With the python use flag, sci-libs/grib_api-1.9.16 fails to compile in configuration phase with the error message "checking whether numpy is installed... no configure: error: NumPy is not installed. Use --disable-numpy if you want to disable Numpy from the build." importing numpy from python 3 and 2 works fine as numpy is installed. If I do eselect python set python2.7 I can compile the package, switch back to python 3.2 and grib_api works fine. emerge --info: Portage 2.2.0_alpha142 (default/linux/amd64/10.0, gcc-4.5.4, glibc-2.15-r3, 3.6.0 x86_64) ================================================================= System uname: Linux-3.6.0-x86_64-Intel-R-_Core-TM-_i7_CPU_860_@_2.80GHz-with-gentoo-2.1 Timestamp of tree: Tue, 27 Nov 2012 11:00:01 +0000 ld GNU ld (GNU Binutils) 2.22 ccache version 3.1.8 [enabled] app-shells/bash: 4.2_p37 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.3-r2, 3.2.3 dev-util/ccache: 3.1.8 dev-util/cmake: 2.8.9 dev-util/pkgconfig: 0.27.1 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.11.5 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.11.6 sys-devel/binutils: 2.22-r1 sys-devel/gcc: 4.3.6-r1, 4.5.4 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 3.6 (virtual/os-headers) sys-libs/glibc: 2.15-r3 Repositories: gentoo science sunrise swegener pentoo graph-tool-overlay ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -mtune=native -pipe -fomit-frame-pointer" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.4/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="-O2 -march=native -mtune=native -pipe -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs ccache 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" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/swegener /var/lib/layman/pentoo /home/scholz/graphtooloverlay" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit R X aac acl acpi alsa amd64 applet audio avahi bash-completion berkdb blas boost brasero bzip2 cairo cdda cddb cdio cdparanoia cdr cdrom cli clisp connection-sharing consolekit cracklib crypt cups cxx daap dap dbus declarative detex device-mapper djvu dmx dnotify dri dvd ebook edit elisp emacs emf encode exif extra extras fat ffmpeg fftw firefox flac fontconfig foomaticdb fortran fuse gcj gconf gd gdbm gdu ginac git gmail gmp gnome gnome-keyring gnome-print gnuplot gnus gnutls gpg gpm gpu graphics graphite gsl gstreamer gtk guile gzip gzip-el h323 hdf hdf5 humanities iconv id3 id3tag inkjar inotify ipod ipv6 jabber jpeg jpeg2k kde kpathsea kvm lame lapack latex libnotify lua lzma mathml matroska mdnsresponder-compat meanwhile mmx mng modules mp3 mp4 mpeg mplayer mudflap multilib nautilus ncurses netcdf networking new-login nls nptl nsplugin ntfsprogs ogg openexr opengl openmp openssl openstreetmap pam patented pcre pdf pgf plotutils plugins png pnm policykit posix postgres pppd preview-latex pstoedit pstricks publishers pulseaudio qhull qt3support qt4 quicktime raw rdesktop readline reiser4 reiserfs romio samba samba4 schroedinger science scrobbler sdl sdl-image server session sip sipim smp speex sql sqlite sqlite3 sse sse2 sse3 sse4 sse4a sse5 ssl ssse3 stars startup-notification subtitles subversion svg svgz syslog tcpd telepathy tex tex4ht theora thesaurus threads tiff tk toolame toolbar toolkit-scroll-bars tools truetype twolame udev umfpack unicode usb video vnc vorbis wav webdav webkit wmf wxwidgets x264 xcb xcf xcomposite xface xft xine xinerama xml xrandr xterm xulrunner xv xvid xvmc yahoo youtube zeroconf zip zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" 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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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 ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="fbdev radeon vesa fglrx" 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON Reproducible: Always Steps to Reproduce: 1. USE="python" emerge grib_api # Fails 2. eselect python set python2.7 3. USE="python" emerge grib_api # Works, and the library works after eselect python3.2 again
I should probably add that it is stated on grib_api's wiki that grib_api does not work with python3. After install on python2 and eselecting back to python3, the package still works fine from python2, though. Anders
Please attach the entire build log to this bug report.
(In reply to comment #2) > Please attach the entire build log to this bug report. Here it is: * Package: sci-libs/grib_api-1.9.16 * Repository: gentoo * Maintainer: sci@gentoo.org * USE: amd64 elibc_glibc fortran jpeg2k kernel_linux multilib netcdf openmp png python userland_GNU * FEATURES: ccache preserve-libs sandbox >>> Unpacking source... >>> Unpacking grib_api-1.9.16.tar.gz to /var/tmp/portage/sci-libs/grib_api-1.9.16/work >>> Source unpacked in /var/tmp/portage/sci-libs/grib_api-1.9.16/work >>> Preparing source in /var/tmp/portage/sci-libs/grib_api-1.9.16/work/grib_api-1.9.16 ... * Applying grib_api-1.9.9-ieeefloat.patch ... [ ok ] * Applying grib_api-1.9.16-autotools.patch ... [ ok ] * Applying grib_api-1.9.16-jpeg2k.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-libs/grib_api-1.9.16/work/grib_api-1.9.16' ... * Running libtoolize --install --copy --force --automake ... [ ok ] * Running aclocal ... [ ok ] * Running autoconf ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy ... [ ok ] * Running elibtoolize in: grib_api-1.9.16/config/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... * Applying as-needed/2.2.6 patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/grib_api-1.9.16/work/grib_api-1.9.16 ... * econf: updating grib_api-1.9.16/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating grib_api-1.9.16/config/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --disable-dependency-tracking --without-perl --enable-jpeg --with-openjpeg=system --without-jasper --enable-fortran --enable-omp-packing --enable-python --enable-numpy --disable-static --with-netcdf=/usr --with-png-support 1.9.16 configuring grib_api 1.9.16 checking whether build environment is sane... yes checking for a BSD-compatible install... /usr/bin/install -c checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for x86_64-pc-linux-gnu-xlc_r... no checking for x86_64-pc-linux-gnu-xlc... no checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... none checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking for bison... bison -y checking for flex... flex checking lex output file root... lex.yy checking lex library... -lfl checking whether yytext is a pointer... yes checking for x86_64-pc-linux-gnu-pgf90... no checking for x86_64-pc-linux-gnu-pgf77... no checking for x86_64-pc-linux-gnu-xlf... no checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran checking whether we are using the GNU Fortran 77 compiler... yes checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes checking for x86_64-pc-linux-gnu-pgf90... no checking for x86_64-pc-linux-gnu-xlf90... no checking for x86_64-pc-linux-gnu-gfortran... x86_64-pc-linux-gnu-gfortran checking whether we are using the GNU Fortran compiler... yes checking whether x86_64-pc-linux-gnu-gfortran accepts -g... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... (cached) x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/nm -B output from x86_64-pc-linux-gnu-gcc object... ok checking for sysroot... no checking for x86_64-pc-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for x86_64-pc-linux-gnu-gfortran option to produce PIC... -fPIC checking if x86_64-pc-linux-gnu-gfortran PIC flag -fPIC works... yes checking if x86_64-pc-linux-gnu-gfortran static flag -static works... yes checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-gfortran supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-gfortran linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if Fortran 90 compiler capitalizes .mod filenames... no checking if double and float are ieee big endian... no checking if double and float are ieee little endian... yes checking if Big Endian... no checking if inline in C... yes checking if bus error on unaligned pointers... no checking for posix_memalign... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for nc_open in -lnetcdf... yes checking for jas_stream_memopen in -ljasper... yes checking for opj_image_create in -lopenjpeg... yes checking for PNG ... checking png.h usability... yes checking png.h presence... yes checking for png.h... yes checking for png_read_png in -lpng... yes checking if PNG support package is complete... yes checking for a Python interpreter with version >= 2.5... python checking for python... /usr/bin/python checking for python version... 3.2 checking for python platform... linux2 checking for python script directory... ${prefix}/lib64/python3.2/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python3.2/site-packages checking whether numpy is installed... no configure: error: NumPy is not installed. Use --disable-numpy if you want to disable Numpy from the build. !!! Please attach the following file when seeking support: !!! /var/tmp/portage/sci-libs/grib_api-1.9.16/work/grib_api-1.9.16/config.log * ERROR: sci-libs/grib_api-1.9.16 failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 93: Called src_configure * environment, line 2838: Called econf '--without-perl' '--enable-jpeg' '--with-openjpeg=system' '--without-jasper' '--enable-fortran' '--enable-omp-packing' '--enable-python' '--enable-numpy' '--disable-static' '--with-netcdf=/usr' '--with-png-support' * phase-helpers.sh, line 501: Called die * The specific snippet of code: * die "econf failed" * * If you need support, post the output of `emerge --info '=sci-libs/grib_api-1.9.16'`, * the complete build log and the output of `emerge -pqv '=sci-libs/grib_api-1.9.16'`. * The complete build log is located at '/var/tmp/portage/sci-libs/grib_api-1.9.16/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/grib_api-1.9.16/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/grib_api-1.9.16/work/grib_api-1.9.16' * S: '/var/tmp/portage/sci-libs/grib_api-1.9.16/work/grib_api-1.9.16'
+ 29 Nov 2012; Sébastien Fabbro <bicatali@gentoo.org> + -files/grib_api-1.9.5-32bit.patch, -files/grib_api-1.9.5-autotools.patch, + -files/grib_api-1.9.9-autotools.patch, grib_api-1.9.16.ebuild: + Do not build for python-3 (bug #445047) +
