Error in Ops.data.frame

[AGibsonV]

Hi dartR Team,

I've encountered an error which I am unsure on how to fix. It occurs when trying to do any sort of gl.report or gl.filter step. For example:

> gl.report.rdepth(platypus.gl)

Starting gl.report.rdepth 
  Processing genlight object with SNP data
  Warning: data include loci that are scored NA across all individuals.
  Consider filtering using gl <- gl.filter.allna(gl)
  Reporting Read Depth by Locus
  No. of loci = 1000 
  No. of individuals = 81 
    Minimum      :  2.5 
    1st quartile :  7.975 
    Median       :  19 
    Mean         :  31.3504 
    3r quartile  :  46.2 
    Maximum      :  207.5 
    Missing Rate Overall:  0.07 

Error in Ops.data.frame(guide_loc, panel_loc) : 
  ‘==’ only defined for equally-sized data frames

I am currently using version 2.9.7 of dartR and using R version 4.1.1

What is strange is that these were working, but when I got to the gl.report.hwe/gl.filter.hwe step I needed the package "ggtern". Once I installed that package, this error emerged and now I am unable to a whole host of functions!

I tried installing the developing version of dartR (devtools::install_github("green-striped-gecko/dartR@dev")) and this updated a lot of other dependent packages. But still no luck.

Any help is appreciated.

Cheers,

Aline

[green-striped-gecko]

Hi AlineSounds like the ggplot2 error. Can you try to update to the latest ggplot2restart R and install.packages(“ggplot2”)Regards Bernd---------On 10 Jun 2024, at 22:58, AGibsonV @.***> wrote: Hi dartR Team, I've encountered an error which I am unsure on how to fix. It occurs when trying to do any sort of gl.report or gl.filter step. For example:

gl.report.rdepth(platypus.gl)

Starting gl.report.rdepth Processing genlight object with SNP data Warning: data include loci that are scored NA across all individuals. Consider filtering using gl <- gl.filter.allna(gl) Reporting Read Depth by Locus No. of loci = 1000 No. of individuals = 81 Minimum : 2.5 1st quartile : 7.975 Median : 19 Mean : 31.3504 3r quartile : 46.2 Maximum : 207.5 Missing Rate Overall: 0.07

Error in Ops.data.frame(guide_loc, panel_loc) : ‘==’ only defined for equally-sized data frames

I am currently using version 2.9.7 of dartR and using R version 4.1.1 What is strange is that these were working, but when I got to the gl.report.hwe/gl.filter.hwe step I needed the package "ggtern". Once I installed that package, this error emerged and now I am unable to a whole host of functions! I tried installing the developing version of dartR @.***")) and this updated a lot of other dependent packages. But still no luck. Any help is appreciated. Cheers, Aline

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>

[AGibsonV]

Hi Bernd,

Thanks for the advice, that worked! I had updated tidyverse which made me think ggplot2 was up-to-date when making this post, since ggplot2 resides within that broader package. However, that was not the case and updating it via the install.packages("ggplot2") resolved the issue.

Cheers,

Aline

---

From: Bernd Gruber @.> Sent: Tuesday, 11 June 2024 5:52 AM To: green-striped-gecko/dartR @.> Cc: Aline Gibson Vega @.>; Author @.> Subject: Re: [green-striped-gecko/dartR] Error in Ops.data.frame (Issue #665)

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Hi AlineSounds like the ggplot2 error. Can you try to update to the latest ggplot2restart R and install.packages(“ggplot2”)Regards Bernd---------On 10 Jun 2024, at 22:58, AGibsonV @.***> wrote: Hi dartR Team, I've encountered an error which I am unsure on how to fix. It occurs when trying to do any sort of gl.report or gl.filter step. For example:

gl.report.rdepth(platypus.gl)

Starting gl.report.rdepth Processing genlight object with SNP data Warning: data include loci that are scored NA across all individuals. Consider filtering using gl <- gl.filter.allna(gl) Reporting Read Depth by Locus No. of loci = 1000 No. of individuals = 81 Minimum : 2.5 1st quartile : 7.975 Median : 19 Mean : 31.3504 3r quartile : 46.2 Maximum : 207.5 Missing Rate Overall: 0.07

Error in Ops.data.frame(guide_loc, panel_loc) : ‘==’ only defined for equally-sized data frames

I am currently using version 2.9.7 of dartR and using R version 4.1.1 What is strange is that these were working, but when I got to the gl.report.hwe/gl.filter.hwe step I needed the package "ggtern". Once I installed that package, this error emerged and now I am unable to a whole host of functions! I tried installing the developing version of dartR @.***")) and this updated a lot of other dependent packages. But still no luck. Any help is appreciated. Cheers, Aline

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/green-striped-gecko/dartR/issues/665#issuecomment-2159351513, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A6QXQGKHGZOW5KV2TZCZC43ZGYNZ7AVCNFSM6AAAAABJCIJOLOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJZGM2TCNJRGM. You are receiving this because you authored the thread.Message ID: @.***>

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