Warning message: In data(GenomeOfNl_raw) : data set 'GenomeOfNl_raw' not found

[ghost]

I could not find the indel dataset in your "data" repository. It's not in the package as well. Where could I find it?

[Marc-Ruebsam]

The data seems to load without problems in the latest Bioconductor version of YAPSA.
Please update your package and report any further errors there: https://support.bioconductor.org/tag/YAPSA/

> suppressPackageStartupMessages(library("YAPSA"))
> data(GenomeOfNl_raw)
> head(GenomeOfNl_raw)
   CHROM   POS          ID   REF ALT QUAL FILTER                                           INFO
32     2 12320 rs147364131   AAT   A    .   PASS    AC=31;AF=0.031;AN=998;DB;NUMALT=1;set=INDEL
53     2 13613           .    AG   A    .   PASS    AC=3;AF=3.006e-03;AN=998;NUMALT=1;set=INDEL
92     2 17012 rs144550470 TAAAG   T    .   PASS AC=6;AF=6.012e-03;AN=998;DB;NUMALT=1;set=INDEL
94     2 17128 rs140420760     T  TG    .   PASS AC=1;AF=1.002e-03;AN=998;DB;NUMALT=1;set=INDEL
95     2 17142           .     G  GA    .   PASS    AC=9;AF=9.018e-03;AN=998;NUMALT=1;set=INDEL
96     2 17151           .  TCAC   T    .   PASS    AC=1;AF=1.002e-03;AN=998;NUMALT=1;set=INDEL

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/ruebsam/.conda/envs/bioconductor_yapsa/lib/libopenblasp-r0.3.20.so

locale:
[1] C

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

other attached packages:
[1] YAPSA_1.19.0         Biobase_2.54.0       ggplot2_3.3.6        GenomicRanges_1.46.1 GenomeInfoDb_1.30.0  IRanges_2.28.0       S4Vectors_0.32.3     BiocGenerics_0.40.0 

loaded via a namespace (and not attached):
  [1] backports_1.4.1                   circlize_0.4.15                   Hmisc_4.7-0                       corrplot_0.92                     NMF_0.21.0                        BiocFileCache_2.2.0              
  [7] plyr_1.8.7                        lazyeval_0.2.2                    splines_4.1.3                     BiocParallel_1.28.3               gridBase_0.4-7                    gtrellis_1.26.0                  
 [13] digest_0.6.29                     foreach_1.5.2                     ensembldb_2.18.1                  htmltools_0.5.2                   viridis_0.6.2                     fansi_1.0.3                      
 [19] magrittr_2.0.3                    checkmate_2.1.0                   memoise_2.0.1                     BSgenome_1.62.0                   cluster_2.1.3                     doParallel_1.0.17                
 [25] ComplexHeatmap_2.10.0             Biostrings_2.62.0                 matrixStats_0.62.0                limSolve_1.5.6                    ggbio_1.42.0                      lpSolve_5.6.15                   
 [31] prettyunits_1.1.1                 jpeg_0.1-9                        colorspace_2.0-3                  blob_1.2.3                        rappdirs_0.3.3                    xfun_0.31                        
 [37] dplyr_1.0.9                       crayon_1.5.1                      RCurl_1.98-1.6                    graph_1.72.0                      SomaticSignatures_2.30.0          survival_3.3-1                   
 [43] VariantAnnotation_1.40.0          iterators_1.0.14                  glue_1.6.2                        registry_0.5-1                    gtable_0.3.0                      zlibbioc_1.40.0                  
 [49] XVector_0.34.0                    GetoptLong_1.0.5                  DelayedArray_0.20.0               shape_1.4.6                       scales_1.2.0                      rngtools_1.5.2                   
 [55] DBI_1.1.2                         GGally_2.1.2                      Rcpp_1.0.8.3                      xtable_1.8-4                      viridisLite_0.4.0                 progress_1.2.2                   
 [61] htmlTable_2.4.0                   clue_0.3-60                       proxy_0.4-26                      foreign_0.8-82                    bit_4.0.4                         OrganismDbi_1.36.0               
 [67] PMCMR_4.4                         Formula_1.2-4                     htmlwidgets_1.5.4                 httr_1.4.3                        RColorBrewer_1.1-3                ellipsis_0.3.2                   
 [73] pkgconfig_2.0.3                   reshape_0.8.9                     XML_3.99-0.9                      nnet_7.3-17                       dbplyr_2.2.0                      utf8_1.2.2                       
 [79] tidyselect_1.1.2                  rlang_1.0.2                       reshape2_1.4.4                    AnnotationDbi_1.56.1              munsell_0.5.0                     tools_4.1.3                      
 [85] cachem_1.0.6                      cli_3.3.0                         generics_0.1.2                    RSQLite_2.2.8                     stringr_1.4.0                     fastmap_1.1.0                    
 [91] yaml_2.3.5                        knitr_1.39                        bit64_4.0.5                       purrr_0.3.4                       KEGGREST_1.34.0                   AnnotationFilter_1.18.0          
 [97] dendextend_1.15.2                 RBGL_1.70.0                       pracma_2.3.8                      xml2_1.3.3                        biomaRt_2.50.0                    compiler_4.1.3                   
[103] rstudioapi_0.13                   beeswarm_0.4.0                    filelock_1.0.2                    curl_4.3.2                        png_0.1-7                         tibble_3.1.7                     
[109] stringi_1.7.6                     GenomicFeatures_1.46.1            lattice_0.20-45                   ProtGenerics_1.26.0               Matrix_1.4-1                      vctrs_0.4.1                      
[115] pillar_1.7.0                      lifecycle_1.0.1                   BiocManager_1.30.18               GlobalOptions_0.1.2               data.table_1.14.2                 bitops_1.0-7                     
[121] rtracklayer_1.54.0                pcaMethods_1.86.0                 R6_2.5.1                          BiocIO_1.4.0                      latticeExtra_0.6-29               gridExtra_2.3                    
[127] vipor_0.4.5                       codetools_0.2-18                  dichromat_2.0-0.1                 MASS_7.3-57                       assertthat_0.2.1                  SummarizedExperiment_1.24.0      
[133] pkgmaker_0.32.2                   rjson_0.2.21                      withr_2.5.0                       GenomicAlignments_1.30.0          Rsamtools_2.10.0                  GenomeInfoDbData_1.2.7           
[139] parallel_4.1.3                    hms_1.1.1                         quadprog_1.5-8                    rpart_4.1.16                      BSgenome.Hsapiens.UCSC.hg19_1.4.3 MatrixGenerics_1.6.0             
[145] biovizBase_1.42.0                 base64enc_0.1-3                   ggbeeswarm_0.6.0                  restfulr_0.0.14