Bug 530746 – sci-libs/hdf5-1.8.14 - links against its own installed libraries

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Ulenrich 2014-11-26 11:15:19 UTC]

sci-libs/hdf5-1.8.14 when updating creates a
/var/lib/portage/preserved_libs_registry
where itself is dependend on libs of its own predecessor.

The way to update this beast for me was to
emerge -C hdf5 vigra enblend
Thus the next world update pulls all of it back cleanly.

[Comment 1 Jeroen Roovers (RETIRED) 2014-11-26 17:13:03 UTC]

1) Please attach the entire build log to this bug report.
2) Please post your `emerge --info' output in a comment.

[Comment 2 Jouni Kosonen 2014-11-27 08:11:45 UTC]

Created attachment 390376 [details]
build.log.bz2

Build log from the merge where /usr/lib64/libhdf5_hl.so.9.0.0 ended up linking against /usr/lib64/libhdf5.so.8.0.2 from package version 1.8.13 installed earlier.

To me line 18444 from the log seems to show the reason:
libtool: link: x86_64-pc-linux-gnu-gcc -shared  -fPIC -DPIC  .libs/H5DO.o .libs/H5DS.o .libs/H5IM.o .libs/H5LT.o .libs/H5LTanalyze.o .libs/H5LTparse.o .libs/H5PT.o .libs/H5TB.o   -L/usr/lib ../../src/.libs/libhdf5.so -lpthread -lsz -lz -ldl -lm  -O3 -march=amdfam10 -O2 -Wl,-O1 -Wl,--as-needed   -Wl,-soname -Wl,libhdf5_hl.so.9 -o .libs/libhdf5_hl.so.9.0.0

[Comment 3 Jouni Kosonen 2014-11-27 08:15:17 UTC]

emerge --info sci-libs/hdf5

Portage 2.2.14 (python 2.7.7-final-0, default/linux/amd64/13.0/desktop, gcc-4.8.3, glibc-2.19-r1, 3.14.24-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-3.14.24-gentoo-x86_64-AMD_Phenom-tm-_II_X4_945_Processor-with-gentoo-2.2
KiB Mem:    16433544 total,   3742684 free
KiB Swap:    4200992 total,   4166992 free
Timestamp of tree: Wed, 26 Nov 2014 16:45:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
ccache version 3.1.9 [disabled]
app-shells/bash:          4.2_p53
dev-java/java-config:     2.2.0
dev-lang/perl:            5.18.2-r2
dev-lang/python:          2.7.7, 3.4.1
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           3.0.2
dev-util/pkgconfig:       0.28-r2
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.13.5
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6-r1, 1.13.4
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.7.3-r1, 4.8.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.3-r2
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.16 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: cross-compilers gentoo-haskell gentoo gentoo-opm local-repo
Installed sets: @binary, @dune, @extradb, @fonts, @fs, @gst10plugins, @lang, @math, @net_analyze, @qt5, @s6, @video, @wayland
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA Oracle-BCLA-JavaSE skype-eula skype-4.0.0.7-copyright google-chrome googleearth AdobeFlash-11.x PUEL cadsoft FraunhoferFDK TeamViewer"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=amdfam10 -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /opt/openfire/resources/security/ /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-2.2/conf /usr/share/maven-bin-3.0/conf /var/bind /var/lib/hsqldb /var/spool/torque"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/php/cli-php5.5/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=amdfam10 -O2 -pipe"
DISTDIR="/work/distfiles"
EMERGE_DEFAULT_OPTS="--quiet-build=y --with-bdeps=y"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://trumpetti.atm.tut.fi/gentoo/ http://mirror.mdfnet.se/gentoo http://gentoo.mneisen.org/ ftp://ftp.ntua.gr/pub/linux/gentoo/ http://gentoo.mirrors.hoobly.com/ http://mirror.yandex.ru/gentoo-distfiles/"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/cross-compilers /var/lib/layman/haskell /usr/portage /usr/local/gentoo-opm /usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext X a52 aac acl acpi aio alsa amd64 amr berkdb bluetooth branding bzip2 cairo cdda cdf cdr cleartype cli consolekit corefonts cracklib crypt cups curl cxx dbus dot dri dts dvd dvdr eigen emacs emboss encode exif expat fam firefox flac fontforge fortran gcj gdbm gif git gl2ps glamor glib gnutls gpm gsl gstreamer gtk iconv icu ipv6 java jpeg jpeg2k kde kpathsea ladspa lcms ldap libass libkms libnotify libsamplerate lzo mad matroska metric mmx mmxext mng modules mp3 mp4 mpeg multilib ncurses nls nptl nscd octave ogg ogm openexr opengl openmp opus pam pango pcre pdf physfs png policykit ppds pulseaudio qml qt3support qt4 readline sdl session sndfile source spell sqlite3 sse sse2 sse4a ssl startup-notification svg tbb tcpd theora threads tiff tk truetype type1 udev udisks unicode upower usb v4l vorbis wavpack webkit webm webp win32codecs wmf wxwidgets x264 xcb xinerama xml xrandr xv xvid zlib" ABI_X86="64 32" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" ELIBC="glibc" ENLIGHTENMENT_MODULES="backlight battery clock comp conf-applications conf-dialogs conf-display conf-edgebindings conf-interaction conf-intl conf-keybindings conf-menus conf-paths conf-performance conf-randr conf-shelves conf-theme conf-window-manipulation conf-window-remembers cpufreq dropshadow everything fileman fileman-opinfo gadman ibar ibox illume2 mixer msgbus notification pager quickaccess shot start syscon systray tasks temperature tiling winlist wizard xkbswitch" 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 ublox ubx" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver pdfimport scripting-beanshell scripting-javascript" LINGUAS="en en_US fi fi_FI" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-4 php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_USER_TARGETS="arm" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="radeon vesa vga" 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, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

=================================================================
                        Package Settings
=================================================================

sci-libs/hdf5-1.8.14 was built with the following:
USE="szip threads zlib -cxx -debug -examples -fortran -fortran2003 -mpi -static-libs" ABI_X86="64"

[Comment 4 Kacper Kowalik (Xarthisius) (RETIRED) 2014-11-27 20:50:48 UTC]

+*hdf5-1.8.14-r1 (27 Nov 2014)
+
+  27 Nov 2014; Kacper Kowalik <[e-mail]>
+  +files/hdf5-1.8.14-ldflags.patch, +hdf5-1.8.14-r1.ebuild, -hdf5-1.8.14.ebuild:
+  Prevent injection of -L{prefix}/lib to LDFLAGS. Fixes bug #530746 by Ulenrich
+  <[e-mail]>. Thanks to Jouni Kosonen <[e-mail]> for
+  the hint