Bug 588706 – sci-libs/avogadrolibs-0.8.0 : CMake Error at avogadro/.../CMakeLists.txt:5 (include_directories):

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2016-07-12 17:18:07 UTC]

-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /usr/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.8.15.1") 
CMake Error at avogadro/io/CMakeLists.txt:5 (include_directories):
  include_directories given empty-string as include directory.




$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-plasma-unstable_20160710-112417) at a hardened host acting as a tinderbox.

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

  make.conf: USE="pax_kernel xtpax -cdinstall -oci8 -bindist btrfs cgi cups -egl emacs ffmpeg gles gnomecanvas -gpg gstreamer gui gzip haptic imlib ipv6 isag -logrotate minimal -mng -mysql odbc -opencv pam pcre16 php policykit -pulseaudio rendering scrypt source ssh svg system-ffmpeg -system-icu system-jpeg system-llvm -szip timidity tools vaapi vala x265 -xkb zenmap -ziffy"

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

Portage 2.3.0 (python 3.4.4-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-5.4.0, glibc-2.23-r2, 4.6.3-hardened-r2 x86_64)
=================================================================
System uname: Linux-4.6.3-hardened-r2-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16155840 total,   1978820 free
KiB Swap:   16777212 total,  16716712 free
Timestamp of repository gentoo: Tue, 12 Jul 2016 15:42:46 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p46::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.11-r2::gentoo, 3.4.4::gentoo
dev-util/cmake:           3.6.0::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.2-r1::gentoo
sys-apps/openrc:          0.21.2::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.10.3-r2::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 5.4.0::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: 4.6::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

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

local
    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/rancid/.cloginrc"
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=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--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 berkdb bluetooth branding btrfs bzip2 cairo cdda cdr cgi cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emacs emboss encode exif fam ffmpeg firefox flac fortran gdbm gif glamor gles gnomecanvas gpm gstreamer gtk gui gzip haptic iconv imlib ipv6 isag jpeg kde kipi lcms ldap libnotify mad minimal mmx mmxext modules mp3 mp4 mpeg multilib ncurses nls nptl odbc ogg opengl openmp pam pango pax_kernel pcre pcre16 pdf phonon php plasma png policykit ppds qml qt3support qt4 qt5 readline rendering scrypt sdl seccomp semantic-desktop session source spell sse sse2 ssh ssl startup-notification svg system-ffmpeg system-jpeg system-llvm tcpd tiff timidity tools truetype udev udisks unicode upower usb vaapi vala vorbis widgets wxwidgets x264 x265 xattr xcb xcomposite xinerama xml xscreensaver xtpax xv xvid zenmap 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" 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_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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 2016-07-12 17:18:10 UTC]

Created attachment 440496 [details]
CMakeOutput.log

[Comment 2 Toralf Förster 2016-07-12 17:18:14 UTC]

Created attachment 440498 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2016-07-12 17:18:17 UTC]

Created attachment 440500 [details]
environment

[Comment 4 Toralf Förster 2016-07-12 17:18:21 UTC]

Created attachment 440502 [details]
sci-libs:avogadrolibs-0.8.0:20160712-164007.log

[Comment 5 milan hodoscek 2017-05-26 12:43:05 UTC]

Created attachment 474364 [details, diff]
fixes avogadrolibbs-0.8.0 & 0.9.0 to compile with gcc-6 & gcc-7

fixes a cmake file to compile with gcc-6 and gcc-7

This patch fixes the build of avogadrolibs, I think both 0.8.0 and 0.9.0 versions. However there is a problem with the cmake refering to /usr/lib64/libjson.a and /usr/lib64/libjsoncpp.a

The/usr/lib64/libjson.a problem may be fixed by making a link to it from libjson-c.a

The /usr/lib64/libjsoncpp.a problem may be fixed by deleting the line -DBUILD_STATIC_LIBS=OFF in jsoncpp-1.8.0.build

Then also avogadro2 will build

[Comment 6 Rolf Eike Beer 2017-12-18 20:19:35 UTC]

See also bug 619544. As I said there:

The code should use CMAKE_C_COMPILER_VERSION or CMAKE_CXX_COMPILER_VERSION (depending on the language here) instead. These variables are determined by CMake itself and are available since CMake 2.8.10. No need to parse anything from the compiler.

[Comment 7 Larry the Git Cow 2018-04-08 09:55:04 UTC]

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

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9a80747f1a93efa92be9944ba77feafd4650c7ea

commit 9a80747f1a93efa92be9944ba77feafd4650c7ea
Author:     Andreas Sturmlechner <[e-mail]>
AuthorDate: 2018-04-07 19:01:22 +0000
Commit:     Andreas Sturmlechner <[e-mail]>
CommitDate: 2018-04-08 09:53:52 +0000

    sci-libs/avogadrolibs: Add 1.91.0_p20180406 snapshot
    
    Closes: https://bugs.gentoo.org/645248
    Closes: https://bugs.gentoo.org/649862
    Closes: https://bugs.gentoo.org/588706
    Closes: https://bugs.gentoo.org/577214
    Package-Manager: Portage-2.3.28, Repoman-2.3.9

 sci-libs/avogadrolibs/Manifest                     |  1 +
 .../avogadrolibs-1.91.0_pre20180406.ebuild         | 71 ++++++++++++++++++++++
 ...gadrolibs-1.91.0_pre20180406-underlinking.patch | 18 ++++++
 sci-libs/avogadrolibs/metadata.xml                 |  3 +-
 4 files changed, 92 insertions(+), 1 deletion(-)