Error in as(chain, "Chain") : no method or default for coercing "NULL" to "Chain"

[bschilder]

Hi there,

I seem to be having some issues running XGR's liftover function, which now returns some errors related to "Chain". Is there something else I need to install?

Example

## Construct example data
library(echolocatoR)

build.conversion="hg19.to.hg38"
chrom_col="CHR"
start_col="POS"
end_col="POS"
chr_format="NCBI"

dat <- echolocatoR::CORCES_2020.scATACseq_celltype_peaks
dat[,paste0("POS.",strsplit(build.conversion, "\\.")[[1]][1])] <- dat[[start_col]]

gr.dat <- GenomicRanges::makeGRangesFromDataFrame(df = dat,
                                                   keep.extra.columns = T,
                                                   seqnames.field = "chrom",
                                                   start.field = start_col,
                                                   end.field = end_col)

## Liftover
gr.lifted <- XGR::xLiftOver(data.file = gr.dat,
                               format.file = "GRanges",
                               build.conversion = "hg38.to.hg19",
                               verbose = F ,
                               merged = F)  # merge must =F in order to work

Error in as(chain, "Chain") : 
  no method or default for coercing "NULL" to "Chain"

packageVersion("XGR")

[1] '1.1.7'

I tried installing the BioConductor version, but it looks like it's not available for the last couple versions of R (currently up to v4.0.3):

BiocManager::install("XGR")

package 'XGR' is not available (for R version 3.6.3)

Thanks for your help!

Session Info

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

loaded via a namespace (and not attached):
  [1] readxl_1.3.1                backports_1.2.1            
  [3] Hmisc_4.4-2                 corrplot_0.84              
  [5] BiocFileCache_1.10.2        RCircos_1.2.1              
  [7] plyr_1.8.6                  igraph_1.2.6               
  [9] lazyeval_0.2.2              splines_3.6.3              
 [11] echolocatoR_0.1.0           BiocParallel_1.20.1        
 [13] GenomeInfoDb_1.22.1         ggnetwork_0.5.8            
 [15] ggplot2_3.3.3               digest_0.6.27              
 [17] ensembldb_2.10.2            htmltools_0.5.1            
 [19] fansi_0.4.2                 magrittr_2.0.1             
 [21] checkmate_2.0.0             memoise_1.1.0              
 [23] BSgenome_1.54.0             cluster_2.1.0              
 [25] Biostrings_2.54.0           matrixStats_0.57.0         
 [27] R.utils_2.10.1              ggbio_1.34.0               
 [29] askpass_1.1                 prettyunits_1.1.1          
 [31] jpeg_0.1-8.1                colorspace_2.0-0           
 [33] blob_1.2.1                  rappdirs_0.3.1             
 [35] ggrepel_0.9.1               xfun_0.20                  
 [37] dplyr_1.0.3                 crayon_1.3.4               
 [39] RCurl_1.98-1.2              hexbin_1.28.2              
 [41] graph_1.64.0                Exact_2.1                  
 [43] supraHex_1.24.0             survival_3.2-7             
 [45] VariantAnnotation_1.32.0    ape_5.4-1                  
 [47] glue_1.4.2                  gtable_0.3.0               
 [49] zlibbioc_1.32.0             XVector_0.26.0             
 [51] DelayedArray_0.12.3         Rgraphviz_2.30.0           
 [53] BiocGenerics_0.32.0         scales_1.1.1               
 [55] mvtnorm_1.1-1               DBI_1.1.1                  
 [57] GGally_2.1.0                Rcpp_1.0.6                 
 [59] progress_1.2.2              htmlTable_2.1.0            
 [61] foreign_0.8-75              bit_4.0.4                  
 [63] OrganismDbi_1.28.0          Formula_1.2-4              
 [65] stats4_3.6.3                DT_0.17                    
 [67] htmlwidgets_1.5.3           httr_1.4.2                 
 [69] RColorBrewer_1.1-2          ellipsis_0.3.1             
 [71] pkgconfig_2.0.3             reshape_0.8.8              
 [73] XML_3.99-0.3                R.methodsS3_1.8.1          
 [75] nnet_7.3-14                 dbplyr_2.0.0               
 [77] tidyselect_1.1.0            rlang_0.4.10               
 [79] reshape2_1.4.4              AnnotationDbi_1.48.0       
 [81] cellranger_1.1.0            munsell_0.5.0              
 [83] tools_3.6.3                 cli_2.2.0                  
 [85] generics_0.1.0              RSQLite_2.2.2              
 [87] evaluate_0.14               stringr_1.4.0              
 [89] yaml_2.2.1                  knitr_1.30                 
 [91] bit64_4.0.5                 purrr_0.3.4                
 [93] AnnotationFilter_1.10.0     rootSolve_1.8.2.1          
 [95] RBGL_1.62.1                 nlme_3.1-151               
 [97] R.oo_1.24.0                 biomaRt_2.42.1             
 [99] compiler_3.6.3              rstudioapi_0.13            
[101] curl_4.3                    png_0.1-7                  
[103] e1071_1.7-4                 tibble_3.0.5               
[105] DescTools_0.99.39           stringi_1.5.3              
[107] GenomicFeatures_1.38.2      lattice_0.20-41            
[109] ProtGenerics_1.18.0         Matrix_1.3-2               
[111] vctrs_0.3.6                 pillar_1.4.7               
[113] lifecycle_0.2.0             BiocManager_1.30.10        
[115] data.table_1.13.6           bitops_1.0-6               
[117] dnet_1.1.7                  lmom_2.8                   
[119] patchwork_1.1.1             rtracklayer_1.46.0         
[121] GenomicRanges_1.38.0        R6_2.5.0                   
[123] latticeExtra_0.6-29         XGR_1.1.7                  
[125] gridExtra_2.3               IRanges_2.20.2             
[127] gld_2.6.2                   sessioninfo_1.1.1          
[129] dichromat_2.0-0             boot_1.3-25                
[131] MASS_7.3-53                 assertthat_0.2.1           
[133] SummarizedExperiment_1.16.1 openssl_1.4.3              
[135] withr_2.4.0                 GenomicAlignments_1.22.1   
[137] Rsamtools_2.2.3             S4Vectors_0.24.4           
[139] GenomeInfoDbData_1.2.2      expm_0.999-6               
[141] parallel_3.6.3              hms_1.0.0                  
[143] grid_3.6.3                  rpart_4.1-15               
[145] tidyr_1.1.2                 class_7.3-17               
[147] rmarkdown_2.6               biovizBase_1.34.1          
[149] Biobase_2.46.0              base64enc_0.1-3   

[bschilder]

Hi @hfang-bristol , just wondering if there's been any headway with this. XGR was one of the dependencies for my R package echolocatoR but I've had to remove it due to these issues, especially those pertaining to installation 😢 . I'd really like to add it back in because I think it offers a lot!

Thanks again,
Brian