liana_wrap error!

[achilessss]

Hi there!

I encountered the following error when running the sample data when using liana_wrap .

Expression from the RNA assay will be used
Running LIANA with seurat_annotations as labels!
Error in (function (cond) :
error in evaluating the argument 'object' in selecting a method for function 'na.omit': :1:7: unexpected symbol
1: Using an
^
In addition: Warning message:
In exec(output, ...) :
3465 genes and/or 0 cells were removed as they had no counts!

[dbdimitrov]

Hi @achilessss,

Can you please post a reproducible example or your rlang::last_error_trace + R session info?
I could then check if there is something different, etc.

[sakinaamin]

Hi, I got the same error, this is my rlang::last_error_trace

Error in 'select()':
! :1:7: unexpected symbol
1:Using an

This error came for both testdata and my own object as well.

sessionInfo()
locale:
[1] C

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

other attached packages:
[1] liana_0.1.11 magrittr_2.0.3 forcats_0.5.1 stringr_1.4.0
[5] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[9] tibble_3.1.7 ggplot2_3.3.6 tidyverse_1.3.1

loaded via a namespace (and not attached):
[1] readxl_1.4.0 backports_1.4.1
[3] circlize_0.4.15 igraph_1.3.2
[5] sp_1.5-0 BiocParallel_1.30.3
[7] listenv_0.8.0 GenomeInfoDb_1.32.2
[9] digest_0.6.29 foreach_1.5.2
[11] htmltools_0.5.2 OmnipathR_3.8.0
[13] fansi_1.0.3 checkmate_2.1.0
[15] ScaledMatrix_1.4.0 cluster_2.1.3
[17] doParallel_1.0.17 tzdb_0.3.0
[19] limma_3.52.2 ComplexHeatmap_2.12.0
[21] globals_0.15.0 modelr_0.1.8
[23] matrixStats_0.62.0 prettyunits_1.1.1
[25] colorspace_2.0-3 rvest_1.0.2
[27] rappdirs_0.3.3 haven_2.5.0
[29] xfun_0.31 crayon_1.5.1
[31] RCurl_1.98-1.7 jsonlite_1.8.0
[33] progressr_0.10.1 iterators_1.0.14
[35] glue_1.6.2 gtable_0.3.0
[37] zlibbioc_1.42.0 XVector_0.36.0
[39] GetoptLong_1.0.5 DelayedArray_0.22.0
[41] BiocSingular_1.12.0 future.apply_1.9.0
[43] shape_1.4.6 SingleCellExperiment_1.18.0
[45] BiocGenerics_0.42.0 scales_1.2.0
[47] DBI_1.1.3 edgeR_3.38.1
[49] Rcpp_1.0.8.3 progress_1.2.2
[51] clue_0.3-61 reticulate_1.25
[53] dqrng_0.3.0 rsvd_1.0.5
[55] stats4_4.2.1 metapod_1.4.0
[57] httr_1.4.3 dir.expiry_1.4.0
[59] RColorBrewer_1.1-3 ellipsis_0.3.2
[61] pkgconfig_2.0.3 scuttle_1.6.2
[63] dbplyr_2.2.0 locfit_1.5-9.5
[65] utf8_1.2.2 tidyselect_1.2.0
[67] rlang_1.0.4 later_1.3.0
[69] munsell_0.5.0 cellranger_1.1.0
[71] tools_4.2.1 cli_3.3.0
[73] generics_0.1.2 broom_0.8.0
[75] evaluate_0.15 fastmap_1.1.0
[77] yaml_2.3.5 knitr_1.39
[79] fs_1.5.2 future_1.26.1
[81] sparseMatrixStats_1.8.0 scran_1.24.0
[83] xml2_1.3.3 compiler_4.2.1
[85] rstudioapi_0.13 filelock_1.0.2
[87] curl_4.3.2 png_0.1-7
[89] reprex_2.0.1 statmod_1.4.36
[91] stringi_1.7.6 basilisk.utils_1.8.0
[93] logger_0.2.2 rgeos_0.5-9
[95] lattice_0.20-45 bluster_1.6.0
[97] Matrix_1.4-1 vctrs_0.4.1
[99] pillar_1.7.0 lifecycle_1.0.1
[101] GlobalOptions_0.1.2 BiocNeighbors_1.14.0
[103] bitops_1.0-7 irlba_2.3.5
[105] GenomicRanges_1.48.0 R6_2.5.1
[107] IRanges_2.30.0 parallelly_1.32.0
[109] codetools_0.2-18 assertthat_0.2.1
[111] SummarizedExperiment_1.26.1 rjson_0.2.21
[113] withr_2.5.0 SeuratObject_4.1.0
[115] S4Vectors_0.34.0 GenomeInfoDbData_1.2.8
[117] parallel_4.2.1 hms_1.1.1
[119] grid_4.2.1 beachmat_2.12.0
[121] basilisk_1.8.1 rmarkdown_2.14
[123] DelayedMatrixStats_1.18.0 MatrixGenerics_1.8.1
[125] Biobase_2.56.0 lubridate_1.8.0

[dbdimitrov]

Hi @sakinaamin,

Sorry for the delayed response, I must've missed it. I can't see anything in the session that might be out of the ordinary, perhaps if you could provide the full error trace so that I can see where the error occurs?

Thanks.
Daniel

[nsdelablancac]

Hi all!

I also have an error in this function, but different: "Error: cnd is not a condition object."

No other issue seems to occur. Do you know why it could happen? rlang is installed.

Thank you in advance!
Best.

[M-Arafat]

I got the same error but when I normalized the data, it got resolved!

[nsdelablancac]

Thank you for your response :)

Could you please tell me how you normalize the Seurat object? I took my annotated cells from a processed (and integrated) single cell analysis which include normalization, scaling, etc. Should I normalize again?

Thanks again!