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Joined: 01 Jul 2010
Posts: 34
Location: NJ, USA

PostPosted: Thu Apr 23, 2015 6:15 pm    Post subject: sci-physics/root-6.02.05-r2: PCH generation failed Reply with quote


It looks like
(from the science overlay) doesn't build on x86.


# emerge -1av --jobs 2 --emptytree root

<... snip ...>

 * ERROR: sci-physics/root-6.02.05-r2::gentoo failed (install phase):
 *   PCH generation failed
 * Call stack:
 *, line   93:  Called src_install
 *   environment, line 3979:  Called cleanup_install
 *   environment, line  910:  Called die
 * The specific snippet of code:
 *       etc/root/dictpch/ etc/root/allDict.cxx.pch || die "PCH generation failed"
 * If you need support, post the output of `emerge --info '=sci-physics/root-6.02.05-r2::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-physics/root-6.02.05-r2::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sci-physics/root-6.02.05-r2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-physics/root-6.02.05-r2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-physics/root-6.02.05-r2/image'
 * S: '/var/tmp/portage/sci-physics/root-6.02.05-r2/work/root-6.02.05'

The compilation works fine, but it seems to fail in the 'install' phase:


Generating PCH for core/base core/thread io/io math/mathcore net/net math/matrix hist/hist tree/tree graf2d/graf graf2d/gpad gui/gui math/minuit hist/histpainter tree/treeplayer tree/treeviewer math/physics graf2d/postscript core/rint math/smatrix math/smatrix hist/spec\
trum hist/spectrumpainter gui/fitpanel graf2d/x11 graf2d/x11ttf graf3d/gl graf2d/asimage graf2d/asimage bindings/pyroot math/genvector math/genvector math/mathmore math/minuit2 roofit/roofitcore roofit/roofit roofit/roostats roofit/histfactory hist/hbook tmva math/genet\

   ===                ROOT BUILD SUCCESSFUL.                ===
   === Run 'make install' now.                              ===
Installing binaries in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/bin
Installing libraries in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/lib/root
Installing headers in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/include/root
Installing /var/tmp/portage/sci-physics/root-6.02.05-r2/work/root-6.02.05/main/src/rmain.cxx in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/include/root
Installing icons in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/root/icons
Installing fonts in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/root/fonts
Installing misc docs in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/doc/root-6.02.05
Installing tutorials in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/doc/root-6.02.05/examples/tutorials
Installing tests in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/doc/root-6.02.05/examples/tests
Installing macros in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/root/macros
Installing man(1) pages in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/man/man1
Installing config files in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//etc/root
Installing Autoconf macro in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/aclocal
Installing Emacs Lisp library in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/share/emacs/site-lisp
Installing GDML conversion scripts in /var/tmp/portage/sci-physics/root-6.02.05-r2/image//usr/lib/root
Warning in cling::CIFactory::createCI():
  C++ ABI mismatch, compiled with __GLIBCXX__ v20140522 running with v20141219

Processing hsimple.C...
hsimple   : Real Time =   0.16 seconds Cpu Time =   0.14 seconds
(class TFile *) 0xac1c338
 * Installing Elisp files for GNU Emacs support ...
 [ ok ]
ERROR in cling::CIFactory::createCI():
  resource directory /etc/root/cling/lib/clang/3.6.0 not found!
In file included from input_line_3:2:
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.8.4/include/g++-v4/string:40:
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.8.4/include/g++-v4/bits/char_traits.h:40:
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.8.4/include/g++-v4/bits/postypes.h:40:
In file included from /usr/lib/gcc/i686-pc-linux-gnu/4.8.4/include/g++-v4/cwchar:44:
^[[1m/usr/include/wchar.h:39:11: ^[[0m^[[0;1;31mfatal error: ^[[0m^[[1m'stdarg.h' file not found^[[0m
# include <stdarg.h>
^[[0;1;32m          ^
^[[0m^[[ ^[[0m^[[0;1;31merror: ^[[0m^[[1munknown type name 'Double32_t'^[[0m
 *** Break *** segmentation violation

The complete build log is at

The error seems to be due to root looking for ' /etc/root/cling/lib/clang/3.6.0' while I only
have '/etc/root/cling/lib/clang/3.5/'.

However, clang-3.6.0 is blocked:

# USE="~x86" emerge -1av --jobs 2 =sys-devel/clang-3.6.0-r100

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild     U ~] sys-devel/llvm-3.6.0:0/3.6 [3.5.0:0/3.5] USE="clang libffi ncurses static-analyzer -debug -doc -gold -libedit -multitarget -ocaml -python {-test} -xml" PYTHON_TARGETS="python2_7 -pypy" VIDEO_CARDS="-radeon" 22282 KiB
[ebuild     U ~] sys-devel/clang-3.6.0-r100:0/3.6 [3.5.0-r100:0/3.5] USE="static-analyzer -debug -multitarget -python" 0 KiB
[blocks B      ] <=sys-devel/clang-3.6.0-r99 ("<=sys-devel/clang-3.6.0-r99" is blocking sys-devel/llvm-3.6.0)

Total: 2 packages (2 upgrades), Size of downloads: 22282 KiB
Conflict: 1 block (1 unsatisfied)

!!! Multiple package instances within a single package slot have been pulled
!!! into the dependency graph, resulting in a slot conflict:


  (sys-devel/llvm-3.6.0:0/3.6::gentoo, ebuild scheduled for merge) pulled in by
    ~sys-devel/llvm-3.6.0[clang(-),debug=,multitarget?,python?,static-analyzer,abi_x86_32(-)?,abi_x86_64(-)?,abi_x86_x32(-)?,abi_mips_n32(-)?,abi_mips_n64(-)?,abi_mips_o32(-)?,abi_ppc_32(-)?,abi_ppc_64(-)?,abi_s390_32(-)?,abi_s390_64(-)?] required by (sys-devel/clang-3.6.0-r100:0/3.6::gentoo, ebuild scheduled for merge)
    ^               ^^^^^                                                                                                                                                                                                                                                                                                                                                               

  (sys-devel/llvm-3.5.0:0/3.5::gentoo, installed) pulled in by
    <sys-devel/llvm-3.6 required by (media-libs/mesa-10.3.7-r1:0/0::gentoo, installed)
    ^               ^^^                                                                                                                     
    >=sys-devel/llvm-3.3-r3:0/3.5=[abi_x86_32(-)] required by (media-libs/mesa-10.3.7-r1:0/0::gentoo, installed)
    ~sys-devel/llvm-3.5.0[clang(-),debug=,multitarget?,python?,static-analyzer,abi_x86_32(-)?,abi_x86_64(-)?,abi_x86_x32(-)?,abi_mips_n32(-)?,abi_mips_n64(-)?,abi_mips_o32(-)?,abi_ppc_32(-)?,abi_ppc_64(-)?,abi_s390_32(-)?,abi_s390_64(-)?] required by (sys-devel/clang-3.5.0-r100:0/3.5::gentoo, installed)
    ^               ^^^^^                                                                                                                                                                                                                                                                                                                                             


  (sys-devel/clang-3.6.0-r100:0/3.6::gentoo, ebuild scheduled for merge) pulled in by
    =sys-devel/clang-3.6.0-r100 (Argument)
    (and 1 more with the same problem)

  (sys-devel/clang-3.5.0-r100:0/3.5::gentoo, installed) pulled in by
    =sys-devel/clang-3.5.0-r100 required by (sys-devel/llvm-3.5.0:0/3.5::gentoo, installed)
    ^                ^^^^^^^^^^                                                                                                                   

It may be possible to solve this problem by using package.mask to
prevent one of those packages from being selected. However, it is also
possible that conflicting dependencies exist such that they are
impossible to satisfy simultaneously.  If such a conflict exists in
the dependencies of two different packages, then those packages can
not be installed simultaneously. You may want to try a larger value of
the --backtrack option, such as --backtrack=30, in order to see if
that will solve this conflict automatically.

For more information, see MASKED PACKAGES section in the emerge man
page or refer to the Gentoo Handbook.

 * Error: The above package list contains packages which cannot be
 * installed at the same time on the same system.

For more information about Blocked Packages, please refer to the following
section of the Gentoo Linux x86 Handbook (architecture is irrelevant):

Any suggestion on how to go about this?
Perhaps sys-devel/clang-3.6.0 is a dependence that is missing from root's ebuild?
I am pasting below my emerge --info.

Thank you,



# emerge --info '=sci-physics/root-6.02.05-r2::gentoo'
Portage 2.2.14 (python 2.7.9-final-0, default/linux/x86/13.0, gcc-4.8.4, glibc-2.19-r1, 3.14.16-gentoo i686)
                         System Settings
System uname: Linux-3.14.16-gentoo-i686-Intel-R-_Core-TM-_i5-3427U_CPU_@_1.80GHz-with-gentoo-2.2
KiB Mem:     3328828 total,    282688 free
KiB Swap:    3999996 total,   3263584 free
Timestamp of tree: Sat, 18 Apr 2015 06:45:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.2_p53
dev-java/java-config:     2.2.0
dev-lang/perl:            5.20.2
dev-lang/python:          2.7.9-r1, 3.3.5-r1
dev-util/pkgconfig:       0.28-r2
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.13.11
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:            4.5.4, 4.7.3-r1, 4.8.4
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.6
sys-devel/make:           4.1-r1
sys-kernel/linux-headers: 3.18 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo science x-portage
CFLAGS="-O2 -march=i686 -pipe"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
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="-O2 -march=i686 -pipe"
FCFLAGS="-O2 -march=i686 -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 -march=i686 -pipe"
GENTOO_MIRRORS=" rsync://"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
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"
PORTDIR_OVERLAY="/var/lib/layman/science /usr/local/portage"
USE="X a52 aac acl acpi alsa berkdb bzip2 cdr cli consolekit cracklib crypt cxx dbus divx djvu dri dvd emacs flac fortran gdbm gif iconv icu id3 ipv6 jpeg kde kerberos lame midi mmx modules mp3 mp4 mplayer ncurses nls nptl ogg opengl openmp pam pcre policykit pulseaudio qt3support qt4 readline realmedia session sse sse2 ssl svg tcpd tiff udev unicode v4l v4l2 webkit wicd x86 zlib" ABI_X86="32" ALSA_CARDS="hda-intel usb-audio" 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" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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 ublox ubx" INPUT_DEVICES="keyboard mouse evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_US" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel" 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"
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