Question: Error when using "Module_A.r" of TCGA-assembler
0
gravatar for ytian
2.1 years ago by
ytian0
ytian0 wrote:

Dear everyone I use TCGA assembler to retrieve some data. But when I tried Methylation 450K data. The code i used are: filename_READ_Methylation450 = DownloadMethylationData(cancerType = "LUAD", assayPlatform = "methylation_450", saveFolderName = "./Methyl",inputPatientIDs = rownamesLUAD.ID)) It recurrently went to error. Here is the indication by R studio:

[1] "*.tar.gz file: downloading & unzipping ..."

[1] "*.tar.gz file: downloading & unzipping done!"

[1] "*.tar.gz file: downloading & unzipping ..."

**[1] "error (download): check the proxy"

Error: is.null(attr(s_stdout, "status")) is not TRUE Called from: f_v_barcode2filename_downloadedById(v_id2barcode[(n * n_each + 1):ifelse(n == ceiling(length(v_id2barcode)/n_each) - 1, length(v_id2barcode), (n + 1) * n_each)], s_dir = s_dir, s_archive = s_archive) Browse[1]> Q**

Have any one encounter such a problem??

R • 745 views
ADD COMMENTlink modified 2.0 years ago by Biostar ♦♦ 20 • written 2.1 years ago by ytian0

I also faced such an error

DownloadRNASeqData(cancerType = "COAD", assayPlatform = "gene.normalized_RNAseq",

tissueType = NULL, saveFolderName = ".", outputFileName = "", inputPatientIDs = NULL)

[1] "metadata file: preparing ..."

[1] "metadata file: preparing done!"

[1] "*.tar.gz file: downloading & unzipping ..."

[1] "error (download): check the proxy"

Error: is.null(attr(s_stdout, "status")) is not TRUE

Called from: f_v_barcode2filename_downloadedById(v_id2barcode, s_dir = s_dir,

s_archive = s_archive)

Browse[1]> c

c function (..., recursive = FALSE) .Primitive("c")

I am in windows and read something about limitation on the length of file path in windows but I did not solve the problem yet

ADD REPLYlink written 2.1 years ago by F3.4k

Maybe it is related to this:

Version 2.0.2 release - 04/05/2017

Bug fixed

Because GDC recently changed the format of meta file for biospecimen and clinical data, we updated TCGA-Assembler code so that
  

the DownloadBiospecimenClinicalData function can work correctly.

ADD REPLYlink written 2.0 years ago by h.mon24k
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