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Question: BiocManager::install() breaks; can't install bioc-devel
0
gravatar for Kyle Johnsen
3 months ago by
Kyle Johnsen20
United States/Brigham Young University
Kyle Johnsen20 wrote:

BiocManger::install(version='devel') doesn't work for me.

This is what happens:

> BiocManager::install(version = 'devel')
Error: $ operator is invalid for atomic vectors
 

I was able to identify the problem on line 23 of the install package, when .install_n_invalid_pkgs is called. When I run install, `valist` in install (and thus `valid` in .install_n_invalid_pkgs) is just TRUE, rather than a list, as the function expects. So the problem seems to lie in the .valid() function.

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.7.0
LAPACK: /usr/lib/lapack/liblapack.so.3.7.0

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] BiocManager_1.30.2

loaded via a namespace (and not attached):
[1] compiler_3.5.1 tools_3.5.1 
ADD COMMENTlink modified 3 months ago • written 3 months ago by Kyle Johnsen20
0
gravatar for Kyle Johnsen
3 months ago by
Kyle Johnsen20
United States/Brigham Young University
Kyle Johnsen20 wrote:

I installed Bioconductor first, and then it worked. I didn't know Bioconductor needed to already be installed.

ADD COMMENTlink written 3 months ago by Kyle Johnsen20

What exactly do you mean by 'installed Bioconductor'?  Can you provide the code you ran, so if anyone else finds this post they can run it to?

ADD REPLYlink written 3 months ago by Mike Smith3.1k

I can see the problem in the code and we will fix, thanks for the report. See this issue.

ADD REPLYlink written 3 months ago by Martin Morgan ♦♦ 22k

This:

source("https://bioconductor.org/biocLite.R")
biocLite()
ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by Kyle Johnsen20
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