BiocManager::install() breaks; can't install bioc-devel
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Kyle Johnsen ▴ 20
@kyle-johnsen-11443
Last seen 2.6 years ago
United States/Brigham Young University

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 
biocmanager installation • 906 views
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Entering edit mode
Kyle Johnsen ▴ 20
@kyle-johnsen-11443
Last seen 2.6 years ago
United States/Brigham Young University

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

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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?

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

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This:

source("https://bioconductor.org/biocLite.R")
biocLite()
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