Bug 420777 – sci-mathematics/octave-3.6.2-r1 with sys-cluster/openmpi-1.6-r1 - At global scope: /usr/include/openmpi/ompi/mpi/cxx/mpicxx.h:188:9: error: expected identifier before 'int'

• Status: RESOLVED TEST-REQUEST
• Product: Gentoo Linux

[Description Juergen Rose 2012-06-12 07:58:22 UTC]

'emerge octave' fails with:
...
libtool: compile:  mpicxx -DHAVE_CONFIG_H -I. -I.. -I../libgnu -I../libgnu -I../libcruft/misc -I../liboctave -I../liboctave -I. -I. -I/usr/include/fltk-1 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -march=amdfam10 -O2 -pipe -DHAVE_CONFIG_H -I/usr/include/freetype2 -Wall -W -Wshadow -Wold-style-cast -Wformat -Wpointer-arith -Wwrite-strings -Wcast-align -Wcast-qual -march=amdfam10 -O2 -pipe -march=amdfam10 -O2 -pipe -c DLD-FUNCTIONS/__init_fltk__.cc  -fPIC -DPIC -o DLD-FUNCTIONS/.libs/DLD_FUNCTIONS___init_fltk___la-__init_fltk__.o
In file included from /usr/include/mpi.h:2087:0,
                 from /usr/include/H5public.h:61,
                 from /usr/include/hdf5.h:24,
                 from ./oct-hdf5.h:27,
                 from ./ov.h:43,
                 from ./oct-obj.h:34,
                 from ./ov-fcn.h:32,
                 from ./ov-builtin.h:28,
                 from ./defun-int.h:28,
                 from ./defun-dld.h:30,
                 from DLD-FUNCTIONS/__fltk_uigetfile__.cc:42:
/usr/include/openmpi/ompi/mpi/cxx/mpicxx.h: At global scope:
/usr/include/openmpi/ompi/mpi/cxx/mpicxx.h:188:9: error: expected identifier before 'int'
/usr/include/openmpi/ompi/mpi/cxx/mpicxx.h:188:9: error: multiple types in one declaration
In file included from /usr/include/openmpi/ompi/mpi/cxx/mpicxx.h:234:0,
                 from /usr/include/mpi.h:2087,
                 from /usr/include/H5public.h:61,
                 from /usr/include/hdf5.h:24,
                 from ./oct-hdf5.h:27,
                 from ./ov.h:43,
                 from ./oct-obj.h:34,
                 from ./ov-fcn.h:32,
                 from ./ov-builtin.h:28,
                 from ./defun-int.h:28,
                 from ./defun-dld.h:30,
                 from DLD-FUNCTIONS/__fltk_uigetfile__.cc:42:
/usr/include/openmpi/ompi/mpi/cxx/status.h:22:7: error: expected identifier before 'int'
/usr/include/openmpi/ompi/mpi/cxx/status.h:22:14: error: expected unqualified-id before '{' token
DLD-FUNCTIONS/__fltk_uigetfile__.cc:135:1: error: expected '}' at end of input
make[3]: *** [DLD-FUNCTIONS/DLD_FUNCTIONS___fltk_uigetfile___la-__fltk_uigetfile__.lo] Error 1
make[3]: *** Waiting for unfinished jobs....
In file included from /usr/include/fltk-1/FL/Fl.H:40:0,
                 from DLD-FUNCTIONS/__init_fltk__.cc:52:



mpicxx is from openmpi-1.6-r1.


root@impala:/usr/local/portage/dev-vcs(62)# emerge --info '=sci-mathematics/octave-3.6.2-r1'
Portage 2.1.10.65 (default/linux/amd64/10.0, gcc-4.6.3, glibc-2.15-r2, 3.4.0-gentoo x86_64)
=================================================================
                        System Settings
=================================================================
System uname: Linux-3.4.0-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.1
Timestamp of tree: Tue, 12 Jun 2012 07:00:01 +0000
app-shells/bash:          4.2_p29
dev-java/java-config:     2.1.12
dev-lang/python:          2.7.3-r2, 3.2.3-r1
dev-util/cmake:           2.8.8-r2
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.10.3
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.5, 1.12.1
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.3-r2, 4.6.3
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.4 (virtual/os-headers)
sys-libs/glibc:           2.15-r2
Repositories: gentoo x11 lordvan bicatali science sage-on-gentoo dilfridge sunrise lisp java-overlay x-portage x-cpan g-octave
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.3 cadsoft Oracle-BCLA-JavaSE"
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 /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
CONFIG_PROTECT_MASK="${EPREFIX}/etc/gconf /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/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="-march=amdfam10 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch xattr"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LC_ALL="C"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j5"
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/x11 /var/lib/layman/lordvan /var/lib/layman/bicatali /var/lib/layman/science /var/lib/layman/sage-on-gentoo /var/lib/layman/dilfridge /var/lib/layman/sunrise /var/lib/layman/lisp /var/lib/layman/java-overlay /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac accessibility acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boo boost bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc 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 ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse g3dvl galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gtk3 gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate live lm_sensors lua lzo mad mail maildir mapnik math matroska media-library mkl mmx mmxext mng modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript pppd preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime 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 smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4a ssl subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter vaapi video virtualbox visio vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xorg xpm xv xvid xvmc yaml zlib zvbi" 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="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file 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 log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump" CAMERAS="canon fuji" 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 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" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nv nouveau vesa" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON



root@impala:/usr/local/portage/dev-vcs(63)# emerge -pqv '=sci-mathematics/octave-3.6.2-r1'
[ebuild     U ] sci-mathematics/octave-3.6.2-r1 [3.6.2] USE="X curl doc fftw glpk gnuplot hdf5%* imagemagick opengl qhull qrupdate readline sparse zlib -static-libs"

[Comment 1 Juergen Rose 2012-06-12 08:02:48 UTC]

Created attachment 315075 [details]
bzip2ed /var/tmp/portage/sci-mathematics/octave-3.6.2-r1/temp/build.log

[Comment 2 Kacper Kowalik (Xarthisius) (RETIRED) 2012-06-13 19:00:28 UTC]

+*hdf5-1.8.9-r2 (13 Jun 2012)
+
+  13 Jun 2012; Kacper Kowalik <[e-mail]>
+  +files/hdf5-1.8.9-mpicxx.patch, +hdf5-1.8.9-r2.ebuild, -hdf5-1.8.9-r1.ebuild:
+  Prevent accidental inclusion of mpi c++ headers when hdf5.h is included by
+  third party C++ program/library. Fixes #420777 Juergen Rose <[e-mail]-
+  potsdam.de>
+

Please update hdf5 and check if that fixes it for you.

[Comment 3 Juergen Rose 2012-06-16 11:48:22 UTC]

Works now.