Hi,
I installed "StructuralVariantAnnotation" package and tried to read "representations.vcf" but I got an error message below. I am using R 4.5.0, so I think it should work. Could help me solve this issue?
library(StructuralVariantAnnotation)
vcf <- VariantAnnotation::readVcf(system.file("extdata", "representations.vcf", package = "StructuralVariantAnnotation"))
Error in validObject(.Object) :
invalid class “CollapsedVCF” object: superclass "ExpData" not defined in the environment of the object's class
sessionInfo()
R version 4.5.0 (2025-04-11)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.4
Matrix products: default
BLAS: System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] StructuralVariantAnnotation_1.24.0 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 MatrixGenerics_1.20.0
[9] matrixStats_1.5.0 rtracklayer_1.68.0 GenomicRanges_1.60.0 GenomeInfoDb_1.44.0
[13] IRanges_2.42.0 S4Vectors_0.46.0 BiocGenerics_0.54.0 generics_0.1.3
loaded via a namespace (and not attached):
[1] KEGGREST_1.48.0 rjson_0.2.23 lattice_0.22-7 vctrs_0.6.5 tools_4.5.0 bitops_1.0-9
[7] curl_6.2.2 parallel_4.5.0 tibble_3.2.1 AnnotationDbi_1.70.0 RSQLite_2.3.9 blob_1.2.4
[13] pkgconfig_2.0.3 Matrix_1.7-3 BSgenome_1.76.0 lifecycle_1.0.4 GenomeInfoDbData_1.2.14 compiler_4.5.0
[19] codetools_0.2-20 RCurl_1.98-1.17 yaml_2.3.10 pillar_1.10.2 crayon_1.5.3 BiocParallel_1.42.0
[25] DelayedArray_0.34.1 cachem_1.1.0 abind_1.4-8 tidyselect_1.2.1 dplyr_1.1.4 restfulr_0.0.15
[31] fastmap_1.2.0 grid_4.5.0 cli_3.6.5 SparseArray_1.8.0 magrittr_2.0.3 S4Arrays_1.8.0
[37] GenomicFeatures_1.60.0 XML_3.99-0.18 UCSC.utils_1.4.0 bit64_4.6.0-1 pwalign_1.4.0 httr_1.4.7
[43] bit_4.6.0 png_0.1-8 memoise_2.0.1 BiocIO_1.18.0 rlang_1.1.6 glue_1.8.0
[49] DBI_1.2.3 BiocManager_1.30.25 rstudioapi_0.17.1 jsonlite_2.0.0 R6_2.6.1 GenomicAlignments_1.44.0
Thank you,
Sanghoon
Hi,
I installed "StructuralVariantAnnotation" package and tried to read "representations.vcf" but I got an error message below. I am using R 4.5.0, so I think it should work. Could help me solve this issue?
Error in validObject(.Object) :
invalid class “CollapsedVCF” object: superclass "ExpData" not defined in the environment of the object's class
R version 4.5.0 (2025-04-11)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.4
Matrix products: default
BLAS: System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] StructuralVariantAnnotation_1.24.0 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 MatrixGenerics_1.20.0
[9] matrixStats_1.5.0 rtracklayer_1.68.0 GenomicRanges_1.60.0 GenomeInfoDb_1.44.0
[13] IRanges_2.42.0 S4Vectors_0.46.0 BiocGenerics_0.54.0 generics_0.1.3
loaded via a namespace (and not attached):
[1] KEGGREST_1.48.0 rjson_0.2.23 lattice_0.22-7 vctrs_0.6.5 tools_4.5.0 bitops_1.0-9
[7] curl_6.2.2 parallel_4.5.0 tibble_3.2.1 AnnotationDbi_1.70.0 RSQLite_2.3.9 blob_1.2.4
[13] pkgconfig_2.0.3 Matrix_1.7-3 BSgenome_1.76.0 lifecycle_1.0.4 GenomeInfoDbData_1.2.14 compiler_4.5.0
[19] codetools_0.2-20 RCurl_1.98-1.17 yaml_2.3.10 pillar_1.10.2 crayon_1.5.3 BiocParallel_1.42.0
[25] DelayedArray_0.34.1 cachem_1.1.0 abind_1.4-8 tidyselect_1.2.1 dplyr_1.1.4 restfulr_0.0.15
[31] fastmap_1.2.0 grid_4.5.0 cli_3.6.5 SparseArray_1.8.0 magrittr_2.0.3 S4Arrays_1.8.0
[37] GenomicFeatures_1.60.0 XML_3.99-0.18 UCSC.utils_1.4.0 bit64_4.6.0-1 pwalign_1.4.0 httr_1.4.7
[43] bit_4.6.0 png_0.1-8 memoise_2.0.1 BiocIO_1.18.0 rlang_1.1.6 glue_1.8.0
[49] DBI_1.2.3 BiocManager_1.30.25 rstudioapi_0.17.1 jsonlite_2.0.0 R6_2.6.1 GenomicAlignments_1.44.0
Thank you,
Sanghoon