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Bug 593310

Summary: sci-libs/shogun-4.1.0 - CMake Error: The following variables are used in this project, but they are set to NOTFOUND. - HDF5_hdf5_cpp_LIBRARY
Product: Gentoo Linux Reporter: Juergen Rose <rose>
Component: Current packagesAssignee: Gentoo Science Related Packages <sci>
Status: RESOLVED FIXED    
Severity: normal    
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Attachments: build.log

Description Juergen Rose 2016-09-09 19:08:58 UTC 
Created attachment 445322 [details]
build.log

'MAKEOPTS=-j1 emerge -v1 shogun' fails with:
...
Compiler flags:
C               -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated -march=native -O2 -pipe  -fopenmp
C++             -std=c++11 -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated -march=native -O2 -pipe  -fopenmp
Linker flags:
Executable       -Wl,-O1 -Wl,--as-needed 
Module           -Wl,-O1 -Wl,--as-needed
Shared           -Wl,-O1 -Wl,--as-needed

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
HDF5_hdf5_cpp_LIBRARY
    linked by target "shogun" in directory /var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0/src/shogun

-- Configuring incomplete, errors occurred!
See also "/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build/CMakeFiles/CMakeOutput.log".
See also "/var/tmp/portage/sci-libs/shogun-4.1.0/work/shogun-4.1.0_build/CMakeFiles/CMakeError.log".
 * ERROR: sci-libs/shogun-4.1.0::gentoo failed (configure phase):



This Bug is similar to 
https://bugs.gentoo.org/show_bug.cgi?id=588850 .





root@condor:/root(69)# emerge --info '=sci-libs/shogun-4.1.0::gentoo'
Portage 2.3.0 (python 2.7.12-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.23-r2, 4.7.2-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.7.2-gentoo-x86_64-Intel-R-_Core-TM-2_CPU_6600_@_2.40GHz-with-gentoo-2.3
KiB Mem:     7068408 total,    520236 free
KiB Swap:   25173848 total,  24385960 free
Timestamp of repository gentoo: Fri, 09 Sep 2016 04:00:02 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
distcc 3.2rc1 x86_64-pc-linux-gnu [disabled]
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:          2.7.12-r100::sage-on-gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/cmake:           3.6.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.21.7::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.12.6-r1::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.26.1::gentoo
sys-devel/gcc:            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: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage_condor
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

local
    location: /usr/local/portage
    masters: gentoo
    priority: 0

g-cpan
    location: /var/lib/cpan
    masters: gentoo
    priority: 1

sage-on-gentoo
    location: /var/lib/layman/sage-on-gentoo
    masters: gentoo science
    priority: 50

science
    location: /var/lib/layman/science
    masters: gentoo
    priority: 50

sunrise
    location: /var/lib/layman/sunrise
    masters: gentoo
    priority: 50

x11
    location: /var/lib/layman/x11
    masters: gentoo
    priority: 50

Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /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/php/apache2-php7.0/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php7.0/ext-active/ /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="/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 xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ rsync://ftp.fi.muni.cz/pub/linux/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo rsync://gd.tuwien.ac.at/opsys/linux/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo http://gentoo.oregonstate.edu"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j3"
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="64bit R X Xaw3d a52 aac accessibility acl acpi admin afs alsa amd64 amr ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audacious audiofile aufs automap automount barcode bash-completion berkdb blas blast bluetooth bluray boost branding btrfs bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cilk cli cmake collada consolekit contrib cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia digitalradio djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples excel exif expat extensions extra extras faac faad fam fbcon fbcondecor ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx ftp fuse gcj gd gdal gdbm gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jadetex java jbig jit john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libgda libkms libnotify libsamplerate lirc live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg opencl opencv openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm pstricks pulseaudio python q16 q32 qemu qhull qml qt3support qt4 qt5 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool rtlsdr sage samba sasl schroedinger science sdk sdl seccomp secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tbb tcl tcpd tex tex4ht theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l v4l2 vaapi vala valgrind vdpau video vim-syntax virt-network virtualbox visio vorbis vpx vtk wav wayland webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xetex xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zsh-completion zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog sensors thermal" CPU_FLAGS_X86="mmx mmxext sse sse2 sse3 ssse3" CURL_SSL="nss" DVB_CARDS="tda10045 tda10046lifeview" 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" KERNEL="linux" L10N="de en fr ru" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd SureElec" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="radeon radeonsi" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

=================================================================
                        Package Settings
=================================================================

sci-libs/shogun-4.1.0::gentoo was built with the following:
USE="examples lua python -R -doc -mono -octave -ruby -static-libs -test" ABI_X86="64" PYTHON_SINGLE_TARGET="python2_7 -python3_4 -python3_5" PYTHON_TARGETS="python2_7 python3_4 -python3_5"




root@condor:/root(70)# emerge -pqv '=sci-libs/shogun-4.1.0::gentoo'
[ebuild   R   ] sci-libs/shogun-4.1.0  USE="examples lua python -R -doc -mono -octave -ruby -static-libs {-test}" PYTHON_SINGLE_TARGET="python2_7 -python3_4 -python3_5" PYTHON_TARGETS="python2_7 python3_4 -python3_5"
Comment 1 Juergen Rose 2016-09-17 07:31:35 UTC 
After downgrading to cmake-3.5.2 this issue disappeared.
Comment 2 David Seifert gentoo-dev 2017-02-04 21:09:26 UTC 
Fixed for me in 5.0.0, reopen if issue persists with latest version.

commit 8d85f22fd38976093c4b3d3a9f5d30954e689c14
Author: David Seifert <soap@gentoo.org>
Date:   Sat Feb 4 22:02:10 2017 +0100

    sci-libs/shogun: Version bump to 5.0.0
    
    Gentoo-bug: 550134, 570014, 587324, 593310,
                602534, 604670, 606770, 607122