It fails running aclocal: ***** aclocal ***** ***** aclocal -I gl/m4 -I m4 -I m4 -I gl/m4 configure.in:44: error: AC_REQUIRE: circular dependency of AC_GNU_SOURCE gl/m4/extensions.m4:19: AC_USE_SYSTEM_EXTENSIONS is expanded from... ../../lib/autoconf/specific.m4:332: AC_GNU_SOURCE is expanded from... gl/m4/gnulib-comp.m4:21: gl_EARLY is expanded from... configure.in:44: the top level autom4te-2.63: /usr/bin/m4 failed with exit status: 1 aclocal-1.10: autom4te failed with exit status: 1 Portage 2.2_rc20 (default/linux/x86/2008.0, gcc-4.3.2, glibc-2.7-r2, 2.6.27-gentoo-r7 i686) ================================================================= System uname: Linux-2.6.27-gentoo-r7-i686-Intel-R-_Pentium-R-_D_CPU_2.80GHz-with-glibc2.0 Timestamp of tree: Tue, 06 Jan 2009 07:15:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p39 dev-java/java-config: 1.3.7-r1, 2.1.6-r1 dev-lang/python: 2.5.2-r8 dev-util/ccache: 2.4-r7 sys-apps/baselayout: 2.0.0 sys-apps/openrc: 0.4.1-r1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.63 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.27-r2 ACCEPT_KEYWORDS="x86" ALSA_CARDS="hda-intel" 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" ANT_HOME="/usr/share/ant" 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 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" ARCH="x86" AUTOCLEAN="yes" BINSORT_SCR="/tmp/justin" BINTYPE="linux9" CBIN="/usr/bin" CBUILD="i686-pc-linux-gnu" CCACHE_DIR="/home/ccache" CCACHE_SIZE="3G" CCP4="/usr" CCP4I_HELP="/usr/lib/ccp4/ccp4i/help" CCP4I_TCLTK="/usr/bin" CCP4I_TOP="/usr/lib/ccp4/ccp4i" CCP4_BIN="/usr/bin" CCP4_BROWSER="mozilla" CCP4_HELPDIR="/usr/help/" CCP4_LIB="/usr/lib" CCP4_MASTER="/usr" CCP4_OPEN="UNKNOWN" CCP4_SCR="/tmp/justin" CDOC="/usr/doc" CETC="/usr/etc" CEXAM="/usr/examples" CFLAGS="-O2 -pipe -march=prescott -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CHTML="/usr/html" CINCL="/usr/share/ccp4/include" CLASSPATH="/usr/bin:." CLEAN_DELAY="5" CLIB="/usr/lib" CLIBD="/usr/share/ccp4/data" CLIBD_MON="/share/ccp4/data/monomers/" CLIBS="/usr/lib/src" CNS_CONFDB="/usr/share/cns/libraries/confdb" CNS_DATA="/usr/share/cns" CNS_DOC="/usr/share/doc/cns-1.2.1-r1" CNS_HELPLIB="/usr/share/cns/helplib" CNS_LIB="/usr/share/cns/libraries" CNS_MODULE="/usr/share/cns/modules" CNS_NMRLIB="/usr/share/cns/libraries/nmr" CNS_NMRMODULE="/usr/share/cns/modules/nmr" CNS_ROOT="/usr" CNS_SOLVE="/usr" CNS_TOPPAR="/usr/share/cns/libraries/toppar" CNS_XRAYLIB="/usr/share/cns/libraries/xray" CNS_XTALLIB="/usr/share/cns/libraries/xtal" CNS_XTALMODULE="/usr/share/cns/modules/xtal" COLLISION_IGNORE="/lib/modules" COLORFGBG="7;0" COLORTERM="rxvt" COLUMNS="166" CONFIG_PROTECT="/etc /usr/share/hddtemp/hddtemp.db /usr/share/nano/ /var/lib/hsqldb" 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/splash /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CPROG="/usr/src" CRANK="/usr/ccp4i/crank" CVS_RSH="ssh" CXXFLAGS="-O2 -pipe -march=prescott -fomit-frame-pointer" DBUS_SESSION_BUS_ADDRESS="unix:abstract=/tmp/dbus-Tva3kZdBYv,guid=863f270cf704cb57da64444449631075" DESKTOP_SESSION="gnome" DISPLAY=":0.0" DISTDIR="/usr/portage/distfiles" DYLD_LIBRARY_PATH="/usr/lib:/usr/lib" DYNAMO_DIR="${NMRBASE}/dynamo" DYNAMO_KEY="2002084" DYNAMO_PARAMS="${DYNAMO_DIR}/params" ECHANGELOG_USER="justin Lecher (jlec) <jlec@j-schmitz.net>" EDITOR="/bin/nano" ELIBC="glibc" EMERGE_DEFAULT_OPTS="-t --verbose --jobs=3 --load-average=3 --keep-going" EMERGE_WARNING_DELAY="10" F77="gfortran" FCFLAGS="-O2 -pipe -march=prescott -fomit-frame-pointer" FEATURES="ccache distlocks fixpackages noinfo notitles parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch" FETCHCOMMAND="/usr/bin/axel -a -o ${DISTDIR}/${FILE} ${URI}" FFLAGS="-O2 -pipe -march=prescott -fomit-frame-pointer" FORTANC="gfortran" GCC_SPECS="" GDK_USE_XFT="1" GDMSESSION="gnome" GDM_LANG="en_GB.UTF-8" GDM_XSERVER_LOCATION="local" GENTOO_MIRRORS="http://gentoo.j-schmitz.net/mirror/ ftp://ftp.gentoo.mesh-solutions.com/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo/ http://mirror.switch.ch/ftp/mirror/gentoo/" GKLIB="/opt/usf-lib/" GNOME_DESKTOP_SESSION_ID="Default" GNOME_KEYRING_SOCKET="/tmp/keyring-MrIENd/socket" GPG_AGENT_INFO="/tmp/gpg-ambNS6/S.gpg-agent:23760:1" GTK_RC_FILES="/etc/gtk/gtkrc:/home/justin/.gtkrc-1.2-gnome2" HELPDIR="/usr/help/" HISTCONTROL="ignoredups" HISTFILESIZE="1000" HISTIGNORE="fg:bg" HISTSIZE="1000" HOME="/home/justin" INFOPATH="/usr/share/info:/usr/share/binutils-data/i686-pc-linux-gnu/2.18/info:/usr/share/gcc-data/i686-pc-linux-gnu/4.3.2/info" INPUT_DEVICES="keyboard mouse evdev" INTEL_BATCH="1" JAVAC="/home/justin/.gentoo/java-config-2/current-user-vm/bin/javac" JAVA_HOME="/home/justin/.gentoo/java-config-2/current-user-vm" JDK_HOME="/home/justin/.gentoo/java-config-2/current-user-vm" KERNEL="linux" LANG="en_GB.UTF-8" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LC_CTYPE="en_GB.UTF-8" LDFLAGS="-Wl,-O1,--hash-style=gnu,--sort-common" LD_LIBRARY_PATH="/usr/lib:/usr/lib" LESS="-R -M --shift 5" LESSOPEN="|lesspipe.sh %s" LINES="76" LINGUAS="en" LOGNAME="justin" LS_COLORS="no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.svgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:" MAKEOPTS="-j3 -l3" MANPATH="/home/justin/.gentoo/java-config-2/current-user-vm/man:/usr/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/i686-pc-linux-gnu/2.18/man:/usr/share/gcc-data/i686-pc-linux-gnu/4.3.2/man:/opt/intel/cc/10.1.018/man:/opt/intel/fc/10.1.018/man:/etc/java-config/system-vm/man/:${NMRBASE}/man" MCTYPE="unix" MMCIFDIC="/usr/lib/cif_mmdic.lib" MOLREPLIB="/share/ccp4/data/monomers/" MOSHELPFILE="mosflm" MP_SET_NUMTHREADS="1" NETBEANS="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" NMRBASE="/opt/nmrpipe" NMRTXT="${NMRBASE}/nmrtxt" NOCOLOR="true" OMP_NUM_THREADS="2" OPENGL_PROFILE="xorg-x11" PAGER="/usr/bin/less" PATH="/usr/lib/ccp4/ccp4i/bin:/usr/etc:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/4.3.2:/opt/intel/cc/10.1.018/bin:/opt/intel/fc/10.1.018/bin:/opt/cara/:/opt/usf-dejavu-bin/:/opt/usf-rave-bin/:/opt/usf-voidoo-bin/:/opt/usf-xutil-bin/:/opt/xds-bin/:${PATH}:${DYNAMO_DIR}/tcl:/usr/games/bin:/data/scripts" PDBH_BASE="${NMRBASE}/pdb" PDBH_DIR="${PDBH_BASE}/pdbH" PDBH_LIST="${PDBH_BASE}/pdbH.list" PDBH_TAB="${PDBH_BASE}/resolution.tab" PKGDIR="/usr/portage/packages" PLOT_COMMAND="lp -s -dmicrolaser" PORTAGE_ARCHLIST="ppc s390 amd64 x86 ppc64 x86-fbsd m68k arm sparc sh mips ia64 alpha hppa sparc-fbsd" PORTAGE_BINHOST_CHUNKSIZE="3000" PORTAGE_BIN_PATH="/usr/lib/portage/bin" PORTAGE_COMPRESS="lzma" PORTAGE_COMPRESS_EXCLUDE_SUFFIXES="css gif htm[l]? jp[e]?g js pdf png" PORTAGE_COMPRESS_FLAGS="-z -9 -f -S .lzma -v" PORTAGE_CONFIGROOT="/" PORTAGE_COUNTER_HASH="a3121bca91fcb3123f5ed772a5edc77b" PORTAGE_DEBUG="0" PORTAGE_DEPCACHEDIR="/var/cache/edb/dep" PORTAGE_ECLASS_WARNING_ENABLE="0" PORTAGE_ELOG_CLASSES="info warn error log * qa" PORTAGE_ELOG_MAILFROM="portage@localhost" PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}" PORTAGE_ELOG_MAILURI="root" PORTAGE_ELOG_SYSTEM="save echo" PORTAGE_FETCH_CHECKSUM_TRY_MIRRORS="5" PORTAGE_FETCH_RESUME_MIN_SIZE="350K" PORTAGE_GID="250" PORTAGE_INST_GID="0" PORTAGE_INST_UID="0" PORTAGE_PYM_PATH="/usr/lib/portage/pym" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_RSYNC_RETRIES="3" PORTAGE_TMPDIR="/var/tmp" PORTAGE_VERBOSE="1" PORTAGE_WORKDIR_MODE="0700" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/dberkholz /usr/portage/local/private-overlay /usr/portage/local/molmod/trunk /usr/portage/local/molmod/branches /usr/portage/local/sunrise/reviewed /usr/portage/local/science/overlay" PRELINK_PATH_MASK="/lib/modules:/usr/lib/locale:/usr/lib/wine:/usr/lib/valgrind:*.la:*.png:*.py:*.pl:*.pm:*.sh:*.xml:*.xslt:*.a:*.js:/usr/lib/klibc" PRINT_COMMAND="lp -s -denscript" PROFILE_ONLY_VARIABLES="ARCH ELIBC KERNEL USERLAND" PUBLIC_FONT84="/usr/lib/font84.dat" PWD="/home/justin" PYMOL_DATA="/usr/share/pymol/data" PYMOL_PATH="/usr/lib/python2.5/site-packages/pymol" PYMOL_SCRIPTS="/usr/share/pymol/scripts" RASMOLPATH="/usr/x-windows/RasMol/src" RESUMECOMMAND="/usr/bin/axel -a -o ${DISTDIR}/${FILE} ${URI}" ROOT="/" ROOTPATH="/opt/bin:/usr/i686-pc-linux-gnu/gcc-bin/4.3.2:/opt/intel/cc/10.1.018/bin:/opt/intel/fc/10.1.018/bin:/data/scripts" RPMDIR="/usr/portage/rpm" SESSION_MANAGER="local/kancheli:/tmp/.ICE-unix/23534" SGML_CATALOG_FILES="/etc/sgml/openjade-1.3.2.cat:/etc/sgml/xml-docbook-4.4.cat:/etc/sgml/xml-docbook-4.1.2.cat:/etc/sgml/sgml-docbook.cat:/etc/sgml/sgml-lite.cat:/etc/sgml/sgml-ent.cat:/etc/sgml/dsssl-docbook-stylesheets.cat:/etc/sgml/sgml-docbook-3.1.cat" SHELL="/bin/bash" SHLVL="2" SSH_AGENT_PID="23708" SSH_ASKPASS="/usr/bin/ssh-askpass-fullscreen" SSH_AUTH_SOCK="/tmp/ssh-AkQni23706/agent.23706" SURF_DIR="${DYNAMO_DIR}/surface" SYNC="rsync://rsync.j-schmitz.net/gentoo-portage" TERM="rxvt-unicode" TRAP_FPE="OVERFL=ABORT; DIVZERO=ABORT; INVALID=ABORT" USE="7zip X acpi additions alsa bash-completion berkdb branding bzip2 c++ cblas ccache cli command-args cracklib crypt cups cupsddk custom-optimization cxx dri dts fbcondecor fortran gdbm gif glibc-omitfp gnome gpm graphics gtk hddtemp iconv icu isdnlog java javascript jpeg kdeenablefinal kqemu lapack lcms libnotify libsexy lm_sensors mailtrain md5sum midi mmx mp3 mpi mudflap multiuser nagios-dns nagios-ntp nagios-ping nagios-ssh nano-syntax ncurses nis nls nptl nptlonly nsplugin objc objc++ opengl openmp openntpd oss pam pcre pdf perl png pppd pymol python qt-static qt3support readline reflection replytolist restrict-javascript rrdcgi rrdtool science sensord session smp spl sqlite sqlite3 sse sse2 ssl swat symlink sysfs tcpd threads tiff truetype type1 unicode x86 xcomposite xorg xulrunner zlib" ALSA_CARDS="hda-intel" 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 authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" USERLAND="GNU" VIDEO_CARDS="intel" USER="justin" USERLAND="GNU" USERNAME="justin" USE_EXPAND="ALSA_CARDS ALSA_PCM_PLUGINS APACHE2_MODULES APACHE2_MPMS CAMERAS CROSSCOMPILE_OPTS DVB_CARDS ELIBC FCDSL_CARDS FOO2ZJS_DEVICES FRITZCAPI_CARDS INPUT_DEVICES KERNEL LCD_DEVICES LINGUAS LIRC_DEVICES MISDN_CARDS NETBEANS_MODULES USERLAND VIDEO_CARDS" USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND" USE_ORDER="env:pkg:conf:defaults:pkginternal:env.d" VIDEO_CARDS="intel" WINDOWID="27263064" WINDOWPATH="7" WINEPREFIX="/home/justin/.wine" XAUTHORITY="/home/justin/.Xauthority" XCURSORS_THEME="Jimmac" XDG_DATA_DIRS="/usr/local/share/:/usr/share/:/usr/share/gdm/" XSESSION="Gnome" XUSERFILESEARCHPATH="/usr/lib/X11/app-defaults/%N:/usr/lib/X11/app-defaults/%N:/usr/lib/X11/app-defaults" _="/usr/bin/emerge" _POSIX2_VERSION="199209"
please try 1.4.13 and report back if this one works for you.
Hi Tobi, please see bug 253955.
(In reply to comment #2) > Hi Tobi, > please see bug 253955. > so this issue doesn't show up with 1.4.13, right?
re-open
re-assign
and test-request again. sorry for that noise ...
(In reply to comment #6) > and test-request again. sorry for that noise ... > No 1.4.13 has no aclocal problems.
