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Question: Unable to install TCGAbiolinks
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gravatar for rfes
7 months ago by
rfes0
rfes0 wrote:

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
    ‘C:\Users\ui.ent\AppData\Local\Temp\RtmpM1UrrV\downloaded_packages’
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
ADD COMMENTlink modified 7 months ago by shepherl ♦♦ 560 • written 7 months ago by rfes0
0
gravatar for rfes
7 months ago by
rfes0
rfes0 wrote:

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

 

Source: A: package or namespace load failed for TCGAbiolinks

ADD COMMENTlink written 7 months ago by rfes0
0
gravatar for shepherl
7 months ago by
shepherl ♦♦ 560
shepherl ♦♦ 560 wrote:

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. 

ADD COMMENTlink written 7 months ago by shepherl ♦♦ 560
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