Error in params_into_BioGeoBEARS_model_object(BioGeoBEARS_model

Pete Darwin

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Aug 3, 2015, 10:51:21 PM8/3/15

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Hey there, I'm getting the following error msg and am just wondering what I need to do to resolve it. I've attached the files. The tree was a *BEAST tree with some very short branch lengths that I substituted with 0.001. The analysis gets halfway through and then gives me the error msg pasted below. Any advice would be much appreciated! Cheers

Error in params_into_BioGeoBEARS_model_object(BioGeoBEARS_model_object, :

replacement has length zero

In addition: Warning message:

In (function (npt = min(n + 2L, 2L * n), rhobeg = NA, rhoend = NA, :

unused control arguments ignored

sBEASTtree.newick

sBEAST.txt

Nick Matzke

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Aug 3, 2015, 11:11:29 PM8/3/15

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Hi -- this issue is something minor with counting the free parameters, I think after the main calculations have been done. Very likely this is due to missing one of the source() updates, see:

http://phylo.wikidot.com/biogeobears-mistakes-to-avoid#source_everything2

Nick

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Pete Darwin

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Aug 3, 2015, 11:38:16 PM8/3/15

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Thanks Nick. Turned out you were right. Firewall here where I work won't allow the sources to be used in R so did it on my telephones connection and it works fine now. Cheers.

Frank Koehler

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Dec 11, 2018, 3:25:11 AM12/11/18

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Hi

I have exactly the same problem. Have downloaded all updated libraries, but the error message stays.

Pete seemed to have a problem with his firewall, so I also turned my firewall off... still the same.

The scripts worked fine before the update.

I wonder if it was possible to download and locally source the updates from github to prevent the firewall problems?!

Cheers

Frank

Nick Matzke

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Dec 11, 2018, 5:03:54 PM12/11/18

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Hi -- the firewall issue shouldn't matter all all now that the script uses the GitHub install instead of source() on online files -- assuming you actually successfully installed the updated version from GitHub, *and* removed any old versions installed in R, see hints on doing this: https://groups.google.com/forum/#!searchin/biogeobears/detach%7Csort:date/biogeobears/2f9etrphhmg/0Jg1YIoOBwAJ

But, if you want to download all the updated BioGeoBEARS R files that you used to use source() opn, all you have to do is:

1. https://github.com/nmatzke/BioGeoBEARS

2. Go to the green Clone or download button

3. Click Download Zip

4. Unzip somewhere. The R source files are in the "R" subdirectory

5a. write out a bunch of source() commands to source the exact location on your hard drive for each file, or (easier)

5b. use the BioGeoBEARS sourceall() command to source everything in that R directory

All that said, it would be easier to just make sure the old installs are gone (just keep repeating library(BioGeoBEARS) and the various detach / remove.packages commands at

https://groups.google.com/forum/#!searchin/biogeobears/detach%7Csort:date/biogeobears/2f9etrphhmg/0Jg1YIoOBwAJ

...until library(BioGeoBEARS) no longer works, then and then just install the new GitHub version, assuming your firewall lets you install anything from GitHub.

Cheers,

Nick

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Nicolas Brignone

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Dec 12, 2018, 10:01:11 AM12/12/18

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Hi,

I have the same problem. So, I did all of this, even I uninstalled R and RStudio from my laptop (and deleted the R folder), then I have installed R/RStudio again. I don't know why I cannot install the version 1.1 of BGB from github; only the version 0.2 from CRAN.

I'm new in R, and probably because of this I don't know what I'm not doing well.

The files are OK, because both the dated tree and the distribution file are read.

Any suggestions for a new user?

Thanks in advance

Nico

Nick Matzke

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Dec 12, 2018, 6:34:12 PM12/12/18

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Hi,

I can't help if I don't see an error message on the GitHub install. The instructions to install from GitHub are here: https://github.com/nmatzke/BioGeoBEARS

...pasting below...

========================

(first, install devtools, and MAKE SURE all previous BioGeoBEARS installs are removed, i.e. "library(BioGeoBEARS)" should return an error indicating no package)

...then...

library(devtools)

devtools::install_github(repo="nmatzke/BioGeoBEARS")

========================

The BioGeoBEARS R package is "pure R" and so should install very easily (no compilers etc. needed).

Cheers,

Nick

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Nicolas Brignone

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Dec 13, 2018, 6:38:02 AM12/13/18

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Hi Nick,

Thanks for your reply.

First, I uninstalled BioGeoBEARS, rexpokit and cladoRcpp.

Then, I have installed again rexpokit and cladoRcpp, as is indicated at https://github.com/nmatzke/BioGeoBEARS.

This message appears:

> library(devtools)

> devtools::install_github(repo="nmatzke/BioGeoBEARS")

Downloading GitHub repo nmatzke/BioGeoBEARS@master

These packages have more recent versions available.

Which would you like to update?

1: rexpokit (0.26.6 -> 1701a011b...) [GitHub]

2: cladoRcpp (0.15.1 -> 202e0a393...) [GitHub]

3: CRAN packages only

4: All

5: None

Enter one or more numbers separated by spaces, or an empty line to cancel

1:

I don´t know what set, because I have already installed rexpokit and cladoRcpp.

If I leave empty the line (so, I press enter), this message appears:

√ checking for file 'C:\Users\Nicolás\AppData\Local\Temp\RtmpYTBmsJ\remotes10246d20a7a\nmatzke-BioGeoBEARS-6780624/DESCRIPTION' ...

- preparing 'BioGeoBEARS': (2.3s)

√ checking DESCRIPTION meta-information ...

Warning in .write_description(db, ldpath) :

Unknown encoding with non-ASCII data: converting to ASCII

- checking for LF line-endings in source and make files and shell scripts

- checking for empty or unneeded directories

- building 'BioGeoBEARS_1.1.1.tar.gz'

Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L, :