Question

Error in installing BiocManager

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biok0423 ▴ 20

@biok0423-23341

Last seen 4.6 years ago

I have tried to install BiocManager to ubuntu 18.04. When I run the command in bash terminal:

install.packages('BiocManager')

I got an error saying:

** testing if installed package can be loaded 
Error : .onAttach failed in attachNamespace() for 'BiocManager', details:
call: .version_map_get_online_config(config)
error: could not find function "startsWith"
Error: loading failed

When I do the same thing on Rstudio, no error happened to me, and I am not sure what is the difference. I need to do this because I got another error on Rstudio recommending to run the code on bash terminal.

Please kindly give me advice to fix this error. Thank you.

software error • 2.4k views

ADD COMMENT • link 4.6 years ago biok0423 ▴ 20

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What version of R are you using

R.version.string

? startsWith() is a function in base R, so will always be available. It was introduced in 2016 (R version 3.3, I think).

ADD REPLY • link 4.6 years ago Martin Morgan 25k

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R 3.6. And I figured out how to solve this. I will update this slot later. Thanks a lot

ADD REPLY • link 4.6 years ago biok0423 ▴ 20

score 0 · Answer 1 · 2020-04-18

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biok0423 ▴ 20

@biok0423-23341

Last seen 4.6 years ago

My error was solved by re-install BiocManager by running the following command:

conda install -c conda-forge r-biocmanager

Originally BiocManager was installed by apt install or pip install. After installing miniconda3, many errors happened to me and most of them were solved by re-install them by conda install.

I am not sure the difference in a package installed by apt and the one installed by conda. But it worked now.