'emerge hdf5' fails with: ... make -j1 DESTDIR=/var/tmp/portage/sci-libs/hdf5-1.8.3/image/ install-examples + for d in examples fortran + cd examples + make install-examples make[1]: Entering directory `/var/tmp/portage/sci-libs/hdf5-1.8.3/work/hdf5-1.8.3/examples' + /usr/bin/install -c -m 644 ./h5_write.c /var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3/image//usr/share/doc/hdf5-1.8.3/examples/c/.': No such file or directory + exit 1 The same version was installed with gcc-4.3.3. Now it fails with gcc-4.3.4. With USE='-examples' I can emerge hdf5. Reproducible: Always root@lynx:/root(12)# emerge -pvD hdf5 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/hdf5-1.8.3 USE="examples fortran szip threads zlib -cxx -mpi" 0 kB [1] root@lynx:/root(13)# emerge --info Portage 2.1.6.13 (default/linux/amd64/2008.0/desktop, gcc-4.3.4, glibc-2.10.1-r0, 2.6.30-gentoo-r4 x86_64) ================================================================= System uname: Linux-2.6.30-gentoo-r4-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T8300_@_2.40GHz-with-gentoo-2.0.1 Timestamp of tree: Wed, 12 Aug 2009 06:00:01 +0000 app-shells/bash: 4.0_p28 dev-java/java-config: 2.1.8-r1 dev-lang/python: 2.6.2-r1, 3.1 dev-python/pycrypto: 2.0.1-r8 dev-util/cmake: 2.6.4-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe" CHOST="x86_64-pc-linux-gnu" 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/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-ph p5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.d ef.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks fixpackages parallel-fetch protect-owned sandbox sfperms strict unmerge-orphans userfetch" FFLAGS="-march=nocona -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/distributions/gentoo" LDFLAGS="-Wl,-O1" 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="/usr/local/portage/layman/n4g /usr/local/portage/layman/dotnet /usr/local/portage/layman/science /usr/local/portage/layman/java-overlay /usr/local/portage /layman/suka /usr/local/portage/layman/zugaina /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X Xaw3d a52 aac acl acpi administrator afs aiglx alsa amd64 amrr ao aotuv apache2 asf atlas auctex audacious audiofile automount bash-completion beagle berkdb bjam bl as bluetooth bonobo boo boost branding bzip2 c++ cairo cardbus cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib cran crypt cups curl cxx daap dbus d evice-mapper dga dia divx djvu dlloader dmi doc dri ds3490 dv dvb dvd dvdr dvi dxr3 dynagraph eds effects elf emacs emboss encode epiphany esd evo examples exif expat extr a fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fuse galago garmin gd gdal gdbm geos gif gimp gimpprint ginac glade glib glitz gml gmp gnokii gnome gn ome-keyring gnuplot gnutls gphoto2 gpm graphics graphviz gs gsl gsm gstreamer gtk guile hal hardened harness hddtemp hdf hdf5 hlapi http httpd hvm iconv icq icu id3 ide im agemagick imap innodb ipod ipv6 irda irmc isdnlog ithreads jabber java java5 java6 jbig john jpeg jpeg2k kde kde4 kerberos kexi keyring kvm ladspa lame lapack laptop latex lcms ldap libffi libgda libnotify libsamplerate lirc lua lzo lzw mad maildir mailwrapper math matroska mikmod mmx mmxext mng mod mono motif mozdevelop mozilla mozsvg mozx mlterm mp3 mp4 mp4live mpeg mpeg2 mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networkmanager nfs nls nntp nptl nptlon ly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp pae pam pcre pda pdf perl pipechan plotutils plugins png podcas t policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python qhull qt3 qt3support qt4 quicktime readline reflection reiserfs rhyt hmbox rle rpc rrdcgi rrdtool samba sasl science sdl server session slang slp smp sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg sysfs szip t1lib tcl tcpd tex theora threads thunderbird tidy tiff tk tntc truetype unicode usb userlocales utempter v4l2 vorbis wav webda v 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_PLUG INS="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_ow ner 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" DVB_CARDS="usb-wt220u" ELIBC="glibc" INPUT_DEVICES="keyboard mouse synaptics " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd4478 0 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="ide websvccommon nb harness apisupport groovy gsf j2ee java xml" USERLAND="GNU" VIDEO_CARDS="nv nvid ia vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
After succesfull doing 'USE=-examples emerge hdf5', also 'USE=examples emerge hdf5' finishes succesfull.
Same here: $ emerge --info Portage 2.2_rc38 (default/linux/x86/2008.0, gcc-4.4.1, glibc-2.10.1-r0, 2.6.29.2-yoruichi i686) ================================================================= System uname: Linux-2.6.29.2-yoruichi-i686-AMD_Athlon-tm-_XP_3200+-with-gentoo-2.0.1 Timestamp of tree: Fri, 14 Aug 2009 12:15:02 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] ccache version 2.4 [enabled] app-shells/bash: 4.0_p28 dev-java/java-config: 2.1.8-r1 dev-lang/python: 2.6.2-r1, 3.1 dev-python/pycrypto: 2.0.1-r8 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.6.4-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.4.3-r3 sys-apps/sandbox: 2.0 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2, 1.11 sys-devel/binutils: 2.19.1-r1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6a virtual/os-headers: 2.6.29 ACCEPT_KEYWORDS="x86 ~x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=athlon-xp -m32 --param l1-cache-line-size=64 --param l1-cache-size=64 --param l2-cache-size=512 -O2 -funswitch-loops -fpredictive-commoning -fgcse-after-reload -ftree-vectorize -fomit-frame-pointer -mfpmath=sse -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/bind /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/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=athlon-xp -m32 --param l1-cache-line-size=64 --param l1-cache-size=64 --param l2-cache-size=512 -O2 -funswitch-loops -fpredictive-commoning -fgcse-after-reload -ftree-vectorize -fomit-frame-pointer -mfpmath=sse -pipe" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps y" FEATURES="assume-digests ccache collision-protect distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch userpriv usersandbox" FFLAGS="-march=athlon-xp -m32 --param l1-cache-line-size=64 --param l1-cache-size=64 --param l2-cache-size=512 -O2 -funswitch-loops -fpredictive-commoning -fgcse-after-reload -ftree-vectorize -fomit-frame-pointer -mfpmath=sse -pipe" GENTOO_MIRRORS=" ftp://orionis/distributions/1Linux/gentoo/portage ftp://ftp.chg.ru/pub/Linux/gentoo http://mirror.yandex.ru/gentoo-distfiles ftp://ftp.corbina.net/pub/Linux/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo http://mirror.netcologne.de/gentoo" LANG="en_US.UTF-8" LC_ALL="" LDFLAGS="-Wl,-O1" LINGUAS="ru en ja" MAKEOPTS="-j4" 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/layman/science /usr/local/portage/layman/java-overlay /usr/local/portage/layman/sunrise /usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="3dnow X a52 aac aalib acl acpi adns afs aften aim alsa amr amrnb amrwb ao audiofile bash-completion bcmath bidi binfilter blas bluetooth branding bzip2 cairo calendar canna caps ccache cddb cdinstall cdparanoia cdr chasen cjk cli clisp colordiff cracklib crypt cscope css ctype cups curl curlwrappers cvs cxx cyrillic dbus device-mapper dga dia dirac directfb djvu dmx doc dri dts dv dvd dvdr dvdread dvi editor elf encode enscript ermt examples exif expat faac faad fbcon festival ffmpeg fftw firefox flac fontconfig foomaticdb fortran fpx freetds freetype ftp gcj gcrypt gd gdbm geoip ggi gif gimp ginac git glut gmp gnuplot gnutls gpgme gphoto2 gpm gps graphviz gs gsl gsm gtk gucharmap h224 h281 h323 hdf5 hdri iconv icq icu id3tag idn imagemagick imap imlib immqt-bc inkjar ipod iproute2 ipv6 isdnlog jabber jack jadetex java6 javascript jbig jingle jpeg jpeg2k kdehiddenvisibility kerberos keyscrub kpathsea kqemu ladspa lame lapack lash latex lcms libcaca libnotify libsamplerate libwww lm_sensors logrotate lzo mad maildir mailwrapper matroska mbox md5sum mhash mikmod mime mjpeg mmap mmx mng modplug mp3 mpeg mplayer mppe-mppc msn mudflap musepack musicbrainz mysql mysqli nas ncurses netcdf network network-cron nls nntp nocd nodrm nptlonly nsplugin nuv objc objc++ offensive ogg openal openexr opengl oscar otr pam pango pch pcntl pcre pda pdf perl pgf plotutils png pop portaudio posix postproc postscript ppds pppd pronounce pstricks qt3 qt3support qt4 quicktime raw rdesktop readline recode reflection restrict-javascript rle rrdtool samba scanner schroedinger sdl session sharedmem shorten sip sipim slang slp smi smime sms smtp sndfile sockets socks5 soundtouch sox sparse speex spell spl sqlite sqlite3 srtp sse ssl startup-notification subversion supernodal svg svga sysfs syslog szip t1lib taglib tcpd theora tiff timezone timidity tordns truetype twolame type3 unicode usb v4l v4l2 vamp vcd videos vim vim-syntax vnc vorbis wav wavpack wifi win32codecs wireshark wmf x264 x86 xattr xcb xface xft xinerama xorg xosd xpm xprint xrandr xscreensaver xulrunner xv xvid yahoo yaz ziffy zlib" 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="authz_host dir mime" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="ru en ja" USERLAND="GNU" VIDEO_CARDS="nvidia nv vesa" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Unable to reproduce, but should be fixed with the just committed portage tree version (the one used here was from the science overlay). Re-open if not. Thanks.
