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Kyle Johnsen
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20
@kyle-johnsen-11443
Last seen 5.2 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 |
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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
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?
I can see the problem in the code and we will fix, thanks for the report. See this issue.
This:
source("https://bioconductor.org/biocLite.R") biocLite()