SomaLogic/SomaDataIO

Error when using read_adat() + issue in setup script

Hijinx725 opened this issue · 2 comments

Hijinx725 commented

Checks

  • Please search previous issues before creating a new one,
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  • Please include a minimal reproducible example (AKA a reprex)

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please start by reading https://www.tidyverse.org/help/#reprex.

Description

Please briefly describe the problem you have encountered
and what output you expected ...

I tired this code from the readme:

f <- system.file("extdata", "example_data10.adat",
package = "SomaDataIO", mustWork = TRUE)
my_adat <- read_adat(f)
is.soma_adat(my_adat)
my_adat

Also, in /data_raw/SomaScanObjects.R there is a missing ')' in the second function.

Output

Error in gsub_(st$close, st$open, text, fixed = TRUE, useBytes = TRUE) : 
  could not find function "gsub_"
In addition: Warning message:
In is_string(left) : restarting interrupted promise evaluation

Expected Output

table

Steps

Please describe any steps you have already taken that may
assist in reproducing the (unexpected) behavior:

  • installed SomaDataIO from R ( version 4.1.2 )
  • installed missing required packages listed in readme

Priority Level

  • High
  • Medium
  • Low

Thanks for reporting 🥳!

stufield commented

Hi @Hijinx725 ,

  • unfortunately I am unable to reproduce the error you are experiencing. Could you please generate a proper reprex that reproduces the error? Specifically, which version of SomaDataIO you are using (v6.0.0?)
  • the SomaScanObjects.R script is meant for updating package objects only, and is not intended for end user interaction (see .Rbuildignore). However, thank you for the catch, I will fix in an upcoming PR.

Thank you!

stufield commented

@Hijinx725 was this issue resolved?

I'm re-opening this issue so the PR can close it when merged

  • 👀1