- using R version 4.5.3 (2026-03-11 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.3.0
GNU Fortran (GCC) 14.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'immundata/DESCRIPTION' ... OK
- this is package 'immundata' version '0.1.0'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'immundata' can be installed ... OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s] OK
- checking whether the package can be unloaded cleanly ... [2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s] OK
- checking loading without being on the library search path ... [3s] OK
- checking whether startup messages can be suppressed ... [2s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [11s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking examples ... [38s] ERROR
Running examples in 'immundata-Ex.R' failed
The error most likely occurred in:
> ### Name: read_repertoires
> ### Title: Read immune repertoire files into ImmunData
> ### Aliases: read_repertoires
>
> ### ** Examples
>
> library(immundata)
> library(dplyr)
>
> options(immundata.verbose = FALSE)
>
> # Read one bulk AIRR file and preserve its abundance column
> bulk_file <- system.file(
+ "extdata/tsv",
+ "sample_0_1k.tsv",
+ package = "immundata"
+ )
>
> bulk_idata <- read_repertoires(
+ path = bulk_file,
+ schema = c("cdr3_aa", "v_call"),
+ count_col = "counts",
+ output_folder = tempfile("immundata-bulk-")
+ )
>
> tibble(
+ n_records = bulk_idata |> count() |> pull(n),
+ n_receptors = bulk_idata$receptors |> count() |> collect() |> pull(n),
+ n_repertoires = nrow(bulk_idata$repertoires)
+ )
Warning in file(file, ifelse(append, "a", "w")) :
cannot open file 'C:\Users\CRAN\AppData\Local/R/cache/R/duckplyr/telemetry/79372.ndjson': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
Calls: tibble ... arrange.data.frame -> rel_try -> tel_collect -> cat -> file
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [216s] OK
Running 'testthat.R' [216s]
- checking PDF version of manual ... [19s] OK
- checking HTML version of manual ... [8s] OK
- DONE
Status: 1 ERROR