Re: [R-sig-phylo] RMesquite package

2017-12-03 Thread Ayelet Salman 
Dear Hilmar, Jeannine and r-sig-phylo members,

Here's the error I get when trying to load RMesquite package on R, from
RStudio with R version 3.4.2
(the same error occurs when I try to load it on Linux with R versions: 215,
301, 310, 322, 342)

I have tried two loading options:

> install.packages("RMesquite", repos="http://R-Forge.R-project.org;)
Installing package into ‘D:/My Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘RMesquite’ is not available (for R version 3.4.1)

> install.packages("RMesquite")
Installing package into ‘D:/My Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘RMesquite’ is not available (for R version 3.4.1)

Thanks for the help
Best,
Ayelet

On Fri, Dec 1, 2017 at 7:54 PM, Hilmar Lapp  wrote:

> Ayelet - If you provide the exact error that prevents you from loading
> RMesquite, I can try to see what the underlying cause might be. I can’t
> help you with using Mesquite itself , but others on the list may, which is
> why I’m copying the list.
>
> Jeannine - I don’t know right now which version(s) of R won’t work with
> RMesquite. But the rJava package that it’s dependent on has I believe
> undergone some changes recently, so I’m not surprised if recent versions of
> R don’t work. (Can you report the error you were getting?)
>
> I think if there’s some continued interest for this package what would be
> best is to migrate it to being hosted on Github. At the time that would
> have made integration with the R package management difficult, which is why
> we chose R-Forge, but I think now if anything it’s the opposite. And Github
> is what I (and probably most others here) use all the time, so would be
> vastly preferable for maintenance for that reason alone. I’ll look into
> that later this month (unless someone wants to beat me to it).
>
> -hilmar
>
> Sent from away
>
> On Sep 23, 2017, at 3:31 AM, Ayelet Salman 
> wrote:
>
> Dear Hilmar,
>
> I wasn't able to load RMesquite,
> I will very much appreciate your help with the Mesquite software
> Could you please guide me how to us Mesquite tools on batch data?
>
> e.g. applying the pairwise comparison tool on trees and character data,
> for several different genera.
> Currently I am loading the tree and data for every genera separately, and
> appling the pairwise comparison test for every genera. How can I save time
> and apply these same steps on the different genera data?
>
> Thanks,
> Ayelet
>
>
> 
>  בלי
> וירוסים. www.avast.com
> 
> <#m_-6091983636188628197_m_1630277254929088098_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> On Wed, Sep 13, 2017 at 5:28 PM, Hilmar Lapp  wrote:
>
>> Hi Ayelet,
>>
>> Instructions for installing RMesquite are on the project’s homepage:
>> http://rmesquite.r-forge.r-project.org
>> 
>>
>> Let us know if the information there doesn’t answer your question.
>>
>>   -hilmar
>>
>> > On Sep 11, 2017, at 6:10 AM, Ayelet Salman 
>> wrote:
>> >
>> > Dear r-SIG-phylo members,
>> >
>> > I have tried to call the RMesquite package from R but got an error that
>> it
>> > is not available.
>> > Do you know how to download and install RMesquite (on windows or
>> server)?
>> >
>> > Any other idea how to use Mesquite or  the pairwise comparison tool
>> > (Maddison 2000) on a large scale data?
>> >
>> > Best,
>> > Ayelet
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > ___
>> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> hz.ch_mailman_listinfo_r-2Dsig-2Dphylo=DwICAg=imBPVzF25O
>> nBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpq
>> F6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_
>> iyAKw37Moc=DHck5zYgVyyIMKf18p3DZPx7bi7GjTzk9iVikg8hqN4=
>> > Searchable archive at https://urldefense.proofpoint.
>>

Re: [R-sig-phylo] RMesquite package

2017-12-01 Thread Hilmar Lapp 
Ayelet - If you provide the exact error that prevents you from loading 
RMesquite, I can try to see what the underlying cause might be. I can’t help 
you with using Mesquite itself , but others on the list may, which is why I’m 
copying the list.

Jeannine - I don’t know right now which version(s) of R won’t work with 
RMesquite. But the rJava package that it’s dependent on has I believe undergone 
some changes recently, so I’m not surprised if recent versions of R don’t work. 
(Can you report the error you were getting?)

I think if there’s some continued interest for this package what would be best 
is to migrate it to being hosted on Github. At the time that would have made 
integration with the R package management difficult, which is why we chose 
R-Forge, but I think now if anything it’s the opposite. And Github is what I 
(and probably most others here) use all the time, so would be vastly preferable 
for maintenance for that reason alone. I’ll look into that later this month 
(unless someone wants to beat me to it).

-hilmar

Sent from away

On Sep 23, 2017, at 3:31 AM, Ayelet Salman 
> wrote:

Dear Hilmar,

I wasn't able to load RMesquite,
I will very much appreciate your help with the Mesquite software
Could you please guide me how to us Mesquite tools on batch data?

e.g. applying the pairwise comparison tool on trees and character data, for 
several different genera.
Currently I am loading the tree and data for every genera separately, and 
appling the pairwise comparison test for every genera. How can I save time and 
apply these same steps on the different genera data?

Thanks,
Ayelet

[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]
 בלי וירוסים. 
www.avast.com

On Wed, Sep 13, 2017 at 5:28 PM, Hilmar Lapp 
> wrote:
Hi Ayelet,

Instructions for installing RMesquite are on the project’s homepage:
http://rmesquite.r-forge.r-project.org

Let us know if the information there doesn’t answer your question.

  -hilmar

> On Sep 11, 2017, at 6:10 AM, Ayelet Salman 
> > wrote:
>
> Dear r-SIG-phylo members,
>
> I have tried to call the RMesquite package from R but got an error that it
> is not available.
> Do you know how to download and install RMesquite (on windows or server)?
>
> Any other idea how to use Mesquite or  the pairwise comparison tool
> (Maddison 2000) on a large scale data?
>
> Best,
> Ayelet
>
>   [[alternative HTML version deleted]]
>
> ___
> R-sig-phylo mailing list - 
> R-sig-phylo@r-project.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo=DwICAg=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_iyAKw37Moc=DHck5zYgVyyIMKf18p3DZPx7bi7GjTzk9iVikg8hqN4=
> Searchable archive at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject.org_=DwICAg=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_iyAKw37Moc=EjBfROurcmBvQ9sM3pHs1y9fP9PgQG5bBoN54T4tUsY=

--
Hilmar Lapp -:- genome.duke.edu -:- 
lappland.io



[[alternative HTML version deleted]]

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Re: [R-sig-phylo] RMesquite package

2017-09-13 Thread Hilmar Lapp 
Hi Ayelet,

Instructions for installing RMesquite are on the project’s homepage:
http://rmesquite.r-forge.r-project.org

Let us know if the information there doesn’t answer your question.

  -hilmar

> On Sep 11, 2017, at 6:10 AM, Ayelet Salman  wrote:
> 
> Dear r-SIG-phylo members,
> 
> I have tried to call the RMesquite package from R but got an error that it
> is not available.
> Do you know how to download and install RMesquite (on windows or server)?
> 
> Any other idea how to use Mesquite or  the pairwise comparison tool
> (Maddison 2000) on a large scale data?
> 
> Best,
> Ayelet
> 
>   [[alternative HTML version deleted]]
> 
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo=DwICAg=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_iyAKw37Moc=DHck5zYgVyyIMKf18p3DZPx7bi7GjTzk9iVikg8hqN4=
>  
> Searchable archive at 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject.org_=DwICAg=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=eGWUXrFTNKFQ_7iv2ZZTsTpqF6jBUoOs67dzNTy0W_Y=nLcvm2XyiPq2SigT7Kkz_OgewmzetB3W_iyAKw37Moc=EjBfROurcmBvQ9sM3pHs1y9fP9PgQG5bBoN54T4tUsY=
>  

-- 
Hilmar Lapp -:- genome.duke.edu -:- lappland.io

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[R-sig-phylo] RMesquite package

2017-09-13 Thread Ayelet Salman 
Dear r-SIG-phylo members,

I have tried to call the RMesquite package from R but got an error that it
is not available.
Do you know how to download and install RMesquite (on windows or server)?

Any other idea how to use Mesquite or  the pairwise comparison tool
(Maddison 2000) on a large scale data?

Best,
Ayelet

[[alternative HTML version deleted]]

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Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/