treebase-guts

[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

[SourceForge.net <no...@so...>]

Bugs item #2798604, was opened at 2009-05-29 23:21
Message generated for change (Tracker Item Submitted) made by blaiseli
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
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Category: data
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Mark Dominus (mjdominus)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

[SourceForge.net <no...@so...>]

Bugs item #2798604, was opened at 2009-05-29 17:21
Message generated for change (Settings changed) made by sfrgpiel
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
>Priority: 8
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Mark Dominus (mjdominus)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

----------------------------------------------------------------------

>Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 10:29

Message:
This looks like a difficult bug to fix because the problem stems from
Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from
a tree block that does not use a translation table. I've tried opening
trees like this in Mesquite v. 2 with no success... 

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 10:29

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

[SourceForge.net <no...@so...>]

Bugs item #2798604, was opened at 2009-05-29 21:21
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
Priority: 8
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Mark Dominus (mjdominus)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-06-27 07:31

Message:
The issue is because, although mesquite *can* create a taxa block on the
fly while reading a tree block without a translation table, it doesn't want
to. It prods the user for feedback, which makes the import hang in headless
mode. Bill has emailed the Maddisons about this, and it looks like the
issue could certainly be fixed in their code (even if that would make it
some sort of treebase special). But - then we have to fold that change into
our previous treebase special version of mesquite, which was a snapshot
roughly at version 2.1, and we're now at 2.6. I did some testing and some
methods have changed or have been removed, so we would need to adapt our
code base to that new api.

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
This looks like a difficult bug to fix because the problem stems from
Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from
a tree block that does not use a translation table. I've tried opening
trees like this in Mesquite v. 2 with no success... 

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

[SourceForge.net <no...@so...>]

Bugs item #2798604, was opened at 2009-05-29 21:21
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
>Priority: 7
Private: No
Submitted By: Blaise Li (blaiseli)
>Assigned to: Rutger Vos (rvos)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2009-11-18 18:23

Message:
This has been downgraded. We can't fix this unless mesquite gets fixed. If
people want to upload mrbayes files they will have to run them through
mesquite first on their own machines.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-06-27 07:31

Message:
The issue is because, although mesquite *can* create a taxa block on the
fly while reading a tree block without a translation table, it doesn't want
to. It prods the user for feedback, which makes the import hang in headless
mode. Bill has emailed the Maddisons about this, and it looks like the
issue could certainly be fixed in their code (even if that would make it
some sort of treebase special). But - then we have to fold that change into
our previous treebase special version of mesquite, which was a snapshot
roughly at version 2.1, and we're now at 2.6. I did some testing and some
methods have changed or have been removed, so we would need to adapt our
code base to that new api.

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
This looks like a difficult bug to fix because the problem stems from
Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from
a tree block that does not use a translation table. I've tried opening
trees like this in Mesquite v. 2 with no success... 

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

[SourceForge.net <no...@so...>]

Bugs item #2798604, was opened at 2009-05-29 21:21
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Rutger Vos (rvos)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2010-03-26 11:11

Message:
I think this needs to be closed: there is simply no way we will ever
support all nexus variants. It is a feature of treebase that we support
mesquite-compatible files. We state this very clearly. If people decide to
upload files that are not compatible with mesquite there's not much we can
do.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-11-18 18:23

Message:
This has been downgraded. We can't fix this unless mesquite gets fixed. If
people want to upload mrbayes files they will have to run them through
mesquite first on their own machines.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-06-27 07:31

Message:
The issue is because, although mesquite *can* create a taxa block on the
fly while reading a tree block without a translation table, it doesn't want
to. It prods the user for feedback, which makes the import hang in headless
mode. Bill has emailed the Maddisons about this, and it looks like the
issue could certainly be fixed in their code (even if that would make it
some sort of treebase special). But - then we have to fold that change into
our previous treebase special version of mesquite, which was a snapshot
roughly at version 2.1, and we're now at 2.6. I did some testing and some
methods have changed or have been removed, so we would need to adapt our
code base to that new api.

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
This looks like a difficult bug to fix because the problem stems from
Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from
a tree block that does not use a translation table. I've tried opening
trees like this in Mesquite v. 2 with no success... 

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

[SourceForge.net <no...@so...>]

Bugs item #2798604, was opened at 2009-05-29 17:21
Message generated for change (Comment added) made by hlapp
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
>Priority: 2
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Rutger Vos (rvos)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

----------------------------------------------------------------------

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 12:13

Message:
We won't fix this directly because we can't support all variants of NEXUS.
However, we should better document which NEXUS versions we do support, and
at some point we may also switch out Mesquite as the NEXUS parser to
another one, e.g., NCL. (Though no NEXUS parser can be expected to support
all flavors.)

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2010-03-26 07:11

Message:
I think this needs to be closed: there is simply no way we will ever
support all nexus variants. It is a feature of treebase that we support
mesquite-compatible files. We state this very clearly. If people decide to
upload files that are not compatible with mesquite there's not much we can
do.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-11-18 13:23

Message:
This has been downgraded. We can't fix this unless mesquite gets fixed. If
people want to upload mrbayes files they will have to run them through
mesquite first on their own machines.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-06-27 03:31

Message:
The issue is because, although mesquite *can* create a taxa block on the
fly while reading a tree block without a translation table, it doesn't want
to. It prods the user for feedback, which makes the import hang in headless
mode. Bill has emailed the Maddisons about this, and it looks like the
issue could certainly be fixed in their code (even if that would make it
some sort of treebase special). But - then we have to fold that change into
our previous treebase special version of mesquite, which was a snapshot
roughly at version 2.1, and we're now at 2.6. I did some testing and some
methods have changed or have been removed, so we would need to adapt our
code base to that new api.

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 10:29

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 10:29

Message:
This looks like a difficult bug to fix because the problem stems from
Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from
a tree block that does not use a translation table. I've tried opening
trees like this in Mesquite v. 2 with no success... 

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

[SourceForge.net <no...@so...>]

Bugs item #2798604, was opened at 2009-05-29 21:21
Message generated for change (Settings changed) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
Priority: 2
Private: No
Submitted By: Blaise Li (blaiseli)
>Assigned to: Nobody/Anonymous (nobody)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:56

Message:
OK, I am assigning this to "None". It is pointless to pretend that this is
a fixable bug. To be able to read MrBayes trees we will have to switch to a
newer mesquite. This is not a task that is properly assigned to me. I will
not do this.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:56

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 16:13

Message:
We won't fix this directly because we can't support all variants of NEXUS.
However, we should better document which NEXUS versions we do support, and
at some point we may also switch out Mesquite as the NEXUS parser to
another one, e.g., NCL. (Though no NEXUS parser can be expected to support
all flavors.)

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2010-03-26 11:11

Message:
I think this needs to be closed: there is simply no way we will ever
support all nexus variants. It is a feature of treebase that we support
mesquite-compatible files. We state this very clearly. If people decide to
upload files that are not compatible with mesquite there's not much we can
do.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-11-18 18:23

Message:
This has been downgraded. We can't fix this unless mesquite gets fixed. If
people want to upload mrbayes files they will have to run them through
mesquite first on their own machines.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2009-06-27 07:31

Message:
The issue is because, although mesquite *can* create a taxa block on the
fly while reading a tree block without a translation table, it doesn't want
to. It prods the user for feedback, which makes the import hang in headless
mode. Bill has emailed the Maddisons about this, and it looks like the
issue could certainly be fixed in their code (even if that would make it
some sort of treebase special). But - then we have to fold that change into
our previous treebase special version of mesquite, which was a snapshot
roughly at version 2.1, and we're now at 2.6. I did some testing and some
methods have changed or have been removed, so we would need to adapt our
code base to that new api.

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
This looks like a difficult bug to fix because the problem stems from
Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from
a tree block that does not use a translation table. I've tried opening
trees like this in Mesquite v. 2 with no success... 

----------------------------------------------------------------------

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804