Tiago Chedraoui Silva comments

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                                            Tiago Chedraoui Silva

How do i actually intall the mod?

@seresharp Do you have any info about installing on mac ?

GDCquery_Maf not working

Hi, GDCquery_Maf was removed from the latest version of the package after GDC last update. On Sun, May 1, 2022, 5:14 PM krushnach80 ***@***.***> wrote: > I'm trying to run...

GDCquery_Maf not working

Here is the documentation. https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/mutation.html

GDCprepare problems.

Hello, For the legacy database there were several files. You will need to use `file.type` filter. For example: ``` query.sim_Nuc_Var

Duplicated cases when querying TCGA-CHOL mutation data

It is working for me: https://rpubs.com/tiagochst/TCGAbiolinks_issue_520 The "duplicated cases" is just a warning, since for each MAF file both matched tumor and normal samples were used to produce the file.

GDCPrepare Error

Hi, Could you update to the last version with `BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")`. I don't think any old versions will be working anymore.

GDCPrepare Error

I'll check, I think I know what it might be.

GDCPrepare Error

Thanks, I just fixed it. If you reinstall with `BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")` and restart R it should be working.

Error in strsplit(c(colnames(data)), "-") : non-character argument

The function was mainly created for TCGA data. There are certain functions that will only work with TCGA data. You could still run the function as below: ``` library(TCGAbiolinks) project

Problem with installing the package on Mac and linux

Please, if you try installing openssl with `install.packages("openssl")` what is the output ? It is possibly missing a system dependence to install openssl package.