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10 months 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")


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

modified 9 months ago by wenhuo hu200 • written 10 months ago by jason.yijialin0
2
10 months ago by
Mike Smith2.8k
EMBL Heidelberg / de.NBI
Mike Smith2.8k 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.

I have solved the problem,Thank you very much.

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

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

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10 months ago by
sechenmo0
sechenmo0 wrote:

I have the same problem.

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10 months 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

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

thank you so much!

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10 months 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'"

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9 months ago by
wenhuo hu200
United States
wenhuo hu200 wrote:

Just in case someone is still bothered by this:

Install the TCGAbiolinks from the github solved this problem. It applears github has the more updated version.