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Question: Error in c(DataFrameList(META = meta), tbls[unique(tags)])
0
gravatar for ddzhangzz
7 months ago by
ddzhangzz0
United States
ddzhangzz0 wrote:

I met some issue by running examples in R package VariantAnnotation:

> library(VariantAnnotation)
> fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
> fl
[1] "/usr/local/lib/R/site-library/VariantAnnotation/extdata/ex2.vcf"
> scanVcfHeader(fl)
Error in c(DataFrameList(META = meta), tbls[unique(tags)]) : 
  could not find symbol "recursive" in environment of the generic function
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

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

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

other attached packages:
 [1] VariantAnnotation_1.20.2   Rsamtools_1.26.1           Biostrings_2.42.1          XVector_0.14.0             SummarizedExperiment_1.4.0 Biobase_2.34.0            
 [7] GenomicRanges_1.26.3       GenomeInfoDb_1.10.3        IRanges_2.8.1              S4Vectors_0.12.1           BiocGenerics_0.20.0        setwidth_1.0-4            
[13] colorout_1.1-2            

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9              AnnotationDbi_1.36.2     GenomicAlignments_1.10.0 zlibbioc_1.20.0          BiocParallel_1.8.1       BSgenome_1.42.0          lattice_0.20-34         
 [8] tools_3.3.3              grid_3.3.3               DBI_0.6                  digest_0.6.12            Matrix_1.2-8             rtracklayer_1.34.2       bitops_1.0-6            
[15] biomaRt_2.30.0           RCurl_1.95-4.8           memoise_1.0.0            RSQLite_1.1-2            GenomicFeatures_1.26.3   XML_3.98-1.5       

ADD COMMENTlink modified 7 months ago by Hervé Pagès ♦♦ 13k • written 7 months ago by ddzhangzz0
0
gravatar for Hervé Pagès
7 months ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi,

This problem has been fixed in the latest version of VariantAnnotation (1.20.3). Please update to the latest packages (with biocLite()) and try again.

H.

ADD COMMENTlink written 7 months ago by Hervé Pagès ♦♦ 13k
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