Question: Installation of PharmacoGx on linux fails
0
gravatar for rubi
3.0 years ago by
rubi90
rubi90 wrote:

Trying to install the PharmacoGx package on linux and am getting an error that doesn't male a lot of sense:

    > biocLite("PharmacoGx")
    BioC_mirror: https://bioconductor.org
    Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
    Installing package(s) ‘PharmacoGx’
    Old packages: 'cluster', 'codetools', 'foreign', 'lattice', 'Matrix', 'mgcv',
      'survival'
    Update all/some/none? [a/s/n]: n
    Warning message:
    package ‘PharmacoGx’ is not available (for R version 3.3.1) 

 

> sessionInfo()
    R version 3.3.1 (2016-06-21)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: CentOS Linux 7 (Core)
    
    locale:
     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
     [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
     [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
     [9] LC_ADDRESS=C               LC_TELEPHONE=C            
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
    
    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods   base     
    
    other attached packages:
    [1] devtools_1.12.0      BiocInstaller_1.22.3
    
    loaded via a namespace (and not attached):
    [1] tools_3.3.1   withr_1.0.2   memoise_1.0.0 digest_0.6.10

 

Note - I already updated the  'cluster', 'codetools', 'foreign', 'lattice', 'Matrix', 'mgcv',
      'survival' in previous attempts hence the decline to update them above.

installation pharmacogx • 451 views
ADD COMMENTlink modified 3.0 years ago by Martin Morgan ♦♦ 23k • written 3.0 years ago by rubi90
Answer: Installation of PharmacoGx on linux fails
0
gravatar for Martin Morgan
3.0 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

PharamacoGx was added in Bioconductor 3.4, so you'll need to upgrade your installation (remove.packages("BiocInstaller"), then in a new session source("https://bioconductor.org/biocLite.R"); biocLite() to update (probably many) packages.

ADD COMMENTlink written 3.0 years ago by Martin Morgan ♦♦ 23k
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