Installing BioMap on Mac OS X Tiger

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  • May 23, 2007 at 7:22 am #1122
    Chris Bunch
    Participant

    Update:

    I have figured out a way of launching this from the command line, but now I get a bus error:

    theodora:~ cb$ /Applications/rsi/idl_6.3/bin/idl -rt=/usr/local/biomap/bin/biomap.sav
    IDL Version 6.3, Mac OS X (darwin ppc m32). (c) 2006, Research Systems, Inc.

    % Restored file: IDLRTMAIN.
    pBMT_SetupStructures: Initializing structures…
    % PBMT_READPARAMETER: Reading /Users/cb/.biomap/uparsrc
    % PLIB_READSTRUCTDATA: Error occured, exiting:Variable is undefined: NAME.
    % PBMT_READPARAMETER: Reading /Users/cb/.biomap/infrc
    % PLIB_READSTRUCTDATA: Error occured, exiting:Variable is undefined: NAME.
    % PBMT_READPARAMETER: Reading /Users/cb/.biomap/systemrc
    % PBMT_READPARAMETER: Reading /Users/cb/.biomap/winrc
    % PLIB_READSTRUCTDATA: Type of tag was not recognized
    % PLIB_READSTRUCTDATA: Error occured, exiting:Variable is undefined: NAME.
    Bus error
    theodora:~ cb$

    Any ideas, anyone…?

    May 23, 2007 at 7:53 am #1123
    Markus Stoeckli
    Moderator

    All right, this might be an obvious question, but did you copy the setting files to this location?

    markus

    May 23, 2007 at 7:58 am #1124
    Chris Bunch
    Participant

    My settings files are in ~/.biomap (ie not ~/biomap)

    May 23, 2007 at 9:04 am #1125
    Markus Stoeckli
    Moderator

    So that would be in /Users/cb/.biomap/ ?

    Markus

    May 23, 2007 at 9:09 am #1126
    Chris Bunch
    Participant

    yes, assuming I am logged in as cb (which I am)

    May 23, 2007 at 9:25 am #1129
    Markus Stoeckli
    Moderator

    OK, so far my quick guess… Just to be sure, if you remove the files from this current location, do you get the same error? Do you have permission to edit these files?

    There are not too many mac users for BioMap out there and I’m not one of them. Let’s see if we can get some wisdom from the pros…

    Markus

    September 2, 2009 at 5:50 pm #1263
    Markus Stoeckli
    Moderator

    The following message was received from Akos:

    Dear Peter,

    Few days ago I could manage to install BioMap on my Mac (OS X 10.5) and it works fine ever since. I think the trouble is the licenserc file that seems to best in the biomap system directory (/.biomap).

    I installed the BioMap into my user directory and modified the uparsrc-linux-mac file also in the /.biomap directory.
    Now, my question is how familiar you are with the Mac OS structure (I was not for sure) to be able to find hidden directories and files? The reason is that ALL system directories and files are hidden by default on Macs and there is no simple switch to show and hide them like on PCs in the Folder options. When I realized this I made two plug-ins with the Automator following the description on this site:
    http://theappleblog.com/2007/04/30/quick-tip-showhide-hidden-files/
    Then I could easily find the biomap system dir (/.biomap) and copy the licenserc file into it.

    However, it still did not work for me for the reason that the licenserc file was not correct!
    First I got the message from the Webmaster without any attachment only written the code as text that looked like this:

    TYPE =3D 13571
    ID =3D 725341
    EXP =3D 108075823
    MRI =3D 0
    MSI =3D 67388375
    WIP =3

    Following discussion with Markus he pinpointed that this is not a correct content of a licenserc file and suggested to remove all “3D”s. At this point I have to add that I created this file with TextEdit and removed its extension. So, it became like this:

    TYPE = 13571
    ID = 725341
    EXP = 108075823
    MRI = 0
    MSI = 67388375
    WIP = 0

    After that it still did not work however.
    Then I got the idea to apply for the code again. This time I got the file as attachment as well but to my surprise it looked differently opened by TextEdit (first line was empty!):

    âÌzCz…TYPE = 13571
    ID = 725341
    EXP = 108075823
    MRI =
    MSI = 67388375
    WIP =

    And it did not work but it did after the first (empty) and the garbage in the second line was removed!!!

    In conclusion, my recommendation is to play around with the licenserc file and get it in right format and BioMap will run nicely on Mac.

    Good luck!

    Akos

    September 3, 2009 at 12:20 pm #1264
    Administrator
    Keymaster

    There was a problem with encoding the attachment, which has been solved by now.

    Markus

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