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Question: makeTxdbFromUCSC in genomicfeatures package is broken
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gravatar for arko.sen1
6 months ago by
arko.sen10
arko.sen10 wrote:

> txdb= makeTxDbFromUCSC(genome= "hg19", tablename="ensGene")
Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) :
  'names' attribute [211] must be the same length as the vector [209]

any ideas how to fix this

ADD COMMENTlink modified 6 months ago by Michael Lawrence10.0k • written 6 months ago by arko.sen10

Did you find a way to solve the problem? 

ADD REPLYlink written 6 months ago by mcall0
0
gravatar for Michael Lawrence
6 months ago by
Michael Lawrence10.0k
United States
Michael Lawrence10.0k wrote:

Should be fixed as of rtracklayer 1.38.2.

ADD COMMENTlink written 6 months ago by Michael Lawrence10.0k

Hi. 

I've installed and updated the rtracklayer, but I still get the same error... Anyother ideas? 

ADD REPLYlink written 6 months ago by mcall0
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
 [1] BiocInstaller_1.28.0   rtracklayer_1.38.2     magrittr_1.5           forcats_0.2.0          stringr_1.2.0          dplyr_0.7.4           
 [7] purrr_0.2.4            readr_1.1.1            tibble_1.3.4           ggplot2_2.2.1          tidyverse_1.2.1        broom_0.4.3           
[13] reshape2_1.4.3         annotate_1.56.1        XML_3.98-1.9           org.Hs.eg.db_3.5.0     GenomicFeatures_1.30.0 AnnotationDbi_1.40.0  
[19] Biobase_2.38.0         tidyr_0.7.2            GenomicRanges_1.30.0   GenomeInfoDb_1.14.0    IRanges_2.12.0         S4Vectors_0.16.0      
[25] BiocGenerics_0.24.0    refGenome_1.7.3        RSQLite_2.0            doBy_4.5-15            limma_3.34.3           dtplyr_0.0.2          
[31] genefilter_1.60.0      RColorBrewer_1.1-2     RSkittleBrewer_1.1     plyr_1.8.4            

loaded via a namespace (and not attached):
 [1] nlme_3.1-131               bitops_1.0-6               matrixStats_0.52.2         lubridate_1.7.1            bit64_0.9-7               
 [6] httr_1.3.1                 tools_3.4.0                R6_2.2.2                   DBI_0.7                    lazyeval_0.2.1            
[11] colorspace_1.3-2           mnormt_1.5-5               bit_1.1-12                 compiler_3.4.0             cli_1.0.0                 
[16] rvest_0.3.2                xml2_1.1.1                 DelayedArray_0.4.1         scales_0.5.0               psych_1.7.8               
[21] digest_0.6.12              Rsamtools_1.30.0           foreign_0.8-69             XVector_0.18.0             pkgconfig_2.0.1           
[26] rlang_0.1.4                readxl_1.0.0               rstudioapi_0.7             bindr_0.1                  jsonlite_1.5              
[31] BiocParallel_1.12.0        RCurl_1.95-4.8             GenomeInfoDbData_0.99.1    Matrix_1.2-12              Rcpp_0.12.14              
[36] munsell_0.4.3              stringi_1.1.6              MASS_7.3-47                SummarizedExperiment_1.8.0 zlibbioc_1.24.0           
[41] grid_3.4.0                 blob_1.1.0                 crayon_1.3.4               lattice_0.20-35            Biostrings_2.46.0         
[46] haven_1.1.0                splines_3.4.0              hms_0.4.0                  biomaRt_2.34.0             glue_1.2.0                
[51] modelr_0.1.1               cellranger_1.1.0           gtable_0.2.0               assertthat_0.2.0           xtable_1.8-2              
[56] survival_2.41-3            GenomicAlignments_1.14.1   memoise_1.1.0              bindrcpp_0.2              

> refSeq             <- makeTxDbFromUCSC(genom="hg19",tablename="refGene")
Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : 
  'names' attribute [210] must be the same length as the vector [208]
ADD REPLYlink written 6 months ago by mcall0

https://github.com/lawremi/rtracklayer/issues/4

ADD REPLYlink written 6 months ago by Michael Lawrence10.0k
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