[Mesquitelist] possible bug?
Wayne Maddison
wmaddisn at interchange.ubc.ca
Thu Feb 12 14:12:59 PST 2009
At 12:27 PM -0600 12.2.2009, Scott Monks wrote:
>Hello all,
> I am making the bittersweet move from Maclade to Mesquite
>(Macclade-simple to use and, for me, mostly logical menus vs.
>Mesquite-complicated but much more powerful and for both PC and Mac!)
>and I still have a lot to learn, but I have run into a problem.
Try the new simplification system if you want it to try to simplify
its interface, though its still won't be a simple as MacClade.
>
> I am not sure this is bug or if I am doing something wrong so I
>thought it best to comment here rather than just send it in as a bug.
>
> I use Mesquite 2.6 on several PC's (windows XP), an I-mac (OSX 10.5),
>and on a dual-processor G-5 (OSX 10.3.9), all with recent updates to
>the operating systems. Recently I decided to label groups of taxa
>according to family, each with a different color. In the PC's and the
>I-mac this works fine (taxon names in black, cells in color), but when
>I open the file in the G-5 and view the character matrix the names of
>the taxa are in the same color as the cells and I can't read the names.
> The only way to return the taxon names to black is to remove the group
>designation.
> Is this a bug with the program or just a problem with the particular
>version of Java that runs on this computer? Checking "About this Mac"
>shows Java 1.3.1 Plugin settings as version 2.0.0, Java 1.4.2 Plugin
>settings as version 2.3.0, and Java Web Start as version 2.3.0.
>
> Has anyone else had this problem?
OS X 10.3.9 has so many problems with java that we will probably soon
declare defeat and say we don't support it. Most have to do with
graphical problems of this sort.
If you go to Matrix>Color Taxon Names Background, you can turn off
the cell color (No Color).
>
> There is also another small problem with the program in the same
>machine. Mesquite loads just fine, but when I open a file that had
>been saved in any other machine a small window opens that says "A
>script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: A command ("getInfoPanel;") did not result in the return of
>an object as expected. The script's results may not be as expected.
>More details are written into Mesquite's log file." This does not
>occur with files that were saved on this same machine.
If you open a newer file with an older version of Mesquite, or if you
open a file saved with another copy of Mesquite that had extra
modules installed, then the scripts saved within the files may refer
to modules not in your current copy. The warning is usually
innocent, just to remind you that you should expect the file to
return to the same state in which you saved it in terms of windows
and analyses. The data themselves should be unaffected.
Wayne
> A copy of the info from the log file is given below.
>
>Thanks, Scott Monks
>
>log file--
>(File Dialog: Open file as independent project:
>(/Users/scott/Documents/ aa Manuscritos/ Species
>descriptions/Digenea/Phyllodistomum/aa Cladistic analysis/)) #
>(Mesquite) # Location: /Users/scott/Documents/ aa Manuscritos/ Species
>descriptions/Digenea/Phyllodistomum/aa Cladistic analysis/PUBL-01.NEX
>
>Reading NEXUS file PUBL-01.NEX
>Reading block: TAXA
>Reading block: CHARACTERS
>Reading CHARACTERS block Character Matrix
>Reading block: TREES
>Reading block: MESQUITECHARMODELS
>Reading block: CODONS
>Reading block: ASSUMPTIONS
>Reading block: NOTES
>Reading block: MESQUITE
>Window Project did not respond to command setResourcesState with
>arguments (false false 100)
>Window Project did not respond to command setPopoutState with arguments
>(400)
>Module Tree Window
>(mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker) did not
>respond to command suppressEPCResponse with arguments ()
>Module Basic Draw Names for Tree Display
>(mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames) did not
>respond to command namesAngle with arguments (?)
>Window Tree Window 2 showing Stored Trees did not respond to command
>getInfoPanel with arguments ()
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command:
>"getInfoPanel;" to object
>mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow at 4da576)
>ALERT: (Mesquite): A script has failed to execute properly, possibly
>because it expected certain modules not available in the current
>configuration of Mesquite. Details: A command ("getInfoPanel;") did
>not result in the return of an object as expected. The script's
>results may not be as expected.
>More details are written into Mesquite's log file.
>
>(Alert) #
>(Mesquite) # Window Tree Window 2 showing Stored Trees did not respond
>to command toggleInfoPanel with arguments (on)
>Module Parsimony Ancestral States
>(mesquite.parsimony.ParsAncestralStates.ParsAncestralStates) did not
>respond to command toggleMPRsMode with arguments (off)
>Module Tree Window
>(mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker) did not
>respond to command desuppressEPCResponse with arguments ()
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command:
>"getEmployee
>#mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles;" to
>object Tree Window (id# 882))
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command:
>"getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;" to object
>Tree Window (id# 882))
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command: "newValue
>#mesquite.trees.TreeValueUsingMatrix.TreeValueUsingMatrix;" to object
>null)
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command:
>"getEmployee
>#mesquite.parsimony.TreelengthForMatrix.TreelengthForMatrix;" to object
>null)
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command:
>"getEmployee #mesquite.parsimony.ParsCharSteps.ParsCharSteps;" to
>object null)
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command:
>"getEmployee
>#mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep;" to
>object null)
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command:
>"setCharacterSource
>#mesquite.charMatrices.StoredMatrices.StoredMatrices;" to object null)
>Window Character Matrix "Character Matrix" did not respond to command
>colorRowNames with arguments
>(#mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor)
>Window Character Matrix "Character Matrix" did not respond to command
>colorColumnNames with arguments
>(#mesquite.charMatrices.NoColor.NoColor)
>Window Character Matrix "Character Matrix" did not respond to command
>toggleAllowAutosize with arguments (on)
>Window Character Matrix "Character Matrix" did not respond to command
>toggleDiagonal with arguments (on)
>Window Character Matrix "Character Matrix" did not respond to command
>setDiagonalHeight with arguments (80)
>A script has failed to execute properly, possibly because it expected
>certain modules not available in the current configuration of Mesquite.
> Details: Object of tell command is null (previous command:
>"getEmployee
>#mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor;" to object
>Character Matrix Editor (id# 945))
>File reading complete (file PUBL-01.NEX)
>
>
>
>-- _____________________________________________________
>
>Correo/ Mail
>
>Dr. Scott Monks
>Universidad Autónoma del Estado de Hidalgo (UAEH)
>Centro de Investigaciones Biológicas (CIB)
>Apdo. Postal 1-69
>Pachuca, C.P. 42001
>Hidalgo, México.
>
>
>Mensajería/ Courier
>
>Universidad Autónoma del Estado de Hidalgo (UAEH)
>Centro de Investigaciones Biológicas (CIB)
>Ciudad Universitaria, Carretera Pachuca-Tulancingo Km. 4.5 S/n
>Pachuca C.P. 42184
>Hidalgo, México
>
>[Tel 01(771)717-2000 Ext. 6658, 6640]
>[Fax 01(771)717-2112]
>
>pagina / web page
>http://www.reduaeh.mx/investigacion/biologia/investigadores/
>monks_sheets.htm
>
>correo electrónico / email
><smonks at uaeh.edu.mx> y <scottmonks at hotmail.com>
>_____________________________________________________
>
>
>--
>_____________________________________________________
>
>Correo/ Mail
>
>Dr. Scott Monks
>Universidad Autónoma del Estado de Hidalgo (UAEH)
>Centro de Investigaciones Biológicas (CIB)
>Apdo. Postal 1-69
>Pachuca, C.P. 42001
>Hidalgo, México.
>
>
>Mensajería/ Courier
>
>Universidad Autónoma del Estado de Hidalgo (UAEH)
>Centro de Investigaciones Biológicas (CIB)
>Ciudad Universitaria, Carretera Pachuca-Tulancingo Km. 4.5 S/n
>Pachuca C.P. 42184
>Hidalgo, México
>
>[Tel 01(771)717-2000 Ext. 6658, 6640]
>[Fax 01(771)717-2112]
>
>pagina / web page
>http://www.reduaeh.mx/investigacion/biologia/investigadores/
>monks_sheets.htm
>
>correo electrónico / email
><smonks at uaeh.edu.mx> y <scottmonks at hotmail.com>
>_____________________________________________________
>
>
>
>_______________________________________________
>Mesquitelist mailing list
>Mesquitelist at mesquiteproject.org
>http://mesquiteproject.org/mailman/listinfo/mesquitelist
--
--------------------------------------------------------
Wayne Maddison
Professor and Canada Research Chair
Depts. of Zoology and Botany and
Biodiversity Research Centre
& Director
Beaty Biodiversity Museum
6270 University Boulevard
University of British Columbia
Vancouver, BC V6T 1Z4 Canada
email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416
Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org
Salticidae: http://salticidae.org
Tree of Life: http://tolweb.org
Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
Home page: http://salticidae.org/wpm/home.html
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