'emerge h5py' fails with root@impala:/usr/local/portage/sci-libs(275)# MAKEOPTS=-j1 emerge -v1 h5py ... x86_64-pc-linux-gnu-gcc -march=amdfam10 -O2 -pipe -fno-strict-aliasing -fPIC -DH5_USE_16_API -I/var/tmp/portage/dev-python/h5py-2.3.1/work/h5py-2.3.1/lzf -I/usr/lib64/python3.3/site-packages/numpy/core/include -I/usr/include/python3.3 -c h5py/defs.c -o /var/tmp/portage/dev-python/h5py-2.3.1/work/h5py-2.3.1-python3_3/temp.linux-x86_64-3.3/h5py/defs.o In file included from /usr/lib64/python3.3/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/lib64/python3.3/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/lib64/python3.3/site-packages/numpy/core/include/numpy/arrayobject.h:4, from h5py/api_compat.h:26, from h5py/defs.c:354: /usr/lib64/python3.3/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from h5py/defs.c:354:0: h5py/api_compat.h:21:21: error: conflicting types for ‘PyMPI_MPI_Message’ #define MPI_Message PyMPI_MPI_Message ^ h5py/api_compat.h:20:15: note: previous declaration of ‘PyMPI_MPI_Message’ was here typedef void *PyMPI_MPI_Message; ^ h5py/defs.c: In function ‘__pyx_f_4h5py_4defs_H5Lunpack_elink_val’: h5py/defs.c:22966:11: warning: passing argument 4 of ‘H5Lunpack_elink_val’ from incompatible pointer type [enabled by default] __pyx_t_8 = H5Lunpack_elink_val(__pyx_v_ext_linkval, __pyx_v_link_size, __pyx_v_flags, __pyx_v_filename, __pyx_v_obj_path); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L7_error;} ^ In file included from /usr/include/H5Opublic.h:33:0, from /usr/include/H5Apublic.h:24, from /usr/include/hdf5.h:25, from h5py/api_compat.h:27, from h5py/defs.c:354: /usr/include/H5Lpublic.h:193:15: note: expected ‘const char **’ but argument is of type ‘char **’ H5_DLL herr_t H5Lunpack_elink_val(const void *ext_linkval/*in*/, size_t link_size, ^ h5py/defs.c:22966:11: warning: passing argument 5 of ‘H5Lunpack_elink_val’ from incompatible pointer type [enabled by default] __pyx_t_8 = H5Lunpack_elink_val(__pyx_v_ext_linkval, __pyx_v_link_size, __pyx_v_flags, __pyx_v_filename, __pyx_v_obj_path); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L7_error;} ^ In file included from /usr/include/H5Opublic.h:33:0, from /usr/include/H5Apublic.h:24, from /usr/include/hdf5.h:25, from h5py/api_compat.h:27, from h5py/defs.c:354: /usr/include/H5Lpublic.h:193:15: note: expected ‘const char **’ but argument is of type ‘char **’ H5_DLL herr_t H5Lunpack_elink_val(const void *ext_linkval/*in*/, size_t link_size, ^ h5py/defs.c: In function ‘__pyx_f_4h5py_4defs_H5Pset_fapl_multi’: h5py/defs.c:33217:11: warning: passing argument 4 of ‘H5Pset_fapl_multi’ from incompatible pointer type [enabled by default] __pyx_t_8 = H5Pset_fapl_multi(__pyx_v_fapl_id, __pyx_v_memb_map, __pyx_v_memb_fapl, __pyx_v_memb_name, __pyx_v_memb_addr, __pyx_v_relax); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1457; __pyx_clineno = __LINE__; goto __pyx_L7_error;} ^ In file included from /usr/include/hdf5.h:47:0, from h5py/api_compat.h:27, from h5py/defs.c:354: /usr/include/H5FDmulti.h:36:15: note: expected ‘const char * const*’ but argument is of type ‘char **’ H5_DLL herr_t H5Pset_fapl_multi(hid_t fapl_id, const H5FD_mem_t *memb_map, ^ h5py/defs.c: In function ‘__pyx_f_4h5py_4defs_H5Pget_cache’: h5py/defs.c:33683:11: warning: passing argument 3 of ‘H5Pget_cache’ from incompatible pointer type [enabled by default] __pyx_t_8 = H5Pget_cache(__pyx_v_plist_id, __pyx_v_mdc_nelmts, __pyx_v_rdcc_nelmts, __pyx_v_rdcc_nbytes, __pyx_v_rdcc_w0); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 1479; __pyx_clineno = __LINE__; goto __pyx_L7_error;} ^ In file included from /usr/include/hdf5.h:36:0, from h5py/api_compat.h:27, from h5py/defs.c:354: /usr/include/H5Ppublic.h:314:15: note: expected ‘size_t *’ but argument is of type ‘int *’ H5_DLL herr_t H5Pget_cache(hid_t plist_id, ^ h5py/defs.c: In function ‘__pyx_f_4h5py_4defs_H5Sselect_elements’: h5py/defs.c:53474:11: warning: passing argument 4 of ‘H5Sselect_elements’ from incompatible pointer type [enabled by default] __pyx_t_8 = H5Sselect_elements(__pyx_v_space_id, __pyx_v_op, __pyx_v_num_elements, __pyx_v_coord); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L7_error;} ^ In file included from /usr/include/hdf5.h:38:0, from h5py/api_compat.h:27, from h5py/defs.c:354: /usr/include/H5Spublic.h:128:15: note: expected ‘const hsize_t *’ but argument is of type ‘hsize_t **’ H5_DLL herr_t H5Sselect_elements(hid_t space_id, H5S_seloper_t op, ^ error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1 * ERROR: dev-python/h5py-2.3.1::gentoo failed (install phase): ... root@impala:/usr/local/portage/sci-libs(277)# emerge --info '=dev-python/h5py-2.3.1::gentoo' Portage 2.2.10 (default/linux/amd64/13.0, gcc-4.8.3, glibc-2.19-r1, 3.15.6-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.15.6-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2 KiB Mem: 8164824 total, 3439108 free KiB Swap: 50331640 total, 49371260 free Timestamp of tree: Wed, 23 Jul 2014 05:30:01 +0000 ld GNU ld (GNU Binutils) 2.24 app-shells/bash: 4.2_p47 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.7, 3.3.5, 3.4.1 dev-util/cmake: 2.8.12.2-r1 dev-util/pkgconfig: 0.28-r1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.10.3, 1.11.6, 1.12.6, 1.14.1 sys-devel/binutils: 2.24-r3 sys-devel/gcc: 4.8.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2-r1 sys-devel/make: 4.0-r1 sys-kernel/linux-headers: 3.15 (virtual/os-headers) sys-libs/glibc: 2.19-r1 Repositories: gentoo x11 science sunrise sage-on-gentoo x-portage g-cpan g-octave 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=amdfam10 -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /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-php5.5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.5/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=amdfam10 -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="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" 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" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage_impala" PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/sage-on-gentoo /usr/local/portage /var/lib/cpan /var/lib/g-octave" USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac accessibility acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print 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 ithreads jabber jadetex java java6 jbig jit john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy nvidia obex objc ocaml ocr octave odbc ofa ogdi ogg 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 python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl 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 stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode usb utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx vtk wav webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" 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" 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" 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" CURL_SSL="nss" DRACUT_MODULES="caps lvm mdraid 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 ublox ubx" INPUT_DEVICES="keyboard mouse evdev void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de 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="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" 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, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON root@impala:/usr/local/portage/sci-libs(278)# emerge -pqv '=dev-python/h5py-2.3.1::gentoo' [ebuild U ] dev-python/h5py-2.3.1 [2.2.1-r1] USE="examples mpi {-test}" PYTHON_TARGETS="python2_7 python3_3 -python3_2" root@impala:/usr/local/portage/sci-libs(279)# qlist -Iv numpy dev-python/numpy-1.8.1 dev-python/numpydoc-0.4-r1 root@impala:/usr/local/portage/sci-libs(280)# qlist -Iv hdf5 sci-libs/hdf5-1.8.12
Hi Jurgen, I've fixed it this morning. Should be fine after next sync. 23 Jul 2014; Kacper Kowalik <xarthisius@gentoo.org> h5py-2.3.1.ebuild: Make sure that --mpi is passed to setup.py during each stage 23 Jul 2014; Kacper Kowalik <xarthisius@gentoo.org> h5py-2.3.1.ebuild: Use mpi wrapper when compiling with parallel hdf5. Tests with USE=mpi are completely fine
This problem is definitely still present (dev-python/h5py/h5py-2.3.1.ebuild revision 1.3). You need USE="-mpi" to reproduce it.
(In reply to Arfrever Frehtes Taifersar Arahesis from comment #2) > This problem is definitely still present (dev-python/h5py/h5py-2.3.1.ebuild > revision 1.3). > You need USE="-mpi" to reproduce it. 23 Jul 2014; Kacper Kowalik <xarthisius@gentoo.org> h5py-2.3.1.ebuild: Introduce subslot and strict mpi= dependency for hdf5, see #302621
