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

[ChishanB]

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]

@ChishanB Thank you. I will look at fixing this with the database update to avoid future issues when it's removed.