: warning: this is the location of the previous
definition
In file included from /usr/include/mysql/my_global.h:84,
                 from myx_library.c:35:
/usr/include/mysql/my_config.h:985:1: warning: "PACKAGE_NAME" redefined
In file included from myx_library.c:28:
../../../config.h:71:1: warning: this is the location of the previous
definition
In file included from /usr/include/mysql/my_global.h:84,
                 from myx_library.c:35:
/usr/include/mysql/my_config.h:988:1: warning: "PACKAGE_STRING" redefined
In file included from myx_library.c:28:
../../../config.h:74:1: warning: this is the location of the previous
definition
In file included from /usr/include/mysql/my_global.h:84,
                 from myx_library.c:35:
/usr/include/mysql/my_config.h:991:1: warning: "PACKAGE_TARNAME" redefined
In file included from myx_library.c:28:
../../../config.h:77:1: warning: this is the location of the previous
definition
In file included from /usr/include/mysql/my_global.h:84,
                 from myx_library.c:35:
/usr/include/mysql/my_config.h:994:1: warning: "PACKAGE_VERSION" redefined
In file included from myx_library.c:28:
../../../config.h:80:1: warning: this is the location of the previous
definition
In file included from /usr/include/mysql/my_global.h:84,
                 from myx_library.c:35:
/usr/include/mysql/my_config.h:1110:1: warning: "VERSION" redefined
In file included from myx_library.c:28:
../../../config.h:86:1: warning: this is the location of the previous
definition
In file included from myx_library.c:35:
/usr/include/mysql/my_global.h:318:24: error: asm/atomic.h: No such file or
directory
 i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I../../.. -I../include
-I../../../library/utilities/shared_include
-I../../../library/utilities/include -I../../../library/sql-parser/include
-I/usr/include/mysql -DHAVE_ERRNO_AS_DEFINE=1 -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/libxml2 -O3 -march=pentium-m
-fomit-frame-pointer -pipe -fexceptions -Wall -Wsign-compare -Wall
-Wsign-compare -MT myx_network.lo -MD -MP -MF .deps/myx_network.Tpo -c
myx_network.c  -fPIC -DPIC -o .libs/myx_network.o
make[4]: *** [myx_library.lo] Error 1
make[4]: *** Waiting for unfinished jobs....
myx_network.c: In function 'myx_ping_host':
myx_network.c:217: warning: dereferencing type-punned pointer will break
strict-aliasing rules
 i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I. -I../../.. -I../include
-I../../../library/utilities/shared_include
-I../../../library/utilities/include -I../../../library/sql-parser/include
-I/usr/include/mysql -DHAVE_ERRNO_AS_DEFINE=1 -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/libxml2 -O3 -march=pentium-m
-fomit-frame-pointer -pipe -fexceptions -Wall -Wsign-compare -Wall
-Wsign-compare -MT myx_network.lo -MD -MP -MF .deps/myx_network.Tpo -c
myx_network.c -o myx_network.o >/dev/null 2>&1
make[4]: Leaving directory
`/var/tmp/portage/dev-db/mysql-gui-tools-5.0_p9/work/mysql-gui-tools-5.0r9/mysql-gui-common/library/base-library/source'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/var/tmp/portage/dev-db/mysql-gui-tools-5.0_p9/work/mysql-gui-tools-5.0r9/mysql-gui-common/library/base-library'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/var/tmp/portage/dev-db/mysql-gui-tools-5.0_p9/work/mysql-gui-tools-5.0r9/mysql-gui-common/library'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/var/tmp/portage/dev-db/mysql-gui-tools-5.0_p9/work/mysql-gui-tools-5.0r9/mysql-gui-common'
make: *** [all] Error 2

!!! ERROR: dev-db/mysql-gui-tools-5.0_p9 failed.
Call stack:
  ebuild.sh, line 1611:   Called dyn_compile
  ebuild.sh, line 968:   Called qa_call 'src_compile'
  environment, line 3742:   Called src_compile
  mysql-gui-tools-5.0_p9.ebuild, line 52:   Called gnome2_src_compile
'--enable-i18n'
  gnome2.eclass, line 71:   Called die

!!! compile failure
!!! If you need support, post the topmost build error, and the call stack if
relevant.
!!! A complete build log is located at
'/var/tmp/portage/dev-db/mysql-gui-tools-5.0_p9/temp/build.log'.


Reproducible: Always




gapon@bobbie ~ $ emerge --info
Portage 2.1.2-r2 (default-linux/x86/2006.0, gcc-4.1.1, glibc-2.3.6-r5,
2.6.19-gentoo-r4 i686)
=================================================================
System uname: 2.6.19-gentoo-r4 i686 Intel(R) Pentium(R) M processor 1.50GHz
Gentoo Base System version 1.12.9
Timestamp of tree: Mon, 22 Jan 2007 01:00:01 +0000
dev-java/java-config: 1.3.7, 2.0.31-r3
dev-lang/python:     2.3.6, 2.4.4
dev-python/pycrypto: 2.0.1-r5
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.14
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.19.2-r1
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O3 -march=pentium-m -fomit-frame-pointer -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /opt/openjms/config /usr/kde/3.5/env
/usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb
/usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf
/etc/java-config/vms/ /etc/revdep-rebuild /etc/splash /etc/terminfo
/etc/texmf/web2c"
CXXFLAGS="-O3 -march=pentium-m -fomit-frame-pointer -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks fixpackages metadata-transfer parallel-fetch
prelink sandbox sfperms strict"
GENTOO_MIRRORS=" http://gentoo.inode.at/
http://pandemonium.tiscali.de/pub/gentoo/
http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/
http://gentoo.mirror.solnet.ch"
LANG="cs_CZ.UTF-8"
LC_ALL="cs_CZ.UTF-8"
LINGUAS="cs"
MAKEOPTS="-j2"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --delete-after --stats --timeout=180
--exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="X a52 aac aalib acpi alsa apache2 arts avi bash-completion berkdb
bitmap-fonts bzip2 cdr cli cracklib crypt cups dbus directfb divx4linux
dlloader dri dvd eds emboss encode examples fam fbcon ffmpeg firebird firefox
foomaticdb fortran ftp gdbm gif gnome gnutls gpm gstreamer gtk gtk2 hal iconv
imap imlib ipv6 isdnlog jabber java java5 jpeg jpeg2k jython kde kdeenablefinal
libg++ libwww logrotate mad mikmod mmx mmx2 mng mono motif mp3 mpeg mysql
ncurses nls nptl nptlonly nsplugin ogg oggvorbis opengl oss pam pcmcia pcre
perl png pnp postgres pppd python qt qt3 qt4 quicktime readline reflection
samba sasl sdl seamonkey session spell spl sqlite sqlite3 sse sse2 ssl svg tcpd
tiff truetype truetype-fonts type1-fonts udev unicode usb utf8 vorbis wifi
wireshark x264 x86 xine xinerama xml xorg xscreensaver xv xvid zlib"
ALSA_CARDS="intel8x0" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop
empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi
null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="keyboard
mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk
hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="cs" USERLAND="GNU"
VIDEO_CARDS="fglrx radeon vga vesa fbdev"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS,
PORTAGE_RSYNC_EXTRA_OPTS

The package builds with this configuration:

norbert ~ # emerge --info
Portage 2.1.1-r2 (default-linux/x86/2006.1, gcc-4.1.1, glibc-2.4-r4,
2.6.18-gentoo-r6 i686)
=================================================================
System uname: 2.6.18-gentoo-r6 i686 Intel(R) Core(TM)2 CPU         T7200  @
2.00GHz
Gentoo Base System version 1.12.6
Last Sync: Mon, 22 Jan 2007 13:59:01 +0000
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632)
[disabled]
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: [Not Present]
dev-lang/python:     2.4.3-r4
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.61
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.14
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.17-r2
ACCEPT_KEYWORDS="x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=nocona -pipe -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo"
CXXFLAGS="-O2 -march=nocona -pipe -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="ftp://gentoo.risq.qc.ca http://adelie.polymtl.ca
http://gentoo.mirrored.ca ftp://cs.ubishops.ca/pub/gentoo"
LINGUAS="en"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --delete-after --stats --timeout=180
--exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="x86 X acpi alsa alsa_cards_hda-intel alsa_pcm_plugins_adpcm
alsa_pcm_plugins_alaw alsa_pcm_plugins_asym alsa_pcm_plugins_copy
alsa_pcm_plugins_dmix alsa_pcm_plugins_dshare alsa_pcm_plugins_dsnoop
alsa_pcm_plugins_empty alsa_pcm_plugins_extplug alsa_pcm_plugins_file
alsa_pcm_plugins_hooks alsa_pcm_plugins_iec958 alsa_pcm_plugins_ioplug
alsa_pcm_plugins_ladspa alsa_pcm_plugins_lfloat alsa_pcm_plugins_linear
alsa_pcm_plugins_meter alsa_pcm_plugins_mulaw alsa_pcm_plugins_multi
alsa_pcm_plugins_null alsa_pcm_plugins_plug alsa_pcm_plugins_rate
alsa_pcm_plugins_route alsa_pcm_plugins_share alsa_pcm_plugins_shm
alsa_pcm_plugins_softvol berkdb bitmap-fonts cdr cli cracklib crypt cups dbus
dlloader dri dvdr elibc_glibc firefox fortran gdbm gnome gpm iconv
input_devices_keyboard input_devices_mouse isdnlog jpeg kernel_linux
lcd_devices_bayrad lcd_devices_cfontz lcd_devices_cfontz633 lcd_devices_glk
lcd_devices_hd44780 lcd_devices_lb216 lcd_devices_lcdm001 lcd_devices_mtxorb
lcd_devices_ncurses lcd_devices_text libg++ linguas_en mysql ncurses nls nptl
nptlonly ogg opengl pam pcre perl png ppds pppd python readline reflection
session spl ssl tcpd tiff truetype-fonts type1-fonts udev unicode userland_GNU
video_cards_nvidia xinerama xorg zlib"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS,
MAKEOPTS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY

Ther has been a change to the kernel headers to remove asm/atomic.h from user
vsisibility. See http://lkml.org/lkml/2006/7/10/417

*** Bug 165790 has been marked as a duplicate of this bug. ***

I get the same atomic.h error when trying to compile Thousand Parsec C++ server
(tpserver-cpp) with MySQL support. This is with MySQL 5.0.32 and Linux kernel
2.6.20.

It looks like the problem is that when you compile MySQL there is no problems
with new linux-headers-2.6.20 I'm using. But MySQL headers that reference
atomic.h Linux header (which is gone in new versions) still get installed. So I
guess MySQl should be fixed (and probably some other applications that still
reference these Linux headers that they shouldn't) in a way that they don't
reference these removed headers anymore.

If you recompile MySQL with the new linux-headers installed the asm/atomic.h
include should be gone and mysql-gui-tools shoul compile fine.

I've tried recompiling 5.0.32 before and just upgraded to 5.0.34 today, but I
still get the error:

i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I/usr/include/mysql
-DHAVE_ERRNO_AS_DEFINE=1 -g -Wall -c mysqlemptyobject.cpp -o mysqlemptyobject.o
>/dev/null 2>&1
/bin/sh ../../../libtool --mode=compile i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H
-I. -I. -I../../..    -I/usr/include/mysql -DHAVE_ERRNO_AS_DEFINE=1 -g -Wall -c
mysqlfleet.cpp
 i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I/usr/include/mysql
-DHAVE_ERRNO_AS_DEFINE=1 -g -Wall -c mysqlfleet.cpp  -fPIC -DPIC -o
.libs/mysqlfleet.o
In file included from mysqlfleet.cpp:20:
/usr/include/mysql/my_global.h:353:24: error: asm/atomic.h: No such file or
directory
 i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I/usr/include/mysql
-DHAVE_ERRNO_AS_DEFINE=1 -g -Wall -c mtsec.cpp -o mtsec.o >/dev/null 2>&1
mysqlfleet.cpp: In member function 'virtual void
MysqlFleet::initialise(MysqlPersistence*, MYSQL*)':
mysqlfleet.cpp:160: warning: unused variable 'ver'
mysqlfleet.cpp:172: warning: unused variable 'ver'
make[4]: *** [mysqlfleet.lo] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory
`/var/tmp/portage/games-server/tpserver-cpp-0.4.0/work/tpserver-cpp-0.4.0/modules/games/mtsec'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/var/tmp/portage/games-server/tpserver-cpp-0.4.0/work/tpserver-cpp-0.4.0/modules/games'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/var/tmp/portage/games-server/tpserver-cpp-0.4.0/work/tpserver-cpp-0.4.0/modules'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/var/tmp/portage/games-server/tpserver-cpp-0.4.0/work/tpserver-cpp-0.4.0'
make: *** [all-recursive-am] Error 2

!!! ERROR: games-server/tpserver-cpp-0.4.0 failed.
Call stack:
  ebuild.sh, line 1614:   Called dyn_compile
  ebuild.sh, line 971:   Called qa_call 'src_compile'
  environment, line 2973:   Called src_compile
  tpserver-cpp-0.4.0.ebuild, line 29:   Called die

*** Bug 171906 has been marked as a duplicate of this bug. ***

This bug is not fixed by comment #6 due to bug 168931, which it should depend
on. Please change this bug's status accordingly. Thanks.

*** Bug 173369 has been marked as a duplicate of this bug. ***

*** Bug 174097 has been marked as a duplicate of this bug. ***

Problem solved for me (bug 174097) by the following:

emerge -C mysql
rm -rf /usr/include/mysql
emerge mysql
emerge mysql-gui-tools

*** Bug 174918 has been marked as a duplicate of this bug. ***

(In reply to comment #12)
> Problem solved for me (bug 174097) by the following:
> rm -rf /usr/include/mysql

I can confirm that it helps, thanks.

*** Bug 176527 has been marked as a duplicate of this bug. ***

*** Bug 185883 has been marked as a duplicate of this bug. ***

(In reply to comment #16)
> *** Bug 185883 has been marked as a duplicate of this bug. ***

That was me - sorry. I did search for related bugs, of course, but this one
didn't turn up.

*** Bug 186677 has been marked as a duplicate of this bug. ***

*** Bug 187254 has been marked as a duplicate of this bug. ***

*** Bug 189713 has been marked as a duplicate of this bug. ***

comment #12 got it to compile for me

(In reply to comment #20)
> *** Bug 189713 has been marked as a duplicate of this bug. ***

Thanks. My solution:

emerge -C mysql
emerge mysql
emerge mysql-gui-tools

Because after "emerge -C mysql" of the directory "/usr/include/mysql" any
longer did not exist.

*** Bug 190508 has been marked as a duplicate of this bug. ***

*** Bug 197004 has been marked as a duplicate of this bug. ***

*** Bug 197342 has been marked as a duplicate of this bug. ***

*** Bug 202864 has been marked as a duplicate of this bug. ***

*** Bug 210779 has been marked as a duplicate of this bug. ***

*** Bug 211641 has been marked as a duplicate of this bug. ***

*** Bug 212410 has been marked as a duplicate of this bug. ***

Why is this still marked as RESOLVED? It's obvious that this is a real bug.

If it's not fixed then it should at least be searchable so people can find the
workaround.

   These appear to be dupes.  

http://bugs.gentoo.org/show_bug.cgi?id=216184
http://bugs.gentoo.org/show_bug.cgi?id=197004


mysql/my_global.h
360,362c360,362
< /*C_MODE_START*/
< /*#include <asm/atomic.h>*/
< /*C_MODE_END*/
---
> C_MODE_START
> #include <asm/atomic.h>
> C_MODE_END

./configure --prefix=/usr/local/mysql/ --exec-prefix=/usr/local/mysql/
--enable- dependency-tracking

The source code from MySQL compiles cleanly (relatively)

So...  on my Turion64 2GHz with 
"dev-db/mysql-gui-tools ~amd64"
in /etc/portage/package.keywords
and
FEATURES="test"

# emerge -Dvp mysql-gui-tools

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

Calculating dependencies... done!
[ebuild     U ] media-libs/libart_lgpl-2.3.20 [2.3.19-r1] USE="-debug" 0
kB [ebuild     U ] dev-libs/libIDL-0.8.10 [0.8.9] USE="-debug" 364 kB
[ebuild     U ] gnome-base/orbit-2.14.12 [2.14.10] USE="-debug -doc" 729
kB [ebuild     U ] gnome-base/libbonobo-2.20.4 [2.20.3] USE="-debug -doc"
1,413 kB [ebuild     U ] sys-apps/usbutils-0.73 [0.72-r4] USE="zlib%*
-network-cron" 170 kB [ebuild     U ] app-text/scrollkeeper-9999
[0.3.14-r2] USE="(-nls%*)" 0 kB [ebuild  N    ] app-text/rarian-0.6.0-r1 
USE="-debug" 305 kB [ebuild  N    ] dev-db/mysql-gui-tools-5.0_p12-r2 
USE="administrator nls query-browser (-workbench)" 0 kB 

Total: 8 packages (6 upgrades, 2 new), Size of downloads: 2,980 kB

-----------------

Compiled Cleanly and is connected over a network!

Research on the issue is that including the atomic.h file from userspace is no
longer allowed.  So, we comment out that reference.  Just seems a little more
graceful than cleaning any other include files.

B.

*** Bug 216184 has been marked as a duplicate of this bug. ***

more easy solution - edit /usr/include/mysql/my_global.h and comment-out the
offending include. This worked for me

*** Bug 235061 has been marked as a duplicate of this bug. ***

(In reply to comment #34)
> *** Bug 235061 has been marked as a duplicate of this bug. ***
> 

Why is this marked as resolved when it is still an issue? At the very least I
would say the ebuild should suggest on failure that the user come look at this
bug.

*** Bug 236123 has been marked as a duplicate of this bug. ***

This bug references a change to kernel headers that happened in 2006. If I use
a box that I just installed MySQL on against very new kernel headers. It's
bogus to say I've got to comment out a section from installed headers.

emerge -C mysql
emerge mysql
emerge mysql-gui-tools

Doesn't fix it for me. re bug #236123

emerge -C mysql
rm -rf /usr/include/mysql
emerge mysql
emerge mysql-gui-tools

Versions:
dev-db/mysql-5.0.60-r1
dev-db/mysql-gui-tools-5.0_p12-r2

I can confirm that it helps, thanks.

I tried to emerge these tools over a year ago and had the same issue, but
rather than report them to the bugzilla I simply used the tools installed on my
laptop. Removing and re-emerging mysql fixed the problem. Perhaps after there
is a new MySQL release that would force installation of the new headers this
bug could be closed, but for now it seems as if it should remain open.  

*** Bug 240966 has been marked as a duplicate of this bug. ***

*** Bug 243278 has been marked as a duplicate of this bug. ***

*** Bug 244865 has been marked as a duplicate of this bug. ***

mysql itself had a bug, it's been fixed for months, try again.