Bug 334069 – sci-chemistry/avogadro-1.0.1: Crash adding hydrogen

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

[Description Reinis Danne 2010-08-23 13:02:06 UTC]

Avogadro crashes when drawing molecule with 'Adjust Hydrogens' option enabled adding a proton to NH2 to make NH3+. If this option is disabled, then it works without problems.

Reproducible: Always

Steps to Reproduce:
1. Select nitrogen in drawing mode
2. Click to draw amonia
3. Select hydrogen
4. Click on nitrogen and drag to make a N-H bond
5. Release mouse button

Actual Results:  
Avogadro crashes:
Qt has caught an exception thrown from an event handler. Throwing
exceptions from an event handler is not supported in Qt. You must
reimplement QApplication::notify() and catch all exceptions there.

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc


Expected Results:  
Draw the molecule and continue working.

$ emerge --info
Portage 2.1.8.3 (default/linux/amd64/10.0/desktop, gcc-4.4.4, glibc-2.11.2-r0, 2.6.32-gentoo-r7 x86_64)
=================================================================
System uname: Linux-2.6.32-gentoo-r7-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7300_@_2.00GHz-with-gentoo-1.12.13
Timestamp of tree: Mon, 23 Aug 2010 07:15:02 +0000
ccache version 2.4 [disabled]
app-shells/bash:     4.0_p37
dev-java/java-config: 2.1.11
dev-lang/python:     2.5.4-r4, 2.6.5-r3, 3.1.2-r4
dev-util/ccache:     2.4-r7
dev-util/cmake:      2.8.1-r2
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:  2.20.1-r1
sys-devel/gcc:       4.3.4, 4.4.4
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
sys-devel/make:      3.81-r2
virtual/os-headers:  2.6.30-r1
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -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/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /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=core2 -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch userpriv usersandbox"
GENTOO_MIRRORS="ftp://mirror.yandex.ru/gentoo-distfiles/ http://ftp.linux.ee/pub/gentoo/distfiles/ ftp://ftp.linux.ee/pub/gentoo/distfiles/ ftp://trumpetti.atm.tut.fi/gentoo/distfiles/ "
LANG="lv_LV.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="lv en"
MAKEOPTS="-s -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="/var/lib/layman/science /var/lib/layman/sunrise /usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="7zip X a52 aac aalib accessibility acl acpi alsa amd64 avahi avi bash-completion berkdb bluethooth bluetooth branding bzip2 cairo cdparanoia cdr cjk cli consolekit cracklib crypt css cups cxx dbus divx dri dts dv dvd dvdr dvdread eds emboss encode evo exif fam ffmpeg flac fontconfig fortran freetype gdbm gif gnome gnutls gpm gstreamer gtk gtk2 hal iconv ieee1394 ipv6 java jpeg kerberos lame lcms ldap libnotify live lm_sensors mad matroska mikmod mjpeg mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses networkmanager nls nptl nptlonly nsplugin nvidia ogg opengl openmp pam pango pcmcia pcre pdf perl png ppds pppd python qt3support quicktime rar readline reflection sdl session spell spl sse sse2 sse3 ssl ssse3 startup-notification subversion svg sysfs tcl tcpd theora tiff tk truetype udev unicode usb v4l v4l2 vaapi vcd vorbis wifi wmf x264 xcb xft xml xmms xorg xulrunner xv xvid zlib" ALSA_CARDS="via82xx 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 authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" FOO2ZJS_DEVICES="hp1018" INPUT_DEVICES="evdev keyboard mouse synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="lv en" NETBEANS_MODULES="apisupport harness ide java nb websvccommon cnd dlight" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" 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

[Comment 1 Eric Johnson 2010-08-24 16:14:37 UTC]

This also occurs on x86.

[Comment 2 Marcus D. Hanwell (RETIRED) 2011-01-28 20:35:31 UTC]

I am preparing a 1.0.2 release, and I think we have this issue fixed in the 1.0 branch. It doesn't do what you want, in that the hydrogens then go back to 3 rather than 4 we adjust the number of hydrogens.

[Comment 3 Justin Lecher (RETIRED) 2011-03-26 17:11:47 UTC]

Please retest with avogadro-1.0.2_rc1 and report if the issue is fixed.

[Comment 4 urcindalo 2011-04-06 10:06:26 UTC]

I also experience this crash in 1.0.2_rc1

[Comment 5 Justin Lecher (RETIRED) 2011-04-26 16:21:33 UTC]

(In reply to comment #4)
> I also experience this crash in 1.0.2_rc1

please test 1.0.3. Upstreams reslease notes say:

Fixed some crashes when drawing with adjust hydrogens on

[Comment 6 Alexey Shvetsov 2011-08-14 17:16:13 UTC]

If its not fixed in 1.0.3 please reopen