GENtle/Bug reports

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Linux (Ubuntu 8.10 with MySQL 4.1 installed extra), GENtle v. 1.9.3

please update the software so that it can cope with MySQL 5, MySQL is already outdated and difficult to install on current Linux systems
When using the PCR tool, adding primers (that have been loaded from the database first) causes a program crash, so the PCR-tool option is unfortunately not usable...

This is the output on the console:


*** glibc detected *** ./GENtle: munmap_chunk(): invalid pointer: 0x096af51c ***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0xb75753f4]
/usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb776c031]
./GENtle[0x8155fd8]
/usr/lib/libwx_baseu-2.6.so.0(_ZNK12wxAppConsole11HandleEventEP12wxEvtHandlerMS0_FvR7wxEventES3_+0x28)[0xb79c04c8]
/usr/lib/libwx_baseu-2.6.so.0(_ZN12wxEvtHandler21ProcessEventIfMatchesERK21wxEventTableEntryBasePS_R7wxEvent+0x9d)[0xb7a452bd]
/usr/lib/libwx_baseu-2.6.so.0(_ZN16wxEventHashTable11HandleEventER7wxEventP12wxEvtHandler+0x84)[0xb7a46424]
/usr/lib/libwx_baseu-2.6.so.0(_ZN12wxEvtHandler12ProcessEventER7wxEvent+0xeb)[0xb7a4653b]
/usr/lib/libwx_gtk2u_core-2.6.so.0(_ZN12wxWindowBase9TryParentER7wxEvent+0x6d)[0xb7cd77ad]
/usr/lib/libwx_baseu-2.6.so.0(_ZN12wxEvtHandler12ProcessEventER7wxEvent+0x81)[0xb7a464d1]
/usr/lib/libwx_gtk2u_core-2.6.so.0(_ZN13wxToolBarBase11OnLeftClickEib+0x62)[0xb7ccec02]
/usr/lib/libwx_gtk2u_core-2.6.so.0[0xb7c60d5d]
/usr/lib/libgobject-2.0.so.0(g_cclosure_marshal_VOID__VOID+0x84)[0xb6eee3d4]
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x1ab)[0xb6ee0c4b]
/usr/lib/libgobject-2.0.so.0[0xb6ef7095]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x7dc)[0xb6ef87ac]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x26)[0xb6ef8c26]
/usr/lib/libgtk-x11-2.0.so.0(gtk_button_clicked+0x8a)[0xb71c6eaa]
/usr/lib/libgtk-x11-2.0.so.0[0xb71c7f58]
/usr/lib/libgobject-2.0.so.0(g_cclosure_marshal_VOID__VOID+0x84)[0xb6eee3d4]
/usr/lib/libgobject-2.0.so.0[0xb6edf3c9]
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x1ab)[0xb6ee0c4b]
/usr/lib/libgobject-2.0.so.0[0xb6ef68ee]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x7dc)[0xb6ef87ac]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x26)[0xb6ef8c26]
/usr/lib/libgtk-x11-2.0.so.0(gtk_button_released+0x8a)[0xb71c6f4a]
/usr/lib/libgtk-x11-2.0.so.0[0xb71c6f83]
/usr/lib/libgtk-x11-2.0.so.0[0xb727b036]
/usr/lib/libgobject-2.0.so.0[0xb6edf3c9]
/usr/lib/libgobject-2.0.so.0(g_closure_invoke+0x1ab)[0xb6ee0c4b]
/usr/lib/libgobject-2.0.so.0[0xb6ef6d3d]
/usr/lib/libgobject-2.0.so.0(g_signal_emit_valist+0x65b)[0xb6ef862b]
/usr/lib/libgobject-2.0.so.0(g_signal_emit+0x26)[0xb6ef8c26]
/usr/lib/libgtk-x11-2.0.so.0[0xb739033e]
/usr/lib/libgtk-x11-2.0.so.0(gtk_propagate_event+0xec)[0xb7273b4c]
/usr/lib/libgtk-x11-2.0.so.0(gtk_main_do_event+0x2e7)[0xb7274ef7]
/usr/lib/libgdk-x11-2.0.so.0[0xb710a50a]
/usr/lib/libglib-2.0.so.0(g_main_context_dispatch+0x1e8)[0xb6e436f8]
/usr/lib/libglib-2.0.so.0[0xb6e46da3]
/usr/lib/libglib-2.0.so.0(g_main_loop_run+0x1d2)[0xb6e472c2]
/usr/lib/libgtk-x11-2.0.so.0(gtk_main+0xb9)[0xb72753a9]
/usr/lib/libwx_gtk2u_core-2.6.so.0(_ZN11wxEventLoop3RunEv+0x5b)[0xb7bdec1b]
/usr/lib/libwx_gtk2u_core-2.6.so.0(_ZN9wxAppBase8MainLoopEv+0x4e)[0xb7c6980e]
/usr/lib/libwx_gtk2u_core-2.6.so.0(_ZN9wxAppBase5OnRunEv+0x21)[0xb7c69441]
/usr/lib/libwx_baseu-2.6.so.0(_Z7wxEntryRiPPw+0x6a)[0xb79f31ba]
/usr/lib/libwx_baseu-2.6.so.0(_Z7wxEntryRiPPc+0x36)[0xb79f3276]
./GENtle[0x81d30c0]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe5)[0xb751c685]
./GENtle(__gxx_personality_v0+0x301)[0x8063ac1]
======= Memory map: ========
08048000-08325000 r-xp 00000000 08:07 755375     /home/myusername/GENtle/GENtle
08325000-0832d000 rw-p 002dc000 08:07 755375     /home/myusername/GENtle/GENtle
0832d000-08348000 rw-p 0832d000 00:00 0 
08fdd000-09735000 rw-p 08fdd000 00:00 0          [heap]
b504e000-b50d0000 rw-p b504e000 00:00 0 
b50d0000-b511c000 r--p 00000000 08:06 237822     /usr/share/fonts/truetype/ttf-dejavu/DejaVuSansMono.ttf
b511c000-b512b000 r-xp 00000000 08:06 90150      /lib/libbz2.so.1.0.4
b512b000-b512c000 r--p 0000f000 08:06 90150      /lib/libbz2.so.1.0.4
b512c000-b512d000 rw-p 00010000 08:06 90150      /lib/libbz2.so.1.0.4
b512d000-b515e000 r-xp 00000000 08:06 109316     /usr/lib/libcroco-0.6.so.3.0.1
b515e000-b5161000 rw-p 00030000 08:06 109316     /usr/lib/libcroco-0.6.so.3.0.1
b5161000-b5191000 r-xp 00000000 08:06 109593     /usr/lib/libgsf-1.so.114.0.8
b5191000-b5193000 r--p 0002f000 08:06 109593     /usr/lib/libgsf-1.so.114.0.8
b5193000-b5194000 rw-p 00031000 08:06 109593     /usr/lib/libgsf-1.so.114.0.8
b5194000-b5195000 rw-p b5194000 00:00 0 
b5195000-b51ad000 r-xp 00000000 08:06 139594     /usr/lib/gio/modules/libgvfsdbus.so
b51ad000-b51ae000 r--p 00017000 08:06 139594     /usr/lib/gio/modules/libgvfsdbus.so
b51ae000-b51af000 rw-p 00018000 08:06 139594     /usr/lib/gio/modules/libgvfsdbus.so
b51b6000-b51e7000 r-xp 00000000 08:06 109955     /usr/lib/librsvg-2.so.2.22.3
b51e7000-b51e8000 r--p 00030000 08:06 109955     /usr/lib/librsvg-2.so.2.22.3
b51e8000-b51e9000 rw-p 00031000 08:06 109955     /usr/lib/librsvg-2.so.2.22.3
b51e9000-b5249000 rw-s 00000000 00:09 27983940   /SYSV00000000 (deleted)
b5249000-b5260000 r--s 00000000 08:06 188625     /usr/share/mime/mime.cache
b5260000-b5262000 r-xp 00000000 08:06 107548     /lib/tls/i686/cmov/libutil-2.8.90.so
b5262000-b5263000 r--p 00001000 08:06 107548     /lib/tls/i686/cmov/libutil-2.8.90.so
b5263000-b5264000 rw-p 00002000 08:06 107548     /lib/tls/i686/cmov/libutil-2.8.90.so
b5264000-b5271000 r-xp 00000000 08:06 109686     /usr/lib/libgvfscommon.so.0.0.0
b5271000-b5272000 r--p 0000d000 08:06 109686     /usr/lib/libgvfscommon.so.0.0.0
b5272000-b5273000 rw-p 0000e000 08:06 109686     /usr/lib/libgvfscommon.so.0.0.0
b5273000-b52a9000 r-xp 00000000 08:06 90164      /lib/libdbus-1.so.3.4.0
b52a9000-b52aa000 r--p 00035000 08:06 90164      /lib/libdbus-1.so.3.4.0
b52aa000-b52ab000 rw-p 00036000 08:06 90164      /lib/libdbus-1.so.3.4.0
b52ba000-b52bd000 r-xp 00000000 08:06 90178      /lib/libgpg-error.so.0.3.0
b52bd000-b52be000 rw-p 00002000 08:06 90178      /lib/libgpg-error.so.0.3.0
b52be000-b5324000 r-xp 00000000 08:06 90176      /lib/libgcrypt.so.11.4.4
b5324000-b5325000 r--p 00065000 08:06 90176      /lib/libgcrypt.so.11.4.4
b5325000-b5327000 rw-p 00066000 08:06 90176      /lib/libgcrypt.so.11.4.4
b5327000-b5337000 r-xp 00000000 08:06 110024     /usr/lib/libtasn1.so.3.0.15
b5337000-b5339000 rw-p 0000f000 08:06 110024     /usr/lib/libtasn1.so.3.0.15
b5339000-b5349000 r-xp 00000000 08:06 107542     /lib/tls/i686/cmov/libresolv-2.8.90.so
b5349000-b534a000 r--p 0000f000 08:06 107542     /lib/tls/i686/cmov/libresolv-2.8.90.so
b534a000-b534b000 rw-p 00010000 08:06 107542     /lib/tls/i686/cmov/libresolv-2.8.90.so
b534b000-b534d000 rw-p b534b000 00:00 0 
b534d000-b534f000 r-xp 00000000 08:06 90183      /lib/libkeyutils-1.2.so
b534f000-b5351000 rw-p 00001000 08:06 90183      /lib/libkeyutils-1.2.so
b5351000-b5358000 r-xp 00000000 08:06 109744     /usr/lib/libkrb5support.so.0.1
b5358000-b5359000 r--p 00006000 08:06 109744     /usr/lib/libkrb5support.so.0.1
b5359000-b535a000 rw-p 00007000 08:06 109744     /usr/lib/libkrb5support.so.0.1
b535a000-b53f1000 r-xp 00000000 08:06 106617     /usr/lib/libgnutls.so.26.4.5
b53f1000-b53f6000 r--p 00096000 08:06 106617     /usr/lib/libgnutls.so.26.4.5
b53f6000-b53f7000 rw-p 0009b000 08:06 106617     /usr/lib/libgnutls.so.26.4.5
b53f7000-b5419000 r-xp 00000000 08:06 109736     /usr/lib/libk5crypto.so.3.1
b5419000-b541a000 r--p 00022000 08:06 109736     /usr/lib/libk5crypto.so.3.1
b541a000-b541b000 rw-p 00023000 08:06 109736     /usr/lib/libk5crypto.so.3.1
b541b000-b54aa000 r-xp 00000000 08:06 109742     /usr/lib/libkrb5.so.3.3
b54aa000-b54ac000 r--p 0008e000 08:06 109742     /usr/lib/libkrb5.so.3.3
b54ac000-b54ad000 rw-p 00090000 08:06 109742     /usr/lib/libkrb5.so.3.3
b54ad000-b54d5000 r-xp 00000000 08:06 109599     /usr/lib/libgssapi_krb5.so.2.2
b54d5000-b54d6000 r--p 00028000 08:06 109599     /usr/lib/libgssapi_krb5.so.2.2
b54d6000-b54d7000 rw-p 00029000 08:06 109599     /usr/lib/libgssapi_krb5.so.2.2
b54d7000-b550a000 r-xp 00000000 08:06 107651     /usr/lib/libcups.so.2
b550a000-b550b000 ---p 00033000 08:06 107651     /usr/lib/libcups.so.2
b550b000-b550c000 r--p 00033000 08:06 107651     /usr/lib/libcups.so.2
b550c000-b550d000 rw-p 00034000 08:06 107651     /usr/lib/libcups.so.2
b550d000-b551a000 r-xp 00000000 08:06 109541     /usr/lib/libgnomecups-1.0.so.1.0.0
b551a000-b551b000 r--p 0000c000 08:06 109541     /usr/lib/libgnomecups-1.0.so.1.0.0
b551b000-b551c000 rw-p 0000d000 08:06 109541     /usr/lib/liAborted

The BLAST-page still hangs...

Bernd (talk) 12:51, 20 January 2009 (UTC)

Using GENtle on WinXP Pro. Attempting to BLAST anything results in immediate shutdown of the software. No prompting for save or anything... Any suggestions? Patches?

Fixed in CVS, will go live with the next version. --Magnus Manske 14:33, 30 January 2007 (UTC)

Under Mac OSx 10.4.8 (PPC platform), when starting GENtle the program hangs while displaying the introductory splash screen.

I can not reproduce this bug on my G4 PowerBook (PPC, 10.4.8). It also runs well on PPC iMac 10.3.9. Was GENtle installed under the same user name you're using? It could potentially be a write access conflict. --Magnus Manske 14:33, 30 January 2007 (UTC)

Under OpenSuSE 10.2 x86 the CVS version GENtle builds and works fine. One problem: when blasting a sequence GENtle hangs. Probably a threading issue? This is also the case on OpenSuSE 10.2 x86_64. Follow-up: I tested the latest CVS version (17 Feb 2009) on openSUSE 11.0 and openSUSE 11.1, both x86 and x86_64. Still, when BLASTing anything, GENtle hangs. I used wxWidgets-2.8.9.1 to build. I can send you additional data if you like.