Bug 604604 – sci-chemistry/avogadro-1.1.1 : /.../Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Toralf Förster 2017-01-04 09:15:49 UTC]

In file included from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1_build/libavogadro/include/avogadro/primitive.h:34:0,
                 from /var/tmp/portage/sci-chemistry/avogadro-1.1.1/work/avogadro-1.1.1/libavogadro/src/colors/elementcolor.cpp:27:
/usr/include/eigen3/Eigen/Core:321:2: error: #error Eigen2-support is only available up to version 3.2. Please go to "http://eigen.tuxfamily.org/index.php?title=Eigen2" for further information
 #error Eigen2-support is only available up to version 3.2. Please go to "http:/
  ^
make[2]: *** [libavogadro/src/colors/CMakeFiles/elementcolor.dir/build.make:68: libavogadro/src/colors/CMakeFiles/elementcolor.dir/elementcolor.cpp.o] Error 1

  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named gnome-systemd-unstable_20161228-205023) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------
  from make.conf:
USE="  pax_kernel xtpax -cdinstall -oci8 -bindist ssp avformat btrfs clang dvb -eglfs fax ftp gif -gtk help -infinality inifile mpeg2 mysqli ois osc pam -qt5 semantic-desktop sqlite -system-libevent -thinkpad usbredir vorbis x265 -xcb -xz"

gcc-config -l:
 [1] x86_64-pc-linux-gnu-5.4.0 *
llvm-config --version:
3.9.1
Available Java Virtual Machines:
  [1]   icedtea-bin-8  system-vm
Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python3.5 (fallback)
  [3]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby21 (with Rubygems) *
java-config:
The following VMs are available for generation-2:
*)	IcedTea JDK 3.2.0 [icedtea-bin-8]
  -----------------------------------------------------------------



$ cat emerge-info.txt
Portage 2.3.3 (python 3.4.5-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-5.4.0, glibc-2.24, 4.8.15-hardened x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.8.15-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3
KiB Mem:    65285560 total,   3358696 free
KiB Swap:   67108860 total,  67091628 free
Timestamp of repository gentoo: Tue, 03 Jan 2017 20:02:48 +0000
sh bash 4.4_p5-r1
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.4_p5-r1::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.1_rc4::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/cmake:           3.7.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.23::gentoo
sys-apps/sandbox:         2.10-r3::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo, 2.27::gentoo
sys-devel/gcc:            5.4.0-r2::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.9::gentoo (virtual/os-headers)
sys-libs/glibc:           2.24::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: 1

tinderbox
    location: /tmp/tb/data/portage
    masters: gentoo
    priority: 2

local
    location: /usr/local/portage
    masters: gentoo
    priority: 99

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native -Wall"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/omega.conf /etc/stunnel/stunnel.conf /opt/openfire/resources/security/ /usr/lib64/fax /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf /usr/share/qpsmtpd/plugins /var/lib/hsqldb /var/spool/fax/etc"
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"
CXXFLAGS="-O2 -pipe -march=native"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 avformat berkdb bluetooth branding btrfs bzip2 cairo cdda cdr clang cli colord cracklib crypt cups cxx dbus dri dts dvb dvd dvdr eds emboss encode evo exif fam fax firefox flac fortran ftp gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpm gstreamer help iconv inifile introspection ipv6 jpeg lcms ldap libnotify libsecret mad mmx mmxext mng modules mp3 mp4 mpeg mpeg2 multilib mysqli nautilus ncurses nls nptl ogg ois opengl openmp osc pam pango pax_kernel pcre pdf png policykit ppds pulseaudio qt3support qt4 readline sdl seccomp semantic-desktop session spell sqlite sse sse2 ssl ssp startup-notification svg systemd tcpd tiff tracker truetype udev udisks unicode upower usb usbredir vorbis wxwidgets x264 x265 xattr xml xtpax xv xvid zlib" ABI_X86="64" ALSA_CARDS="hda-intel" 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="evdev synaptics" KERNEL="linux" L10N="cak ff sk zh" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" 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:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Toralf Förster 2017-01-04 09:15:52 UTC]

Created attachment 458644 [details]
emerge-history.txt

[Comment 2 Toralf Förster 2017-01-04 09:15:55 UTC]

Created attachment 458646 [details]
environment

[Comment 3 Toralf Förster 2017-01-04 09:15:58 UTC]

Created attachment 458648 [details]
etc.portage.tbz2

[Comment 4 Toralf Förster 2017-01-04 09:16:01 UTC]

Created attachment 458650 [details]
sci-chemistry:avogadro-1.1.1:20170103-214520.log

[Comment 5 Attila Tóth 2017-01-24 23:14:49 UTC]

Looks like upstream is having difficulties:
https://github.com/cryos/avogadro/issues/842

[Comment 6 Juergen Rose 2017-03-15 13:20:17 UTC]

Any news?

[Comment 7 Attila Tóth 2017-12-25 22:54:21 UTC]

(In reply to Juergen Rose from comment #6)
> Any news?

https://bugs.gentoo.org/594630

[Comment 8 Larry the Git Cow 2018-01-16 13:05:08 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=de6524a1b675617ebcf587d9fb5ba515eb675026

commit de6524a1b675617ebcf587d9fb5ba515eb675026
Author:     Andreas Sturmlechner <[e-mail]>
AuthorDate: 2018-01-16 13:03:09 +0000
Commit:     Andreas Sturmlechner <[e-mail]>
CommitDate: 2018-01-16 13:04:51 +0000

    sci-chemistry/avogadro: 1.2.0_p20170207 version bump
    
    Thanks-to: Michelangelo Scopelliti <[e-mail]>
    Closes: https://bugs.gentoo.org/594630
    Closes: https://bugs.gentoo.org/604604
    Package-Manager: Portage-2.3.19, Repoman-2.3.6

 sci-chemistry/avogadro/Manifest                    |  1 +
 .../avogadro/avogadro-1.2.0_p20170207.ebuild       | 80 ++++++++++++++++++++++
 .../avogadro/files/avogadro-1.2.0-numpy.patch      | 13 ++++
 3 files changed, 94 insertions(+)