Error in c(DataFrameList(META = meta), tbls[unique(tags)])
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ddzhangzz • 0
@ddzhangzz-8982
Last seen 6.1 years ago
United States

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       

VariantAnnotation • 1.2k views
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@herve-pages-1542
Last seen 20 hours ago
Seattle, WA, United States

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.

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Hi,

I still have this problem with the new version of VariantAnnotation (1.20.3).

> fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> vcf <- readVcf(fl, genome="hg19")
Error in c(DataFrameList(META = meta), tbls[unique(tags)]) : 
  could not find symbol "recursive" in environment of the generic function
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] 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              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] VariantAnnotation_1.20.3   SummarizedExperiment_1.4.0 Rsamtools_1.26.2          
 [4] Biostrings_2.42.1          XVector_0.14.1             GenomicRanges_1.26.4      
 [7] GenomeInfoDb_1.10.3        proxysnps_0.0.1            BiocInstaller_1.24.0      
[10] kinship2_1.6.4             quadprog_1.5-5             Matrix_1.2-11             
[13] lattice_0.20-35            xtable_1.8-2               bindrcpp_0.2              
[16] DT_0.2                     purrr_0.2.4                fmsb_0.6.1                
[19] tidyr_0.7.2                biomaRt_2.30.0             IRanges_2.8.2             
[22] S4Vectors_0.12.2           Biobase_2.34.0             BiocGenerics_0.20.0       
[25] limma_3.30.13              dplyr_0.7.4                ggplot2_2.2.1             
[28] knitr_1.17                

loaded via a namespace (and not attached):
 [1] httr_1.3.1               bit64_0.9-7              jsonlite_1.5             Formula_1.2-1           
 [5] assertthat_0.2.0         latticeExtra_0.6-28      blob_1.1.0               BSgenome_1.42.0         
 [9] yaml_2.1.14              RSQLite_2.0              glue_1.1.1               digest_0.6.9            
[13] RColorBrewer_1.1-2       colorspace_1.2-4         htmltools_0.3.6          plyr_1.8.3              
[17] XML_3.98-1.3             pkgconfig_2.0.1          devtools_1.13.4          myvariant_1.4.0         
[21] zlibbioc_1.20.0          scales_0.5.0             BiocParallel_1.8.2       git2r_0.19.0            
[25] tibble_1.3.4             withr_2.1.0              GenomicFeatures_1.26.4   nnet_7.3-12             
[29] lazyeval_0.2.0           survival_2.41-3          magrittr_1.5             memoise_1.1.0           
[33] foreign_0.8-69           tools_3.4.2              munsell_0.4.3            cluster_2.0.6           
[37] AnnotationDbi_1.36.2     compiler_3.4.2           rlang_0.1.2              grid_3.4.2              
[41] RCurl_1.95-4.7           htmlwidgets_0.9          bitops_1.0-6             gtable_0.2.0            
[45] DBI_0.7                  curl_3.0                 R6_2.2.2                 GenomicAlignments_1.10.1
[49] gridExtra_2.0.0          rtracklayer_1.34.2       bit_1.1-12               bindr_0.1               
[53] Hmisc_3.17-1             Rcpp_0.12.13             rpart_4.1-11             acepack_1.3-3.3   
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If it's not solved yet, Martin Morgan 's solution A: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC) worked well for me. :D 

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