Error when downloading files

[cherlynty]

Hi, I keep getting this error when trying to download files.

Error: lexical error: invalid char in json text. <?xml version="1.0" encoding="U (right here) ------^

this is my code: ge_manifest_CNV_primarytumour = files() %>% filter( ~ cases.project.project_id == 'TCGA-LIHC' & data_type == 'Masked Copy Number Segment' & cases.samples.sample_type == 'Primary Tumor' & analysis.workflow_type == 'DNAcopy') %>%

Please advise me further. Thank you

Cherlyn

[seandavi]

Thanks for the report, @cherlynty. It looks like your code block might have gotten cut off. Can you try pasting it in again? Also, can you share the output of sessionInfo() and GenomicDataCommons::status()?

[seandavi]

@cherlynty, can you give this a try by:

BiocInstaller::biocLite('Bioconductor/GenomicDataCommons')

and then running your code? If that works, I'll push the changes to the main bioc repositories. '

Thanks!

[cherlynty]

Hi,

Many thanks for your response. I have tried the new installation line, but have gotten a new line of error.

Error in UseMethod("filter") : no applicable method for 'filter' applied to an object of class "c('gdc_files', 'GDCQuery', 'list')"

This is an example of my code, I have tried to get other data types as well.

ge_manifest_mRNA_counts_primarytumour = files() %>% filter( ~ cases.project.project_id == 'TCGA-LIHC' & data_type == 'Gene Expression Quantification' & cases.samples.sample_type == 'Primary Tumor' & analysis.workflow_type == 'HTSeq - Counts') %>% manifest()

This is my session info.

R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=English_Singapore.1252 LC_CTYPE=English_Singapore.1252
[3] LC_MONETARY=English_Singapore.1252 LC_NUMERIC=C
[5] LC_TIME=English_Singapore.1252

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

other attached packages: [1] dplyr_0.7.5 BiocInstaller_1.30.0 GenomicDataCommons_1.5.3 [4] magrittr_1.5

loaded via a namespace (and not attached): [1] Rcpp_0.12.17 pillar_1.2.3 compiler_3.5.0 GenomeInfoDb_1.16.0
[5] XVector_0.20.0 bindr_0.1.1 remotes_1.1.1 bitops_1.0-6
[9] tools_3.5.0 zlibbioc_1.26.0 digest_0.6.15 jsonlite_1.5
[13] tibble_1.4.2 pkgconfig_2.0.1 rlang_0.2.0 curl_3.2
[17] yaml_2.1.19 parallel_3.5.0 bindrcpp_0.2.2 GenomeInfoDbData_1.1.0 [21] httr_1.3.1 knitr_1.20 xml2_1.2.0 S4Vectors_0.18.2
[25] IRanges_2.14.10 rappdirs_0.3.1 hms_0.4.2 stats4_3.5.0
[29] rprojroot_1.3-2 tidyselect_0.2.4 glue_1.2.0 R6_2.2.2
[33] purrr_0.2.4 readr_1.1.1 backports_1.1.2 htmltools_0.3.6
[37] BiocGenerics_0.26.0 GenomicRanges_1.32.3 assertthat_0.2.0 RCurl_1.95-4.10
[41] lazyeval_0.2.1

the status: $commit [1] "53012d00624a8dcf06b6ad47c31b51017094f517"

$data_release [1] "Data Release 11.0 - May 21, 2018"

$status [1] "OK"

$tag [1] "1.14.1"

$version [1] 1

thank you.

cherlyn

[cherlynty]

Hi,

I have tried the code again without the Rcurl package and it seem to run alright. Thank you for your help.

Cheers, Cherlyn

[seandavi]

Just a note that this was, indeed, a bug introduced by changes to the URL on the server (and an incorrect redirect). Version 1.4.1 (or later) or 1.5.3 (developer) will fix the issue.