Comments (6)
from labs.
Please close this issue if it resolves for you @gillsignals
Thanks
from labs.
This change did not correct the error. First, running ldblock::stack1kg
generated this error:
Error in Seqinfo(chrs) : could not find function "Seqinfo"
I resolved that by loading the GenomeInfoDb package, which contains the Seqinfo
function with capital S. (If that's the function intended for use here, perhaps GenomeInfoDb should be imported as a dependency.)
However, then my original VcfStack
error recurred:
Error in validObject(.Object): invalid class “VcfStack” object: all rownames(object) must be in seqlevels(object)
I haven't found the source code for stack1kg
yet, but I'm wondering if the Seqinfo
function call was supposed to be seqinfo
. This is just a guess, but looks like some data is not being correctly assigned to seqlevels
of an object.
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomeInfoDb_1.20.0 IRanges_2.18.1 S4Vectors_0.22.0 BiocGenerics_0.30.0 stringr_1.4.0 pdftools_2.2
loaded via a namespace (and not attached):
[1] Biobase_2.44.0 httr_1.4.1 bit64_0.9-7
[4] splines_3.6.1 GenomicFiles_1.20.0 shiny_1.3.2
[7] assertthat_0.2.1 askpass_1.1 BiocManager_1.30.4
[10] RBGL_1.60.0 blob_1.2.0 BSgenome_1.52.0
[13] GenomeInfoDbData_1.2.1 Rsamtools_2.0.0 progress_1.2.2
[16] qpdf_1.1 Homo.sapiens_1.3.1 pillar_1.4.2
[19] RSQLite_2.1.2 backports_1.1.4 lattice_0.20-38
[22] glue_1.3.1 digest_0.6.20 GenomicRanges_1.36.0
[25] promises_1.0.1 XVector_0.24.0 colorspace_1.4-1
[28] htmltools_0.3.6 httpuv_1.5.1 Matrix_1.2-17
[31] OrganismDbi_1.26.0 ldblock_1.14.0 XML_3.98-1.20
[34] pkgconfig_2.0.2 biomaRt_2.40.4 zlibbioc_1.30.0
[37] purrr_0.3.2 xtable_1.8-4 GO.db_3.8.2
[40] scales_1.0.0 erma_1.0.0 later_0.8.0
[43] BiocParallel_1.18.1 tibble_2.1.3 ggplot2_3.2.1
[46] SummarizedExperiment_1.14.1 GenomicFeatures_1.36.4 lazyeval_0.2.2
[49] survival_2.44-1.1 magrittr_1.5 crayon_1.3.4
[52] mime_0.7 memoise_1.1.0 graph_1.62.0
[55] tools_3.6.1 prettyunits_1.0.2 org.Hs.eg.db_3.8.2
[58] hms_0.5.0 matrixStats_0.54.0 munsell_0.5.0
[61] DelayedArray_0.10.0 AnnotationDbi_1.46.1 snpStats_1.34.0
[64] Biostrings_2.52.0 compiler_3.6.1 rlang_0.4.0
[67] grid_3.6.1 RCurl_1.95-4.12 rstudioapi_0.10
[70] VariantAnnotation_1.30.1 bitops_1.0-6 gtable_0.3.0
[73] DBI_1.0.0 R6_2.4.0 GenomicAlignments_1.20.1
[76] dplyr_0.8.3 rtracklayer_1.44.2 bit_1.1-14
[79] zeallot_0.1.0 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 stringi_1.4.3
[82] Rcpp_1.0.1 vctrs_0.2.0 tidyselect_0.2.5
from labs.
from labs.
from labs.
This fixed the issue - thanks!
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