Question: How to install BiocManger commandline ?
0
gravatar for maddy
9 weeks ago by
maddy0
maddy0 wrote:

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

normalization • 159 views
ADD COMMENTlink modified 9 weeks ago by James W. MacDonald51k • written 9 weeks ago by maddy0
Answer: How to install BiocManger commandline ?
0
gravatar for James W. MacDonald
9 weeks ago by
United States
James W. MacDonald51k wrote:
R -e "install.packages('BiocManager'); library('BiocManager'); BiocManager::install('DESeq2')"

ADD COMMENTlink written 9 weeks ago by James W. MacDonald51k

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

ADD REPLYlink written 9 weeks ago by maddy0
1

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

ADD REPLYlink written 9 weeks ago by Lorena Pantano100

Thanks Lorena ! It worked after specifying nearest CRAN mirror url. R -e "install.packages('BiocManager', repos = 'https://mirrors.nic.cz/R/')"

Cheers!!

ADD REPLYlink written 9 weeks ago by maddy0
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