Error running the test and getProfileData functions following the vignette

[asmagen]

Hello,

I get the following error with the test function:

> test(mycgds)
getCancerStudies...  OK
getCaseLists (1/2) ...  OK
getCaseLists (2/2) ...  OK
getGeneticProfiles (1/2) ...  OK
getGeneticProfiles (2/2) ...  OK
getClinicalData (1/1) ...  OK
Error in read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t",  : 
  more columns than column names

[asmagen]

I also get the same error when running this example from the vignette:

> getProfileData(mycgds, c("MDM2","MDM4"), "gbm_tcga_mrna", "gbm_tcga_all")[c(1:5),]
Error in read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t",  : 
  more columns than column names

[jjgao]

@asmagen I had no problem running either function. Have you updated to the latest code?

[asmagen]

I did. Just forced a new installation from GitHub.
I'm still getting the same error.

[jjgao]

@asmagen I was using the cgdsr package from CRAN: https://cran.r-project.org/web/packages/cgdsr/index.html. Have you tried that?

[asmagen]

It works with this version from Cran. So there's a problem with the GitHub version.
Thanks

[asmagen]

What does NaN mean when I run getProfileData(mycgds, c("MDM2","MDM4"), "gbm_tcga_mrna", "gbm_tcga_all")[c(1:5),]? Are the values missing originally in TCGA or is it a bug / problem of the download?

[jjgao]

@asmagen got it. thanks.

[jjgao]

@asmagen these samples are missing expression data in the gbm_tcga_mrna profile.

[asmagen]

Got it, thanks.

[jjgao]

I am reopening this since the originally reported issue is not solved in the code here.

[avicens]

I have tried both GitHub (cgdsr_1.2.8) and CRAN (cgdsr_1.2.10 versions and I got the same error here reported when running the example from vignettes.

> getProfileData(mycgds, c("MDM2","MDM4"), "gbm_tcga_mrna", "gbm_tcga_all")[c(1:5),]
Error in read.table(url, skip = 0, header = TRUE, as.is = TRUE, sep = "\t",  : 
  more columns than column names

Could you tell me what version did you get run this function with?