emerge vmd doesn't compile because there are issues with python. I guess it is related to python-2.5 vs python2.4 Reproducible: Always Steps to Reproduce: 1.emerge vmd 2. 3. Actual Results: echo "Compiling " py_atomsel.C " --> " py_atomsel.o " ..."; \ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=k8 -DARCH_LINUX -DVMDOPENGL -DVMDGRAPHICS -DVMDIMD -DVMDPYTHON -DVMDTHREADS -DUSEPOSIXTHREADS -D_REENTRANT -DVMDSURF -DVMDMSMS -DVMDFIELDLINES -DVMDVOLUMETEXTURE -DVMDTCL -DVMDTK -DVMDSTATICPLUGINS -DVMDGUI -DVMDFLTK -I/usr/X11R6/include -I/usr/include/python2.5 -I../lib/tcl/include -I../lib/tk/include -I/var/tmp/portage/sci-chemistry/vmd-1.8.6/work/plugins/include -I/var/tmp/portage/sci-chemistry/vmd-1.8.6/work/plugins/compile/lib_LINUX/molfile -I/usr/include -I/usr/include/fltk-1.1 -I. -c py_atomsel.C -o ../LINUX/py_atomsel.o Compiling py_atomsel.C --> py_atomsel.o ... py_atomsel.C:941: error: invalid conversion from 'int (*)(PyObject*)' to 'Py_ssize_t (*)(PyObject*)' make: *** [py_atomsel.o] Error 1
Portage 2.1.3.9 (default-linux/amd64/2006.1, gcc-4.1.2, glibc-2.6.1-r0, 2.6.22-gentoo-r4 x86_64) ================================================================= System uname: 2.6.22-gentoo-r4 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ Timestamp of tree: Sun, 16 Sep 2007 07:00:01 +0000 app-shells/bash: 3.2_p17-r1 dev-java/java-config: 1.3.7, 2.0.33-r1 dev-lang/python: 2.4.4-r4, 2.5.1-r2 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.10-r4 sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18 sys-devel/gcc-config: 1.4.0-r2 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.22-r2 ACCEPT_KEYWORDS="amd64 ~amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=k8" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2 -pipe -march=k8" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://mirrors.sec.informatik.tu-darmstadt.de/gentoo/" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://a/portage" USE="X a52 aac aalib acpi aiglx alsa amd64 amr amrnb amrr amrwb ansi applet berkdb bitmap-fonts bitmapfonts branding breakme bzip2 cdparanoia cdr cjk cli clisp cracklib crypt css cups dar64 dbus dc1394 dpms dri dv dvd dvdr dvdread dvi eds emacs emovix encode exif f77 faac faad ffmpeg firefox flac fontconfig foomaticdb fortran gcj gdbm gif gimp gimpprint gkrellm gnome gnuplot gpm grammar gstreamer gtk gtkhtml hal iconv imagemagick immqt-bc ipod ipv6 isdnlog java javascript jpeg jpeg2k kde lame lapack latex lcd lcms leim libgda libnotify mad mailbox math matroska mbox midi mng mozilla mp2 mp3 mp4 mp4live mpeg mpeg2 mplayer mudflap musepack musicbrainz nautilus ncurses nls nptl nptlonly nsplugin ogg oggvorbis old-crypt opengl openmp oss pam pcre pdf perl png ppds pppd python qt-static qt3 qt3support qt4 rar readline reflection reiserfs rtc sdl session smp speex spell spl ssl svg t1lib tagwriting tcltk tcpd tetex tga theora thesaurus tiff tk totem transcode truetype truetype-fonts type1-fonts unicode usb vcd vorbis wmf wordperfect x264 xine xorg xv xvid 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 mulaw multi null plug rate route share shm softvol" ELIBC="glibc" INPUT_DEVICES="mouse keyboard evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="nv nvidia" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Yeah, vmd won't compile with python-2.5. I reported it on the vmd mailing list, but no solutions yet.
(In reply to comment #2) > Yeah, vmd won't compile with python-2.5. I reported it on the vmd mailing list, > but no solutions yet. > OK, so the problem is in PYVER in .ebuild There is a partial implementation of PYTHON_OVERRIDE_PYVER variable which doesn't work for VMD, ie I tryed: PYTHON_OVERRIDE_PYVER="2.4" emerge vmd and it doesn't work. However if I change the PYVER in the ebuild itself emerge vmd works OK! I guess I'll file a bug against eclass/python.eclass If I understand vmd history file correctly they fixed the problem in their development version :-)
*** Bug 193154 has been marked as a duplicate of this bug. ***
Hm, that must be an amd64 specific "int thingy" since it compiles just fine on my x86 boxes. Anyway, I'll post a possible fix below. Please let me know if it works since I don't have an amd64 box to test. Markus
Created attachment 131376 [details] possible fix for amd64 + python-2.5
Created attachment 131434 [details] vmd-1.8.6.ebuild for python-2.5 support
(In reply to comment #6) > Created an attachment (id=131376) [edit] > possible fix for amd64 + python-2.5 > I think it is just python-2.5 issue. I made some more changes in order to really fix the problem. Please check new attachments.
Created attachment 131435 [details, diff] patch for vmd-1.8.6 to support python-2.5
Hi milan, That looks good to me, thanks! I'll commit it to portage tonight. Best, Markus
In cvs, thanks! Markus
