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Question: Error in c(DataFrameList(META = meta), tbls[unique(tags)])
0
gravatar for ddzhangzz
17 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 17 months ago by Hervé Pagès ♦♦ 13k • written 17 months ago by ddzhangzz0
0
gravatar for Hervé Pagès
17 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 17 months ago by Hervé Pagès ♦♦ 13k

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   
ADD REPLYlink written 9 months ago by michele.filosi0

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 

ADD REPLYlink written 6 months ago by ehsueh19930
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