Error in give_feedback(msg = msg, verbose = verbose, fdb.fn = fdb.fn, :

[acazelles]

Hi, I am using Spata2 for Visium data since several months. I use 2.0.4 version. And i also use Seurat version 4.1.1. Since yesterday i had no problem to create spata_object and work. Today, i have this error :

_spata295B1_SCT <- initiateSpataObject10X( _+ directory_10X = datadir, _+ sample_name = "Ech_295B1", + SCTransform = T, + verbose = T) 22:58:35 Starting initiation. Error in givefeedback(msg = msg, verbose = verbose, fdb.fn = fdb.fn, :

I really dont know how to solve it. I tried to reinstall packages etc ... No solution ... Huge tkanks for your help.

Antoine

[PIGAsHIT]

I have same problem too :(

[acazelles]

Hi I (almost) found the problem. I removed all my packages and re-installed SPATA2 without updating any packages. And it works now. But I don't know which specific package is not compatible with SPATA. Sorry ! Antoine

[PIGAsHIT]

not works :(

[ayushbharati]

Same problem. There are so many errors with the package nowadays!

[sylee623]

not working for me also.... T.T

[emcramer]

I am having the same problem as well. I previously solved it by updating the original older spata object with updateSpataObject(), but since then I've updated the package. Now I get the error when I use the function plotSurface(). I believe it is an issue with the confuns package. Is there any way to disable this?

[kueckelj]

Hello everybody, thanks for reaching out and sorry for the late reply. Can you install the confuns package again and see if the error persists?

[emcramer]

@kueckelj I have reinstalled the confuns package, but I get the same error with the SPATA2 functions (imageAnnotationToSegmentation, runCnvAnalysis, etc.).

The error message is just: Error in give_feedback(msg = msg, verbose = verbose, fdb.fn = fdb.fn, :

Here's an example of the traceback:

Error in give_feedback(msg = msg, verbose = verbose, fdb.fn = fdb.fn,  :
4.
base::stop(msg) at input-check.R#100
3.
give_feedback(msg = msg, verbose = verbose, fdb.fn = fdb.fn,
with.time = FALSE) at input-check.R#498
2.
confuns::are_values(c("save_infercnv_object"), mode = "logical")
1.
runCnvAnalysis(object = o, ref_annotation = cnv_ref[["annotation"]],
ref_mtr = cnv_ref[["mtr"]], ref_regions = cnv_ref[["regions"]],
gene_pos_df = SPATA2::gene_pos_df, n_pcs = 30, directory_cnv_folder = "results",
cnv_prefix = "Chr", save_infercnv_object = TRUE, )

[sylee623]

Hello everybody, thanks for reaching out and sorry for the late reply. Can you install the confuns package again and see if the error persists?

I reinstalled confuns package, but I got same error. Both downloading or loading for existing sample are not working with same error.

Error in give_feedback(msg = msg, verbose = verbose, fdb.fn = fdb.fn, : 
4. base::stop(msg) 
3. give_feedback(msg = msg, verbose = verbose, fdb.fn = fdb.fn, with.time = FALSE) 
2. confuns::are_values(c("folder", "file"), mode = "character", skip.allow = TRUE, skip.val = NULL) 
1. downloadSpataObject(sample_name = "269_T")

[kueckelj]

Can you reinstall confuns once again and try it?

[emcramer]

It is now working for me on my installation. Do you know if this was an issue due to updates with base R or another package? Thank you!

> sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-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: America/Los_Angeles
tzcode source: internal

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

other attached packages:
 [1] infercnv_1.18.1             lubridate_1.9.3             forcats_1.0.0               stringr_1.5.1              
 [5] dplyr_1.1.4                 purrr_1.0.2                 readr_2.1.5                 tidyr_1.3.1                
 [9] tibble_3.2.1                tidyverse_2.0.0             SPATAData_0.0.0.9000        ggplot2_3.4.4              
[13] Seurat_5.0.1                SeuratObject_5.0.1          sp_2.1-2                    SpatialExperiment_1.11.2   
[17] SingleCellExperiment_1.24.0 topicmodels_0.2-16          SPATA2_2.0.4                SummarizedExperiment_1.32.0
[21] Biobase_2.62.0              GenomicRanges_1.54.1        GenomeInfoDb_1.38.5         IRanges_2.36.0             
[25] S4Vectors_0.40.2            BiocGenerics_0.48.1         MatrixGenerics_1.14.0       matrixStats_1.2.0          
[29] Matrix_1.6-5               

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22        splines_4.3.2           later_1.3.2             bitops_1.0-7            polyclip_1.10-6        
  [6] fastDummies_1.7.3       lifecycle_1.0.4         fastcluster_1.2.6       edgeR_4.0.12            doParallel_1.0.17      
 [11] globals_0.16.2          NLP_0.2-1               lattice_0.22-5          MASS_7.3-60.0.1         magrittr_2.0.3         
 [16] limma_3.58.1            plotly_4.10.4           yaml_2.3.8              httpuv_1.6.14           sctransform_0.4.1      
 [21] spam_2.10-0             spatstat.sparse_3.0-3   reticulate_1.34.0       cowplot_1.1.3           pbapply_1.7-2          
 [26] RColorBrewer_1.1-3      multcomp_1.4-25         abind_1.4-5             zlibbioc_1.48.0         Rtsne_0.17             
 [31] RCurl_1.98-1.14         TH.data_1.1-2           sandwich_3.1-0          GenomeInfoDbData_1.2.11 tm_0.7-11              
 [36] ggrepel_0.9.5           irlba_2.3.5.1           listenv_0.9.0           spatstat.utils_3.0-4    units_0.8-5            
 [41] goftest_1.2-3           RSpectra_0.16-1         spatstat.random_3.2-2   fitdistrplus_1.1-11     parallelly_1.36.0      
 [46] coin_1.4-3              leiden_0.4.3.1          codetools_0.2-19        DelayedArray_0.28.0     xml2_1.3.6             
 [51] tidyselect_1.2.0        futile.logger_1.4.3     farver_2.1.1            rjags_4-15              spatstat.explore_3.2-5 
 [56] jsonlite_1.8.8          ellipsis_0.3.2          progressr_0.14.0        iterators_1.0.14        ggridges_0.5.6         
 [61] survival_3.5-7          dbscan_1.1-12           foreach_1.5.2           tools_4.3.2             ica_1.0-3              
 [66] Rcpp_1.0.12             glue_1.7.0              gridExtra_2.3           SparseArray_1.2.3       EBImage_4.44.0         
 [71] withr_3.0.0             formatR_1.14            BiocManager_1.30.22     fastmap_1.1.1           fansi_1.0.6            
 [76] caTools_1.18.2          digest_0.6.34           parallelDist_0.2.6      timechange_0.3.0        R6_2.5.1               
 [81] mime_0.12               colorspace_2.1-0        scattermore_1.2         gtools_3.9.5            tensor_1.5             
 [86] jpeg_0.1-10             spatstat.data_3.0-4     anndata_0.7.5.6         utf8_1.2.4              generics_0.1.3         
 [91] renv_1.0.3              data.table_1.15.0       httr_1.4.7              htmlwidgets_1.6.4       S4Arrays_1.2.0         
 [96] uwot_0.1.16             pkgconfig_2.0.3         gtable_0.3.4            modeltools_0.2-23       lmtest_0.9-40          
[101] XVector_0.42.0          htmltools_0.5.7         dotCall64_1.1-1         fftwtools_0.9-11        scales_1.3.0           
[106] png_0.1-8               phyclust_0.1-34         lambda.r_1.2.4          rstudioapi_0.15.0       tzdb_0.4.0             
[111] reshape2_1.4.4          rjson_0.2.21            curl_5.2.0              coda_0.19-4             nlme_3.1-164           
[116] zoo_1.8-12              KernSmooth_2.23-22      concaveman_1.1.0        libcoin_1.0-10          parallel_4.3.2         
[121] miniUI_0.1.1.1          pillar_1.9.0            grid_4.3.2              vctrs_0.6.5             gplots_3.1.3           
[126] RANN_2.6.1              slam_0.1-50             promises_1.2.1          xtable_1.8-4            cluster_2.1.6          
[131] magick_2.8.2            mvtnorm_1.2-4           futile.options_1.0.1    cli_3.6.2               locfit_1.5-9.8         
[136] compiler_4.3.2          rlang_1.1.3             crayon_1.5.2            confuns_1.0.3           future.apply_1.11.1    
[141] labeling_0.4.3          argparse_2.2.2          plyr_1.8.9              stringi_1.8.3           viridisLite_0.4.2      
[146] deldir_2.0-2            assertthat_0.2.1        munsell_0.5.0           lazyeval_0.2.2          tiff_0.1-12            
[151] spatstat.geom_3.2-8     V8_4.4.1                RcppHNSW_0.5.0          hms_1.1.3               patchwork_1.2.0        
[156] future_1.33.1           statmod_1.5.0           shiny_1.8.0             ROCR_1.0-11             igraph_1.6.0           
[161] RcppParallel_5.1.7      ape_5.7-1    

[kueckelj]

Please install SPATA2 again and try again.