Bug 437680 – app-admin/collectd-5.1.0-r1 USE=-collectd_plugins_perl - configure: error: "Some plugins are missing dependencies - see the summary above for details"

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Fabio Coatti 2012-10-09 07:29:02 UTC]

collectd fails to emerge when collectd_plugins_perl is enabled.
the messages:

configure: error: "Some plugins are missing dependencies - see the summary above for details"

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/app-admin/collectd-5.1.0-r1/work/collectd-5.1.0/config.log
 * ERROR: app-admin/collectd-5.1.0-r1 failed (configure phase):
 *   econf failed
 * 
 * Call stack:
 *          ebuild.sh, line   89:  Called src_configure
 *        environment, line 4201:  Called econf '--config-cache' '--without-included-ltdl' '--disable-static' '--localstatedir=/var' '--disable-debug' '--disable-netapp' '--disable-pinba' '--disable-xmms' '--disable-ipvs' '--disable-apple_sensors' '--disable-tape' '--disable-zfs_arc' '--disable-modbus' '--disable-amqp' '--disable-genericjmx' '--disable-lpar' '--disable-redis' '--disable-threshold' '--disable-write_redis' '--disable-v5upgrade' '--disable-apache' '--enable-apcups' '--disable-ascent' '--disable-battery' '--disable-bind' '--disable-conntrack' '--disable-contextswitch' '--enable-cpu' '--enable-cpufreq' '--disable-curl' '--disable-curl_json' '--disable-curl_xml' '--disable-dbi' '--enable-df' '--disable-disk' '--disable-dns' '--disable-email' '--disable-entropy' '--enable-ethstat' '--disable-exec' '--disable-filecount' '--disable-fscache' '--disable-gmond' '--enable-hddtemp' '--enable-interface' '--disable-ipmi' '--disable-iptables' '--enable-irq' '--disable-java' '--disable-libvirt' '--enable-load' '--disable-madwifi' '--disable-mbmon' '--disable-md' '--disable-memcachec' '--disable-memcached' '--enable-memory' '--disable-multimeter' '--enable-mysql' '--disable-netlink' '--enable-network' '--disable-nfs' '--enable-nginx' '--enable-ntpd' '--enable-numa' '--disable-nut' '--disable-olsrd' '--disable-onewire' '--disable-openvpn' '--enable-perl' '--enable-ping' '--disable-postgresql' '--disable-powerdns' '--disable-processes' '--disable-protocols' '--enable-python' '--disable-rrdcached' '--enable-sensors' '--disable-serial' '--enable-snmp' '--enable-swap' '--enable-table' '--enable-tail' '--enable-tcpconns' '--disable-teamspeak2' '--disable-ted' '--enable-thermal' '--disable-tokyotyrant' '--disable-uptime' '--disable-users' '--disable-varnish' '--disable-vmem' '--disable-vserver' '--disable-wireless' '--disable-csv' '--disable-exec' '--enable-logfile' '--enable-network' '--enable-notify_desktop' '--disable-notify_email' '--disable-oracle' '--enable-perl' '--enable-python' '--disable-routeros' '--disable-rrdcached' '--enable-rrdtool' '--enable-syslog' '--disable-unixsock' '--enable-write_graphite' '--enable-write_http' '--disable-write_mongodb' '--disable-match_empty_counter' '--disable-match_hashed' '--disable-match_regex' '--disable-match_timediff' '--disable-match_value' '--disable-target_notification' '--disable-target_replace' '--disable-target_scale' '--disable-target_set' '--disable-uuid' '--with-libiptc=no' '--with-perl-bindings'
 *   phase-helpers.sh, line  501:  Called die
 * The specific snippet of code:
 *                      die "econf failed"
 * 
 * If you need support, post the output of `emerge --info '=app-admin/collectd-5.1.0-r1'`,
 * the complete build log and the output of `emerge -pqv '=app-admin/collectd-5.1.0-r1'`.
 * The complete build log is located at '/var/tmp/portage/app-admin/collectd-5.1.0-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/app-admin/collectd-5.1.0-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/app-admin/collectd-5.1.0-r1/work/collectd-5.1.0'
 * S: '/var/tmp/portage/app-admin/collectd-5.1.0-r1/work/collectd-5.1.0'


looking at config.log:
configure:22390: x86_64-pc-linux-gnu-gcc -o conftest -march=native -mtune=native -O2 -msse4a -pipe -ftree-loop-linear -floop-interchange -floop-strip-mine -fgraphite-identity -floop-block   -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64  -I/usr/lib64/perl5/5.16.1/x86_64-linux-thread-multi/CORE   -Wl,-O1 -Wl,--as-needed -Wl,-E -Wl,-O1 -Wl,--as-needed  -L/usr/lib64/perl5/5.16.1/x86_64-linux-thread-multi/CORE -lperl -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc conftest.c -ldl  -lperl >&5
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/../../../../x86_64-pc-linux-gnu/bin/ld: /var/tmp/portage/app-admin/collectd-5.1.0-r1/temp/ccABGKX7.o: undefined reference to symbol 'pthread_getspecific@@GLIBC_2.2.5'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/../../../../x86_64-pc-linux-gnu/bin/ld: note: 'pthread_getspecific@@GLIBC_2.2.5' is defined in DSO /lib64/libpthread.so.0 so try adding it to the linker command line
/lib64/libpthread.so.0: could not read symbols: Invalid operation
collect2: ld returned 1 exit status

So it seems that the pthread is not located properly, but I'm not sure about the right way to fix it.



Reproducible: Always




kefk ~ # emerge --info
Portage 2.2.0_alpha135 (default/linux/amd64/10.0/desktop, gcc-4.6.3, glibc-2.15-r3, 3.5.4 x86_64)
=================================================================
System uname: Linux-3.5.4-x86_64-AMD_Phenom-tm-_9850_Quad-Core_Processor-with-gentoo-2.2
Timestamp of tree: Tue, 09 Oct 2012 06:00:01 +0000
app-shells/bash:          4.2_p37
dev-java/java-config:     2.1.12
dev-lang/python:          2.6.8, 2.7.3-r2, 3.2.3-r1
dev-util/cmake:           2.8.9-r1
dev-util/pkgconfig:       0.27.1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.10.5
sys-apps/sandbox:         2.6
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.6, 1.12.4
sys-devel/binutils:       2.22.90
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.6 (virtual/os-headers)
sys-libs/glibc:           2.15-r3
Repositories: gentoo gamerlay-stable hacking-gentoo kormoc overlay
Installed sets: @kde
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -mtune=native -O2 -msse4a -pipe -ftree-loop-linear -floop-interchange -floop-strip-mine -fgraphite-identity -floop-block "
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
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/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-march=native -mtune=native -O2 -msse4a -pipe -ftree-loop-linear -floop-interchange -floop-strip-mine -fgraphite-identity -floop-block "
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.wheel.sk/ http://gentoo.mneisen.org/ http://gentoo.supp.name/"
LANG="it_IT.utf8"
LC_ALL="it_IT.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="it en"
MAKEOPTS="-j6"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --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="/var/lib/layman/gamerlay /var/lib/layman/hacking-gentoo /var/lib/layman/kormoc /usr/overlay"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext 3dnowprefetch X a52 aac aalib acl acpi aim alsa amd64 amr amrnb amrwb apache2 apng ares asf ass audiofile avahi bash-completion berkdb bidi bl bluetooth branding bri bzip2 cairo caps cdda cdparanoia cdr cjk cli consolekit cracklib crypt cups curl cxx dba dbus declarative device-mapper dga dirac directfb divx divx4linux dri dts dv dvb dvd dvdnav dvdr dvdread edl embedded emboss enca encode ethereal exif expat faac faad fam fame fbcon ffmpeg fftw firefox flac fontconfig force-cgi-redirect fortran ftp garmin gd gdbm gif gimp gmedia gmp gnutls gpm gps gsm gtk iconv icq icu id3tag idn ifp ilbc imagemagick imap innodb ipod iproute2 ipv6 ithreads jabber java javascript jpeg kde kontact kvm ladspa lcms ldap libcaca libnotify libv4l2 live lm_sensors lua lvm lxc lzo mad maildir matroska mbox md5sum mdnsresponder-compat mhash mime mjpeg mmap mmx mmxext mng modules mozdevelop mozilla mp3 mp4 mpeg msn mtp mudflap multilib musepack mysql ncurses nemesi nepomuk network nfsv4 njb nls nptl nptlonly nsplugin numa nut nvidia offensive ofx ogg oggvorbis ogm openal openexr opengl openmp oscar pam pango parted pcap pcre pdf php plasma plotutils png pnm policykit ppds pppd pulseaudio pvr qemu qt3support qt4 radio rar readline rtc rtmp rtsp ruby samba sasl schroedinger sdl semantic-desktop session sha512 sl slang slp sms sndfile snmp sox speex spell srt sse sse2 sse4a ssh ssl startup-notification stream svg symlink taglib tcltk tcpd theora threads tiff tk tremor truetype udev udisks unicode upower usb utempter v4l v4l2 vcd vdpau vhosts videos vim-syntax virtualbox vorbis wmf wmp wxwidgets wxwindows x264 xanim xcb xface xft xine xml xosd xpm xscreensaver xsl xulrunner xv xvid xvmc yahoo zlib zoran zpm" 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" 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="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog apcups cpu cpufreq ethstat hddtemp logfile mysql network nginx notify_desktop ntpd numa perl ping python sensors snmp table tail tcpconns thermal write_graphite write_http" 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="it en" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" SANE_BACKENDS="epjitsu epson epson2" USERLAND="GNU" VIDEO_CARDS="nv nvidia vesa" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Jeroen Roovers (RETIRED) 2012-10-09 14:52:33 UTC]

1) Please attach the entire build log to this bug report.
2) Please attach the entire config.log to this bug report.

[Comment 2 Fabio Coatti 2012-10-09 19:47:27 UTC]

Created attachment 326118 [details]
config.log

[Comment 3 Fabio Coatti 2012-10-09 19:48:13 UTC]

Created attachment 326120 [details]
build.log

[Comment 4 Fabio Coatti 2012-10-09 19:48:56 UTC]

(In reply to comment #1)
> 1) Please attach the entire build log to this bug report.
> 2) Please attach the entire config.log to this bug report.

You're right, done.

[Comment 5 Jeroen Roovers (RETIRED) 2012-10-09 22:24:53 UTC]

Comment on attachment 326120 [details]
build.log

It looks like you need to attach this file:

/var/tmp/portage/app-admin/collectd-5.1.0-r1/work/collectd-5.1.0/libltdl/config.log

[Comment 6 Fabio Coatti 2012-10-10 06:58:21 UTC]

Created attachment 326158 [details]
libltdl config.log

Here you go,thanks.

[Comment 7 Johan Bergström 2012-10-10 22:04:28 UTC]

Created attachment 326242 [details, diff]
collectd-5.10.1-libperl.patch

I was able to reproduce this with perl 5.12.4-r1 and 5.16.1. It is most likely due to --as-needed and the lack of -lpthread. Anyway, please try replacing the old collectd-4.10.1-libperl.patch with the attached one.

Also, make this minor change to your ebuild:

old	2012-05-31 12:31:01.000000000 +1000
+++ new	2012-10-11 09:03:44.261772434 +1100
@@ -104,10 +104,10 @@
 	collectd_plugins_syslog?		( virtual/logger )"
 
 PATCHES=(
-	"${FILESDIR}/${PN}-4.10.1"-libperl.patch
 	"${FILESDIR}/${PN}-4.10.2"-{libocci,nohal}.patch
 	"${FILESDIR}/${PN}-4.10.3"-{lt,werror}.patch
 	"${FILESDIR}/${PN}-5.1.0"-netlink.patch
+	"${FILESDIR}/${PN}-5.1.0"-libperl.patch
 	)
 
 # @FUNCTION: collectd_plugin_kernel_linux

[Comment 8 Fabio Coatti 2012-10-11 13:58:03 UTC]

With this patch the compilation went just fine with perl plugin, many thanks!

[Comment 9 Markos Chandras (RETIRED) 2012-10-30 19:34:27 UTC]

+*collectd-5.1.0-r2 (30 Oct 2012)
+
+  30 Oct 2012; Markos Chandras <[e-mail]> +collectd-5.1.0-r2.ebuild,
+  +files/collectd-5.1.0-libperl.patch, +files/collectd-5.1.0-mongoc06.patch:
+  Revbump for #436538 and #437680. Thanks to Johan Bergström
+  <[e-mail]>
+