'emerge -v1 viewmol' fails with: ... x86_64-pc-linux-gnu-gcc -c -Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing -I/usr/include -I/usr/include -I/usr/include/python3.1 -march=nocona -O2 -pipe ../annotate.c In file included from /usr/include/python3.1/Python.h:8, from ../viewmol.h:38, from ../annotate.c:35: /usr/include/python3.1/pyconfig.h:1111:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdio.h:28, from ../annotate.c:29: /usr/include/features.h:210:1: warning: this is the location of the previous definition ../annotate.c: In function 'modifyAnnotation': ../annotate.c:128: warning: cast to pointer from integer of different size ../annotate.c: In function 'getAnnotation': ../annotate.c:144: warning: cast from pointer to integer of different size x86_64-pc-linux-gnu-gcc -c -Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing -I/usr/include -I/usr/include -I/usr/include/python3.1 -march=nocona -O2 -pipe ../atommodule.c In file included from /usr/include/python3.1/Python.h:8, from ../viewmol.h:38, from ../atommodule.c:24: /usr/include/python3.1/pyconfig.h:1111:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/ctype.h:27, from ../atommodule.c:20: /usr/include/features.h:210:1: warning: this is the location of the previous definition ../atommodule.c:53: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'PyTypeObject' ../atommodule.c: In function 'atom_new': ../atommodule.c:96: error: 'PyAtomSpec_Type' undeclared (first use in this function) ../atommodule.c:96: error: (Each undeclared identifier is reported only once ../atommodule.c:96: error: for each function it appears in.) ../atommodule.c: In function 'atom_coordinates': ../atommodule.c:174: warning: implicit declaration of function 'PyString_FromString' ../atommodule.c:174: warning: passing argument 3 of 'PyTuple_SetItem' makes pointer from integer without a cast /usr/include/python3.1/tupleobject.h:44: note: expected 'struct PyObject *' but argument is of type 'int' ../atommodule.c: In function 'atom_name': ../atommodule.c:310: warning: return makes pointer from integer without a cast ../atommodule.c: In function 'atom_getattr': ../atommodule.c:382: warning: implicit declaration of function 'Py_FindMethod' ../atommodule.c:382: warning: return makes pointer from integer without a cast ../atommodule.c: In function 'initAtomModule': ../atommodule.c:390: error: 'PyAtomSpec_Type' undeclared (first use in this function) ../atommodule.c:392: warning: implicit declaration of function 'Py_InitModule' ../atommodule.c:392: warning: assignment makes pointer from integer without a cast make[1]: *** [atommodule.o] Error 1 ... x86_64-pc-linux-gnu-gcc -c -Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing -I/usr/include -I/usr/include -I/usr/include/python3.1 -march=nocona -O2 -pipe ../readgamess.c ../readgamess.c: In function 'main': ../readgamess.c:86: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result ... cp: cannot stat `Linux/viewmol': No such file or directory chmod: cannot access `/var/tmp/portage/sci-chemistry/viewmol-2.4.1/image//usr/bin/viewmol': No such file or directory ... * ERROR: sci-chemistry/viewmol-2.4.1 failed: Reproducible: Always root@moose:/root(176)# emerge --info =sci-chemistry/viewmol-2.4.1 Portage 2.1.8.2 (default/linux/amd64/10.0/desktop, gcc-4.4.3, glibc-2.11-r1, 2.6.32-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-gentoo-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.0.1 Timestamp of tree: Tue, 09 Mar 2010 13:30:01 +0000 app-shells/bash: 4.1_p2 dev-java/java-config: 2.1.10 dev-lang/python: 2.6.4-r1, 3.1.1-r1 dev-python/pycrypto: 2.1.0 dev-util/cmake: 2.8.0-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.0-r1 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1 sys-devel/gcc: 4.4.3 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.33 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/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 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" FFLAGS="-march=nocona -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1" LINGUAS="de fr" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/n4g /var/lib/layman/java-overlay /var/lib/layman/zugaina /var/lib/layman/sunrise /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit X Xaw3d a52 aac abiword acl acpi administrator afs alsa amd64 ao aotuv apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 c++ 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 designer devhelp device-mapper dga dia djvu doc dri ds2490 dts dv dvb dvd dvdr dvi eds elf emacs emboss empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm geolocation geos gif gimp ginac git glade glib glitz gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kde kdrive kerberos kexi kpathsea kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mkl mmx mmxext mng modules mono moonlight motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python qhull qt3support qt4 quicktime readline reflection reiserfs rle romio rpc rrdcgi rrdtool samba sasl science sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora threads thunar thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" 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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="nv nvidia nouveau vesa" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS root@moose:/root(177)# emerge -pqv =sci-chemistry/viewmol-2.4.1 [ebuild N ] sci-chemistry/viewmol-2.4.1
Created attachment 222861 [details] /var/tmp/portage/sci-chemistry/viewmol-2.4.1/temp/build.log
(In reply to comment #1) > Created an attachment (id=222861) [details] > /var/tmp/portage/sci-chemistry/viewmol-2.4.1/temp/build.log > Does it compile with <python:3 ?
I tried the followong: root@moose:/root(15)# eselect python set 2 root@moose:/root(16)# eselect python list Available Python interpreters: [1] python2.6 [2] python3.1 * root@moose:/root(18)# emerge -vuDN viewmol But I get the same error: ... x86_64-pc-linux-gnu-gcc -c -Wall -I/usr/X11R6/include -DLINUX -Wno-strict-aliasing -I/usr/include -I/usr/include -I/usr/include/python3.1 -march=nocona -O2 -pipe ../atommodule.c In file included from /usr/include/python3.1/Python.h:8, from ../viewmol.h:38, from ../atommodule.c:24: /usr/include/python3.1/pyconfig.h:1111:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/ctype.h:27, from ../atommodule.c:20: /usr/include/features.h:210:1: warning: this is the location of the previous definition ../atommodule.c:53: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'PyTypeObject' ... make[1]: *** [atommodule.o] Error 1 ... >>> Install viewmol-2.4.1 into /var/tmp/portage/sci-chemistry/viewmol-2.4.1/image/ category sci-chemistry cp: cannot stat `Linux/viewmol': No such file or directory chmod: cannot access `/var/tmp/portage/sci-chemistry/viewmol-2.4.1/image//usr/bin/viewmol': No such file or directory
(In reply to comment #3) > I tried the followong: > > root@moose:/root(15)# eselect python set 2 > root@moose:/root(16)# eselect python list > Available Python interpreters: > [1] python2.6 > [2] python3.1 * My question was: does it compile with python2.6? eselect python set 1 and try again. I don't think it's good idea to set python3.1 as system interpreter...
I had one i686 system, where I installed viewmol last october: root@cheetah:/root(10)# genlop -t viewmol * sci-chemistry/viewmol Fri Oct 16 17:34:39 2009 >>> sci-chemistry/viewmol-2.4.1 merge time: 6 minutes and 36 seconds. but this was after the first installation of python-3*: root@cheetah:/root(12)# genlop -t python | grep python-3 Mon Aug 3 11:06:10 2009 >>> dev-lang/python-3.1 Tue Aug 18 21:10:27 2009 >>> dev-lang/python-3.1.1 Fri Sep 25 11:58:55 2009 >>> dev-lang/python-3.1.1-r1 Mon Dec 7 04:41:03 2009 >>> dev-lang/python-3.1.1-r1 It seems me, that I can install viewmol-2.4.1 at i686 systems, but it fails at all x86_64 systems. Regards
To correct myself. I can install viewmol-2.4.1 at i686 systems, but it is incomplete. There is no viewmol binary. I just tried once more: root@tiger:/usr(16)# emerge -vD viewmol ... >>> Source unpacked in /var/tmp/portage/sci-chemistry/viewmol-2.4.1/work >>> Compiling source in /var/tmp/portage/sci-chemistry/viewmol-2.4.1/work/viewmol-2.4.1/source ... dirname: missing operand Try `dirname --help' for more information. make: *** No rule to make target `_'. Stop. make -j1 COMPILER=i686-pc-linux-gnu-gcc 'OPT=-O2 -march=pentium4 -fomit-frame-pointer' /bin/sh getmachine viewmol ... /usr/include/features.h:210:1: warning: this is the location of the previous definition ../atommodule.c:53: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'PyTypeObject' ../atommodule.c: In function 'atom_new': ... ../atommodule.c:392: warning: assignment makes pointer from integer without a cast make[1]: *** [atommodule.o] Error 1 ... >>> Install viewmol-2.4.1 into /var/tmp/portage/sci-chemistry/viewmol-2.4.1/image/ category sci-chemistry cp: cannot stat `Linux/viewmol': No such file or directory chmod: cannot access `/var/tmp/portage/sci-chemistry/viewmol-2.4.1/image//usr/bin/viewmol': No such file or directory >>> Completed installing viewmol-2.4.1 into /var/tmp/portage/sci-chemistry/viewmol-2.4.1/image/ ... >>> Installing (1 of 1) sci-chemistry/viewmol-2.4.1 * checking 170 files for package collisions --- /usr/ --- /usr/bin/ --- /usr/lib/ >>> /usr/lib/viewmol/ ... * GNU info directory index is up-to-date. root@tiger:/usr/(17)# genlop -t viewmol * sci-chemistry/viewmol Wed Mar 10 14:44:46 2010 >>> sci-chemistry/viewmol-2.4.1 merge time: 1 minute and 36 seconds. Strange!
Fixed in tree thanks for reporting.
