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.