[Mesquitelist] possible bug?
Scott Monks
scottmonks at hotmail.com
Thu Feb 12 10:27:09 PST 2009
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.
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?
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.
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>
_____________________________________________________
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