Unable to install TCGAbiolinks
Entering edit mode
rf • 0
Last seen 8 months ago

I am trying to install and load TCGAbiolinks. It was working before, but probably due to some package that was installed, it suddenly stopped working. This happened before, but unninstalling and reinstalling R and RStudio solved the problem. But not now...

I already tried unninstalling R and RStudio twice, to no avail. The last time I installed ROpen 3.4 and RStudio-1.1.359. 

> biocLite("TCGAbiolinks")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.0 (2017-04-21).
Installing package(s) ‘TCGAbiolinks’

  There is a binary version available but the source version is later:
             binary source needs_compilation
TCGAbiolinks  2.4.3  2.5.7             FALSE

installing the source package ‘TCGAbiolinks’

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/TCGAbiolinks_2.5.7.tar.gz'
Content type 'application/x-gzip' length 48880035 bytes (46.6 MB)
downloaded 46.6 MB

* installing *source* package 'TCGAbiolinks' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : object 'rbind.gtable' is not exported by 'namespace:gridExtra'
ERROR: lazy loading failed for package 'TCGAbiolinks'
* removing 'C:/Program Files/Microsoft/R Open/R-3.4.0/library/TCGAbiolinks'

The downloaded source packages are in
Warning messages:
1: running command '"C:/PROGRA~1/MICROS~3/ROPEN~1/R-34~1.0/bin/x64/R" CMD INSTALL -l "C:\Program Files\Microsoft\R Open\R-3.4.0\library" C:\Users\UI~1.EN\AppData\Local\Temp\RtmpM1UrrV/downloaded_packages/TCGAbiolinks_2.5.7.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘TCGAbiolinks’ had non-zero exit status
tcgabiolinks • 2.4k views
Entering edit mode
rf • 0
Last seen 8 months ago

The solution was to install an older version of `gridExtra`. Version 2.2.1 worked


Source: A: package or namespace load failed for TCGAbiolinks

Entering edit mode
shepherl 3.5k
Last seen 1 day ago
United States

gridExtra changed some of their function names which TCGAbiolinks imported;  Until TCGAbiolinks updates their NAMESPACE and code this ERROR will occur.  The Bioconductor team is in the process of reaching out to TCGAbiolinks to make the appropriate changes.  For now installing the older version of gridExtra will also work. 


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