Question: GDCdownload error in TCGAbiolinks: Invalid zip name argument
1
gravatar for fawazfebin
23 months ago by
fawazfebin30
fawazfebin30 wrote:

 

 

Hi

I was analysing TNBC data sets usin TCGAbiolinks and got the following error while running GDCdownload command:

> GDCdownload(query = queryDown,
+             directory = DataDirectory)
Downloading data for project TCGA-BRCA
trying URL 'https://gdc.cancer.gov/system/files/authenticated%20user/0/gdc-client_v1.3.0_Windows_x64.zip'
Content type 'application/zip' length 16576709 bytes (15.8 MB)
downloaded 15.8 MB

Error in unzip(basename(bin)) : invalid zip name argument
In addition: Warning message:
In if (grepl("^https?://", url)) { :
  the condition has length > 1 and only the first element will be used

 

Can anyone help please? Thanks in advance .

 

ADD COMMENTlink modified 23 months ago by Tiago Chedraoui Silva240 • written 23 months ago by fawazfebin30

I have this same problem using Rstudio in windows 10 and the following code:

library(TCGAbiolinks)

data <- read.table('./R/JWCI/pc/data/prad_tcga_clinical_data.tsv', sep='\t', header=TRUE)

barcode_header <- "Patient.ID"
# get the barcodes that belong to the non-null lymph findings
barcodes <- data[barcode_header][which(!is.na(data[lymph_header]), arr.ind=TRUE)]

query <- GDCquery(project="TCGA-PRAD", data.category="Raw Sequencing Data",

                  barcode=barcodes)

GDCdownload(query, method = "api", directory="./R/GDCdata/")

Everything works until the end of the GDCdownload function in  which i get the same error as the user above: 

> GDCdownload(query, method = "api", directory="./R/GDCdata/")
Downloading data for project TCGA-PRAD
trying URL 'https://gdc.cancer.gov/system/files/authenticated%20user/0/gdc-client_v1.3.0_Windows_x64.zip'
Content type 'application/zip' length 16576709 bytes (15.8 MB)
downloaded 15.8 MB

Error in unzip(basename(bin)) : invalid zip name argument
In addition: Warning message:
In if (grepl("^https?://", url)) { :
  the condition has length > 1 and only the first element will be used

ADD REPLYlink written 23 months ago by cmanughian10
Answer: GDCdownload error in TCGAbiolinks: Invalid zip name argument
1
gravatar for Tiago Chedraoui Silva
23 months ago by
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Tiago Chedraoui Silva240 wrote:

 GDC client version was updated and a GUI version was also added (https://github.com/NCI-GDC/dtt-ui).

That addition broke the code, but I just fixed it. TCGAbiolinks versions 2.7.8 and 2.6.8 are fixed.

For the moment you can install from github with:

devtools::install_github('BioinformaticsFMRP/TCGAbiolinks')
ADD COMMENTlink modified 23 months ago • written 23 months ago by Tiago Chedraoui Silva240
1

Awesome, thanks! Appreciate for your quick response and fix!

ADD REPLYlink written 23 months ago by cmanughian10

Great thanks!

ADD REPLYlink written 23 months ago by fawazfebin30

 

I get the following error while installing from GitHub:

> devtools::install_github('BioinformaticsFMRP/TCGAbiolinks')
Downloading GitHub repo BioinformaticsFMRP/TCGAbiolinks@master
from URL https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/zipball/master
Installing TCGAbiolinks
Installation failed: error reading from connection
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 (build 9200)

Matrix products: default

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

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

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] httr_1.3.1      compiler_3.4.3  R6_2.2.2        Matrix_1.2-12   tools_3.4.3    
 [6] withr_2.1.1     curl_3.1        memoise_1.1.0   grid_3.4.3      git2r_0.20.0   
[11] digest_0.6.13   devtools_1.13.4 lattice_0.20-35

Any comments please , @tiagochst  ? Thanks.

ADD REPLYlink written 23 months ago by fawazfebin30
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