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Question: package or namespace load failed for TCGAbiolinks
0
gravatar for jason.yijialin
14 days ago by
jason.yijialin0 wrote:

I am using R version 3.4.1 (2017-06-30), Bioconductor 3.5 and RStudio to use TCGAbiolinks package.   

source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinks")

Above are the code I used to install TCGAbiolinks package, but when I enter library(TCGAbiolinks)

The error showed up as

Error: package or namespace load failed for ‘TCGAbiolinks’:
 object ‘rbind.gtable’ is not exported by 'namespace:gridExtra'

Could anyone help solve this problem?

Thanks

ADD COMMENTlink modified 12 days ago by lji04280 • written 14 days ago by jason.yijialin0
2
gravatar for Mike Smith
14 days ago by
Mike Smith2.0k
EMBL Heidelberg / de.NBI
Mike Smith2.0k wrote:

It looks like this function was renamed in gridExtra two days ago, see https://cran.r-project.org/web/packages/gridExtra/news.html

I guess it will take the TCGAbiolinks maintainer a couple of days to update the relevant lines, and get a new release through the BioC build system.  In the meantime, maybe you can manually install the previous version of gridExtra (version 2.2.1) and ignore requests to update it until a patch to TCGAbiolinks is released too.

ADD COMMENTlink modified 14 days ago • written 14 days ago by Mike Smith2.0k

I have solved the problem,Thank you very much.

ADD REPLYlink written 14 days ago by sechenmo0

Thank you so much! I will wait for TCGAbiolinks maintainer to update their package.

 

ADD REPLYlink written 13 days ago by jason.yijialin0

Thanks, I have also faced this problem and this solved it!

ADD REPLYlink written 12 days ago by rfes0
0
gravatar for sechenmo
14 days ago by
sechenmo0
sechenmo0 wrote:

I have the same problem.

ADD COMMENTlink written 14 days ago by sechenmo0
0
gravatar for lji0428
12 days ago by
lji04280
lji04280 wrote:

Hi all, R newbie here. Any kind soul willing to provide the code for installing gridExtra_2.2.1? I'm using Rstudio.

 

Thanks so much

ADD COMMENTlink written 12 days ago by lji04280

install.packages("https://cran.r-project.org/src/contrib/Archive/gridExtra/gridExtra_2.2.1.tar.gz", repos=NULL)

 

ADD REPLYlink written 12 days ago by Martin Morgan ♦♦ 20k

thank you so much!

ADD REPLYlink written 12 days ago by lji04280
0
gravatar for lji0428
12 days ago by
lji04280
lji04280 wrote:

Unfortunately, I'm still getting the error message (see below) even after I've installed gridExtra_2.0.0 successfully when I try to then call library(TCGAbiolinks). I guess I'll have to wait for the TCGAbiolinks to be updated too....

 

Error: package or namespace load failed for ‘TCGAbiolinks’:
 object ‘rbind.gtable’ is not exported by 'namespace:gridExtra'"

 

ADD COMMENTlink written 12 days ago by lji04280

Yes until TCGAbiolinks updates their NAMESPACE file, this ERROR will occur.  

ADD REPLYlink written 12 days ago by shepherl ♦♦ 380
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