Hi everyone, I'm trying to use referencePrepare function in IntEREst package on a mouse gtf file downloaded from gencode doing this:

   Mouse_ref<- referencePrepare (sourceBuild="file", filePath="gencode.vM19.primary_assembly.annotation.gtf",collapseExons=TRUE,fileFormat="gtf",annotateGeneIds=FALSE)

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Error in validObject(.Object) : 
  invalid class “GRangesList” object: superclass "list_OR_List" not defined in the environment of the object's class
In addition: Warning message:
In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.

This is the error I got...can someone help me to figure out what is happening?

Thanks in advance

Eva

> traceback()
23: stop(msg, ": ", errors, domain = NA)
22: validObject(.Object)
21: initialize(value, ...)
20: initialize(value, ...)
19: new(...)
18: new2(Class, unlistData = unlistData, partitioning = partitioning, 
        check = FALSE)
17: newCompressedList0(ans_class, flesh, skeleton)
16: relist(x, f)
15: relist(x, f)
14: .splitAsList_by_integer(x, f, drop)
13: splitAsList_default(x, f, drop = drop)
12: .local(x, f, drop, ...)
11: IRanges::splitAsList(x, f, drop = drop)
10: IRanges::splitAsList(x, f, drop = drop)
9: .local(x, f, drop, ...)
8: split(gr, f)
7: split(gr, f)
6: .split_df_into_GRL(txdb, df, mcolumns, by, use.names)
5: .extract_features_by(x, "exon", by, use.names = use.names)
4: .local(x, by, ...)
3: GenomicFeatures::exonsBy(human.txdb, by = "tx", use.names = TRUE)
2: GenomicFeatures::exonsBy(human.txdb, by = "tx", use.names = TRUE)
1: referencePrepare(sourceBuild = "file", filePath = "/storage-daredevil/SammySeq/Data/gencode.vM19.primary_assembly.annotation.gtf", 
       collapseExons = TRUE, fileFormat = "gtf", annotateGeneIds = FALSE)


>sessionInfo()
    R version 3.4.3 (2017-11-30)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: CentOS Linux 7 (Core)

    Matrix products: default
    BLAS: /opt/R/R-3.4.3/lib64/R/lib/libRblas.so
    LAPACK: /opt/R/R-3.4.3/lib64/R/lib/libRlapack.so

    locale:
     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
     [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
     [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
     [9] LC_ADDRESS=C               LC_TELEPHONE=C            
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

    other attached packages:
     [1] IntEREst_1.2.2             edgeR_3.20.9              
     [3] limma_3.34.9               SummarizedExperiment_1.8.1
     [5] DelayedArray_0.4.1         matrixStats_0.54.0        
     [7] Biobase_2.38.0             Rsamtools_1.30.0          
     [9] Biostrings_2.46.0          XVector_0.18.0            
    [11] GenomicRanges_1.30.3       GenomeInfoDb_1.14.0       
    [13] IRanges_2.12.0             S4Vectors_0.16.0          
    [15] BiocGenerics_0.24.0       

    loaded via a namespace (and not attached):
     [1] bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2      
     [4] progress_1.2.0           httr_1.3.1               tools_3.4.3             
     [7] backports_1.1.3          R6_2.2.2                 rpart_4.1-13            
    [10] Hmisc_4.1-1              seqLogo_1.44.0           DBI_1.0.0               
    [13] lazyeval_0.2.1           colorspace_1.3-2         ade4_1.7-13             
    [16] nnet_7.3-12              tidyselect_0.2.4         gridExtra_2.3           
    [19] prettyunits_1.0.2        DESeq2_1.18.1            RMySQL_0.10.15          
    [22] bit_1.1-14               compiler_3.4.3           htmlTable_1.12          
    [25] rtracklayer_1.38.3       scales_0.5.0             checkmate_1.8.5         
    [28] genefilter_1.60.0        stringr_1.3.1            digest_0.6.15           
    [31] foreign_0.8-70           base64enc_0.1-3          pkgconfig_2.0.2         
    [34] htmltools_0.3.6          htmlwidgets_1.2          rlang_0.2.1             
    [37] rstudioapi_0.8           RSQLite_2.1.1            bindr_0.1.1             
    [40] DEXSeq_1.24.4            hwriter_1.3.2            BiocParallel_1.12.0     
    [43] acepack_1.4.1            dplyr_0.7.6              RCurl_1.95-4.10         
    [46] magrittr_1.5             GenomeInfoDbData_1.0.0   Formula_1.2-3           
    [49] Matrix_1.2-15            Rcpp_0.12.17             munsell_0.4.3           
    [52] stringi_1.2.2            MASS_7.3-50              zlibbioc_1.24.0         
    [55] plyr_1.8.4               grid_3.4.3               blob_1.1.1              
    [58] crayon_1.3.4             lattice_0.20-38          splines_3.4.3           
    [61] annotate_1.56.2          GenomicFeatures_1.30.3   hms_0.4.2               
    [64] locfit_1.5-9.1           knitr_1.21               pillar_1.2.3            
    [67] seqinr_3.4-5             geneplotter_1.56.0       biomaRt_2.34.2          
    [70] XML_3.98-1.11            glue_1.3.0               latticeExtra_0.6-28     
    [73] data.table_1.11.4        gtable_0.2.0             purrr_0.2.5             
    [76] assertthat_0.2.0         ggplot2_3.0.0            xfun_0.4                
    [79] xtable_1.8-3             survival_2.42-4          tibble_1.4.2            
    [82] GenomicAlignments_1.14.2 AnnotationDbi_1.40.0     memoise_1.1.0           
    [85] bindrcpp_0.2.2