Bug 482408 – sci-mathematics/rstudio-0.97.551 with dev-libs/boost-1.53.0* - Process.cpp:(.text+0x3f59): undefined reference to `boost::this_thread::sleep(boost::posix_time::ptime const&)'

• Status: RESOLVED TEST-REQUEST
• Product: Gentoo Linux

[Description rainer 2013-08-25 11:44:44 UTC]

emerge yields errors, errros may be related to boost

Part of the build log:

PosixOutputCapture.cpp:(.text._ZN5boost6threadC2INS_3_bi6bind_tIvPFviRKNS_8functionIFvRKSsEEEiSA_ENS2_5list4INS2_5valueIiEENSE_IS8_EESF_SG_EEEEEET_NS_10disable_ifINS_14is_convertibleIRSJ_NS_6detail13thread_move_tISJ_EEEEPNS0_5dummyEE4typeE[_ZN5boost6threadC5INS_3_bi6bind_tIvPFviRKNS_8functionIFvRKSsEEEiSA_ENS2_5list4INS2_5valueIiEENSE_IS8_EESF_SG_EEEEEET_NS_10disable_ifINS_14is_convertibleIRSJ_NS_6detail13thread_move_tISJ_EEEEPNS0_5dummyEE4typeE]+0x84): undefined reference to `boost::thread::start_thread()'
collect2: error: ld returned 1 exit status
make[2]: *** [src/cpp/session/rsession] Error 1

Reproducible: Always




# emerge --info
Portage 2.2.1 (default/linux/amd64/13.0/desktop, gcc-4.7.3, glibc-2.17, 3.9.0-gentoocfg-2013-05-07 x86_64)
=================================================================
System uname: Linux-3.9.0-gentoocfg-2013-05-07-x86_64-Intel-R-_Core-TM-_i7_CPU_860_@_2.80GHz-with-gentoo-2.2
KiB Mem:    16426172 total,   1990748 free
KiB Swap:          0 total,         0 free
Timestamp of tree: Sun, 25 Aug 2013 09:45:01 +0000
ld GNU ld (GNU Binutils) 2.23.2
ccache version 3.1.9 [enabled]
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.5-r2, 3.2.5-r2, 3.3.2-r2
dev-util/ccache:          3.1.9
dev-util/cmake:           2.8.11.1
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.10.3, 1.11.6, 1.12.6, 1.14
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.7.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.10 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo local
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -msse4 -mcx16 -msahf -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /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/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=core2 -msse4 -mcx16 -msahf -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs ccache 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 xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="ftp://gentoo.imj.fr/pub/gentoo/ http://mirrors.linuxant.fr/distfiles.gentoo.org/ ftp://mirrors.linuxant.fr/distfiles.gentoo.org/ http://gentoo.modulix.net/gentoo/ ftp://mirror.ovh.net/gentoo-distfiles/ http://mirror.ovh.net/gentoo-distfiles/ ftp://de-mirror.org/gentoo/ http://de-mirror.org/gentoo/ rsync://de-mirror.org/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j9"
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/local/portage"
SYNC="rsync://rsync.de.gentoo.org/gentoo-portage"
USE="X a52 aac acl acpi aim alsa amd64 ao audiofile avahi bash-completion bcmath berkdb blas bluetooth branding bzip2 cairo calendar caps cdda cddb cdparanoia cdr cli consolekit cracklib crypt css cups curl curlwrappers cxx dbus dga directfb djvu dri dts dv dvd dvdr emacs emboss encode exif fam fbcon ffmpeg firefox flac fontconfig fortran ftp gcj gd gdbm gif gimp ginac glut gnome gnome-keyring gnuplot gnutls gphoto2 gpm graphviz gsm gstreamer gtk gtkhtml gzip hddtemp iconv icq icu ieee1394 imagemagick imap imlib iodbc ipv6 jabber java java6 javascript jbig jingle jpeg jpeg2k kde kontact lame lapack lash latex lcms ldap libgda libnotify lirc lm_sensors lzo mad matroska mikmod mime mmx mng modules mono mozilla mp3 mp4 mpeg mpi mplayer msn mtp mudflap mule multilib musepack musicbrainz mysql mysqli nas ncurses neXt nls nntp nocd nptl nsplugin odbc offensive ofx ogg openal openexr opengl openmp osc oscar oss pam pango pcre pdf perl php plasma plotutils png policykit ppds pulseaudio python qt3support qt4 quicktime raw readline rss ruby samba scanner sdl semantic-desktop session smp sockets socks5 sox speex spell sqlite sqlite3 sse sse2 ssl startup-notification svg symlink syslog sysvipc szip tcl tcpd theora threads tiff truetype udev udisks unicode upower usb v4l v4l2 vcd vde video vnc vorbis wmf wxwidgets x264 xattr xcb xcomposite xemacs xft xml xosd xpm xsl xv xvid yahoo 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" 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="de en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2 python3_3" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="radeon" 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"
USE_PYTHON="2.7 3.2 3.3"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 rainer 2013-08-25 11:46:07 UTC]

Created attachment 356964 [details]
build log

[Comment 2 Julian Ospald 2013-09-25 13:10:25 UTC]

what useflags do you have boost compiled with?

[Comment 3 Christopher Fair 2013-09-25 14:25:55 UTC]

I cannot emerge r-studio either....here is the info file emerge told me to post.

Portage 2.2.1 (default/linux/amd64/13.0/desktop/gnome, gcc-4.6.3, glibc-2.17, 3.10.7-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.10.7-gentoo-x86_64-Intel-R-_Core-TM-_i5-2400_CPU_@_3.10GHz-with-gentoo-2.2
KiB Mem:    16401940 total,  10043272 free
KiB Swap:    4194300 total,   4194300 free
Timestamp of tree: Tue, 24 Sep 2013 16:00:01 +0000
ld GNU ld (GNU Binutils) 2.23.1
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.5-r2, 3.2.5-r1
dev-util/cmake:           2.8.10.2-r2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.11.8
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.10.3, 1.11.6, 1.12.6
sys-devel/binutils:       2.23.1
sys-devel/gcc:            4.6.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4-r1
sys-devel/make:           3.82-r4
sys-kernel/linux-headers: 3.7 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo x-portage
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /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"
CXXFLAGS="-O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs 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://ftp.heanet.ie/pub/gentoo/ ftp://ftp.heanet.ie/pub/gentoo/ rsync://ftp.heanet.ie/pub/gentoo/ ftp://gentoo.mirrors.tds.net/gentoo http://gentoo.mirrors.tds.net/gentoo http://ftp.ucsb.edu/pub/mirrors/linux/gentoo/ ftp://ftp.ucsb.edu/pub/mirrors/linux/gentoo/ ftp://ftp.lug.udel.edu/pub/gentoo/ http://mirror.lug.udel.edu/pub/gentoo/ http://gentoo.cites.uiuc.edu/pub/gentoo/ ftp://gentoo.cites.uiuc.edu/pub/gentoo/"
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="/etc/local/portage"
USE="X a52 aac acl acpi additions aio alsa amd64 ati berkdb bindist bluetooth branding bzip2 cairo caps caps-ng cdda cdr cli clisp colord consolekit cracklib crypt cups curl cxx dbus doc dri dts dvd dvdr dvi2tty dvipdfm eds emboss encode evo exif extensions fam filecaps firefox flac fontconfig fortran freerdp gdbm gif glx gnome gnome-keyring gnome-online-accounts gpm graphics gstreamer gtk iconv icu introspection ipv6 jpeg kerberos lcms ldap libkms libnotify libsecret mad minizip mmx mng modules mp3 mp4 mpeg mudflap multilib nautilus ncurses nls nptl nsplugin ogg opengl openmp opus pam pango pcre pdf png policykit ppds pstricks pulseaudio qt3support qt4 readline samba science sdl seccomp session socialweb spell sqlite sse sse2 ssl startup-notification static-libs svg tcpd tiff truetype udev udisks unicode upower usb vhost-net vorbis wxwidgets x264 xa xcb xfce4 xml xv xvid zlib ~amd64" ABI_X86="64" 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" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="radeon" 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

[Comment 4 Julian Ospald 2013-09-25 16:01:20 UTC]

if no one gives me info on their boost installation, then I cannot help, because I am unable to reproduce

[Comment 5 Christopher Fair 2013-09-26 16:25:16 UTC]

  I got mine to emerge after I attempted to run from the tarball from the rstudio website.  I noticed that it had a direct dependency on libpng12 but my installation has libpng15.


  The emerge does not pull in the backdependency and so it fials.  I ran  "emerge -1 libpng:1.2" then did : "emerge rstudio" I now have a correctly functioning installation of rstudio.

[Comment 6 Julian Ospald 2013-09-26 16:35:06 UTC]

(In reply to Christopher Fair from comment #5)
>   I got mine to emerge after I attempted to run from the tarball from the
> rstudio website.  I noticed that it had a direct dependency on libpng12 but
> my installation has libpng15.
> 
> 
>   The emerge does not pull in the backdependency and so it fials.  I ran 
> "emerge -1 libpng:1.2" then did : "emerge rstudio" I now have a correctly
> functioning installation of rstudio.

That doesn't make any sense. Rstudio does not need libpng:1.2.

Please check that your compile error is similar to this one, otherwise open a new bug.

[Comment 7 cruzki 2013-11-03 09:14:50 UTC]

I have the same problem. I have boost compiled with the following CFLAGS

dev-libs/boost
     Available versions:  1.49.0-r2 1.52.0-r6(0/1.52) (~)1.53.0(0/1.53) [M](~)1.54.0(0/1.54) {debug doc icu mpi +nls python static-libs +threads tools PYTHON_TARGETS="python2_6 python2_7 python3_2 python3_3"}
     Installed versions:  1.53.0(22:33:40 06/09/13)(icu nls threads -debug -doc -mpi -python -static-libs -tools PYTHON_TARGETS="python2_7 -python2_6 -python3_2 -python3_3")

Thanks for your help

[Comment 8 Jeroen Roovers (RETIRED) 2014-01-12 13:47:08 UTC]

*** Bug 497884 has been marked as a duplicate of this bug. ***

[Comment 9 Julian Ospald 2014-02-03 01:13:25 UTC]

is this still an issue?

[Comment 10 Julian Ospald 2014-07-07 17:32:50 UTC]

reopen if it still happens with latest rstudio