TCGABiolinks::GDCquery() suddenly sending back unknown error
2
1
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jrlarsen ▴ 10
@jrlarsen-14308
Last seen 3.4 years ago

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.

software error error tcgabiolinks GDCquery • 872 views
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Biologist ▴ 90
@biologist-9801
Last seen 20 months ago

Use this: This should work

query <- GDCquery(project = "TCGA-BRCA", 
                  data.category = "Clinical")
GDCdownload(query)
clinical <- GDCprepare_clinic(query, clinical.info = "patient")

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eshelden ▴ 20
@eshelden-14132
Last seen 2.5 years ago

I also "suddenly" encountered an error in GDCquery today. However, installing the version currently available on github solved my problem. You may find that version at the following link:

https://github.com/BioinformaticsFMRP/TCGAbiolinks

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