RepLoad select() error - Githubissues

🐛 Bug

The RepLoad function used to work great for me but since updating my R version it now gives me the below error any time I try and load in data. The data is all the same as the data that used to work. Any help would be much appreciated!

> TCRdata <- repLoad("dummy_data.csv")

== Step 1/3: loading repertoire files... ==

Processing "data_1/" ...
  -- [1/14] Parsing "dummy_data.csv" -- airr
Error in `select()`:                                                                                                                                                                     
! Can't subset columns that don't exist.
✖ Column `cdr1` doesn't exist.
Run `rlang::last_trace()` to see where the error occurred.
Warning message:
`select_()` was deprecated in dplyr 0.7.0.
ℹ Please use `select()` instead.
ℹ The deprecated feature was likely used in the immunarch package.
  Please report the issue at <https://github.com/immunomind/immunarch/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. 
> 
> lifecycle::last_lifecycle_warnings()
[[1]]
<warning/lifecycle_warning_deprecated>
Warning:
`select_()` was deprecated in dplyr 0.7.0.
ℹ Please use `select()` instead.
ℹ The deprecated feature was likely used in the immunarch package.
  Please report the issue at <https://github.com/immunomind/immunarch/issues>.
---
Backtrace:
    ▆
 1. ├─immunarch::repLoad("data_1/")
 2. │ └─immunarch (local) .process_batch(batches[[batch_i]], .mode, .coding)
 3. │   └─immunarch (local) .read_repertoire(.filepath, .mode, .coding, ...)
 4. │     └─immunarch (local) parse_fun(.path, .mode, ...)
 5. │       └─df %<>% ...
 6. └─dplyr::select_(...)
 7.   └─dplyr:::lazy_deprec("select", hint = FALSE)

Additional context

Added my session info in if that helps.

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] immunarch_0.9.0   patchwork_1.1.2   data.table_1.14.8 dtplyr_1.3.1      pheatmap_1.0.12   lubridate_1.9.2   forcats_1.0.0     stringr_1.5.0    
 [9] dplyr_1.1.2       purrr_1.0.1       readr_2.1.4       tidyr_1.3.0       tibble_3.2.1      ggplot2_3.4.2     tidyverse_2.0.0  

loaded via a namespace (and not attached):
  [1] airr_1.4.1          gridExtra_2.3       phangorn_2.11.1     readxl_1.4.3        rlang_1.1.1         magrittr_2.0.3      compiler_4.3.1     
  [8] flexmix_2.3-19      vctrs_0.6.3         reshape2_1.4.4      ggalluvial_0.12.5   quadprog_1.5-8      crayon_1.5.2        pkgconfig_2.0.3    
 [15] shape_1.4.6         fastmap_1.1.1       ellipsis_0.3.2      backports_1.4.1     ggraph_2.1.0        utf8_1.2.3          promises_1.2.0.1   
 [22] tzdb_0.4.0          UpSetR_1.4.0        bit_4.0.5           modeltools_0.2-23   ggseqlogo_0.1       jsonlite_1.8.7      later_1.3.1        
 [29] uuid_1.1-0          fpc_2.2-10          tweenr_2.0.2        broom_1.0.5         parallel_4.3.1      prabclus_2.3-2      cluster_2.1.4      
 [36] R6_2.5.1            stringi_1.7.12      RColorBrewer_1.1-3  rlist_0.4.6.2       car_3.1-2           diptest_0.76-0      cellranger_1.1.0   
 [43] Rcpp_1.0.11         iterators_1.0.14    timechange_0.2.0    httpuv_1.6.11       Matrix_1.6-0        nnet_7.3-19         igraph_1.5.0       
 [50] tidyselect_1.2.0    yaml_2.3.7          stringdist_0.9.10   rstudioapi_0.15.0   abind_1.4-5         viridis_0.6.3       doParallel_1.0.17  
 [57] codetools_0.2-19    lattice_0.21-8      plyr_1.8.8          shiny_1.7.4.1       withr_2.5.0         polyclip_1.10-4     circlize_0.4.15    
 [64] mclust_6.0.0        kernlab_0.9-32      pillar_1.9.0        ggpubr_0.6.0        carData_3.0-5       foreach_1.5.2       stats4_4.3.1       
 [71] generics_0.1.3      vroom_1.6.3         hms_1.1.3           munsell_0.5.0       scales_1.2.1        xtable_1.8-4        class_7.3-22       
 [78] glue_1.6.2          tools_4.3.1         robustbase_0.99-0   ggsignif_0.6.4      graphlayouts_1.0.0  fastmatch_1.1-3     tidygraph_1.2.3    
 [85] grid_4.3.1          ape_5.7-1           colorspace_2.1-0    nlme_3.1-162        ggforce_0.4.1       cli_3.6.1           fansi_1.0.4        
 [92] viridisLite_0.4.2   gtable_0.3.3        DEoptimR_1.1-0      rstatix_0.7.2       digest_0.6.33       ggrepel_0.9.3       farver_2.1.1       
 [99] htmltools_0.5.5     lifecycle_1.0.3     factoextra_1.0.7    GlobalOptions_0.1.2 mime_0.12           bit64_4.0.5         shinythemes_1.2.0  
[106] MASS_7.3-60

data is attached here: dummy_data.csv

immunomind / immunarch

RepLoad select() error #368

🐛 Bug

Additional context