getting error in summarise_rm_ID

[Ravindra-Raut]

hello Sir, I was analyzing repeat masker output for Oryza_sativa_HR12, was faced the following error, please suggest a solution. Should I share RMasker output file?

Oryza_sativa_HR12_aggregated <- summarise_rm_ID(Oryza_sativa_HR12)
Error in [.data.table(setDT(rm_table), , list(score = sum(score), p_sub = mean_psub(p_sub, :
Supplied 2 items for column 11 of group 380702 which has 3 rows. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code.

[dwinter]

Hi @Ravindra-Raut ,

Thanks for filing this issue. Just dropping you a note to say it's come at a very busy time, so it will be a little while until I can get to the bottom of what's going on. But it is in the TODO list!

[Ravindra-Raut]

Thank you for your consideration and response. I appreciate your time and efforts. Waiting for the solution.

[drhoads]

Figured out how to back track and get this installed in a Win10 running R4.0. Working on repeatMasker output on scorpion genome. Got to the
rm_file <- system.file("extdata", " Rat-FlyeP5-Final-101320.fasta.out", package="repeatR")
cvitattus <- read_rm(rm_file) #unfortunately, this line throws an error
error output:
Error in [.data.frame(raw_data, , 9) : undefined columns selected
In addition: Warning message:
In file(con, "r") :
file("") only supports open = "w+" and open = "w+b": using the former

[drhoads]

This was posted not for you but for dwinter, the developer. I am having a similar problem as you are. ***@***.*** From: Ravindra Raut ***@***.***> Sent: Monday, August 30, 2021 8:10 AM To: dwinter/repeatR ***@***.***> Cc: Douglas Duane Rhoads ***@***.***>; Comment ***@***.***> Subject: Re: [dwinter/repeatR] getting error in summarise_rm_ID (#4) Thank you sir, I will fallow your suggestions and I will try on rice genome assembly. Let's see how it goes. With regards Ravindra

On Mon, 30 Aug, 2021, 6:14 pm drhoads, ***@***.***<mailto:***@***.***>> wrote: Figured out how to back track and get this installed in a Win10 running R4.0. Working on repeatMasker output on scorpion genome. Got to the rm_file <- system.file("extdata", " Rat-FlyeP5-Final-101320.fasta.out", package="repeatR") cvitattus <- read_rm(rm_file) #unfortunately, this line throws an error error output: Error in [.data.frame(raw_data, , 9) : undefined columns selected In addition: Warning message: In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former - You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AICDXCLSIRHYQ2JNLJUACQLT7N4L7ANCNFSM5BF5YR7A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

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[Ravindra-Raut]

This was posted not for you but for dwinter, the developer. I am having a similar problem as you are. @.*** From: Ravindra Raut @.> Sent: Monday, August 30, 2021 8:10 AM To: dwinter/repeatR @.> Cc: Douglas Duane Rhoads @.>; Comment @.> Subject: Re: [dwinter/repeatR] getting error in summarise_rm_ID (#4) Thank you sir, I will fallow your suggestions and I will try on rice genome assembly. Let's see how it goes. With regards Ravindra
On Mon, 30 Aug, 2021, 6:14 pm drhoads, @.***mailto:***@***.***> wrote: Figured out how to back track and get this installed in a Win10 running R4.0. Working on repeatMasker output on scorpion genome. Got to the rm_file <- system.file("extdata", " Rat-FlyeP5-Final-101320.fasta.out", package="repeatR") cvitattus <- read_rm(rm_file) #unfortunately, this line throws an error error output: Error in [.data.frame(raw_data, , 9) : undefined columns selected In addition: Warning message: In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former - You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AICDXCLSIRHYQ2JNLJUACQLT7N4L7ANCNFSM5BF5YR7A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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I am waiting for the solution from dr david winter like you.

[simone-says]

I'm having this same issue: Error in [.data.table(setDT(rm_table), , list(score = sum(score), p_sub = mean_psub(p_sub, : Supplied 2 items for column 11 of group 1570388 which has 3 rows. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code.

[pgonzale60]

Hello dear developer,

I'm having the same error. I think that the function setDT is not defined in this repo at the moment. You must have it somewhere else. Could you share the function?

Best,
P