maybe a problem to download

hibarikyouya commented 8 years ago

Hi all !

Hope everybody is ok, thanks for the guys who are active here :) There might a problem with the TCGAdownload function at the moment. Code that used to work before don't work anymore on my machine. For example :

query <- TCGAquery(tumor="BRCA", level=3, platform="MDA_RPPA_Core") TCGAdownload(query, path="rppa")

or :

TCGAdownload(query, path="rppa", samples=c("TCGA-E2-A14V-01A-21-A13E-20"))

gives me :

-=-=-=-=-=-= | Downloading:5 folders | Path:rppa -=-=-=-=-=-= | | 0% Downloading:mdanderson.org_BRCA.MDA_RPPA_Core.Level_3.1.3.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 240 100 240 0 0 40 0 0:00:06 0:00:05 0:00:01 54 100 2060 100 2060 0 0 343 0 0:00:06 0:00:05 0:00:01 343 Error in fread(paste0(root, data[i, "deployLocation"], ".md5"), header = F, : Expected sep (',') but new line or EOF ends field 1 on line 33 when reading data: --> De plus : Warning messages: 1: In fread(paste0(root, data[i, "deployLocation"], ".md5"), header = F, : Unable to find 5 lines with expected number of columns (+ middle) 2: In fread(paste0(root, data[i, "deployLocation"], ".md5"), header = F, : Unable to find 5 lines with expected number of columns (+ last)

Can somebody try to see if I'm dumb or it's not me. Thanks :)

labrazil commented 8 years ago

Hi, it's due to a maintenance issue over at TCGA.

https://tcga-data.nci.nih.gov/maintenance_deploying.html

Houtan

\hn cell (USA): +1-310-570-2362 cell (BRA): +55-16-99779-2362

Sent from my nexus 6p On Jun 21, 2016 07:36, "hibarikyouya" notifications@github.com wrote:

Hi all !

Hope everybody is ok, thanks for the guys who are active here :) There might a problem with the TCGAdownload function at the moment. Code that used to work before don't work anymore on my machine. For example : query <- TCGAquery(tumor="BRCA", level=3, platform="MDA_RPPA_Core") TCGAdownload(query, path="rppa") or : TCGAdownload(query, path="rppa", samples=c("TCGA-E2-A14V-01A-21-A13E-20")) gives me : -=-=-=-=-=-= | Downloading:5 folders | Path:rppa -=-=-=-=-=-= | | 0% Downloading:mdanderson.org_BRCA.MDA_RPPA_Core.Level_3.1.3.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 240 100 240 0 0 40 0 0:00:06 0:00:05 0:00:01 54 100 2060 100 2060 0 0 343 0 0:00:06 0:00:05 0:00:01 343 Error in fread(paste0(root, data[i, "deployLocation"], ".md5"), header = F, : Expected sep (',') but new line or EOF ends field 1 on line 33 when reading data: --> De plus : Warning messages: 1: In fread(paste0(root, data[i, "deployLocation"], ".md5"), header = F, : Unable to find 5 lines with expected number of columns (+ middle) 2: In fread(paste0(root, data[i, "deployLocation"], ".md5"), header = F, : Unable to find 5 lines with expected number of columns (+ last) Can somebody try to see if I'm dumb or it's not me. Thanks :)

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tiagochst commented 8 years ago

Our team updated TCGAbiolinks to work with the new GDC portal. We had to rewrite almost all the code again, but we hope this will help improve our tool which we are dedicated to improving. Unfortunately, the changes are not in the Bioconductor repository, but we anticipate the codes will be updated within the coming weeks. For the moment, if you require the new package, you can install it from our GitHub repository with the following command:

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

The protein expression data is only available in the legacy database, this code will work for you:

query <- GDCquery(project = "TCGA-BRCA", 
                  data.category = "Protein expression",
                  platform = "MDA_RPPA_Core", legacy = TRUE) 
GDCdownload(query)
data <- GDCprepare(query)

BioinformaticsFMRP / TCGAbiolinks

maybe a problem to download #7