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maddy
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@maddy-21872
Last seen 5.2 years ago
Hello,
We have upgraded R 3.2 to R 3.6 version . I order to install few packages it is asking to install BiocManger. I know how to do it inside R commandline :
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
But I need to do it outside R commandline. Is it possible to install "BiocManager" command line via bash command ? We used this command for biocLite :
R -e "source('http://bioconductor.org/biocLite.R'); biocLite(); biocLite(c('DESeq'))”
Is it possible to have similar command for BiocManger ?
Thanks,
Madhura
Thanks James. But it is giving following error: Error in contrib.url(repos, "source") : trying to use CRAN without setting a mirror Calls: install.packages -> contrib.url Execution halted
Maybe you need to setup the repo as well inside the install command:
install.packages(‘BiocManager', repos='http://cran.us.r-project.org')
https://stackoverflow.com/a/11488224
From: maddy [bioc] noreply@bioconductor.org noreply@bioconductor.org Reply: reply+99d6cb2e+code@bioconductor.org <reply+99d6cb2e+code@bioconductor.org> <reply+99d6cb2e+code@bioconductor.org> Date: September 11, 2019 at 4:49:44 PM To: lorena.pantano@gmail.com lorena.pantano@gmail.com lorena.pantano@gmail.com Subject: [bioc] C: How to install BiocManger commandline ?
Activity on a post you are following on support.bioconductor.org
User maddy https://support.bioconductor.org/u/21872/ wrote Comment: How to install BiocManger commandline ? https://support.bioconductor.org/p/124606/#124619:
Thanks James. But it is giving following error: Error in contrib.url(repos, "source") : trying to use CRAN without setting a mirror Calls:
install.packages -> contrib.url Execution halted
Post tags: normalization
You may reply via email or visit https://support.bioconductor.org/p/124606/#124619
Thanks Lorena ! It worked after specifying nearest CRAN mirror url. R -e "install.packages('BiocManager', repos = 'https://mirrors.nic.cz/R/')"
Cheers!!