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get_multimiR() nor working: get_multimiR may use as_data_frame(), which deprecated in tibble 2.0.0 for as_tibble() #51

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ChishanB opened this issue Oct 1, 2023 · 1 comment
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@ChishanB
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ChishanB commented Oct 1, 2023

get_multimiR() may use as_data_frame(), which deprecated in tibble 2.0.0 for as_tibble()

The source code is attached as a UTF-8 text file, and the main problem areas are pasted below. The file attached also shows the data frame contained by mature_miRNA_ids.
multimiR_problem.txt
Below are a snippet of my code (one where summary = FALSE and one where summary = TRUE), and the corresponding error message.

CONTEXT (output):

str(mature_miRNA_ids)
Classes ‘data.table’ and 'data.frame': 3 obs. of 1 variable:
$ miRNA_ids: chr "mmu-let-7f-5p_mature" "mmu-miR-199b-3p_mature" "mmu-miR-211-5p_mature"

  • attr(*, ".internal.selfref")=

ISSUE:
(When summary = FALSE)
multimiR_results <- get_multimir(org = "mmu",
mirna = mature_miRNA_ids,
table = "validated",
summary = FALSE)
Warning message:
as_data_frame() was deprecated in tibble 2.0.0.
ℹ Please use as_tibble() (with slightly different semantics) to convert to a tibble, or as.data.frame() to convert to a
data frame.
ℹ The deprecated feature was likely used in the multiMiR package.
Please report the issue at https://github.com/KechrisLab/multiMiR/issues.

(When summary = TRUE)
multimiR_problem.txt

multimiR_results <- get_multimir(org = "mmu",
mirna = mature_miRNA_ids,
table = "validated",
summary = TRUE)
Error in validObject(.Object) :
invalid class “mmquery_bioc” object: invalid object for slot "summary" in class "mmquery_bioc": got class "NULL", should be or extend class "data.frame"

@smahaffey smahaffey self-assigned this Oct 26, 2023
@smahaffey
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@ChishanB
Thank you. I will look at fixing this with the database update to avoid future issues when it's removed.

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