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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.
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"
The text was updated successfully, but these errors were encountered:
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):
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, oras.data.frame()
to convert to adata 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"
The text was updated successfully, but these errors were encountered: