Question: GenomicDatacommon execution error
0
gravatar for jarod_v6@libero.it
15 months ago by
Italy
jarod_v6@libero.it40 wrote:

I Run this example:

resp = cases() %>% filter(~ project.project_id=='TCGA-BRCA' &
                              samples.sample_type=='Solid Tissue Normal') %>%
    GenomicDataCommons::select(c(default_fields(cases()),'samples.sample_type')) %>%
    response_all()
count(resp)

 

I have this error:

Error: lexical error: invalid char in json text.
                                       <?xml version="1.0" encoding="U
                     (right here) ------^
> count(resp)
Error in count(resp) : object 'resp' not found

 sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 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=it_IT.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenomicDataCommons_1.2.0 magrittr_1.5            

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17           rstudioapi_0.7         xml2_1.2.0            
 [4] XVector_0.18.0         GenomicRanges_1.30.3   BiocGenerics_0.24.0   
 [7] hms_0.4.2              zlibbioc_1.24.0        IRanges_2.12.0        
[10] R6_2.2.2               rlang_0.2.0            httr_1.3.1            
[13] GenomeInfoDb_1.14.0    tools_3.4.4            parallel_3.4.4        
[16] data.table_1.11.2      utf8_1.1.3             yaml_2.1.19           
[19] lazyeval_0.2.1         tibble_1.4.2           crayon_1.3.4          
[22] GenomeInfoDbData_1.0.0 readr_1.1.1            S4Vectors_0.16.0      
[25] bitops_1.0-6           curl_3.2               RCurl_1.95-4.10       
[28] compiler_3.4.4         pillar_1.2.2           stats4_3.4.4          
[31] jsonlite_1.5           pkgconfig_2.0.1    




 

 

genomicdatacommon • 208 views
ADD COMMENTlink written 15 months ago by jarod_v6@libero.it40

I am not able to reproduce this on the most recent version of GenomicDataCommons. You might try updating to R 3.5 and using the latest version of the package.

ADD REPLYlink modified 14 months ago • written 14 months ago by shepherl ♦♦ 1.4k
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