seurat v5 compatibility issues

[onetaoneryan]

HI，
Thanks for creating augur. I was able to run augur successfully a few months ago, but can't do it these days. Is this related to the version of Seurat？ any input is appreciated!

augur = calculate_auc(sc_sim)
using default assay: RNA ...
| | 0%, ETA NA
Error in filter():
ℹ In argument: metric == "roc_auc".
Caused by error:
! object 'metric' not found
Run rlang::last_trace() to see where the error occurred.
Warning message:
In mclapply(X, function(...) { :
all scheduled cores encountered errors in user code

Best，

Ran

[AlanTeoYueYang]

Hi Ran,

I managed to get Augur to run on Seurat V5.0.1 with just a warning message.
Can you share with me your data so I can see what the issue might be?
Thanks.

Best,
Alan

[TuoCai2000]

Hi,I also encountered the same issue,can you help me?
My Seurat version is ‘5.1.0’

[onetaoneryan]

Thank you for reply.

library(Augur)

augur = calculate_auc(sc_sim)
using default assay: RNA ...
| | 0%, ETA NA
Error in filter():
ℹ In argument: metric == "roc_auc".
Caused by error:
! object 'metric' not found
Run rlang::last_trace() to see where the error occurred.
Warning message:
In mclapply(X, function(...) { :
all scheduled cores encountered errors in user code

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.5.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

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: America/Chicago
tzcode source: internal

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] Augur_1.0.3 lubridate_1.9.3 forcats_1.0.0
[4] stringr_1.5.1 purrr_1.0.2 readr_2.1.5
[7] tibble_3.2.1 tidyverse_2.0.0 tidyr_1.3.1
[10] DESeq2_1.44.0 patchwork_1.3.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3
[13] BSgenome_1.72.0 rtracklayer_1.64.0 BiocIO_1.14.0
[16] Biostrings_2.72.1 XVector_0.44.0 TFBSTools_1.42.0
[19] JASPAR2020_0.99.10 shiny_1.9.1 Matrix_1.7-0
[22] monocle3_1.3.7 SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0
[25] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 IRanges_2.38.1
[28] S4Vectors_0.42.1 MatrixGenerics_1.19.0 matrixStats_1.4.1
[31] Biobase_2.64.0 BiocGenerics_0.50.0 dplyr_1.1.4
[34] ggplot2_3.5.1 Signac_1.13.0 Seurat_5.1.0
[37] SeuratObject_5.0.2 sp_2.1-4

loaded via a namespace (and not attached):
[1] R.methodsS3_1.8.2 dichromat_2.0-0.1 urlchecker_1.0.1
[4] nnet_7.3-19 poweRlaw_0.80.0 goftest_1.2-3
[7] vctrs_0.6.5 spatstat.random_3.3-2 digest_0.6.37
[10] png_0.1-8 proxy_0.4-27 ggrepel_0.9.6
[13] deldir_2.0-4 parallelly_1.38.0 MASS_7.3-60.2
[16] reshape2_1.4.4 httpuv_1.6.15 withr_3.0.1
[19] ggrastr_1.0.2 ellipsis_0.3.2 survival_3.6-4
[22] memoise_2.0.1 s2_1.1.7 ggbeeswarm_0.7.2
[25] parsnip_1.2.1 profvis_0.3.8 systemfonts_1.1.0
[28] ragg_1.3.2 zoo_1.8-12 gtools_3.9.5
[31] pbapply_1.7-2 R.oo_1.26.0 spData_2.3.3
[34] KEGGREST_1.44.1 promises_1.3.0 httr_1.4.7
[37] restfulr_0.0.15 globals_0.16.3 fitdistrplus_1.2-1
[40] ps_1.7.7 rstudioapi_0.16.0 UCSC.utils_1.0.0
[43] units_0.8-5 miniUI_0.1.1.1 generics_0.1.3
[46] processx_3.8.4 curl_5.2.3 zlibbioc_1.50.0
[49] randomForest_4.7-1.2 polyclip_1.10-7 GenomeInfoDbData_1.2.12
[52] SparseArray_1.4.8 xtable_1.8-4 desc_1.4.3
[55] pracma_2.4.4 S4Arrays_1.4.1 hms_1.1.3
[58] irlba_2.3.5.1 colorspace_2.1-1 ROCR_1.0-11
[61] reticulate_1.39.0 spatstat.data_3.1-2 magrittr_2.0.3
[64] lmtest_0.9-40 spdep_1.3-6 later_1.3.2
[67] viridis_0.6.5 lattice_0.22-6 mapproj_1.2.11
[70] spatstat.geom_3.3-3 future.apply_1.11.2 scattermore_1.2
[73] XML_3.99-0.17 cowplot_1.1.3 RcppAnnoy_0.0.22
[76] class_7.3-22 pillar_1.9.0 nlme_3.1-164
[79] pwalign_1.0.0 caTools_1.18.3 compiler_4.4.1
[82] RSpectra_0.16-2 stringi_1.8.4 gower_1.0.1
[85] sf_1.0-17 tensor_1.5 minqa_1.2.8
[88] devtools_2.4.5 GenomicAlignments_1.40.0 plyr_1.8.9
[91] crayon_1.5.3 abind_1.4-8 locfit_1.5-9.10
[94] pals_1.9 bit_4.0.5 fastmatch_1.1-4
[97] codetools_0.2-20 textshaping_0.4.0 recipes_1.1.0
[100] bslib_0.8.0 slam_0.1-53 e1071_1.7-16
[103] plotly_4.10.4 mime_0.12 leidenbase_0.1.31
[106] rsample_1.2.1 splines_4.4.1 Rcpp_1.0.13
[109] fastDummies_1.7.4 sparseMatrixStats_1.17.2 blob_1.2.4
[112] utf8_1.2.4 seqLogo_1.70.0 lme4_1.1-35.5
[115] fs_1.6.4 listenv_0.9.1 DelayedMatrixStats_1.26.0
[118] pkgbuild_1.4.4 callr_3.7.6 statmod_1.5.0
[121] tzdb_0.4.0 tweenr_2.0.3 pkgconfig_2.0.3
[124] tools_4.4.1 cachem_1.1.0 RSQLite_2.3.7
[127] viridisLite_0.4.2 DBI_1.2.3 fastmap_1.2.0
[130] scales_1.3.0 grid_4.4.1 usethis_3.0.0
[133] pbmcapply_1.5.1 ica_1.0-3 Rsamtools_2.20.0
[136] sass_0.4.9 BiocManager_1.30.25 dotCall64_1.1-1
[139] rpart_4.1.23 RANN_2.6.2 farver_2.1.2
[142] wk_0.9.3 yaml_2.3.10 cli_3.6.3
[145] tester_0.2.0 leiden_0.4.3.1 lifecycle_1.0.4
[148] uwot_0.2.2 lava_1.8.0 sessioninfo_1.2.2
[151] BiocParallel_1.38.0 annotate_1.82.0 timechange_0.3.0
[154] gtable_0.3.5 rjson_0.2.23 yardstick_1.3.1
[157] ggridges_0.5.6 progressr_0.14.0 parallel_4.4.1
[160] limma_3.60.4 jsonlite_1.8.9 RcppHNSW_0.6.0
[163] bitops_1.0-8 bit64_4.0.5 assertthat_0.2.1
[166] Rtsne_0.17 spatstat.utils_3.1-0 CNEr_1.40.0
[169] jquerylib_0.1.4 spatstat.univar_3.0-1 R.utils_2.12.3
[172] timeDate_4041.110 lazyeval_0.2.2 htmltools_0.5.8.1
[175] GO.db_3.19.1 sctransform_0.4.1 glue_1.7.0
[178] TFMPvalue_0.0.9 spam_2.10-0 RCurl_1.98-1.16
[181] classInt_0.4-10 gridExtra_2.3 boot_1.3-30
[184] igraph_2.0.3 R6_2.5.1 RcppRoll_0.3.1
[187] labeling_0.4.3 cluster_2.1.6 pkgload_1.4.0
[190] ipred_0.9-15 nloptr_2.1.1 DirichletMultinomial_1.46.0
[193] DelayedArray_0.30.1 tidyselect_1.2.1 vipor_0.4.7
[196] maps_3.4.2.1 ggforce_0.4.2 AnnotationDbi_1.66.0
[199] future_1.34.0 munsell_0.5.1 KernSmooth_2.23-24
[202] furrr_0.3.1 data.table_1.16.0 htmlwidgets_1.6.4
[205] RColorBrewer_1.1-3 rlang_1.1.4 spatstat.sparse_3.1-0
[208] spatstat.explore_3.3-2 remotes_2.5.0 fansi_1.0.6
[211] hardhat_1.4.0 prodlim_2024.06.25 beeswarm_0.4.0

[mesposit]

I encountered exactly the same error message with Seurat version 5.0.2.

EDIT: sorry I meant SeuratObject version 5.0.2. But apparently I was using an old version of Seurat, after updating Seurat to version 5.2.1 the problem disappeared and I was able to run Augur without any issues.

Thanks a lot for the great package!