'emerge hdf5' fails with: ... make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.3-r1/work/hdf5-1.8.3/perform' make -j1 -j1 DESTDIR=/var/tmp/portage/sci-libs/hdf5-1.8.3-r1/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-r1/work/hdf5-1.8.3/examples' + /usr/bin/install -c -m 644 ./h5_write.c /var/tmp/portage/sci-libs/hdf5-1.8.3-r1/image//usr/share/doc/hdf5-1.8.3-r1/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3-r1/image//usr/share/doc/hdf5-1.8.3-r1/examples/c/.': No such file or directory + exit 1 ... + exit 1 + /usr/bin/install -c -m 644 ./ph5example.c /var/tmp/portage/sci-libs/hdf5-1.8.3-r1/image//usr/share/doc/hdf5-1.8.3-r1/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3-r1/image//usr/share/doc/hdf5-1.8.3-r1/examples/c/.': No such file or directory + exit 1 make[1]: *** [install-examples] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-libs/hdf5-1.8.3-r1/work/hdf5-1.8.3/examples' + exit 1 make: *** [install-examples] Error 1 Reproducible: Always root@condor:/root(4)# emerge --info Portage 2.1.6.13 (default/linux/amd64/2008.0/desktop, gcc-4.4.1, 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_CPU_6600_@_2.40GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 24 Sep 2009 22:55:01 +0000 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.0_p33 dev-java/java-config: 2.1.9-r1 dev-lang/python: 2.6.2-r2, 3.1.1-r1 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: 2.1 sys-devel/autoconf: 2.13, 2.63-r1 sys-devel/automake: 1.4_p6, 1.5, 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: 2.6.30-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-php5/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.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=nocona -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/zugaina /usr/local/portage/layman/dotnet /usr/local/portage/layman/science /usr/local/portage/layman/lordvan /usr/local/portage/layman/java-overlay /usr/local/portage/layman/perl-experimental /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 blas bluetooth bonobo boo boost branding bzip2 c++ cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib cran crypt cups curl cxx daap dbus device-mapper dga dia divx djvu dlloader dmi doc dri ds3490 dts dv dvb dvd dvdr dvi dxr3 dynagraph eds effects elf emacs emboss encode epiphany esd evo examples exif expat extra extras 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 gnome-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 imagemagick 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 latex lcms ldap libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo lzw mad maildir mailwrapper math matroska mikmod mmx mmxext mng mod modules mono motif mozdevelop mozilla mozsvg mozxmlterm mp3 mp4 mp4live mpeg mpeg2 mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networkmanager nfs nls nntp nptl nptlonly 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 podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python qhull qt3 qt3support qt4 quicktime readline reflection reiserfs rhythmbox 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 thunar thunderbird tidy tiff tk tntc truetype unicode usb userlocales utempter v4l2 vorbis wav webdav webdav-serf webkit 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 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="cx8800 cx88xx tda1004x saa713" ELIBC="glibc" INPUT_DEVICES="keyboard mouse " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 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 nvidia vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
I can't reproduce it here. However I added a few fixes in a new version of the ebuild (sill 1.8.5-r1). Please try again when it hits the mirrors
It now works for mee.
Sorry, it works for me only if I remove the examples USE flag. If I have the example flag it fails still with the same error: 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-r1 USE="examples fortran szip threads zlib -cxx -mpi" 0 kB root@lynx:/root(13)# emerge -vuDN --resume world ... + cd examples + make install-examples make[1]: Entering directory `/var/tmp/portage/sci-libs/hdf5-1.8.3-r1/work/hdf5-1.8.3/examples' + /usr/bin/install -c -m 644 ./h5_write.c /var/tmp/portage/sci-libs/hdf5-1.8.3-r1/image///usr/share/doc/hdf5-1.8.3-r1/examples/c/. /usr/bin/install: cannot create regular file `/var/tmp/portage/sci-libs/hdf5-1.8.3-r1/image///usr/share/doc/hdf5-1.8.3-r1/examples/c/.': No such file or directory + exit 1 ... make: *** [install-examples] Error 1
(In reply to comment #1) I was able to reproduce it: 1) emerge -C hdf5 2) USE="examples fortran szip threads zlib -cxx -mpi" emerge -1 hdf5 3) USE="examples fortran szip threads zlib -cxx -mpi" emerge -1 hdf5 2) runs fine and installs everything in a right place. 3) fails. Guess install script detects /usr/share/doc/hdf5 and does something nasty... I was unable to nail it down, yet.
Just committed the 1.8.4. I tried to reproduced according to comment #4, but my build still worked flawlessly.
Now I can emerge hdf5-1.8.4 with the exambles USE flag.
Closing.
It fails again for with the examples USE flag.
(In reply to comment #8) > It fails again for with the examples USE flag. If this fails with 1.8.4-r1, please provide: * full build log and USE flags. * which hdf5 you had installed before. If this is another version, update to 1.8.4-r1. Thanks
Created attachment 212459 [details] gzipped /var/tmp/portage/sci-libs/hdf5-1.8.4-r1/temp/build.log Yes, it fails with hdf5-1.8.4-r1.
My hdf5 history: root@lynx:/root(15)# genlop -t hdf5 | tail -n20 merge time: 5 minutes and 28 seconds. Tue Oct 20 18:55:17 2009 >>> sci-libs/hdf5-1.8.3-r1 merge time: 5 minutes and 52 seconds. Wed Oct 21 14:04:36 2009 >>> sci-libs/hdf5-1.8.3-r1 merge time: 6 minutes and 5 seconds. Thu Oct 22 15:09:43 2009 >>> sci-libs/hdf5-1.8.3-r1 merge time: 5 minutes and 46 seconds. Sat Nov 21 09:47:39 2009 >>> sci-libs/hdf5-1.8.4 merge time: 8 minutes and 46 seconds. Mon Nov 23 16:42:34 2009 >>> sci-libs/hdf5-1.8.4 merge time: 8 minutes and 35 seconds. Fri Dec 4 12:07:27 2009 >>> sci-libs/hdf5-1.8.4-r1 merge time: 8 minutes and 22 seconds. As you can see in the history of this bug I had difficulties with hdf5-1.8.3-r1 in September and October, so I had to remove the example USE flag from hdf5. In november with hdf5-1.8.4, it looks if I could emerge with example USE flag. At Dec 4 I could emerge hdf5-1.8.4-r1 and it is installed now, but I don't with or without examble USE flag (likely without). Now I wanted to add the mpi USE flag, which was not succesful and I found even without mpi but with examples USE flag I can't emerge hdf5.
Created attachment 212464 [details, diff] forcing build to respect DESTDIR Could you use new version of destdir patch and report whether it makes any difference? To use it simply change line 46 of the original ebuild from epatch "${FILESDIR}"/${PN}-1.8.3-destdir.patch to epatch "${FILESDIR}"/${P}-destdir.patch REMARK: You won't be able to concurrently emerge hdf5 with USE="-mpi" and USE="mpi" or vice-versa due to mpi-fortran-wrapper bug. You have to unmerge hdf5 first.
Hello Kacper, corresponding to Comment #12 I created hdf5-1.8.4-r2.ebuild. Then I did: root@lynx:/usr/local/portage/sci-libs/hdf5(74)# emerge -pvuD hdf5 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] sci-libs/hdf5-1.8.4-r2 [1.8.4-r1] USE="cxx examples fortran szip threads zlib -mpi" 0 kB [0=>1] Total: 1 package (1 upgrade), Size of downloads: 0 kB Portage tree and overlays: [0] /usr/portage [1] /usr/local/portage root@lynx:/usr/local/portage/sci-libs/hdf5(76)# emerge -vuD hdf5 ... >>> No outdated packages were found on your system. * GNU info directory index is up-to-date. Thanks, Juergen
Created attachment 212476 [details] My test version of hdf5-1.8.4-r2.ebuild
Hi Kacpar, also thanks for the remark concerning the mpi flag. After deleting hdf5, I could also emerge hdf5 with the mpi flag.
Should be solved by now.
