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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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Lots of warnings when running get_ssm_by_sample example in the vignette #156

Closed rdmorin closed 1 year ago

rdmorin commented 1 year ago

Can someone please determine if these warnings can be safely suppressed or find a way to avoid them happening?

this_sample = "00-15201_tumorA"

this_sample_ssm = get_ssm_by_sample(this_sample_id = this_sample, 
+                                     this_seq_type = "genome",
+                                     projection = "grch37")
you should also run this command to ensure the ssh library is loaded:
library(ssh)
Warning messages:                                                                                                                            
1: In data.table::fread(file = maf_file_path, sep = "\t", stringsAsFactors = FALSE,  :
  Attempt to override column 59 <<DISTANCE>> of inherent type 'float64' down to 'bool8' ignored. Only overrides to a higher type are currently supported. If this was intended, please coerce to the lower type afterwards.
2: In data.table::fread(file = maf_file_path, sep = "\t", stringsAsFactors = FALSE,  :
  Attempt to override column 89 <<MOTIF_NAME>> of inherent type 'string' down to 'bool8' ignored. Only overrides to a higher type are currently supported. If this was intended, please coerce to the lower type afterwards.
3: In data.table::fread(file = maf_file_path, sep = "\t", stringsAsFactors = FALSE,  :
  Attempt to override column 90 <<MOTIF_POS>> of inherent type 'float64' down to 'bool8' ignored. Only overrides to a higher type are currently supported. If this was intended, please coerce to the lower type afterwards.
4: In data.table::fread(file = maf_file_path, sep = "\t", stringsAsFactors = FALSE,  :
  Attempt to override column 91 <<HIGH_INF_POS>> of inherent type 'string' down to 'bool8' ignored. Only overrides to a higher type are currently supported. If this was intended, please coerce to the lower type afterwards.