avogadro-1.0.1 does not allow me to copy & paste structures from a window to another. After pasting a structure nothing happens. The structure is just not there. I keep a virtual machine running Gentoo where the version is still 1.0.0, and that version does not have this problem. I have even rebuilt every avogadro dependency, to no avail. ============== Portage 2.1.8.3 (default/linux/amd64/10.0/desktop/kde, gcc-4.4.3, glibc-2.10.1-r1, 2.6.34-gentoo x86_64) ================================================================= System uname: Linux-2.6.34-gentoo-x86_64-AMD_Athlon-tm-_X2_Dual-Core_QL-65-with-gentoo-1.12.13 Timestamp of tree: Thu, 03 Jun 2010 15:30:01 +0000 app-shells/bash: 4.0_p37 dev-java/java-config: 2.1.10 dev-lang/python: 2.6.5-r2, 3.1.2-r3 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 1.6-r2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.18-r3 sys-devel/gcc: 4.4.3-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=athlon64-sse3 -mtune=athlon64-sse3 -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/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=athlon64-sse3 -mtune=athlon64-sse3 -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="ftp://gentoo.mirror.dkm.cz/pub/gentoo/" LANG="es_ES.utf8" LDFLAGS="-Wl,-O1" LINGUAS="es_ES es en_US en" MAKEOPTS="-j3" 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="/usr/local/portage/layman/science /usr/local/portage/layman/rion /usr/local/portage/layman/vmware /usr/portage/local /usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnowext X a52 aac aalib acl acpi additions adns ads aften aim aio akode akonadi alsa amazon amd64 apbs apm ares arpack ass async atm audio audiofile autoipd autotrace avahi bash-completion battery bcmath beagle berkdb bidi binary-drivers binfilter bittorrent-external blas bluetooth bonjour branding bzip2 cairo caps cblas cdda cddb cdr cgi cgraph charconv chasen chm clamav cleartype cli client-only clisp cmake consolekit context contrib cracklib crypt css cups cupsddk curl custom-optimization cvs cxx daemon dbus desktopglobe detex dga dhclient dhcpcd dia dirac directfb dosformat dri dts dv dvb dvd dvdr dvi dvi2tty dvipdfm eap-sim editor emboss emovix encode exif extra fam fat fbcon ffmpeg fftw firefox firefox3 flac fltk fontconfig foomaticdb fortran ftp fuse gcj gdbm geoip geolocation gif gimp ginac gnuplot gnutls gphoto2 gpm gps graphics graphviz grub gsl gtk gtkhtml gtkstyle gzip hal hddtemp hdri hfs hibernate-script hpcups hpijs iconv icu idn imagemagick imap imlib ioctl ipod ipv6 jack jadetex java java6 javascript jce jpeg jpeg2k justify kate kde kde4 lame lapack laptop lasi latex latex3 lcms ldap lensfun libass libcaca libnotify libv4l libv4l2 libwww live lm_sensors logrotate lqr lzma lzo mad madwifi maildir mailwrapper matroska matrox mbox mcve mdnsresponder-compat memlimit metric mikmod mime mmap mmx mmxext mng modplug modules mono mopac7 motif moznomail mp3 mp4 mpeg mpi mplayer msn mtp mudflap multilib musepack nas ncurses network networkmanager nforce2 nls npp nptl nptlonly nsplugin ntfs numpy octave ods ogg omega opal openal openbabel openexr opengl openmp osc oscar osdmenu oss pam pango pcre pdf perl pkcs11 plasma plotutils pm-utils pmu png policykit portaudio posix postscript povray ppds ppm ps psf pstoedit pstricks publishers pvr pymol python qt3support qt4 quicktime rar raster raw rdesktop readline realmedia recode reflection reiser4 reiserfs remote remoteosd rss rtsp ruby samba sasl scanner schroedinger science sdl sdl-image semantic-desktop session shaders sharedmem shorten simplexml skins skype slang slp smartcard smp sndfile snmp sockets solver sox sparse spell spl sse sse2 sse3 ssl ssse3 startup-notification stats stream subtitles subversion svg svgz sysfs syslog szip taglib tcl tcpd tex4ht tga theora threads thumbnail thumbnails tidy tiff tk transcode trash-plugin truetype twolame type3 udev udev-acl unicode upnp usb userlocales v4l v4l2 vcd vhook video video-file vlm vmd vnc vorbis wavpack webinterface wifi winbind winetriks winpopup wma wma-fixed wmf wpg wps wxwidgets x264 xattr xcb xcomposite xetex xfce xft xindy xine xinerama xls xml xorg xosd xplanet xpm xprint xscreensaver xulrunner xv xvid yahoo zeroconf zip zlib zvbi" ALSA_CARDS="hda-intel" 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" CAMERAS="fuji ptp2" ELIBC="glibc" FOO2ZJS_DEVICES="hp1000" INPUT_DEVICES="synaptics evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="es_ES es en_US en" RUBY_TARGETS="ruby18" SANE_BACKENDS="epson2 hp" USERLAND="GNU" VIDEO_CARDS="radeon 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, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS Reproducible: Always
I forgot to add the error I get in a terminal when pasting a methane molecule from a window to another: ===== ============================== *** Open Babel Warning in ReadMolecule Problems reading an XYZ file: The first line must contain the number of atoms. Format is: "sssssss" setOBMol called. Other atom has a position list of size zero! Other atom has a position list of size zero! Other atom has a position list of size zero!
Downgrading the version to 1.0.0 removes the issue in my boxes. I can provide all the necessary tests. Since I use mostly stable systems, maybe a dependency version has to be updated?
Still no news? I am able to reproduce this bug in THREE different boxes. Avogadro is an extremely important package for me.
(In reply to comment #3) > Still no news? > > I am able to reproduce this bug in THREE different boxes. Avogadro is an > extremely important package for me. > Could you please report the bug upstream and added the url here?
I only just saw your bug report, this looks like a regression in Avogadro.
I don't seem to be able to reproduce the issue in 1.0 or master. I am hoping to put out a 1.0.2_rc0 next week, perhaps you could test that and let me know if you still see the issue there. Otherwise, an example of what is actually in your clipboard would also be helpful (it should be an XYZ file).
Please retest with avogadro-1.0.2_rc1 and report if the issue is fixed.
Sorry for the delay in my answer. I was busy with other tasks. I'm really confused here. When I first filed the bug, I was having the issue with v1.0.1 on my two boxes, laptop and desktop, whereas both of them worked well with 1.0.0. Before upgrading to 1.0.2_rc1 I checked again, and to my surprise the issue was gone with 1.0.1 on my laptop, but still present on my desktop. v1.0.2_rc1 behaves the same: laptop OK, desktop can't copy & paste. Somehow the issue was resolved on my laptop over the weeks after daily world updates. Both boxes are almost identical configuration-wise, but evidently there has to be something causing the issue. Since I'm now at my desktop, here is the clipboard output when I create a methane in an Avogadro's window and select and copy it: === 5 C -9.72186 4.89279 0.00000 H -8.65186 4.89279 0.00000 H -10.07904 5.90142 0.00000 H -10.09231 4.36863 0.85611 H -10.07359 4.39511 -0.87948 === When I open a new window with Avogadro and paste the clipboard, nothing happens. However, I can paste it into KWrite, for instance. Any clues?
To make matters even stranger, copy & paste is working today on my desktop machine!!! I really don't know why. No, wait!! I think I may know why it was working on my laptop but not on my desktop. I rebooted my desktop today after a very long while, whilst I reboot my laptop more often (for obvious reasons). Maybe there was some change in a deep Avogadro's dependency that needed a reboot. Anyway, whatever the problem was, it seems to be over now. I think maybe Avogadro needed a particular version for some of its dependencies.
See whether everything is fine with 1.0.3 and close the bug.
This looks like a neverending story. The bug is still present. Here is the output from the terminal when I create a methane and try to paste it into a new window: === $ avogadro "Avogadro version: 1.0.3 Git: LibAvogadro version: 1.0.3 Git: " Locale: "es_ES" Translation successfully loaded. "El sistema permite OpenGL" "A punto de probar funcionalidades OpenGL." "Funcionalidades OpenGL encontradas: " "Doble búfer." "Renderizado directo." "Antialias." Loading plugins: "/usr/bin/../lib64/avogadro/1_0" Searching for plugins in "/usr/lib64/avogadro/1_0/colors" Searching for plugins in "/usr/lib64/avogadro/1_0/engines" Searching for plugins in "/usr/lib64/avogadro/1_0/extensions" Searching for plugins in "/usr/lib64/avogadro/1_0/tools" Searching for plugins in "" Loading plugins: "/home/ramiro/.avogadro/1_0/plugins" Searching for plugins in "" Searching for plugins in "" Searching for plugins in "" Searching for plugins in "" Searching for plugins in "" QStackedLayout::setCurrentWidget: Widget 0x2cc8800 not contained in stack Avogadro(31707)/ KSycocaPrivate::openDatabase: Trying to open ksycoca from "/var/tmp/kdecache-ramiro/ksycoca4" GLWidget initialisation... GLSL support enabled, OpenGL 2.0 support confirmed. GLWidget initialised... createObjects() libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area QStackedLayout::setCurrentWidget: Widget 0x4c8eff0 not contained in stack GLWidget initialisation... GLSL support enabled, OpenGL 2.0 support confirmed. GLWidget initialised... createObjects() ============================== *** Open Babel Warning in ReadMolecule Problems reading an XYZ file: The first line must contain the number of atoms. Format is: "s" setOBMol called. Other atom has a position list of size zero! Other atom has a position list of size zero! Other atom has a position list of size zero! === This happens with both stable openbabel v2.2.3 and ~amd64 v2.3.0. The clipboard content is: === 5 C -7.71030 2.87870 0.00000 H -6.64030 2.87870 0.00000 H -8.10763 2.19209 0.71805 H -8.07364 2.63420 -0.97627 H -8.03654 3.86069 0.27233 ===
It is still not here. Could you please bug upstream and paste the url here?
What about version 1.1.0?
Created attachment 331676 [details] example disaccharide Mixed results. It does not seem to work when you copy/paste a molecular fragment, due to an incorrect xzy file format passed to the clipper. For instance, take the molecule I attach. Select one of the sugar rings plus the central sulphur atom, leaving the second ring unselected. Then copy that and paste it into another avogadro instance. Nothing happens. In the terminal you can see an error related to an incorrect number of atoms defined in the zxy file format. I got some hypothesis: * Maybe this happens because it is a fragment with an atom other than C's and H's, because it does not seem to happen with a fragment selected from an avogadro-built butane. * Maybe this happens because there are no H's to complete the valences in the fragment. Again, this does not happen in the case of an avogadro-built butane. * Maybe both conditions at the same time. * But, if you add the missing H's and copy the fragment, avogadro exits with a segmentation fault. I just discovered it. A different bug? So, I really don't know what to answer. There are improvements compared to previous versions where you simply couldn't copy/paste normally, but there are still issues, upstream or Gentoo related. Thanks for your efforts.
