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Bug 598416 - net-wireless/gnuradio-3.7.10.1[grc] fails to detect dev-python/numpy-1.10.4, configuration checked fails (sometimes)
Summary: net-wireless/gnuradio-3.7.10.1[grc] fails to detect dev-python/numpy-1.10.4, ...
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2016-10-29 08:37 UTC by Anton Bolshakov
Modified: 2018-10-12 10:53 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (build.log,18.26 KB, text/x-log)
2016-10-29 08:38 UTC, Anton Bolshakov
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Anton Bolshakov 2016-10-29 08:37:20 UTC
-- Configuring gr-ctrlport support...
--   Dependency Boost_FOUND = 1
--   Dependency SWIG_FOUND = TRUE
--   Dependency SWIG_VERSION_CHECK = TRUE
--   Dependency ENABLE_GNURADIO_RUNTIME = ON
--   Disabling gr-ctrlport support.
--   Override with -DENABLE_GR_CTRLPORT=ON/OFF
-- Looking for C++ include sys/resource.h
-- Looking for C++ include sys/resource.h - found
-- Loading build date Sat, 29 Oct 2016 08:12:05 into constants...
-- Loading version 3.7.10.1 into constants...
-- Looking for C++ include windows.h
-- Looking for C++ include windows.h - not found
-- TRY_SHM_VMCIRCBUF set to ON.
-- Performing Test HAVE_WNO_UNUSED_BUT_SET_VARIABLE
-- Performing Test HAVE_WNO_UNUSED_BUT_SET_VARIABLE - Success
-- 
-- Configuring gr-blocks support...
--   Dependency Boost_FOUND = 1
--   Dependency ENABLE_GNURADIO_RUNTIME = ON
--   Enabling gr-blocks support.
--   Override with -DENABLE_GR_BLOCKS=ON/OFF
-- 
-- Python checking for python >= 2.5
-- Python checking for python >= 2.5 - found
-- 
-- Python checking for Cheetah >= 2.0.0
-- Python checking for Cheetah >= 2.0.0 - found
-- 
-- Python checking for lxml >= 1.3.6
-- Python checking for lxml >= 1.3.6 - found
-- 
-- Python checking for pygtk >= 2.10.0
No protocol specified
/usr/lib64/python2.7/site-packages/gtk-2.0/gtk/__init__.py:57: GtkWarning: could not open display
  warnings.warn(str(e), _gtk.Warning)
-- Python checking for pygtk >= 2.10.0 - found
-- 
-- Python checking for numpy
-- Python checking for numpy - not found
-- 
-- Configuring gnuradio-companion support...
--   Dependency ENABLE_GNURADIO_RUNTIME = ON
--   Dependency ENABLE_PYTHON = ON
--   Dependency PYTHON_MIN_VER_FOUND = TRUE
--   Dependency CHEETAH_FOUND = TRUE
--   Dependency LXML_FOUND = TRUE
--   Dependency PYGTK_FOUND = TRUE
--   Dependency NUMPY_FOUND = FALSE
CMake Error at cmake/Modules/GrComponent.cmake:75 (message):
  user force-enabled gnuradio-companion but configuration checked failed
Call Stack (most recent call first):
  grc/CMakeLists.txt:45 (GR_REGISTER_COMPONENT)


-- Configuring incomplete, errors occurred!

--------
emerge --info
Portage 2.3.0 (python 2.7.10-final-0, hardened/linux/amd64, gcc-4.9.3, glibc-2.22-r4, 4.7.10-pentoo x86_64)
=================================================================
System uname: Linux-4.7.10-pentoo-x86_64-Intel-R-_Core-TM-_i5-3320M_CPU_@_2.60GHz-with-gentoo-2.2
KiB Mem:     7981204 total,   2842292 free
KiB Swap:    4194300 total,   4192832 free
Timestamp of repository gentoo: Thu, 27 Oct 2016 13:00:01 +0000
sh bash 4.3_p48
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p48::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.22.2::gentoo
dev-lang/python:          2.7.10-r1::gentoo, 3.4.3-r1::gentoo
dev-util/cmake:           3.5.2-r1::gentoo
dev-util/pkgconfig:       0.28-r2::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.21.7::gentoo
sys-apps/sandbox:         2.10-r1::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            4.9.3::gentoo
sys-devel/gcc-config:     1.7.3::gentoo
sys-devel/libtool:        2.4.6::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc:           2.22-r4::gentoo
Repositories:

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

steam-overlay
    location: /var/lib/layman/steam-overlay
    masters: gentoo
    priority: 0

pentoo
    location: /var/lib/layman/pentoo
    masters: gentoo
    priority: 1

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

ABI="amd64"
ABI_X86="64"
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA OPERA-12 NVIDIA-CUDA PUEL AdobeFlash-11.x Google-TOS dlj-1.1 google-chrome Oracle-BCLA-JavaSE Intel-SDP skype-4.0.0.7-copyright baudline"
ACCEPT_PROPERTIES="*"
ACCEPT_RESTRICT="*"
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ARCH="amd64"
AUTOCLEAN="yes"
BOOTSTRAP_USE="cxx unicode internal-glib python_targets_python3_4 python_targets_python2_7 multilib hardened pax_kernel pic xtpax -jit -orc"
CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author"
CAMERAS="ptp2"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CFLAGS_amd64="-m64"
CFLAGS_x32="-mx32"
CFLAGS_x86="-m32"
CHOST="x86_64-pc-linux-gnu"
CHOST_amd64="x86_64-pc-linux-gnu"
CHOST_x32="x86_64-pc-linux-gnux32"
CHOST_x86="i686-pc-linux-gnu"
CLEAN_DELAY="5"
COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog"
COLLISION_IGNORE="/lib/modules/* *.py[co] *$py.class */dropin.cache"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /opt/sonar/conf /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"
CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3"
CXXFLAGS="-march=native -O2 -pipe"
DEFAULT_ABI="amd64"
DISPLAY=":0"
DISTDIR="/usr/portage/distfiles"
EDITOR="/usr/bin/mcedit"
ELIBC="glibc"
EMERGE_DEFAULT_OPTS=" --ask-enter-invalid --keep-going=y --binpkg-respect-use=y --tree --verbose --with-bdeps=y --autounmask=n --buildpkg-exclude "sys-kernel/compat-drivers sys-kernel/ax88179_178a x11-drivers/ati-drivers x11-drivers/nvidia-drivers sys-fs/zfs-kmod sys-kernel/spl                      sys-power/bbswitch pentoo/pentoo-installer x11-drivers/xf86-video-virtualbox app-emulation/virtualbox-guest-additions                     app-emulation/virtualbox-modules app-emulation/vmware-modules app-emulation/open-vm-tools-kmod sys-kernel/genkernel                       sys-kernel/pentoo-sources dev-python/twisted-web net-analyzer/metasploit sci-libs/lapack-reference x11-base/xorg-drivers app-admin/genmenu" --usepkg-exclude "sys-kernel/compat-drivers sys-kernel/ax88179_178a x11-drivers/ati-drivers x11-drivers/nvidia-drivers sys-fs/zfs-kmod sys-kernel/spl                   sys-power/bbswitch pentoo/pentoo-installer x11-drivers/xf86-video-virtualbox app-emulation/virtualbox-guest-additions                     app-emulation/virtualbox-modules app-emulation/vmware-modules app-emulation/open-vm-tools-kmod sys-kernel/genkernel                       sys-kernel/pentoo-sources dev-python/twisted-web net-analyzer/metasploit sci-libs/lapack-reference x11-base/xorg-drivers app-admin/genmenu""
EMERGE_WARNING_DELAY="10"
EPREFIX=""
EROOT="/"
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"
FETCHCOMMAND="wget -t 3 -T 60 --passive-ftp -O "${DISTDIR}/${FILE}" "${URI}""
FETCHCOMMAND_RSYNC="rsync -avP "${URI}" "${DISTDIR}/${FILE}""
FETCHCOMMAND_SFTP="bash -c "x=\${2#sftp://} ; host=\${x%%/*} ; port=\${host##*:} ; host=\${host%:*} ; [[ \${host} = \${port} ]] && port= ; eval \"declare -a ssh_opts=(\${3})\" ; exec sftp \${port:+-P \${port}} \"\${ssh_opts[@]}\" \"\${host}:/\${x#*/}\" \"\$1\"" sftp "${DISTDIR}/${FILE}" "${URI}" "${PORTAGE_SSH_OPTS}""
FETCHCOMMAND_SSH="bash -c "x=\${2#ssh://} ; host=\${x%%/*} ; port=\${host##*:} ; host=\${host%:*} ; [[ \${host} = \${port} ]] && port= ; exec rsync --rsh=\"ssh \${port:+-p\${port}} \${3}\" -avP \"\${host}:/\${x#*/}\" \"\$1\"" rsync "${DISTDIR}/${FILE}" "${URI}" "${PORTAGE_SSH_OPTS}""
FFLAGS="-O2 -pipe"
GCC_SPECS=""
GENTOO_MIRRORS="http://gentoo.gg3.net"
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"
GRUB_PLATFORMS=""
GSETTINGS_BACKEND="dconf"
GUILE_LOAD_PATH="/usr/share/guile/1.8"
HG="/usr/bin/hg"
HOME="/root"
INFOPATH="/usr/share/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.3/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.25.1/info"
INPUT_DEVICES="evdev keyboard mouse synaptics"
INSTALL_MASK="*.la"
IUSE_IMPLICIT="abi_x86_64 prefix prefix-guest"
JAVAC="/etc/java-config-2/current-system-vm/bin/javac"
JAVA_HOME="/etc/java-config-2/current-system-vm"
JDK_HOME="/etc/java-config-2/current-system-vm"
KERNEL="linux"
L10N="en ru"
LANGUAGE=""
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text"
LC_CTYPE="ru_RU.utf8"
LC_MESSAGES="C"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
LDFLAGS_amd64="-m elf_x86_64"
LDFLAGS_x32="-m elf32_x86_64"
LDFLAGS_x86="-m elf_i386"
LESS="-R -M --shift 5"
LESSOPEN="|lesspipe %s"
LIBDIR_amd64="lib64"
LIBDIR_amd64_fbsd="lib64"
LIBDIR_arm="lib"
LIBDIR_arm64="lib64"
LIBDIR_n32="lib32"
LIBDIR_n64="lib64"
LIBDIR_o32="lib"
LIBDIR_ppc="lib32"
LIBDIR_ppc64="lib64"
LIBDIR_s390="lib32"
LIBDIR_s390x="lib64"
LIBDIR_sparc32="lib32"
LIBDIR_sparc64="lib64"
LIBDIR_x32="libx32"
LIBDIR_x86="lib32"
LIBDIR_x86_fbsd="lib32"
LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer"
LINGUAS="en ru"
LOGNAME="root"
LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.pdf=00;32:*.ps=00;32:*.txt=00;32:*.patch=00;32:*.diff=00;32:*.log=00;32:*.tex=00;32:*.doc=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36:"
MAIL="/var/mail/root"
MAKEOPTS="-j4"
MANPAGER="manpager"
MANPATH="/etc/java-config-2/current-system-vm/man:/usr/local/share/man:/usr/share/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.9.3/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.25.1/man:/etc/java-config-2/current-system-vm/man/:/usr/share/postgresql/man/:/usr/share/postgresql-9.5/man/"
MSF_DATABASE_CONFIG="/usr/lib/metasploit/config/database.yml"
MSF_LOCAL_LIB="/usr/lib/metasploit/lib/metasm"
MSF_ROOT="/usr/lib/metasploit"
MULTILIB_ABIS="amd64 x86"
MULTILIB_STRICT_DENY="64-bit.*shared object"
MULTILIB_STRICT_DIRS="/lib32 /lib /usr/lib32 /usr/lib /usr/kde/*/lib32 /usr/kde/*/lib /usr/qt/*/lib32 /usr/qt/*/lib /usr/X11R6/lib32 /usr/X11R6/lib"
MULTILIB_STRICT_EXEMPT="(perl5|gcc|gcc-lib|binutils|eclipse-3|debug|portage|udev|systemd|clang|python-exec)"
MULTIOSDIRS="../lib64:../lib32"
NETBEANS="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml"
OFFICE_IMPLEMENTATION="libreoffice"
OLDPWD="/var/tmp/portage"
OPENCL_PROFILE="intel"
OPENGL_PROFILE="xorg-x11"
PAGER="/usr/bin/less"
Comment 1 Anton Bolshakov 2016-10-29 08:38:22 UTC
Created attachment 451818 [details]
build.log
Comment 2 Anton Bolshakov 2016-10-29 08:49:51 UTC
somehow, it fails to detect dev-python/numpy-1.10.4

I have upgraded it to the version ~1.11.2-r1 and gnuradio compiled properly:
-- Python checking for numpy
-- Python checking for numpy - found

So the current stable version (1.10.4) could be buggy.
Comment 3 Rick Farina (Zero_Chaos) gentoo-dev 2016-10-30 02:29:02 UTC
odd, I've only hit this problem on x86, and only once.  Since I build two profiles for each arch, that means this has a roughly 25% chance of failing (of course I replicated ~4 times in a row and then it worked... ugh)

Open to suggestions, likely suggestion is upstream bug though.  Anyone have a better explanation though?
Comment 4 Rick Farina (Zero_Chaos) gentoo-dev 2017-01-23 16:05:58 UTC
Science, any ideas why the stable version of numpy may not be detected reliably? is this a gnuradio bug or something known and numpy related?
Comment 5 Alexey Guzeev 2018-10-12 10:53:36 UTC
A possible reason (seen in the wild more than once) is this: numpy depends on sci-libs/lapack-reference (also cblas-reference and blas-reference). [Much later] after numpy is installed, gcc is updated, together with fortran, providing the system with libfortran.so.4* libraries. Once old version of gcc is deinstalled/cleaned, portage apparently does not correctly track references to the now missing library libfortran.so.3* (albeit it does excellent job doing that for other libraries for like a decade I believe). That situation can be easily diagnosed with the following commands:

$ python
> import numpy

if you got a stacktrace, go recompiling numpy and/or its dependencies individually (the stacktrace will suggest which ones to blame) with emerge -av1; once the import works, remerge gnuradio and you will get the desired bin/gnuradio-companion (if numpy was the only problem, yet at the moment gnuradio stays to be a very fragile build dependecies wise).