Error in df[, 2] : object of type 'closure' is not subsettable

[roniweiss12]

Hello,
I'm new to the chromstaR package. when I tried to run the Chromstar function I got the following error:

> Chromstar(inputfolder, experiment.table=experiment_table_GMHM,assembly = "mm10",
+           outputfolder=outputfolder, numCPU=4, binsize=1000, stepsize=500,
+           prefit.on.chr=NULL, chromosomes=NULL,
+           mode='combinatorial')
Setting up parallel execution with 4 threads ... 0.8s
================
Binning the data
================
Obtaining chromosome length information from UCSC ... 0s
Error in df[, 2] : object of type 'closure' is not subsettable

I tried using only a subset of my samples, and also tried specifying 'prefit.on.chr='chr12', chromosomes='chr12'',
none of which helped.

I'm using BAM files, not bed.

Can you tell me what I'm doing wrong? any help is much appreciated!

Thanks!

this is my session info:

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=Hebrew_Israel.1255  LC_CTYPE=Hebrew_Israel.1255   
[3] LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C                  
[5] LC_TIME=Hebrew_Israel.1255    

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

other attached packages:
[1] chromstaR_1.20.2     chromstaRData_1.20.0 ggplot2_3.4.1       
[4] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1  IRanges_2.28.0      
[7] S4Vectors_0.32.4     BiocGenerics_0.40.0 

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.24.0 tidyselect_1.2.0           
 [3] reshape2_1.4.4              lattice_0.20-45            
 [5] colorspace_2.0-3            vctrs_0.5.2                
 [7] generics_0.1.3              utf8_1.2.2                 
 [9] rlang_1.0.6                 pillar_1.8.1               
[11] glue_1.6.2                  withr_2.5.0                
[13] DBI_1.1.3                   BiocParallel_1.28.3        
[15] matrixStats_0.63.0          GenomeInfoDbData_1.2.7     
[17] foreach_1.5.2               lifecycle_1.0.3            
[19] plyr_1.8.8                  stringr_1.5.0              
[21] zlibbioc_1.40.0             MatrixGenerics_1.6.0       
[23] Biostrings_2.62.0           munsell_0.5.0              
[25] gtable_0.3.1                mvtnorm_1.1-3              
[27] codetools_0.2-19            bamsignals_1.26.0          
[29] Biobase_2.54.0              doParallel_1.0.17          
[31] parallel_4.1.3              fansi_1.0.3                
[33] Rcpp_1.0.9                  scales_1.2.1               
[35] DelayedArray_0.20.0         XVector_0.34.0             
[37] Rsamtools_2.10.0            stringi_1.7.12             
[39] dplyr_1.0.10                grid_4.1.3                 
[41] cli_3.6.0                   tools_4.1.3                
[43] bitops_1.0-7                magrittr_2.0.3             
[45] RCurl_1.98-1.9              tibble_3.1.8               
[47] crayon_1.5.2                pkgconfig_2.0.3            
[49] Matrix_1.5-3                assertthat_0.2.1           
[51] rstudioapi_0.14             iterators_1.0.14           
[53] R6_2.5.1                    GenomicAlignments_1.30.0   
[55] compiler_4.1.3