| Summary: | sci-mathematics/glpk: /usr/include/mysql/my_global.h:361:24: error: asm/atomic.h: No such file or directory | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Martin Mokrejš <mmokrejs> |
| Component: | New packages | Assignee: | Robin Johnson <robbat2> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | john, mysql-bugs, paulo, sci-mathematics |
| Priority: | High | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: | build.log | ||
|
Description
Martin Mokrejš
2009-01-07 19:00:08 UTC
# emerge --info Portage 2.1.6.4 (default/linux/x86/2008.0/desktop, gcc-4.3.2, glibc-2.9_p20081201-r1, 2.6.27.7 i686) ================================================================= System uname: Linux-2.6.27.7-i686-Mobile_Intel-R-_Pentium-R-_4_-_M_CPU_1.80GHz-with-glibc2.0 Timestamp of tree: Sat, 03 Jan 2009 12:20:01 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] app-shells/bash: 3.2_p48 dev-java/java-config: 1.3.7-r1, 2.1.6-r1 dev-lang/python: 2.5.2-r8 dev-python/pycrypto: 2.0.1-r6 dev-util/cmake: 2.6.2 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.4.1-r1 sys-apps/sandbox: 1.3.2 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.19 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.28-r1 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /var/bind /var/qmail/alias /var/qmail/control /var/spool/torque /var/vpopmail/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz" LDFLAGS="-Wl,-O1" LINGUAS="en cs cz" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage/layman/sunrise /usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="7zip R X Xaw3d a52 aac aalib ace acl acpi alsa amr amrnb amrwb apache2 audacious audiofile bash-completion bcmath berkdb blas bluetooth boost branding bzip2 cairo cblas cddb cdparanoia cdr clamav cli colordiff compress cpio cracklib crypt cscope css ctype cups curl curlwrappers cxx dbus dga dia directfb djbfft dri dts dv dvb dvd dvdr dvdread eds emacs emboss emf enblend encode enscript exif expat fam fame fat fbcon ffmpeg fftw firefox flac flash foomaticdb fortran fpx ftp gcj gd gdbm ggi gif gimp gimpprint glibc-compat20 glibc-omitfp glitz glut gmp gnuplot gnutls gpgme gphoto2 gpm graphviz gs gsl gstreamer gtk gtkhtml hal hdf hdf5 hp2xx i8x0 icc iconv icu id3 ieee1394 ifc imagemagick imlib inifile innodb isdnlog ithreads jack java javascript jbig jce jikes jpeg jpeg2k kdtree kerberos lame lapack laptop lcms leim libcaca libedit libnotify libwww live lzo lzw mad maildir matroska mhash midi mikmod mime ming mjpeg mmap mmx mng mod_python modperl modplug motif mozilla moznoirc mp2 mp3 mp4 mpeg mpi mpi_njtree mpich2 mplayer mudflap mule musepack mxdatetime mysql mysqli ncurses netcdf netpbm network nls nntp nptl nptlonly nsplugin ntfs numeric ogg opengl openmp pam pango pcmcia pcntl pcre pdf perl plotutils plugin png pnm postproc postscript ppds pppd procmail pymol python qt3 qt3support qt4 quicktime rar raw readline recode reflection reiserfs rpm samba sasl scanner scp seamonkey server session sftp sift slp smime sndfile soap sockets spell spl sqlite srt sse sse2 ssl startup-notification subtitles subversion svg svgz sysfs sysvipc t1lib tcl tcpd tetex theora threads tidy tiff tk transcode truetype unicode urandom usb userlocales uuencode v4l v4l2 vcd vhook vim-syntax vim-with-x vorbis wifi win32codecs wmf wxwindows x264 x86 xanim xcf xfs xft xinerama xinetd xml xorg xpm xprint xsl xslt xulrunner xv xvid xvmc yv12 zip zlib" ALSA_CARDS="intel-8x0m" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config mem_cache mime mime_magic rewrite setenvif speling status unique_id userdir usertrack vhost_alias negotiation" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" USERLAND="GNU" VIDEO_CARDS="radeon" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS Created attachment 177704 [details]
build.log
What is the version of mysql.h? Could you try re-emerging mysql? Thanks. So, I have freshly re-emerged mysql-5.0.72-r1. The problem still appears with currently in portage testing sci-mathematics/glpk-4.35. /bin/sh ../libtool --tag=CC --mode=compile i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe -MT glpsql.lo -MD -MP -MF .deps/glpsql.Tpo -c -o glpsql.lo glpsql.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe -MT glpsql.lo -MD -MP -MF .deps/glpsql.Tpo -c glpsql.c -fPIC -DPIC -o .libs/glpsql.o In file included from glpsql.c:952: /usr/include/mysql/my_global.h:361:24: error: asm/atomic.h: No such file or directory make[2]: *** [glpsql.lo] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-mathematics/glpk-4.35/work/glpk-4.35/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-mathematics/glpk-4.35/work/glpk-4.35' make: *** [all] Error 2 * * ERROR: sci-mathematics/glpk-4.35 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 2385: Called die * The specific snippet of code: * emake || die "emake failed" # ls -al /usr/include/mysql total 416 drwxr-xr-x 2 root root 4096 Jan 20 22:09 . drwxr-xr-x 360 root root 32768 Jan 20 18:27 .. -rw-r--r-- 1 root root 4050 Jan 20 22:07 decimal.h -rw-r--r-- 1 root root 3866 Jan 20 22:07 errmsg.h -rw-r--r-- 1 root root 6791 Jan 20 22:07 keycache.h -rw-r--r-- 1 root root 21374 Jan 20 22:07 m_ctype.h -rw-r--r-- 1 root root 8168 Jan 20 22:07 m_string.h -rw-r--r-- 1 root root 1810 Jan 20 22:07 my_alloc.h -rw-r--r-- 1 root root 1941 Jan 20 22:07 my_attribute.h -rw-r--r-- 1 root root 30344 Jan 20 22:08 my_config.h -rw-r--r-- 1 root root 4547 Jan 20 22:07 my_dbug.h -rw-r--r-- 1 root root 3509 Jan 20 22:08 my_dir.h -rw-r--r-- 1 root root 2962 Jan 20 22:07 my_getopt.h -rw-r--r-- 1 root root 43779 Jan 20 22:07 my_global.h -rw-r--r-- 1 root root 1466 Jan 20 22:07 my_list.h -rw-r--r-- 1 root root 3853 Jan 20 22:07 my_net.h -rw-r--r-- 1 root root 1669 Jan 20 22:07 my_no_pthread.h -rw-r--r-- 1 root root 27519 Jan 20 22:07 my_pthread.h -rw-r--r-- 1 root root 37605 Jan 20 22:07 my_sys.h -rw-r--r-- 1 root root 1958 Jan 20 22:07 my_xml.h -rw-r--r-- 1 root root 33581 Jan 20 22:07 mysql.h -rw-r--r-- 1 root root 17387 Jan 20 22:07 mysql_com.h -rw-r--r-- 1 root root 1175 Jan 20 22:07 mysql_embed.h -rw-r--r-- 1 root root 2097 Jan 20 22:07 mysql_time.h -rw-r--r-- 1 root root 832 Jan 20 22:07 mysql_version.h -rw-r--r-- 1 root root 16849 Jan 20 22:07 mysqld_ername.h -rw-r--r-- 1 root root 16904 Jan 20 22:07 mysqld_error.h -rw-r--r-- 1 root root 5796 Jan 20 22:07 raid.h -rw-r--r-- 1 root root 1846 Jan 20 22:07 sql_common.h -rw-r--r-- 1 root root 11044 Jan 20 22:07 sql_state.h -rw-r--r-- 1 root root 1006 Jan 20 22:07 sslopt-case.h -rw-r--r-- 1 root root 2163 Jan 20 22:07 sslopt-longopts.h -rw-r--r-- 1 root root 1107 Jan 20 22:07 sslopt-vars.h -rw-r--r-- 1 root root 1300 Jan 20 22:07 typelib.h # Really all headers just freshly recreated by the reinstall. Portage 2.1.6.7 (default/linux/x86/2008.0/desktop, gcc-4.3.2, glibc-2.9_p20081201-r1, 2.6.29-rc2-git1 i686) ================================================================= System uname: Linux-2.6.29-rc2-git1-i686-Mobile_Intel-R-_Pentium-R-_4_-_M_CPU_1.80GHz-with-glibc2.0 Timestamp of tree: Tue, 20 Jan 2009 19:45:01 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] app-shells/bash: 3.2_p48 dev-java/java-config: 1.3.7-r1, 2.1.6-r1 dev-lang/python: 2.5.2-r8 dev-python/pycrypto: 2.0.1-r6 dev-util/cmake: 2.6.2 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.4.2 sys-apps/sandbox: 1.3.2 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.19 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.28-r1 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /var/bind /var/qmail/alias /var/qmail/control /var/spool/torque /var/vpopmail/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2 -march=pentium4 -mmmx -msse -msse2 -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz" LDFLAGS="-Wl,-O1" LINGUAS="en cs cz" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage/layman/sunrise /usr/local/portage/layman/science /usr/local/portage/layman/java-overlay /usr/local/portage /usr/local/java-experimental /usr/local/portage/layman/java-overlay" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="7zip R X Xaw3d a52 aac aalib ace acl acpi alsa amr amrnb amrwb apache2 audacious audiofile bash-completion bcmath berkdb blas bluetooth boost branding bzip2 cairo cblas cddb cdparanoia cdr clamav cli colordiff compress cpio cracklib crypt cscope css ctype cups curl curlwrappers cxx dbus dga dia directfb djbfft dri dts dv dvb dvd dvdr dvdread eds emacs emboss emf enblend encode enscript exif expat fam fame fat fbcon ffmpeg fftw firefox flac flash foomaticdb fortran fpx ftp gcj gd gdbm ggi gif gimp gimpprint glibc-compat20 glibc-omitfp glitz glut gmp gnuplot gnutls gpgme gphoto2 gpm graphviz gs gsl gstreamer gtk gtkhtml hal hdf hdf5 hp2xx i8x0 icc iconv icu id3 ieee1394 ifc imagemagick imlib inifile innodb isdnlog ithreads jack java javascript jbig jce jikes jpeg jpeg2k kdtree kerberos lame lapack laptop lcms leim libcaca libedit libnotify libwww live lzo lzw mad maildir matroska mhash midi mikmod mime ming mjpeg mmap mmx mng mod_python modperl modplug motif mozilla moznoirc mp2 mp3 mp4 mpeg mpi mpi_njtree mpich2 mplayer mudflap mule musepack mxdatetime mysql mysqli ncurses netcdf netpbm network nls nntp nptl nptlonly nsplugin ntfs numeric ogg opengl openmp pam pango pcmcia pcntl pcre pdf perl plotutils plugin png pnm postproc postscript ppds pppd procmail pymol python qt3 qt3support qt4 quicktime rar raw readline recode reflection reiserfs rpm samba sasl scanner scp seamonkey server session sftp sift slp smime sndfile soap sockets spell spl sqlite srt sse sse2 ssl startup-notification subtitles subversion svg svgz sysfs sysvipc t1lib tcl tcpd tetex theora threads tidy tiff tk transcode truetype unicode urandom usb userlocales uuencode v4l v4l2 vcd vhook vim-syntax vim-with-x vorbis wifi win32codecs wmf wxwindows x264 x86 xanim xcf xfs xft xinerama xinetd xml xorg xpm xprint xsl xslt xulrunner xv xvid xvmc yv12 zip zlib" ALSA_CARDS="intel-8x0m" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config mem_cache mime mime_magic rewrite setenvif speling status unique_id userdir usertrack vhost_alias negotiation" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" USERLAND="GNU" VIDEO_CARDS="radeon" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS It seems that an old mysql bug was reborn. @mysql: is it the same as bug #252732 or bug #? Thanks (In reply to comment #5) > It seems that an old mysql bug was reborn. > @mysql: is it the same as bug #252732 or bug #? > Thanks > It does seem to be the same bug! :) (In reply to comment #6) > (In reply to comment #5) > > It seems that an old mysql bug was reborn. > > @mysql: is it the same as bug #252732 or bug #? > > Thanks > > > > It does seem to be the same bug! :) > Confirming that it is fixed for me as well with the upgrade of dev-db/mysql (5.0.76). Closing, thanks. |
