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immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
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dbLoad() cannot load #361

Open KforKuma opened 1 year ago

KforKuma commented 1 year ago

🐛 Bug

When I am trying example code tbadb = dbLoad("https://gitlab.com/immunomind/immunarch/raw/dev-0.5.0/private/TBAdb.xlsx", "tbadb", .species = "Homo Sapiens", .chain = c("TRB", "TRA-TRB"), .pathology = "CMV") tbadb it firstly returns an error, same as

Error: path does not exist: ‘https://gitlab.com/immunomind/immunarch/raw/dev-0.5.0/private/TBAdb.xlsx’

After changing the website to the address of local data file, tbadb = dbLoad("/path/to/TBAdb.xlsx", "tbadb", .species = "Homo Sapiens", .chain = c("TRB", "TRA-TRB"), .pathology = "CMV")

Error in if (!is.na(.chain)) { : the condition has length > 1

Another error returns, this time indicating the little problem in annotation.R line 94, that !is.na(.species) returns multiple "TRUE" when a vector is given to .chain.

To Reproduce

Steps to reproduce the behavior:

  1. tbadb = dbLoad("https://gitlab.com/immunomind/immunarch/raw/dev-0.5.0/private/TBAdb.xlsx", "tbadb", .species = "Homo Sapiens", .chain = c("TRB", "TRA-TRB"), .pathology = "CMV") tbadb or tbadb = dbLoad("/path/to/TBAdb.xlsx", "tbadb", .species = "Homo Sapiens", .chain = c("TRB", "TRA-TRB"), .pathology = "CMV")

Expected behavior

Additional context