I have used GCDquery() (from library "TCGAbiolinks" ) for months now with no problems, but now the following:
library("TCGAbiolinks")
PreClin<-GDCquery(project="TCGA-BRCA",data.category = "Clinical",barcode = Breast_Tumor_barcodes)
returns the following error:
> source('~/.active-rstudio-document')
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Warning: 40 parsing failures.
row # A tibble: 5 x 5 col row col expected actual file expected <int> <chr> <chr> <chr> <chr> actual 1 1 <NA> 7 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv' file 2 2 <NA> 7 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv' row 3 3 <NA> 7 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv' col 4 4 <NA> 7 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv' expected 5 5 <NA> 7 columns 71 columns 'https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv'
... ................. ... .............................................................................................. ........ .............................................................................................. ...... .................. [... truncated]
Error: Column index must be at most 7 if positive, not 8
In addition: Warning messages:
1: Unnamed `col_types` should have the same length as `col_names`. Using smaller of the two.
2: In rbind(names(probs), probs_f) :
number of columns of result is not a multiple of vector length (arg 1)
3: Unknown or uninitialised column: 'project_id'.
4: Unknown or uninitialised column: 'project_id'.
I have no idea what has changed nor how it happen. Please help as soon as you can.
