Installation path not writable
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heremin • 0
@heremin-16589
Last seen 2.7 years ago

I am trying to install bioconductor pathview, but it always shows the error message "installation path not writable". Can someone help?

Thank you.

bioconductor • 16k views
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You will have to give us more information than that. How are you trying to install? Show some code. Also, what is the output from sessionInfo()? Can you install other BioC packages?

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I followed the instruction from website http://pathview.r-forge.r-project.org/#fig-2 step by step.

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

biocLite("pathview")

Then it shows me that message:

The downloaded source packages are in
        ‘C:\Users\min.he\AppData\Local\Temp\RtmpkHOG8Q\downloaded_packages’
installation path not writeable, unable to update packages: foreign, survival

 

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This message is about updating packages 'foreign' and 'survival', not 'pathview' or other BioC packages. These two packages come with the R installation and you need to run R as an administrator in order to update them.

If there are no other complaints by biocLite() -- have you tried loading 'pathview' (or other BioC pkgs) after the installation?

> library("pathview")

 

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Thank you so much for your help. It works now.

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I can't install other BioC packages

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@james-w-macdonald-5106
Last seen 7 hours ago
United States

As Axel noted, there is no problem here. You have installed pathview and are just getting a message telling you that you can't update two base packages (foreign, survival). If you care to update those two, you will need to start R as an administrator.

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