RepLoad select() error
annabellaidler opened this issue · 1 comments
annabellaidler commented
🐛 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
vadimnazarov commented
Thank you, on it!