Error: CollapsedVCF superclass ExpData not defined in PureCN

[MaxSimonNm]

Describe the issue
CollapsedVCF object error in PureCN during the usage of the functions runAbsoluteCN and readAllelicCountsFile

The error encountered is:

Error in validObject(.Object) : 
  invalid class “CollapsedVCF” object: superclass "ExpData" not defined in the environment of the object's class

To Reproduce
Copy and paste your complete command line arguments from PureCN.R. If possible and potentially relevant, also copy the output of NormalDB.R and Coverage.R.

• Run PureCN using the PureCN.R wrapper with example inputs (Coverage files, VCF, NormalDB, and Mappability files).
• The error is triggered when runAbsoluteCN or readAllelicCountsFile attempts to process the VCF.

for readAllelicCountsFile :

ac.file <- system.file("extdata", "example_allelic_counts.tsv",
package="PureCN")
vcf.ac <- readAllelicCountsFile(ac.file)

for runAbsoluteCN:

normal.coverage.file <- system.file("extdata", "example_normal.txt.gz",
                                    package = "PureCN")
normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz",
                                     package = "PureCN")
normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)
tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz",
                                   package = "PureCN")
seg.file <- system.file("extdata", "example_seg.txt",
                        package = "PureCN")
vcf.file <- system.file("extdata", "example.vcf.gz", package = "PureCN")
interval.file <- system.file("extdata", "example_intervals.txt",
                             package = "PureCN")

normalDB <- createNormalDatabase(normal.coverage.files)
saveRDS(normalDB, file = "normalDB.rds")
normalDB <- readRDS("normalDB.rds")
pool <- calculateTangentNormal(tumor.coverage.file, normalDB)

ret <-runAbsoluteCN(normal.coverage.file = pool,
                    tumor.coverage.file = tumor.coverage.file, vcf.file = vcf.file,
                    genome = "hg19", sampleid = "Sample1",
                    interval.file = interval.file, normalDB = normalDB,
                    # args.setMappingBiasVcf=list(
                    # mapping.bias.file = mapping.bias.file
                    # ),
                    args.filterVcf=list(
                      # snp.blacklist = snp.blacklist,
                      # stats.file = mutect.stats.file
                    ),
                    args.filterIntervals = list(
                      min.total.counts = 50
                    ),
                    post.optimize = FALSE, plot.cnv = FALSE, verbose = FALSE)

Expected behavior
I expected the ret variable to be created with the example data so that I could proceed with Section 6.1 Plot code:

saveRDS(ret, file = file.rds)
pdf("Sample1_PureCN.pdf", width = 10, height = 11)
plotAbs(ret, type = "all")

Log file
I am not sure if this is created before the successful runs of runAbsoluteCN or readAllelicCountsFile.

B-allele frequency plot
I didnt reach this point yet.

Session Info

R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Kolkata
tzcode source: system (glibc)

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

other attached packages:
 [1] PureCN_2.14.1               VariantAnnotation_1.54.0    Rsamtools_2.24.0            Biostrings_2.76.0          
 [5] XVector_0.48.0              SummarizedExperiment_1.38.1 Biobase_2.68.0              GenomicRanges_1.60.0       
 [9] GenomeInfoDb_1.44.0         IRanges_2.42.0              S4Vectors_0.46.0            MatrixGenerics_1.20.0      
[13] matrixStats_1.5.0           BiocGenerics_0.54.0         generics_0.1.3              DNAcopy_1.82.0             

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1         dplyr_1.1.4              farver_2.1.2             blob_1.2.4               R.utils_2.13.0          
 [6] bitops_1.0-9             fastmap_1.2.0            RCurl_1.98-1.17          GenomicAlignments_1.44.0 XML_3.99-0.18           
[11] lifecycle_1.0.4          KEGGREST_1.48.0          RSQLite_2.3.11           magrittr_2.0.3           compiler_4.5.0          
[16] rlang_1.1.6              tools_4.5.0              yaml_2.3.10              data.table_1.17.0        rtracklayer_1.68.0      
[21] lambda.r_1.2.4           S4Arrays_1.8.0           bit_4.6.0                mclust_6.1.1             curl_6.2.2              
[26] DelayedArray_0.34.1      RColorBrewer_1.1-3       abind_1.4-8              BiocParallel_1.42.0      R.oo_1.27.1             
[31] grid_4.5.0               Rhdf5lib_1.30.0          ggplot2_3.5.2            scales_1.4.0             cli_3.6.5               
[36] crayon_1.5.3             rstudioapi_0.17.1        httr_1.4.7               rjson_0.2.23             DBI_1.2.3               
[41] cachem_1.1.0             rhdf5_2.52.0             splines_4.5.0            parallel_4.5.0           AnnotationDbi_1.70.0    
[46] BiocManager_1.30.25      formatR_1.14             restfulr_0.0.15          vctrs_0.6.5              Matrix_1.7-3            
[51] jsonlite_2.0.0           VGAM_1.1-13              bit64_4.6.0-1            GenomicFeatures_1.60.0   glue_1.8.0              
[56] codetools_0.2-20         gtable_0.3.6             futile.logger_1.4.3      BiocIO_1.18.0            UCSC.utils_1.4.0        
[61] tibble_3.2.1             pillar_1.10.2            rhdf5filters_1.20.0      GenomeInfoDbData_1.2.14  BSgenome_1.76.0         
[66] R6_2.6.1                 lattice_0.22-7           futile.options_1.0.1     png_0.1-8                R.methodsS3_1.8.2       
[71] memoise_2.0.1            gridExtra_2.3            SparseArray_1.8.0        pkgconfig_2.0.3

[lima1]

Apologies, I somehow missed this. How did you install this? This looks like an issue with dependencies. Can you make sure that everything is up to date?

BiocManager::install()
BiocManager::install("PureCN")

[MaxSimonNm]

Hi, thank you for responding. I will try your mentioned method and report back.

I did install it by doing this:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("PureCN")

I will also create a new R environment and see if it resolves my problem.