subject:"\[R\-sig\-phylo\] ape prop.part error malloc\(\)\: memory corruption"

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

2017-06-01 Thread Mario José Marques-Azevedo

Dears,

I removed ape 4.1 and install 4.0 version and the problem with my tree is
gone. I can extract clade even my tree having singletons. But the problem
still occur in example tree, with new error message. With this tree:

A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(E1,E2)E)D),(F1)F)R;

or

(A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),(F1)F)G)R;

I have this new error:

Error in phy$edge[, 2] : incorrect number of dimensions

And with this tree:

((A_1,A_2,)A,(B1,B2,B3)B)C)ABC,((D1,(E1,E2)E)D))DE,(F1)F)G)R;

rsession running infinitely. I need force stop.

Best regards,

Mario



On 1 June 2017 at 16:13, Mario José Marques-Azevedo 
wrote:

> Dear Eliot,
>
> Thank you for your answer! My tree is ok, but to plot is needed to
> collapse singles, as you said.
>
> I use ape/phytools to manipulate my tree for date it after with phylocom.
> Then, all node is important, including single one. For this, collapse
> singletons do not work for me. For instance.
>
> This trees:
>
> A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(E1,E2)E)D),(F1)F)R;
>
> (A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),(F1)F)G)R;
>
> 'collapsed' is:
>
> A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R;
>
> I lost 'F' node, as I said early. D1 is now in 'right' way.
>
> This tree:
>
> ((A_1,A_2,)A,(B1,B2,B3)B)C)ABC,((D1,(E1,E2)E)D))DE,(F1)F)G)R;
>
> 'collapsed' is:
>
> A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D)DE,F1)G;
>
> I lost 'F', 'R' and 'ABC' node.
>
> I have a big tree and some families has polytomies. Then, I extract each
> family (remove tips of this node), resolve plytomies, and I bind families
> tree again. After that, I date tree with phylocon. Phylocon use ages file
> with node age, then each node in my tree is important and collapse
> singletons would be a lost of information.
>
> I created one function to help me with extract node because I have issues
> using drop.tips (https://github.com/MarioJose/
> r-functions/blob/master/drop.clade.label/example.md).
>
> As I said, extract.node was working months ago. I don't know if this error
> is some updated that I did.
>
> Best regards,
>
> Mario
>
>
>
>
> On 1 June 2017 at 11:41, Eliot Miller  wrote:
>
>> Your Newick string is badly formatted. See:
>>
>> plot(t1)
>>
>> Error in plot.phylo(t1) :
>>   there are single (non-splitting) nodes in your tree; you may need to
>> use collapse.singles()
>>
>> On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo <
>> mariojm...@gmail.com> wrote:
>>
>>> Dears,
>>>
>>> I'm using extract.clade from ape package and get some issues. I'm using
>>> phytools package to load tree with single clade like above:
>>>
>>> library(phytools)
>>>
>>> t1 <- read.newick(text='(A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)
>>> E)D),(F1)F)G)R;')
>>>
>>> t2 <- read.newick(text='A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(
>>> E1,E2)E)D),(F1)F)R;
>>>
>>> When I extract 'F' clade, for instance:
>>>
>>> c1 <- extract.clade(t1, 'F')
>>>
>>> or
>>>
>>> c2 <- extract.clade(t2, 'F')
>>>
>>> I have this error:
>>>
>>> Error in prop.part(phy) : attempt to set index 8/8 in SET_VECTOR_ELT
>>>
>>> I have one tree with mode than 300 tips. When I try extract any clade, I
>>> have the same error. If I repeat the command I have this one:
>>>
>>> *** Error in `/usr/lib/rstudio/bin/rsession': malloc(): memory
>>> corruption:
>>> 0x0a3aaa40 ***
>>>
>>> My configurations was:
>>>
>>> platform   x86_64-pc-linux-gnu
>>> arch   x86_64
>>> os linux-gnu
>>> system x86_64, linux-gnu
>>> language   R
>>> version.string R version 3.3.3 (2017-03-06)
>>>
>>> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>>>
>>> I try update R to 3.4 and recompile all my packages, but I get the same
>>> error.
>>>
>>> My new configurations:
>>>
>>> platform   x86_64-pc-linux-gnu
>>> arch   x86_64
>>> os linux-gnu
>>> system x86_64, linux-gnu
>>> language   R
>>> version.string R version 3.4.0 (2017-04-21)
>>>
>>> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>>>
>>> I don't know why I have this error if I can extract with the same
>>> commands
>>> some time ago.
>>>
>>> I have the same error if I run in RStudio or in terminal. When I use
>>> RStudio, it abort after the error.
>>>
>>> I try Google, but I don't found nothing that can help me.
>>>
>>> Thank you and best regards,
>>>
>>> Mario
>>>
>>>
>>> 
>>> Mario José Marques-Azevedo
>>> Ph.D. Candidate in Ecology
>>> Department of Plant Biology, Institute of Biology
>>> University of Campinas, Campinas, São Paulo, Brazil
>>> https://github.com/mariojose 
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>> Searchable archive at

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

2017-06-01 Thread Mario José Marques-Azevedo

Dear Eliot,

Thank you for your answer! My tree is ok, but to plot is needed to collapse
singles, as you said.

I use ape/phytools to manipulate my tree for date it after with phylocom.
Then, all node is important, including single one. For this, collapse
singletons do not work for me. For instance.

This trees:

A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(E1,E2)E)D),(F1)F)R;

(A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),(F1)F)G)R;

'collapsed' is:

A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R;

I lost 'F' node, as I said early. D1 is now in 'right' way.

This tree:

((A_1,A_2,)A,(B1,B2,B3)B)C)ABC,((D1,(E1,E2)E)D))DE,(F1)F)G)R;

'collapsed' is:

A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D)DE,F1)G;

I lost 'F', 'R' and 'ABC' node.

I have a big tree and some families has polytomies. Then, I extract each
family (remove tips of this node), resolve plytomies, and I bind families
tree again. After that, I date tree with phylocon. Phylocon use ages file
with node age, then each node in my tree is important and collapse
singletons would be a lost of information.

I created one function to help me with extract node because I have issues
using drop.tips (https://github.com/MarioJose/r-functions/blob/master/drop.
clade.label/example.md).

As I said, extract.node was working months ago. I don't know if this error
is some updated that I did.

Best regards,

Mario




On 1 June 2017 at 11:41, Eliot Miller  wrote:

> Your Newick string is badly formatted. See:
>
> plot(t1)
>
> Error in plot.phylo(t1) :
>   there are single (non-splitting) nodes in your tree; you may need to use
> collapse.singles()
>
> On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo <
> mariojm...@gmail.com> wrote:
>
>> Dears,
>>
>> I'm using extract.clade from ape package and get some issues. I'm using
>> phytools package to load tree with single clade like above:
>>
>> library(phytools)
>>
>> t1 <- read.newick(text='(A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)
>> E)D),(F1)F)G)R;')
>>
>> t2 <- read.newick(text='A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(
>> E1,E2)E)D),(F1)F)R;
>>
>> When I extract 'F' clade, for instance:
>>
>> c1 <- extract.clade(t1, 'F')
>>
>> or
>>
>> c2 <- extract.clade(t2, 'F')
>>
>> I have this error:
>>
>> Error in prop.part(phy) : attempt to set index 8/8 in SET_VECTOR_ELT
>>
>> I have one tree with mode than 300 tips. When I try extract any clade, I
>> have the same error. If I repeat the command I have this one:
>>
>> *** Error in `/usr/lib/rstudio/bin/rsession': malloc(): memory
>> corruption:
>> 0x0a3aaa40 ***
>>
>> My configurations was:
>>
>> platform   x86_64-pc-linux-gnu
>> arch   x86_64
>> os linux-gnu
>> system x86_64, linux-gnu
>> language   R
>> version.string R version 3.3.3 (2017-03-06)
>>
>> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>>
>> I try update R to 3.4 and recompile all my packages, but I get the same
>> error.
>>
>> My new configurations:
>>
>> platform   x86_64-pc-linux-gnu
>> arch   x86_64
>> os linux-gnu
>> system x86_64, linux-gnu
>> language   R
>> version.string R version 3.4.0 (2017-04-21)
>>
>> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>>
>> I don't know why I have this error if I can extract with the same commands
>> some time ago.
>>
>> I have the same error if I run in RStudio or in terminal. When I use
>> RStudio, it abort after the error.
>>
>> I try Google, but I don't found nothing that can help me.
>>
>> Thank you and best regards,
>>
>> Mario
>>
>>
>> 
>> Mario José Marques-Azevedo
>> Ph.D. Candidate in Ecology
>> Department of Plant Biology, Institute of Biology
>> University of Campinas, Campinas, São Paulo, Brazil
>> https://github.com/mariojose 
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at http://www.mail-archive.com/r-
>> sig-ph...@r-project.org/
>
>
>

[[alternative HTML version deleted]]

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Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

2017-06-01 Thread Mario José Marques-Azevedo

Dear Klaus,

Thank you for your answer and good news that ape/phangorn will load tree
with singletons! Can I send the tree to your email?

My problem with collapse.singles is, for instance, when I have only one
genus/specie. I want the node name with genus and a tip name with species.
When I collapse, genus node name is removed. For instance:

This tree:

A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(E1,E2)E)D),(F1)F)R;

when 'collapsed' will be:

A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R;

Note that I lost node name 'F'.

I don't know why, but month ago I ran extract.clade of my tree without
problem. Maybe some update that I did, but I'm not sure.

Thank you again!

Best regards,
Mario

Mario José Marques-Azevedo
Ph.D. Candidate in Ecology
Department of Plant Biology, Institute of Biology
University of Campinas, Campinas, São Paulo, Brazil
https://github.com/mariojose

On 1 June 2017 at 11:43, Mario José Marques-Azevedo 
wrote:

> Dear Klaus,
>
> Thank you for your answer and good news that ape/phangorn will load tree
> with singletons! Can I send the tree to your email?
>
> My problem with collapse.singles is, for instance, when I have only one
> genus/specie. I want the node name with genus and a tip name with species.
> When I collapse, genus node name is removed. For instance:
>
> This tree:
>
> A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(E1,E2)E)D),(F1)F)R;
>
> when 'collapsed' will be:
>
> A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R;
>
> Note that I lost node name 'F'.
>
> I don't know why, but month ago I ran extract.clade of my tree without
> problem. Maybe some update that I did, but I'm not sure.
>
> Thank you again!
>
> Best regards,
>
> Mario
>
>
> 
> Mario José Marques-Azevedo
> Ph.D. Candidate in Ecology
> Department of Plant Biology, Institute of Biology
> University of Campinas, Campinas, São Paulo, Brazil
> https://github.com/mariojose
>
>
>
>
> On 1 June 2017 at 11:17, Klaus Schliep  wrote:
>
>> Dear Mario,
>> Emmanuel and I are working to allow singletons in ape / phangorn. In the
>> next version will read the tree in with read.tree().
>> Can you send me your larger tree for testing purposes, as it is one which
>> would fail at the moment?
>> Regards,
>> Klaus
>>
>>
>>
>>
>>
>>
>> On Thu, Jun 1, 2017 at 8:51 AM, Klaus Schliep 
>> wrote:
>>
>>> Hi Mario,
>>>
>>> the problem with your tree is that it contains singleton (nodes of
>>> degree 2). Try collapse.singles() before using extract.clade().
>>>
>>> Cheers,
>>> Klaus
>>>
>>>
>>>
>>>
>>> On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo <
>>> mariojm...@gmail.com> wrote:
>>>
 Dears,

 I'm using extract.clade from ape package and get some issues. I'm using
 phytools package to load tree with single clade like above:

 library(phytools)

 t1 <- read.newick(text='(A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)
 E)D),(F1)F)G)R;')

 t2 <- read.newick(text='A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(
 E1,E2)E)D),(F1)F)R;

 When I extract 'F' clade, for instance:

 c1 <- extract.clade(t1, 'F')

 or

 c2 <- extract.clade(t2, 'F')

 I have this error:

 Error in prop.part(phy) : attempt to set index 8/8 in SET_VECTOR_ELT

 I have one tree with mode than 300 tips. When I try extract any clade, I
 have the same error. If I repeat the command I have this one:

 *** Error in `/usr/lib/rstudio/bin/rsession': malloc(): memory
 corruption:
 0x0a3aaa40 ***

 My configurations was:

 platform   x86_64-pc-linux-gnu
 arch   x86_64
 os linux-gnu
 system x86_64, linux-gnu
 language   R
 version.string R version 3.3.3 (2017-03-06)

 phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)

 I try update R to 3.4 and recompile all my packages, but I get the same
 error.

 My new configurations:

 platform   x86_64-pc-linux-gnu
 arch   x86_64
 os linux-gnu
 system x86_64, linux-gnu
 language   R
 version.string R version 3.4.0 (2017-04-21)

 phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)

 I don't know why I have this error if I can extract with the same
 commands
 some time ago.

 I have the same error if I run in RStudio or in terminal. When I use
 RStudio, it abort after the error.

 I try Google, but I don't found nothing that can help me.

 Thank you and best regards,

 Mario

 Mario José Marques-Azevedo
 Ph.D. Candidate in Ecology
 Department of Plant Biology, Institute of Biology

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

2017-06-01 Thread Eliot Miller

Your Newick string is badly formatted. See:

plot(t1)

Error in plot.phylo(t1) :
  there are single (non-splitting) nodes in your tree; you may need to use
collapse.singles()

On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo <
mariojm...@gmail.com> wrote:

> Dears,
>
> I'm using extract.clade from ape package and get some issues. I'm using
> phytools package to load tree with single clade like above:
>
> library(phytools)
>
> t1 <- read.newick(text='(A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)
> E)D),(F1)F)G)R;')
>
> t2 <- read.newick(text='A_1,A_2,)A,(B1,B2,B3)B)C,D1))),(
> E1,E2)E)D),(F1)F)R;
>
> When I extract 'F' clade, for instance:
>
> c1 <- extract.clade(t1, 'F')
>
> or
>
> c2 <- extract.clade(t2, 'F')
>
> I have this error:
>
> Error in prop.part(phy) : attempt to set index 8/8 in SET_VECTOR_ELT
>
> I have one tree with mode than 300 tips. When I try extract any clade, I
> have the same error. If I repeat the command I have this one:
>
> *** Error in `/usr/lib/rstudio/bin/rsession': malloc(): memory corruption:
> 0x0a3aaa40 ***
>
> My configurations was:
>
> platform   x86_64-pc-linux-gnu
> arch   x86_64
> os linux-gnu
> system x86_64, linux-gnu
> language   R
> version.string R version 3.3.3 (2017-03-06)
>
> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>
> I try update R to 3.4 and recompile all my packages, but I get the same
> error.
>
> My new configurations:
>
> platform   x86_64-pc-linux-gnu
> arch   x86_64
> os linux-gnu
> system x86_64, linux-gnu
> language   R
> version.string R version 3.4.0 (2017-04-21)
>
> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10)
>
> I don't know why I have this error if I can extract with the same commands
> some time ago.
>
> I have the same error if I run in RStudio or in terminal. When I use
> RStudio, it abort after the error.
>
> I try Google, but I don't found nothing that can help me.
>
> Thank you and best regards,
>
> Mario
>
>
> 
> Mario José Marques-Azevedo
> Ph.D. Candidate in Ecology
> Department of Plant Biology, Institute of Biology
> University of Campinas, Campinas, São Paulo, Brazil
> https://github.com/mariojose 
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/

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Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

Re: [R-sig-phylo] ape prop.part error malloc(): memory corruption

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