Installation path not writeable.

[BenbenMiao]

RStudio Cloud can't install Rpackages from bioconductor by BiocManager::install() function.

[andy_kipp]

Hi there,

Can you provide more information about the issue? Do you have a screenshot of the error messages you can share?

Thanks
-Andy

[BenbenMiao]

Hi !
Here is the screenshot of the error messages.I don't have the root or sudo permission and do you have other solutions , please!

[andy_kipp]

Can you provide me with the URL for your project?

[BenbenMiao]

Ok,
The URL of my project is https://rstudio.cloud/spaces/15894/project/322821.
Do you know about the bioconductor website and BiocManager package?

[andy_kipp]

I'm familiar with BioConductor. What is interesting is that these packages are being installed to your R library in /home/rstudio-user/R which should be writable. I am not sure why that's not working correctly, so I am going to take a closer look.

[BenbenMiao]

Thanks for your time.The result of libPaths are "/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5" and "/opt/R/3.5.2/lib/R/library" when run .libPaths() command in RScript.I don't have the permission for "/opt/R" dir,but can change the permission to 777 for "/home/rstudio-user/R" dir.

[andy_kipp]

I can see that you changed the permissions on /home/rstudio-user/R. Are you now able to install from BioConductor?

[BenbenMiao]

Still unable to install packages from bioconductor.I think that RStudio Cloud considered the safety of host linux container to present root and sudo permissions.

[josh]

It isn't file permissions, the error message says there is a lock file that needs to be removed first. The lock file is a leftover of a failed installation.