Error during gl.read.dart

Nelia Perry

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Apr 28, 2025, 5:52:01 PMApr 28

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Hi all,

I have been having some issues where I get this same error message for lots of different commands that are very common for dartR and dartRverse packages, specifcially whenever I am trying to conert from one object type to another or input data etc. This is the error:

Error in as.vector(data) : no method for coercing this S4 class to a vector

In this specific case, this was the command line that caused the error:

placo_gl<-gl.read.dart(filename = "Placo_DArT_SNP.csv", ind.metafile = "placo_ind_metrics.csv", topskip = 6, lastmetric = 18)

I have tripled checked with multiple people that everything is correct. In fact, with all the same commands and input files, colleagues are not getting the same errors on their computers. I would really appreciate any help troubleshooting! I can provide any other additional information to make it clearer.

Best,

Nelia

Bernd.Gruber

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Apr 28, 2025, 6:47:51 PMApr 28

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Hi Nelia

Difficult to know what is going on. Can you check

library(adegenet)

packageVersion(“adegenet”)

packageVersion(“dartRverse”)

dartRverse_install()

and post what you get there.

Also maybe try not to use topskip and lastmetric (in theory should work out itself)

Cheers, Bernd

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Nelia Perry

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Apr 28, 2025, 8:13:44 PMApr 28

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Here are the results:

> packageVersion("dartRverse") [1] ‘1.0.6’ > packageVersion("adegenet") [1] ‘2.1.11’ > dartRverse_install() Error in dartRverse_install() : could not find function "dartRverse_install"

Bernd.Gruber

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Apr 28, 2025, 8:16:36 PMApr 28

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Can you load dartRverse via

library(dartRverse)

dartRverse_install()

and check if that works.

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Nelia Perry

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Apr 28, 2025, 11:17:00 PMApr 28

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Yes, here it is. When I was having trouble a few days ago I tried uninstalling all the packages and then reinstalling them (to start fresh) but since then I have not been able to get dartR.spatial or dartR.sexlinked to install again.

Bernd.Gruber

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May 1, 2025, 10:16:18 PMMay 1

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Hi Nelia,

Can you make sure have not loaded the dartR package (the legacy one).

Via packages (and if selected) unclick it.

Might be that you use both of the packages and that can cause trouble.

Cheers, Bernd

From: da...@googlegroups.com <da...@googlegroups.com> On Behalf Of Nelia Perry
Sent: Tuesday, 29 April 2025 10:32 AM
To: dartR <da...@googlegroups.com>
Subject: Re: [dartR] Error during gl.read.dart

Yes, here it is. When I was having trouble a few days ago I tried uninstalling all the packages and then reinstalling them (to start fresh) but since then I have not been able to get dartR.spatial or dartR.sexlinked to install again.

On Tuesday, April 29, 2025 at 10:16:36 AM UTC+10 Bernd. Gruber wrote:

Can you load dartRverse via

library(dartRverse)

dartRverse_install()

and check if that works.

To view this discussion visit https://groups.google.com/d/msgid/dartr/b1b66592-dab9-4bbb-8e7b-12ee057d1b2an%40googlegroups.com.

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Nelia Perry

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May 5, 2025, 1:21:21 AMMay 5

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Hi,

I do not have dartR installed.

Based on the help I have received, it seems the issue is related to the version of R I have relative to the versions of each package in dartRverse. When using a computer that has a newer version of R and of each package, I am not having any issues. I am working with IT at my institution to make sure these can be updated.

Thank you for all the help!

Best,

Nelia

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