Entering edit mode
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
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.