deleted the software folder - PEBKAC

[Ryan Schmidt]

Please remember to Reply All so your reply goes to the mailing list too, not just to me. I'm sending this reply back to the list, in case it helps other users, and also to the maintainer of arb, in case there's something that needs to be changed in the port.

On May 28, 2012, at 03:51, plik wrote:

> Hi Ryan,
> 
> thank you very much for your help.
> 
> I executed "sudo port -f deactivate arb" & "sudo port activate arb". When I tryed to run ARB but I got this message:
> 
> ############
> Environment Variable ARBHOME was empty
> Using ARBHOME='/opt/local'
> Please wait while the program ARB is starting .....
> luis:SH plik$ ARB: Loading '.arb_prop/ntree.arb'
> file .arb_prop/ntree.arb not found
> database .arb_prop/ntree.arb created
> 
> -------------------- ARB-backtrace for 'received signal 11':
> 0   arb_ntree                           0x00000001000c6185 GBK_dump_backtrace + 53
> 1   arb_ntree                           0x00000001000c8395 sigsegv_handler_dump + 53
> 2   libSystem.B.dylib                   0x00007fff89b3d1ba _sigtramp + 26
> 3   arb_ntree                           0x00000001000ef537 gb_search + 1367
> 4   arb_ntree                           0x000000010012a107 _Z15aw_create_shellP9AW_windowbbiiii + 183
> 5   arb_ntree                           0x0000000100132d56 _ZN17AW_window_message4initEP7AW_rootPKcb + 102
> 6   arb_ntree                           0x000000010012433f _Z11aw_questionPKcS0_bS0_ + 303
> 7   arb_ntree                           0x00000001001247e7 _Z11aw_ask_surePKcbS0_ + 23
> 8   arb_ntree                           0x000000010011e65a _Z29aw_create_selection_box_awarsP7AW_rootPKcS2_S2_S2_P17gb_data_base_typeb + 442
> 9   arb_ntree                           0x000000010012b288 _ZN7AW_root14init_variablesEP17gb_data_base_type + 296
> 10  arb_ntree                           0x000000010007db1b main + 139
> 11  arb_ntree                           0x0000000100004348 start + 52
> 12  ???                                 0x0000000000000001 0x0 + 1
> -------------------- End of backtrace
> [Terminating with signal 11]
> file .arb_prop/status.arb not found
> database .arb_prop/status.arb created
> 
> -------------------- ARB-backtrace for 'received signal 11':
> 0   arb_ntree                           0x00000001000c6185 GBK_dump_backtrace + 53
> 1   arb_ntree                           0x00000001000c8395 sigsegv_handler_dump + 53
> 2   libSystem.B.dylib                   0x00007fff89b3d1ba _sigtramp + 26
> 3   arb_ntree                           0x00000001000ef537 gb_search + 1367
> 4   arb_ntree                           0x000000010012a107 _Z15aw_create_shellP9AW_windowbbiiii + 183
> 5   arb_ntree                           0x0000000100132d56 _ZN17AW_window_message4initEP7AW_rootPKcb + 102
> 6   arb_ntree                           0x000000010012433f _Z11aw_questionPKcS0_bS0_ + 303
> 7   arb_ntree                           0x00000001001247e7 _Z11aw_ask_surePKcbS0_ + 23
> 8   arb_ntree                           0x000000010011e65a _Z29aw_create_selection_box_awarsP7AW_rootPKcS2_S2_S2_P17gb_data_base_typeb + 442
> 9   arb_ntree                           0x000000010012b288 _ZN7AW_root14init_variablesEP17gb_data_base_type + 296
> 10  arb_ntree                           0x0000000100124d30 _Z13aw_initstatusv + 192
> 11  arb_ntree                           0x000000010007dad0 main + 64
> 12  arb_ntree                           0x0000000100004348 start + 52
> 13  ???                                 0x0000000000000001 0x0 + 1
> -------------------- End of backtrace
> [Terminating with signal 11]
> ARB done
> ##############
> 
> I googled (is 'googled' correct english?) for "ARB-backtrace for 'received signal 11'" and found a guy who had the same problem and solved it with an update of his .bash_profile - therefore, I put this into my .bash_profile:
> 
> ##############
> ARBHOME=/opt/local/share/arb;export ARBHOME    #specifies your path to the ARB directory
> LD_LIBRARY_PATH=${ARBHOME}/lib:${LD_LIBRARY_PATH} export LD_LIBRARY_PATH
> PATH=${ARBHOME}/bin:${PATH}
> export PATH
> ##############
> 
> After this, ARB started properly. I am still excited how fast this problem has been solved and about the new commands I have learned!
> 
> 
> Thank you very much!
> 
> George
> 
> 
> 
> Am 5/28/12 12:38 AM, schrieb Ryan Schmidt:
>> On May 27, 2012, at 16:51, plik wrote:
>> 
>>> Today I installed Macports for the subsequent installation of ARB. Everything went really fine until I tryed to start ARB. But actually, this is another problem.
>> Once you solve the below, this is what you should tell us more about. What's not working?
>> 
>> 
>>> Herewith, I would like to ask for help for the probably stupid things I did to solve the "ARB won't work" problem.
>>> 
>>> I thought "maybe it is a good idea to re-install arb with Macports". Here is what I did:
>>> 
>>> ###########
>>> luis:~ plik$ sudo port install arb
>>> --->   Computing dependencies for arb
>>> --->   Cleaning arb
>>> --->   Scanning binaries for linking errors: 98.7%
>>> Warning: Error parsing file /opt/local/share/arb/lib/ARB.bundle: Error opening or reading file
>>> --->   Scanning binaries for linking errors: 100.0%
>>> --->   No broken files found.
>> As you see that doesn't actually reinstall arb; it just tells you it's already installed. If you actually want to reinstall arb you need to:
>> 
>> sudo port -n upgrade --force arb
>> 
>> However I don't see any reason to do that at this time, until we hear more about what the actual problem is that started you down this path.
>> 
>> 
>>> I thought "maybe it is a good idea to rm -rf the arb folder in /opt/local/share/". I did so.
>> Not a good idea. :) To get it back, deactivate and re-activate arb:
>> 
>> sudo port -f deactivate arb
>> sudo port activate arb
>> 
>> 
>> 
>