This problem has been happening for me for several weeks at least. I've always ignored it (emerge --skipfirst --resume) in hopes that whatever the problem is would magically get fixed with some new version of gettext, but no such luck. Attempts to update to sys-devel/gettext-0.17 fail with: IOError: [Errno 5] Input/output error. I have searched the bugs database and gentoo forums, but appear to be the only person on the planet with this problem... Sadly, it is not clear to me how to fix the problem. I assume some file is missing, but which one? If I knew what file is missing, then I assume I could figure out what package contains the file and re-emerge it. Reproducible: Always Steps to Reproduce: 1. emerge --sync 2. emerge -uDN world -a Actual Results: speedy pym # emerge -uDN world -a These are the packages that would be merged, in order: Calculating world dependencies... done! [ebuild R ] sys-devel/gettext-0.17 USE="acl* nls openmp -doc -emacs -nocxx" 0 kB [ebuild U ] dev-java/sun-jdk-1.5.0.16 [1.5.0.15] USE="X -alsa -doc -examples -jce (-nsplugin) -odbc" 43,020 kB [ebuild U ] net-dialup/ppp-2.4.4-r15 [2.4.4-r14] USE="gtk ipv6 pam -activefilter -atm -dhcp -eap-tls -mppe-mppc -radius" 47 kB [ebuild U ] app-cdr/cdrdao-1.2.2-r2 [1.2.2] USE="encode -debug -gcdmaster% -pccts (-gnome%)" 0 kB Total: 4 packages (3 upgrades, 1 reinstall), Size of downloads: 43,067 kB Would you like to merge these packages? [Yes/No] yes >>> Verifying ebuild Manifests... >>> starting parallel fetching pid 11148 >>> Emerging (1 of 4) sys-devel/gettext-0.17 to / Traceback (most recent call last): File "/usr/bin/emerge", line 6971, in ? retval = emerge_main() File "/usr/bin/emerge", line 6965, in emerge_main myopts, myaction, myfiles, spinner) File "/usr/bin/emerge", line 6395, in action_build retval = mergetask.merge(pkglist, favorites, mtimedb) File "/usr/bin/emerge", line 3981, in merge return self._merge(mylist, favorites, mtimedb) File "/usr/bin/emerge", line 4259, in _merge prev_mtimes=ldpath_mtimes) File "/usr/lib64/portage/pym/portage.py", line 4675, in doebuild if need_distfiles and not fetch( File "/usr/lib64/portage/pym/portage.py", line 3213, in fetch verified_ok, reason = portage_checksum.verify_all( File "/usr/lib64/portage/pym/portage_checksum.py", line 179, in verify_all myhash = perform_checksum(filename, x, calc_prelink=calc_prelink)[0] File "/usr/lib64/portage/pym/portage_checksum.py", line 225, in perform_checksum myhash, mysize = hashfunc_map[hashname](myfilename) File "/usr/lib64/portage/pym/portage_checksum.py", line 40, in pyhash data = f.read(blocksize) IOError: [Errno 5] Input/output error Expected Results: I would expect the update to gettest-0.17 to complete normally emerge --info Portage 2.1.4.4 (default-linux/amd64/2007.0/desktop, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-gentoo-r8 x86_64) ================================================================= System uname: 2.6.24-gentoo-r8 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 5000+ Timestamp of tree: Sun, 13 Jul 2008 20:32:01 +0000 app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.4.4-r13 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r2 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.24 ABI="amd64" ACCEPT_KEYWORDS="amd64" ALSA_CARDS="via82xx" 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" ANT_HOME="/usr/share/ant-core" 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 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" ARCH="amd64" ASFLAGS_x86="--32" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CDEFINE_amd64="__x86_64__" CDEFINE_x86="__i386__" CFLAGS="-march=athlon64 -O2 -pipe" CFLAGS_x86="-m32 -L/emul/linux/x86/lib -L/emul/linux/x86/usr/lib" CHOST="x86_64-pc-linux-gnu" CHOST_amd64="x86_64-pc-linux-gnu" CHOST_x86="i686-pc-linux-gnu" CLASSPATH="." CLEAN_DELAY="5" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/udev/rules.d" CVS_RSH="ssh" CXXFLAGS="-march=athlon64 -O2 -pipe" DCCC_PATH="/usr/lib/distcc/bin" DEFAULT_ABI="amd64" DISTCC_LOG="" DISTCC_VERBOSE="0" DISTDIR="/usr/portage/distfiles" EDITOR="/bin/nano" ELIBC="glibc" EMERGE_DEFAULT_OPTS="--verbose --with-bdeps y" EMERGE_WARNING_DELAY="10" FEATURES="distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch" FETCHCOMMAND="/usr/bin/wget -t 5 -T 60 --passive-ftp -O ${DISTDIR}/${FILE} ${URI}" GCC_SPECS="" GDK_USE_XFT="1" GENERATION="2" GENTOO_MIRRORS="http://mirror.datapipe.net/gentoo" HISTCONTROL="ignoredups" HISTIGNORE="&:[bf]g:exit:df:cd:h:l:ll:la:au:ad:htop:screen::mc" HOME="/root" INFOPATH="/usr/share/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.18/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2/info" INPUT_DEVICES="keyboard mouse" JAVAC="/etc/java-config-2/current-system-vm/bin/javac" JAVA_HOME="/etc/java-config-2/current-system-vm" JDK_HOME="/etc/java-config-2/current-system-vm" KDEDIRS="/usr:/usr/local:/usr/kde/3.5" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LDFLAGS_x86="-m elf_i386 -L/emul/linux/x86/lib -L/emul/linux/x86/usr/lib" LESS="-R -M --shift 5" LESSOPEN="|lesspipe.sh %s" LIBDIR_amd64="lib64" LIBDIR_x86="lib32" LOGNAME="root" 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" 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/2.18/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.2/man:/opt/blackdown-jdk-1.4.2.03/man:/etc/java-config/system-vm/man/:/usr/lib64/php5/man/:/usr/kde/3.5/share/man:/usr/qt/3/doc/man:/opt/opera/share/man:/opt/vmware/workstation/man" MULTILIB_ABIS="amd64 x86" MULTILIB_STRICT_DENY="64-bit.*shared object" MULTILIB_STRICT_DIRS="/lib /usr/lib /usr/kde/*/lib /usr/qt/*/lib /usr/X11R6/lib" MULTILIB_STRICT_EXEMPT="(perl5|gcc|gcc-lib|binutils|eclipse-3|debug|portage)" OLDPWD="/root" OPENGL_PROFILE="nvidia" PAGER="/usr/bin/less" PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.1.2:/opt/blackdown-jdk-1.4.2.03/bin:/opt/blackdown-jdk-1.4.2.03/jre/bin:/usr/kde/3.5/sbin:/usr/kde/3.5/bin:/usr/qt/3/bin:/opt/vmware/workstation/bin" PKGDIR="/usr/portage/packages" PKG_CONFIG_PATH="/usr/qt/3/lib64/pkgconfig" 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/lib64/portage/bin" PORTAGE_CONFIGROOT="/" PORTAGE_DEBUG="0" PORTAGE_DEPCACHEDIR="/var/cache/edb/dep" PORTAGE_ELOG_CLASSES="warn error log" PORTAGE_ELOG_MAILFROM="portage@localhost" PORTAGE_ELOG_MAILSUBJECT="[portage] ebuild log for ${PACKAGE} on ${HOST}" PORTAGE_ELOG_MAILURI="root" PORTAGE_ELOG_SYSTEM="save" PORTAGE_GID="250" PORTAGE_INST_GID="0" PORTAGE_INST_UID="0" PORTAGE_IUSE="^(3dfx|adabas|alpha|alsa_cards_aoa|alsa_cards_aoa-fabric-layout|alsa_cards_aoa-onyx|alsa_cards_aoa-soundbus|alsa_cards_aoa-soundbus-i2s|alsa_cards_aoa-tas|alsa_cards_aoa-toonie|alsa_cards_armaaci|alsa_cards_at91-soc|alsa_cards_at91-soc-eti-b1-wm8731|alsa_cards_au1x00|alsa_cards_cs5535audio|alsa_cards_harmony|alsa_cards_powermac|alsa_cards_pxa2xx-i2sound|alsa_cards_pxa2xx-soc|alsa_cards_pxa2xx-soc-corgi|alsa_cards_pxa2xx-soc-poodle|alsa_cards_pxa2xx-soc-spitz|alsa_cards_pxa2xx-soc-tosa|alsa_cards_sa11xx-uda1341ts|alsa_cards_sun-amd7930|alsa_cards_sun-cs4231|alsa_cards_sun-dbri|altivec|amd64|aqua|arm|asm|birdstep|bmp|bmpx|bootstrap|build|capslib|clvm|cman|cmucl|coreaudio|crosscompile_opts_.*|dbmaker|doomsday|drac|elibc_.*|elibc_Darwin|elibc_DragonFly|elibc_FreeBSD|elibc_NetBSD|elibc_OpenBSD|elibc_glibc|elibc_uclibc|emf|empress|empress-bcs|esoob|fdftk|filepro|firebird|frontbase|gamess|gcc64|gulm|hppa|ia64|ibm|infopipe|informix|ingres|kernel_.*|kernel_Darwin|kernel_FreeBSD|kernel_linux|lcd_devices_svga|m68k|macbook|mips|multilib|n32|n64|osp|pam_console|pbbuttonsd|pfpro|plugin|ppc|ppc64|ppcsha1|psyco|pvm|real|s390|selinux|sh|solid|sparc|sparc-fbsd|svga|sybase|sybase-ct|tcc|uclibc|ultra1|userland_.*|userland_BSD|userland_Darwin|userland_GNU|video_cards_geode|video_cards_i740|video_cards_impact|video_cards_imstt|video_cards_newport|video_cards_nsc|video_cards_sunbw2|video_cards_suncg14|video_cards_suncg3|video_cards_suncg6|video_cards_sunffb|video_cards_sunleo|video_cards_suntcx|video_cards_vermilion|video_cards_xgi|vidix|vis|win32codecs|x86|x86-fbsd|xmms|yellownet)$" PORTAGE_NICENESS="3" PORTAGE_PYM_PATH="/usr/lib64/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_TMPFS="/dev/shm" PORTAGE_USE="amd64 elibc_glibc kernel_linux userland_GNU" PORTAGE_WORKDIR_MODE="0700" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" PORT_LOGDIR="/var/log/portage" PRELINK_PATH_MASK="/usr/lib/gstreamer-0.10:/usr/lib64/klibc" PWD="/usr/lib64/portage/pym" PYTHONPATH="/usr/lib64/portage/pym" QMAKESPEC="linux-g++" QTDIR="/usr/qt/3" RESUMECOMMAND="/usr/bin/wget -c -t 5 -T 60 --passive-ftp -O ${DISTDIR}/${FILE} ${URI}" ROOT="/" ROOTPATH="/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.1.2:/opt/blackdown-jdk-1.4.2.03/bin:/opt/blackdown-jdk-1.4.2.03/jre/bin:/usr/kde/3.5/sbin:/usr/kde/3.5/bin:/usr/qt/3/bin:/opt/vmware/workstation/bin" RPMDIR="/usr/portage/rpm" SHELL="/bin/bash" SHLVL="1" STAGE1_USE="nptl nptlonly unicode" SYMLINK_LIB="yes" SYNC="rsync://rsync.gentoo.org/gentoo-portage" TERM="xterm" USE="X aac accessibility acl acpi amd amd64 apache2 apm arts automount bash-completion berkdb cairo cdr cdrom cli cracklib crypt cups dbus dri dvd dvdr dvdread eds emboss encode esd evo fam fbcon fbcondecor fbdev firefox fortran ftp gcj gd gdbm gif glibc-omitfp gpm grub gstreamer gtk gutenprint hal iconv ipv6 isdnlog java jpeg kde kerberos ldap lm_sensors logitech-mouse loop-aes mad mdnsresponder-compat midi mikmod mmx mng mp3 mpeg mudflap musicbrainz ncurses nls nptl nptlonly nsplugin nvidia ogg opengl openmp oracle oss pam pascal pcre pdf perl php png ppds pppd python qt3 qt3support qt4 quicktime readline reflection samba sdl server session slp spell spl sse sse2 ssl subversion svg swat syslog tcpd tiff truetype unicode ups vim-with-x visualization vorbis x86emu xcomposite xine xml xorg xv xvmc zeroconf zlib" ALSA_CARDS="via82xx" 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" 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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nvidia vesa fbdev" USER="root" USERLAND="GNU" 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 USERLAND VIDEO_CARDS" USE_EXPAND_HIDDEN="CROSSCOMPILE_OPTS ELIBC KERNEL USERLAND" USE_ORDER="env:pkg:conf:defaults:pkginternal:env.d" VIDEO_CARDS="nvidia vesa fbdev" VMHANDLE="blackdown-jdk-1.4.2" XDG_DATA_DIRS="/usr/share:/usr/kde/3.5/share:/usr/local/share" _="/usr/bin/emerge"
Could be a problem with your filesystem, a dying harddisk, an libata issue, problems with a vendor specifc tool or so.
(In reply to comment #1) > Could be a problem with your filesystem, a dying harddisk, an libata issue, > problems with a vendor specifc tool or so. > I suppose it could be any of those things. However, in all other respects, the system is working without error. I do emerge --sync && emerge -uDN world regulary. If it were a harddisk issue, I guess I would expect to see other errors, not just with gettext. Can you suggest some means by which I could tell exactly what file is being operated on by /usr/lib64/portage/pym/portage_checksum.py at the time of failure? From what I can tell, it looks like emerge is doing checksumming of the gettext ebuild files. Is there some way to delete the existing gettext ebuild files, followed by an emerge --sync, with the idea that a new set of ebuild files would be downloaded?
[ebuild R ] sys-devel/gettext-0.17 USE="acl* nls openmp -doc -emacs -nocxx" 0 kB How long ago did you enable USE=acl and did you rebuild the entire system after that? Many packages come to implicitly depend on sys-apps/acl.
(In reply to comment #3) > [ebuild R ] sys-devel/gettext-0.17 USE="acl* nls openmp -doc -emacs > -nocxx" 0 kB > > How long ago did you enable USE=acl and did you rebuild the entire system after > that? Many packages come to implicitly depend on sys-apps/acl. > I switched to the 2007.0 profile quite recently (can't remember the exact date - I wonder how I can tell...). It is my bet that the acl USE flag was set then. I think all I did was an emerge -uDN world. I apologize for not remembering exact dates. I am not sure if the gettext problem began before or after the change to the 2007.0 profile. Should I do an emerge -e system? Or should I do some selective updates first? I can see that gettext is a system package.
Perhaps you could try `emerge -e system' first.
(In reply to comment #5) > Perhaps you could try `emerge -e system' first. > <BTW - just to be clear - I am doing everything as root> I did: emerge -e system <emerge of gettext failed as documented earlier> emerge --skipfirst --resume <ran to successful completion> emerge gettext <failed as documented earlier> emerge =sys-devel/gettext-0.16.1-r1 <downgrade successful> cd /usr/portage/sys-devel/gettext mkdir ~/gettext cp -pr * ~/gettext <the cp was successful> So this indicates to me that the ebuild files must be readable. Next I moved /usr/portage/sys-devel/gettext to to ~/ . emerge --sync emerge gettext <Failed as before> Next I removed /usr/portage/distfiles/gettext-0.17.tar.gz emerge gettext Success!! All of this for a corrupted gettext-0.17.tar.gz In any case - problem solved. Many thanks for your help, patience and courtesy. Please feel free to close this bug. Thanks.
(In reply to comment #6) > Next I removed /usr/portage/distfiles/gettext-0.17.tar.gz > emerge gettext > Success!! > All of this for a corrupted gettext-0.17.tar.gz That's strange - if the tarball was changed you'd expect a "friendly" checksum error, not a Python backtrace.
(In reply to comment #0) > Attempts to update to sys-devel/gettext-0.17 fail with: > IOError: [Errno 5] Input/output error. This type of failure indicates disk or filesystem trouble. You should check the disk and filesystem where ${DISTDIR} is located.
