revdep-rebuild complains about /usr/lib64/icedtea6/jre/lib/amd64/libnio.so and therefore reemerges dev-java/icedtea: root@moose:/root(7)# revdep-rebuild * Configuring search environment for revdep-rebuild * Checking reverse dependencies * Packages containing binaries and libraries broken by a package update * will be emerged. * Collecting system binaries and libraries * Generated new 1_files.rr * Collecting complete LD_LIBRARY_PATH * Generated new 2_ldpath.rr * Checking dynamic linking consistency ... [ 100% ] * broken /usr/lib64/icedtea6/jre/lib/amd64/libnio.so (no version information available) * Generated new 3_broken.rr * Assigning files to packages * /usr/lib64/icedtea6/jre/lib/amd64/libnio.so -> dev-java/icedtea ... * Generated new 4_raw.rr and 4_owners.rr * Cleaning list of packages to rebuild * Generated new 4_pkgs.rr * Assigning packages to ebuilds * Generated new 4_ebuilds.rr * Evaluating package order * Generated new 5_order.rr * All prepared. Starting rebuild emerge --oneshot dev-java/icedtea:6 ... It happens for about two weeks on all of my systems, eg.: root@lynx:/usr/local/portage/sci-libs/gdal(32)# genlop -t icedtea | tail -n 30 Thu Jan 13 01:56:06 2011 >>> dev-java/icedtea-6.1.9.3 merge time: 34 minutes and 33 seconds. Fri Jan 14 12:52:30 2011 >>> dev-java/icedtea-6.1.9.3 merge time: 34 minutes and 58 seconds. Mon Jan 17 20:01:49 2011 >>> dev-java/icedtea-6.1.9.3 merge time: 35 minutes and 10 seconds. Wed Jan 19 16:03:33 2011 >>> dev-java/icedtea-6.1.9.4 merge time: 34 minutes and 53 seconds. Wed Jan 19 17:24:02 2011 >>> dev-java/icedtea-6.1.9.4 merge time: 34 minutes and 23 seconds. Sat Jan 22 19:30:25 2011 >>> dev-java/icedtea-6.1.9.4 merge time: 34 minutes and 31 seconds. Mon Jan 24 16:20:29 2011 >>> dev-java/icedtea-6.1.9.4 merge time: 41 minutes and 16 seconds. Mon Jan 24 20:10:20 2011 >>> dev-java/icedtea-6.1.9.4 merge time: 36 minutes and 52 seconds. Tue Jan 25 14:45:52 2011 >>> dev-java/icedtea-6.1.9.4 merge time: 34 minutes and 35 seconds. Thu Jan 27 12:18:04 2011 >>> dev-java/icedtea-6.1.9.4 merge time: 47 minutes and 9 seconds. Reproducible: Always root@lynx:/usr/local/portage/sci-libs/gdal(33)# emerge --info Portage 2.1.9.35 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.12.2-r0, 2.6.37-gentoo x86_64) ================================================================= System uname: Linux-2.6.37-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 27 Jan 2011 07:30:15 +0000 app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.1, 3.1.3 dev-util/cmake: 2.8.3-r1 sys-apps/baselayout: 2.0.1-r1 sys-apps/openrc: 0.7.0 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.4.5, 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ " LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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="/var/lib/layman/lordvan /var/lib/layman/x11 /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/arcon /var/lib/layman/science /var/lib/layman/pro-audio /var/lib/layman/qting-edge /var/lib/layman/n4g /var/lib/layman/ibormuth /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cardbus cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack laptop latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mkl mmx mmxext mng modules mono moonlight motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora thinkpad threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" 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 cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DVB_CARDS="usb-wt220u" 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 ubx" INPUT_DEVICES="keyboard mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="nv nvidia nouveau vesa" 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
The issue happens with Sun JDK 1.6.0.23 and OpenJDK6/IcedTea6 1.9.4 as default Java VM, as well.
Don't we put the revdep-rebuild file?
(In reply to comment #2) > Don't we put the revdep-rebuild file? I think so, at least for the mentioned sun-jdk.
I couldn't reproduce the issue. Can you paste "emerge --info icedtea" output for USE flag investigation as well?
root@lynx:/root(5)# emerge --info icedtea Portage 2.1.9.35 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.12.2-r0, 2.6.37-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.37-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.0.1 Timestamp of tree: Sun, 30 Jan 2011 07:30:22 +0000 app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.1, 3.1.3 dev-util/cmake: 2.8.3-r1 sys-apps/baselayout: 2.0.1-r1 sys-apps/openrc: 0.7.0 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.4.5, 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ " LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" 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="/var/lib/layman/lordvan /var/lib/layman/x11 /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/arcon /var/lib/layman/science /var/lib/layman/pro-audio /var/lib/layman/qting-edge /var/lib/layman/n4g /var/lib/layman/ibormuth /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cardbus cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack laptop latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mkl mmx mmxext mng modules mono moonlight motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora thinkpad threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" 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 cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DVB_CARDS="usb-wt220u" 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 ubx" INPUT_DEVICES="keyboard mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="nv nvidia nouveau vesa" 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= dev-java/icedtea-6.1.9.4 was built with the following: USE="doc examples hs19 (multilib) nsplugin nss pulseaudio webstart xrender -cacao -debug -javascript -nio2 -systemtap -zero"
(In reply to comment #2) > Don't we put the revdep-rebuild file? > It seems that we don't do it for icedtea. Let's see why I can't reproduce it. My guess is I'm usişng bleeding edge portage or gentoolkit. Here's what I have for those: portage-2.2.0_alpha19 gentoolkit-0.3.0_rc11-r3 In the meantime should we add a revdep-rebuild control file for icedtea?
Juergen, which gentoolkit version?
rose@lynx:/home/rose(1)$ qlist -Iv gentoolkit app-portage/gentoolkit-0.3.0_rc11-r3 app-portage/gentoolkit-dev-0.2.8
rose@lynx:/home/rose(3)$ qlist -Iv sys-apps/portage sys-apps/portage-2.1.9.35
(In reply to comment #6) > In the meantime should we add a revdep-rebuild control file for icedtea? I think source-based icedtea (not -bin) shouldn't have this control file, as rebuilds really make sense for it and the X and other deps are not optional (as they are for binary JDK's). But if the rebuilds really occur due to missing version information in libnio.so, we should mask the file itself (as rebuilds won't help and the version information is likely really not needed).
Hi Vlastimil, is there a possibility to exclude locally icedtea from rebuilding? It is quite nasty if icedtea is rebuild every day of several PCs.
I still can't reproduce the bug... What's the output of 'ldd /usr/lib64/icedtea6/jre/lib/amd64/libnio.so' ?
At lynx: root@lynx:/root(3)# ldd /usr/lib64/icedtea6/jre/lib/amd64/libnio.so /usr/lib64/icedtea6/jre/lib/amd64/libnio.so: /usr/lib64/libnet.so: no version information available (required by /usr/lib64/icedtea6/jre/lib/amd64/libnio.so) linux-vdso.so.1 => (0x00007fff13506000) libjava.so => /usr/lib64/icedtea6/jre/lib/amd64/libjava.so (0x00007f8d36e8c000) libnet.so => /usr/lib64/libnet.so (0x00007f8d36c72000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f8d369f6000) libdl.so.2 => /lib/libdl.so.2 (0x00007f8d367f2000) libc.so.6 => /lib/libc.so.6 (0x00007f8d36465000) libjvm.so => not found libverify.so => /usr/lib64/icedtea6/jre/lib/amd64/libverify.so (0x00007f8d36255000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007f8d3603c000) /lib64/ld-linux-x86-64.so.2 (0x00007f8d372c8000) libjvm.so => not found root@lynx:/root(4)# java-config -L The following VMs are available for generation-2: *) OpenJDK6/IcedTea6 1.9.6 [icedtea6] 2) Sun JDK 1.6.0.23 [sun-jdk-1.6] At moose: root@moose:/root(15)# ldd /usr/lib/icedtea6/jre/lib/amd64/libnio.so /usr/lib/icedtea6/jre/lib/amd64/libnio.so: /usr/lib64/libnet.so: no version information available (required by /usr/lib/icedtea6/jre/lib/amd64/libnio.so) linux-vdso.so.1 => (0x00007fff775ff000) libjava.so => /usr/lib/icedtea6/jre/lib/amd64/libjava.so (0x00007f70260ef000) libnet.so => /usr/lib64/libnet.so (0x00007f7025ed5000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f7025c59000) libdl.so.2 => /lib/libdl.so.2 (0x00007f7025a55000) libc.so.6 => /lib/libc.so.6 (0x00007f70256c8000) libjvm.so => not found libverify.so => /usr/lib/icedtea6/jre/lib/amd64/libverify.so (0x00007f70254b8000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007f702529f000) /lib64/ld-linux-x86-64.so.2 (0x00007f702652b000) libjvm.so => not found root@moose:/root(18)# java-config -L The following VMs are available for generation-2: *) OpenJDK6/IcedTea6 1.9.6 [icedtea6]
Searching for libjvm.so I found: root@moose:/root(19)# qfile -v libjvm.so dev-java/icedtea-6.1.9.6 (/usr/lib64/icedtea6/jre/lib/amd64/server/libjvm.so) sys-devel/gcc-4.5.2 (/usr/lib64/gcj-4.5.2-11/libjvm.so) sys-devel/gcc-4.4.5 (/usr/lib64/gcj-4.4.5-10/libjvm.so) root@lynx:/root(6)# qfile -v libjvm.so sys-devel/gcc-4.4.5 (/usr/lib64/gcj-4.4.5-10/libjvm.so) sys-devel/gcc-4.5.2 (/usr/lib64/gcj-4.5.2-11/libjvm.so) dev-java/sun-jdk-1.6.0.23 (/opt/sun-jdk-1.6.0.23/jre/lib/amd64/server/libjvm.so) dev-java/icedtea-6.1.9.6 (/usr/lib64/icedtea6/jre/lib/amd64/server/libjvm.so)
Some additional informations about the libjvm.so: root@moose:/usr/local/portage/dev-games(47)# ll /usr/lib64/icedtea6/jre/lib/amd64/server/libjvm.so -rwxr-xr-x 1 root root 9124840 Feb 15 16:21 /usr/lib64/icedtea6/jre/lib/amd64/server/libjvm.so* root@moose:/usr/local/portage/dev-games(48)# ll /usr/lib64/gcj-4.5.2-11/libjvm.so -rwxr-xr-x 1 root root 8095 Jan 3 13:15 /usr/lib64/gcj-4.5.2-11/libjvm.so* root@moose:/usr/local/portage/dev-games(49)# ll /usr/lib64/gcj-4.4.5-10/libjvm.so -rwxr-xr-x 1 root root 8200 Nov 30 23:22 /usr/lib64/gcj-4.4.5-10/libjvm.so* root@moose:/usr/local/portage/dev-games(50)# file /usr/lib64/gcj-4.4.5-10/libjvm.so /usr/lib64/gcj-4.4.5-10/libjvm.so: ELF 64-bit LSB shared object, x86-64, version 1 (GNU/Linux), dynamically linked, not stripped root@moose:/usr/local/portage/dev-games(51)# ldd /usr/lib64/icedtea6/jre/lib/amd64/server/libjvm.so linux-vdso.so.1 => (0x00007fff4bbff000) libm.so.6 => /lib/libm.so.6 (0x00007f90792d5000) libdl.so.2 => /lib/libdl.so.2 (0x00007f90790d1000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f9078eb3000) libc.so.6 => /lib/libc.so.6 (0x00007f9078b27000) /lib64/ld-linux-x86-64.so.2 (0x00007f907a0a6000) root@moose:/usr/local/portage/dev-games(52)# ldd /usr/lib64/gcj-4.5.2-11/libjvm.so linux-vdso.so.1 => (0x00007fffbd1b6000) libgcj.so.11 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.2/libgcj.so.11 (0x00007f2b811c1000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f2b80fa3000) librt.so.1 => /lib/librt.so.1 (0x00007f2b80d9a000) libdl.so.2 => /lib/libdl.so.2 (0x00007f2b80b96000) libz.so.1 => /lib/libz.so.1 (0x00007f2b8097e000) libc.so.6 => /lib/libc.so.6 (0x00007f2b805f2000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f2b803dc000) /lib64/ld-linux-x86-64.so.2 (0x00007f2b8454e000) root@moose:/usr/local/portage/dev-games(53)# ldd /usr/lib64/gcj-4.4.5-10/libjvm.so linux-vdso.so.1 => (0x00007fffb9a1e000) libgcj.so.10 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.4.5/libgcj.so.10 (0x00007fede9db9000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007fede9b9b000) librt.so.1 => /lib/librt.so.1 (0x00007fede9992000) libdl.so.2 => /lib/libdl.so.2 (0x00007fede978e000) libz.so.1 => /lib/libz.so.1 (0x00007fede9576000) libc.so.6 => /lib/libc.so.6 (0x00007fede91ea000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fede8fd4000) /lib64/ld-linux-x86-64.so.2 (0x00007feded0c3000) Looks, if everything is OK with them.
This ldd error with libnio.so occurs even after a fresh and apparently error-free installation of icedtea: root@moose:/root(54)# ldd /usr/lib/icedtea6/jre/lib/amd64/libnio.so /usr/lib/icedtea6/jre/lib/amd64/libnio.so: /usr/lib64/libnet.so: no version information available (required by /usr/lib/icedtea6/jre/lib/amd64/libnio.so) linux-vdso.so.1 => (0x00007fff881ff000) libjava.so => /usr/lib/icedtea6/jre/lib/amd64/libjava.so (0x00007f9377091000) libnet.so => /usr/lib64/libnet.so (0x00007f9376e77000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f9376bfb000) libdl.so.2 => /lib/libdl.so.2 (0x00007f93769f7000) libc.so.6 => /lib/libc.so.6 (0x00007f937666a000) libjvm.so => not found libverify.so => /usr/lib/icedtea6/jre/lib/amd64/libverify.so (0x00007f937645a000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007f9376241000) /lib64/ld-linux-x86-64.so.2 (0x00007f93774cd000) libjvm.so => not found
The problem is not the "missing" libjvm.so, but libnet.so: /usr/lib/icedtea6/jre/lib/amd64/libnio.so: /usr/lib64/libnet.so: no version information available (required by /usr/lib/icedtea6/jre/lib/amd64/libnio.so) libnet.so => /usr/lib64/libnet.so (0x00007f9376e77000) Here's what it says here: $ ldd /usr/lib64/icedtea6/jre/lib/amd64/libnio.so libnet.so => /usr/lib64/icedtea6/jre/lib/amd64/libnet.so (0x00007f402eb90000) Which means correctly linking to the libnet.so that's part of the icedtea itself, and not the system one (which just has the same name but does something different). I wonder why it picks the wrong one in your case. BTW, java-check-environment says something?
java-check-environment says: Java environment is sane. With dev-java/icedtea-6.1.9.7 I get the same issue, too. root@orca:/root(4)# ldd /usr/lib64/icedtea6/jre/lib/amd64/libnio.so /usr/lib64/icedtea6/jre/lib/amd64/libnio.so: /usr/lib64/libnet.so: no version information available (required by /usr/lib64/icedtea6/jre/lib/amd64/libnio.so) linux-vdso.so.1 => (0x00007fff499c5000) libjava.so => /usr/lib64/icedtea6/jre/lib/amd64/libjava.so (0x00007f1918b79000) libnet.so => /usr/lib64/libnet.so (0x00007f191895f000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f19186f2000) libdl.so.2 => /lib/libdl.so.2 (0x00007f19184ee000) libc.so.6 => /lib/libc.so.6 (0x00007f1918161000) libjvm.so => not found libverify.so => /usr/lib64/icedtea6/jre/lib/amd64/libverify.so (0x00007f1917f51000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007f1917d38000) /lib64/ld-linux-x86-64.so.2 (0x00007f1918fb5000) libjvm.so => not found root@orca:/root(5)# genlop -t icedtea | tail -n3 Wed Feb 16 17:54:31 2011 >>> dev-java/icedtea-6.1.9.7 merge time: 15 minutes and 9 seconds.
My /usr/lib64/libnet.so comes from net-libs/libnet-1.1.5: root@orca:/root(8)# qfile -v libnet.so net-libs/libnet-1.1.5 (/usr/lib64/libnet.so) dev-java/sun-jdk-1.6.0.23 (/opt/sun-jdk-1.6.0.23/jre/lib/amd64/libnet.so) dev-java/icedtea-6.1.9.7 (/usr/lib64/icedtea6/jre/lib/amd64/libnet.so) which seems to be a dependency of syslog-ng, arping and virtual/perl-libnet: root@orca:/root(10)# equery d libnet * These packages depend on libnet: app-admin/syslog-ng-3.1.4 (spoof-source ? net-libs/libnet) net-analyzer/arping-2.09-r1 (>=net-libs/libnet-1.1.0-r3) virtual/perl-libnet-1.22 (~perl-core/libnet-1.22)
I find the following java specific settings in my environment: root@orca:/root(15)# env | grep -i jdk JDK_HOME=/etc/java-config-2/current-system-vm root@orca:/root(16)# env | grep -i java MANPATH=/etc/java-config-2/current-system-vm/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.21/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.5.2/man:/etc/java-config/system-vm/man/:/usr/lib64/php5.2/man/:/usr/lib64/php5.3/man/:/usr/share/postgresql-9.0/man:/opt/nvidia-cg-toolkit/man:/usr/local/man CONFIG_PROTECT_MASK=/etc/gentoo-release /etc/sandbox.d /etc/env.d/java/ /etc/php/cli-php5.2/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/apache2-php5.2/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/fonts/fonts.conf /etc/gconf /etc/terminfo /etc/eselect/postgresql /etc/ca-certificates.conf /etc/texmf/web2c /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/revdep-rebuild JAVA_HOME=/etc/java-config-2/current-system-vm JAVAC=/etc/java-config-2/current-system-vm/bin/javac JDK_HOME=/etc/java-config-2/current-system-vm JAVACC_HOME=/usr/share/javacc/ Is there something wrong or missing?
(In reply to comment #20) > Is there something wrong or missing? Probably not. Does /usr/lib64/icedtea6/jre/lib/amd64/libnet.so exist? What's the output of 'ldd ldd /usr/lib64/icedtea6/jre/lib/amd64/libnet.so' ? What's the output of 'scanelf -r /usr/lib64/icedtea6/jre/lib/amd64/libnio.so' ?
/usr/lib64/icedtea6/jre/lib/amd64/libnet.so exists: root@lynx:/root(3)# ldd /usr/lib64/icedtea6/jre/lib/amd64/libnet.so linux-vdso.so.1 => (0x00007fff279ff000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007f7dbc094000) libdl.so.2 => /lib/libdl.so.2 (0x00007f7dbbe8f000) libjvm.so => not found libpthread.so.0 => /lib/libpthread.so.0 (0x00007f7dbbc72000) libjava.so => /usr/lib64/icedtea6/jre/lib/amd64/libjava.so (0x00007f7dbba3f000) libc.so.6 => /lib/libc.so.6 (0x00007f7dbb6b3000) /lib64/ld-linux-x86-64.so.2 (0x00007f7dbc521000) libjvm.so => not found libverify.so => /usr/lib64/icedtea6/jre/lib/amd64/libverify.so (0x00007f7dbb4a2000) libjvm.so => not found root@lynx:/root(4)# scanelf -r /usr/lib64/icedtea6/jre/lib/amd64/libnio.so TYPE RPATH FILE ET_DYN $ORIGIN /usr/lib64/icedtea6/jre/lib/amd64/libnio.so
Do you have LD_LIBRARY_PATH set?
Yes, it is set, on most of my computers I see: root@lynx:/root(1)# env | grep LD LD_LIBRARY_PATH=/usr/lib64 DYLD_LIBRARY_PATH=/usr/lib64: GMXLDLIB=/usr/lib64
It looks like LD_LIBRARY_PATH=/usr/lib64 is set in /etc/profile.d/40ccp4.setup.sh, which is source be /etc/profile and which belongs to sci-libs/ccp4-libs-6.1.3-r7. sci-libs/ccp4-libs is installed as a dependency of sci-chemistry/molrep.
(In reply to comment #24) > Yes, it is set, on most of my computers I see: > root@lynx:/root(1)# env | grep LD > LD_LIBRARY_PATH=/usr/lib64 > DYLD_LIBRARY_PATH=/usr/lib64: > GMXLDLIB=/usr/lib64 So if you unset these variables, will revdep-rebuild stop rebuilding icedtea?
If I unset LD_LIBRARY_PATH, DYLD_LIBRARY_PATH and GMXLDLIB I still get the same result for ldd /usr/lib64/icedtea6/jre/lib/amd64/libnet.so but revdev-rebuild is satisfied with icedtea: root@lynx:/root(10)# env | grep LD LD_LIBRARY_PATH=/usr/lib64 DYLD_LIBRARY_PATH=/usr/lib64: GMXLDLIB=/usr/lib64 root@lynx:/root(11)# dd /usr/lib64/icedtea6/jre/lib/amd64/libnet.so dd: unrecognized operand `/usr/lib64/icedtea6/jre/lib/amd64/libnet.so' Try `dd --help' for more information. root@lynx:/root(12)# ldd /usr/lib64/icedtea6/jre/lib/amd64/libnet.so linux-vdso.so.1 => (0x00007fff969ff000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007f60b2fd0000) libdl.so.2 => /lib/libdl.so.2 (0x00007f60b2dcb000) libjvm.so => not found libpthread.so.0 => /lib/libpthread.so.0 (0x00007f60b2bae000) libjava.so => /usr/lib64/icedtea6/jre/lib/amd64/libjava.so (0x00007f60b297b000) libc.so.6 => /lib/libc.so.6 (0x00007f60b25ef000) /lib64/ld-linux-x86-64.so.2 (0x00007f60b345d000) libjvm.so => not found libverify.so => /usr/lib64/icedtea6/jre/lib/amd64/libverify.so (0x00007f60b23de000) libjvm.so => not found root@lynx:/root(13)# unset LD_LIBRARY_PATH root@lynx:/root(14)# ldd /usr/lib64/icedtea6/jre/lib/amd64/libnet.so linux-vdso.so.1 => (0x00007fffec1ff000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007f0f52fcb000) libdl.so.2 => /lib/libdl.so.2 (0x00007f0f52dc6000) libjvm.so => not found libpthread.so.0 => /lib/libpthread.so.0 (0x00007f0f52ba9000) libjava.so => /usr/lib64/icedtea6/jre/lib/amd64/libjava.so (0x00007f0f52976000) libc.so.6 => /lib/libc.so.6 (0x00007f0f525ea000) /lib64/ld-linux-x86-64.so.2 (0x00007f0f53458000) libjvm.so => not found libverify.so => /usr/lib64/icedtea6/jre/lib/amd64/libverify.so (0x00007f0f523d9000) libjvm.so => not found root@lynx:/root(15)# unset DYLD_LIBRARY_PATH root@lynx:/root(16)# unset GMXLDLIB root@lynx:/root(17)# ldd /usr/lib64/icedtea6/jre/lib/amd64/libnet.so linux-vdso.so.1 => (0x00007fff42d32000) libnsl.so.1 => /lib/libnsl.so.1 (0x00007f785593b000) libdl.so.2 => /lib/libdl.so.2 (0x00007f7855736000) libjvm.so => not found libpthread.so.0 => /lib/libpthread.so.0 (0x00007f7855519000) libjava.so => /usr/lib64/icedtea6/jre/lib/amd64/libjava.so (0x00007f78552e6000) libc.so.6 => /lib/libc.so.6 (0x00007f7854f5a000) /lib64/ld-linux-x86-64.so.2 (0x00007f7855dc8000) libjvm.so => not found libverify.so => /usr/lib64/icedtea6/jre/lib/amd64/libverify.so (0x00007f7854d49000) libjvm.so => not found root@lynx:/root(18)# env | grep LD root@lynx:/root(19)# root@lynx:/root(19)# revdep-rebuild * Configuring search environment for revdep-rebuild * Environment mismatch from previous run, deleting temporary files... * Checking reverse dependencies * Packages containing binaries and libraries broken by a package update * will be emerged. * Collecting system binaries and libraries * Generated new 1_files.rr * Collecting complete LD_LIBRARY_PATH * Generated new 2_ldpath.rr * Checking dynamic linking consistency [ 100% ] * Dynamic linking on your system is consistent... All done. root@lynx:/root(20)#
(In reply to comment #27) > If I unset LD_LIBRARY_PATH, DYLD_LIBRARY_PATH and GMXLDLIB I still get the same > result for ldd /usr/lib64/icedtea6/jre/lib/amd64/libnet.so Yes, the difference should be for ldd on libnio.so. As revdep-rebuild no longer rebuilds, it's really the cause. Thank you for patience, and flameeyes for pointing me to LD_LIBRARY_PATH. So, to sum it up: - /usr/lib/icedtea6/jre/lib/amd64/libnio.so relies on $ORIGIN RPATH to use libnet.so that's in the same directory, and not libnet.so in /usr/lib (which has the same name but is something totally different) - sci-libs/ccp4-libs installs an env file that sets (among other things) LD_LIBRARY_PATH="/usr/lib" - this makes ldd look in /usr/lib first and complain about libnio.so - this makes revdep-rebuild rebuild icedtea I'm CCing maintainers of all relevant packages, and QA for advice. Personally I would say that setting LD_LIBRARY_PATH to /usr/lib(64) is something a package should not do ?
Not an opinion, but rather a fact: packages should _not_ set LD_LIBRARY_PATH in env.d files _at all_. It is an override that should be left to users. If you have to add an extra path in the library search paths list you should set LDPATH that env-update uses to generate ld.so.conf instead. So bottomline, the bug is big in ccp4-libs, and should be solved fast.
(In reply to comment #29) > Not an opinion, but rather a fact: packages should _not_ set LD_LIBRARY_PATH in > env.d files _at all_. It is an override that should be left to users. If you > have to add an extra path in the library search paths list you should set > LDPATH that env-update uses to generate ld.so.conf instead. > > So bottomline, the bug is big in ccp4-libs, and should be solved fast. > I will take care of this. I will be fixed tomorrow night.
sounds like grounds for a new portage qa install check ... i can think of plenty of vars that we should be outright rejecting from /etc/env.d/ ...
+*ccp4-libs-6.1.3-r8 (19 Feb 2011) + + 19 Feb 2011; Justin Lecher <jlec@gentoo.org> -ccp4-libs-6.1.3-r5.ebuild, + -ccp4-libs-6.1.3-r7.ebuild, +ccp4-libs-6.1.3-r8.ebuild: + NEVER set LD_LIBRARY_PATH in /etc/profile.d, 352962 + I didn't follow the bug. Is it fixed with this?
I don;t have a new version of sci-libs/ccp4-libs so the bug is not fixed for me. Revdep-rebuild still reemerged icedtea every time.
(In reply to comment #33) > I don;t have a new version of sci-libs/ccp4-libs so the bug is not fixed for > me. Revdep-rebuild still reemerged icedtea every time. And if you do upgrade to ccp4-libs-6.1.3-r8 ?
Now I have ccp4-libs-6.1.3-r8, the ugly LD_LIBRARY_PATH disappeared and revdep-rebuild does not reemerge icedtea every time. Thanks for solving the issue.
So this issue is fixed?
I would say "yes".
