Created attachment 281373 [details] make.conf file needed to try to reproduce this Several people in #gentoo are reporting issues caused by the /lib directory not being a symbolic link to /lib64. Usually, the issue is that GRUB will not install and certain software will fail saying that they could not execute compiled programs. GCC, sandbox and wine are among some other programs that will fail to compile. This issue has been confirmed in #gentoo as occurring on amd64 stable and testing. The affected users installed gentoo from stage3-amd64-20110721.tar.bz2. This does not appear to be an issue with the tarballs. I checked stage3-amd64-20110721.tar.bz2.CONTENTS and it contains a symbolic link. Aside from doing a new installation and watching it to see if you can catch it do something to the symbolic link, I don't know how to reproduce this. With that said, doing the following as root will fix it: rsync -av /lib/. /lib64/. rm -r /lib/* ln -s /lib64 /lib kerframil in #gentoo suggested using rsync for this, which was much easier than using mv. My system information is as follows: $ emerge --info Portage 2.1.10.7 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.6, glibc-2.11.3-r0, 2.6.39.3 x86_64) ================================================================= System uname: Linux-2.6.39.3-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9550_@_2.83GHz-with-gentoo-2.0.3 Timestamp of tree: Thu, 28 Jul 2011 17:15:01 +0000 ccache version 3.1.5 [enabled] app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r2, 3.2-r2 dev-util/ccache: 3.1.5 dev-util/cmake: 2.8.5-r2 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.0.3 sys-apps/openrc: 0.8.3-r1 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.1-r1 sys-devel/binutils: 2.21.1 sys-devel/gcc: 4.4.6 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 2.6.38 (virtual/os-headers) sys-libs/glibc: 2.11.3 Repositories: gentoo local_overlay sunrise vmware bitcoin ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -mtune=core2 -mcx16 -msahf -msse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=6144 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /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/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=core2 -mtune=core2 -mcx16 -msahf -msse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=6144 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs buildpkg ccache distlocks ebuild-locks fixlafiles fixpackages multilib-strict news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox" FFLAGS="-march=core2 -mtune=core2 -mcx16 -msahf -msse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=6144 -O2 -pipe" GENTOO_MIRRORS="http://mirror.lug.udel.edu/pub/gentoo/ http://gentoo.osuosl.org/ ftp://mirrors.rit.edu/gentoo/" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--sort-common" LINGUAS="en" MAKEOPTS="-j5" 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="/usr/local/portage /var/lib/layman/sunrise /var/lib/layman/vmware /var/lib/layman/bitcoin" SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage" USE="X a52 aac acpi alsa amd64 bash-completion berkdb branding bzip2 cairo cdda cdr cjk cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam ffmpeg fftw firefox flac fontconfig fortran gdbm gdu gif gnutls gpm iconv ipv6 java jpeg kde kipi lcms ldap libnotify lzma mad mmap mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly nsplugin ogg opengl openmp pam pango pcre pdf perl phonon plasma png policykit ppds pppd python qt3support qt4 readline sdl session spell sse sse2 ssl ssse3 startup-notification svg sysfs tcpd theora tiff truetype udev unicode usb vdpau vorbis x264 xcb xcomposite xinerama xml xorg xscreensaver xulrunner xv xvid xvmc zlib zsh-completion" ALSA_CARDS="hda-intel hpet snd-ctxfi" 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 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="braindump flow karbon kexi kpresenter krita tables words" CAMERAS="*" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS If you try to reproduce this, here are some instructions. Boot the system with system rescue cd and follow the manual. Then use my make.conf file (with things like ccache disabled and cflags changed). Set the system profile to default/linux/amd64/10.0/desktop/kde. Make a /etc/portage directory just like mine (a tarball will be attached later). Rebuild @world completely. Then run the following command to install all of the software that I use: emerge --jobs --keep-going -avDuN @world app-admin/sudo app-admin/syslog-ng app-arch/lrzip app-arch/lzop app-arch/rar app-benchmarks/gtkperf app-cdr/k3b app-cdr/k9copy app-crypt/johntheripper app-editors/bluefish app-editors/bvi app-editors/hexedit app-editors/vim app-editors/xemacs app-emulation/vmware-player app-emulation/wine app-laptop/laptop-mode-tools app-misc/anki app-misc/mc app-misc/screen app-misc/tmux app-office/scribus app-portage/eix app-portage/genlop app-portage/gentoolkit app-portage/layman app-portage/mirrorselect app-portage/pfl app-text/acroread app-text/ghostscript-gpl app-text/wgetpaste dev-embedded/upslug2 dev-java/eclipse-ecj dev-java/eclipse-ecj:3.5 dev-java/icedtea dev-java/javatoolkit dev-java/jogl dev-java/sun-jdk dev-lang/smlnj dev-util/ccache dev-util/strace dev-util/valgrind games-arcade/aquaria games-puzzle/osmos games-puzzle/world-of-goo games-strategy/revenge-of-the-titans games-strategy/wesnoth kde-base/kde-l10n kde-base/kdeadmin-meta kde-base/kdebase-meta kde-base/kdegraphics-meta kde-base/kdemultimedia-meta kde-base/kdenetwork-meta kde-base/kdeplasma-addons kde-base/kdesdk-meta kde-base/kdeutils-meta kde-base/kdm kde-base/kmag kde-base/krdc kde-base/kwin kde-base/solid kde-misc/knetworkmanager kde-misc/kwebkitpart media-fonts/arphicfonts media-fonts/artwiz-aleczapka-en media-fonts/corefonts media-fonts/dejavu media-fonts/freefonts media-fonts/liberation-fonts media-fonts/ttf-bitstream-vera media-fonts/ubuntu-font-family media-fonts/unifont media-gfx/digikam media-gfx/gimp media-gfx/inkscape media-libs/libcaca media-sound/alsa-utils media-sound/audacity media-video/kaffeine media-video/smplayer net-analyzer/nmap net-analyzer/tcpdump net-analyzer/traceroute net-analyzer/wireshark net-dialup/ppp net-dialup/pptpclient net-dialup/pptpd net-dialup/wvdial net-dns/bind-tools net-dns/dnsmasq net-ftp/atftp net-ftp/linksys-tftp net-im/skype net-irc/irssi net-misc/dhcpcd net-misc/netkit-telnetd net-misc/ntp net-misc/openvpn net-misc/putty net-misc/rdate net-misc/tightvnc net-misc/tor net-misc/youtube-dl net-p2p/ktorrent net-p2p/rtorrent net-print/gutenprint net-proxy/polipo net-wireless/aircrack-ng sci-mathematics/octave sys-apps/ethtool sys-apps/hdparm sys-apps/lm_sensors sys-apps/lshw sys-apps/microcode-ctl sys-apps/smartmontools sys-apps/usb_modeswitch sys-block/gparted sys-block/parted sys-block/partitionmanager sys-boot/grub sys-boot/unetbootin sys-cluster/mpich2 sys-devel/binutils-config sys-devel/crossdev sys-devel/gcc-config sys-devel/gcc:4.4 sys-devel/gdb sys-fs/btrfs-progs sys-fs/ddrescue sys-fs/dosfstools sys-fs/ntfs3g sys-fs/ntfsprogs sys-fs/sshfs-fuse sys-kernel/genkernel sys-kernel/module-rebuild sys-kernel/vanilla-sources:3.0 sys-power/acpitool sys-power/cpufreqd sys-power/cpufrequtils sys-power/nvclock sys-power/pm-utils sys-power/powertop sys-process/htop sys-process/iotop sys-process/lsof sys-process/time www-client/chromium www-client/firefox www-client/links www-client/opera www-plugins/adobe-flash www-plugins/google-talkplugin x11-apps/mesa-progs x11-apps/xdpyinfo x11-base/xorg-x11 libreoffice This is basically what I did to trigger it.
Created attachment 281375 [details] My /etc/portage directory, which could probably help to reproduce this from my instructions In hindsight, describing my previous attachment as needed to reproduce this was the wrong thing to do. It isn't needed and I am sure that there are other ways of triggering this, but I don't know how to do it.
@amd64 / @base-system, any ideas about this?
I got this on my local testing stages: tar tjvf /home/release/buildroot/amd64-dev/builds/default/stage3-amd64-20110717.tar.bz2 | grep "./lib " lrwxrwxrwx root/root 0 2011-07-17 03:22 ./lib -> lib64 tar tjvf /home/release/buildroot/amd64-dev/builds/hardened/stage3-amd64-hardened-20110717.tar.bz2 | grep "./lib " lrwxrwxrwx root/root 0 2011-07-17 07:31 ./lib -> lib64 tar tjvf /home/release/buildroot/amd64-dev/builds/hardened/stage3-amd64-hardened+nomultilib-20110717.tar.bz2 | grep "./lib " lrwxrwxrwx root/root 0 2011-07-17 09:31 ./lib -> lib64 and on the latest stages in poseidon: tar tjvf /release/buildroot/amd64-dev/builds/default/stage3-amd64-20110728.tar.bz2 | grep "./lib " lrwxrwxrwx root/root 0 2011-07-28 07:50 ./lib -> lib64
For what it is worth, mingdao in #gentoo also had this problem. He had so man issues from it that he started over and the last I know, he was watching things to see if it happened again. I haven't talked to him since yesterday, so I don't know if he tracked down what happened. I assume this is being caused by emerge. I can't think of many other ways such an important symbolic link could turn into a real folder. I normally like to have more useful information to provide when I open a report, but I had seen enough frustrating issues in #gentoo that I thought it would be good idea to have a bug for people in #gentoo to reference. I did not know that the symbolic link was at fault until I had this happen to myself.
@base-system: might this be a dupe of bug 358143 ?
i dont think so. that bug was about multilib.eclass overriding the profile.
your make.conf refers to layman and to /usr/local/portage overlay. what trees exactly are you overlaying ?
(In reply to comment #7) > your make.conf refers to layman and to /usr/local/portage overlay. what trees > exactly are you overlaying ? /usr/local/portage contains some minor modifications that I have done to stuff in the portage tree. Usually, they are revision bumps when I am too impatient to wait for the maintainer. layman is used to install the vmware overlay. I use it to install vmware player.
and what packages exactly are those ? i dont want to waste time tracking down phantom bugs in your overlays. certainly your make.conf+/etc/portage overlay allowed current stage3 to survive `emerge @world` ... especially considering your instructions have broken dep atoms: emerge: there are no ebuilds to satisfy "dev-java/jogl". emerge: there are no ebuilds to satisfy "games-puzzle/osmos". emerge: there are no ebuilds to satisfy "sys-kernel/vanilla-sources:3.0". !!! All ebuilds that could satisfy ">=net-misc/networkmanager-0.8.9997" have been masked. * Error: circular dependencies: (virtual/jdk-1.6.0::gentoo, ebuild scheduled for merge) depends on (dev-java/icedtea-6.1.10.3::gentoo, ebuild scheduled for merge) (runtime) (dev-java/ant-nodeps-1.8.1::gentoo, ebuild scheduled for merge) (buildtime) (virtual/jdk-1.6.0::gentoo, ebuild scheduled for merge) (buildtime)
(In reply to comment #9) > and what packages exactly are those ? i dont want to waste time tracking down > phantom bugs in your overlays. > > certainly your make.conf+/etc/portage overlay allowed current stage3 to survive > `emerge @world` ... > > especially considering your instructions have broken dep atoms: > emerge: there are no ebuilds to satisfy "dev-java/jogl". > emerge: there are no ebuilds to satisfy "games-puzzle/osmos". > emerge: there are no ebuilds to satisfy "sys-kernel/vanilla-sources:3.0". > !!! All ebuilds that could satisfy ">=net-misc/networkmanager-0.8.9997" have > been masked. > * Error: circular dependencies: > (virtual/jdk-1.6.0::gentoo, ebuild scheduled for merge) depends on > (dev-java/icedtea-6.1.10.3::gentoo, ebuild scheduled for merge) (runtime) > (dev-java/ant-nodeps-1.8.1::gentoo, ebuild scheduled for merge) (buildtime) > (virtual/jdk-1.6.0::gentoo, ebuild scheduled for merge) (buildtime) dev-java/jogl is a package in the java-overlay. I have a copy in my local overlay that fixes a major security hole. The fix was published by upstream a few years ago, which I have documented it in bug #143019. Applying it requires resolving bug #170305 to update a component that was put into another package as per Gentoo policy. I have been willing to do all of the work involved in fixing this so it can go into portage for more than a year, but the gentoo-java team has been uncooperative. You can either add the java-overlay to get the vulnerable older version or not emerge that package. The net-misc/networkmanager package issue is an issue that entered portage last week. It is caused because I have kde-misc/knetworkmanager unmasked, but left net-misc/networkmanager set to its default. I solved it on my system by unmasking net-misc/networkmanager. games-puzzle/osmos is a humble indie bundle game. I obtained it from the Gentoo forums, made a small edit and put it into my local overlay. I paid for the games and found the fetch restriction to be hassle, so the edit is to make gentoo fetch the files from the humble bundle servers. Aside from that small change, the ebuild is identical to the one from in the gamerlay overlay. sys-kernel/vanilla-sources:3.0 was how I installed the 3.0 kernel. The portage tree seems to have changed such that doing this no longer works. This likely isn't causing this problem. You can remove the :3.0 to make portage happy. The circular dependency issue is a bug that only affects new installations of icedtea. The workaround is to emerge dev-java/sun-jdk, use it as the system-vm, emerge icedtea and then switch to icedtea afterward. I forgot to file a separate bug report for this issue.
with a recent stage (20110811), and your config files, and dropping packages which don't even exist in the portage tree, things are emerging fine. please narrow it down more than the info you've posted already. if this were a wide ranging problem, i imagine we'd see more reports. as it is, i havent seen any dupes yet.
(In reply to comment #11) > with a recent stage (20110811), and your config files, and dropping packages > which don't even exist in the portage tree, things are emerging fine. please > narrow it down more than the info you've posted already. > > if this were a wide ranging problem, i imagine we'd see more reports. as it > is, i havent seen any dupes yet. I haven't seen any people in IRC with this issue for a while. It is possible that it was resolved unknowingly.
