Question

Can't install Genesis

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winstondunnmd ▴ 10

@winstondunnmd-21581

Last seen 5.4 years ago

I have difficulty installing the Genesis package. Please kindly advise.

BiocManager::install("GENESIS") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'GENESIS' trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GENESIS_2.14.3.zip' Content type 'application/zip' length 3276719 bytes (3.1 MB) downloaded 3.1 MB

package ‘GENESIS’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\winst\AppData\Local\Temp\RtmpGEHmlD\downloaded_packages installation path not writeable, unable to update packages: boot, cluster, foreign, nlme

Genesis Installation • 2.1k views

ADD COMMENT • link updated 5.4 years ago by Mike Smith ★ 6.6k • written 5.4 years ago by winstondunnmd ▴ 10

score 0 · Answer 1 · 2019-08-14

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Mike Smith ★ 6.6k

@mike-smith

Last seen 1 hour ago

EMBL Heidelberg

There doesn't seem to be any errors here, the installation of GENESIS looks like it worked fine.

If you're worried by the part that says:

installation path not writeable, unable to update packages: boot, cluster, foreign, nlme

this is likely because R was installed using administrator privileges, but you're currently running R as a regular user. A small number of packages are installed along with R (these are known as 'base packages') and this message is telling you that they can't be updated as they were created by an administrator. However you can almost certainly ignore the message and things will work fine with the versions that are currently there.

ADD COMMENT • link 5.4 years ago Mike Smith ★ 6.6k

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However, I can't load the library and other functions of Genesis.

library(GENESIS) Error: package or namespace load failed for ‘GENESIS’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘RSQLite’

Is there a way to install using administrator privileges?

ADD REPLY • link 5.4 years ago winstondunnmd ▴ 10

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That message is saying there's a package missing that GENESIS requires, in this case it's RSQLite. R should install any dependencies during installation, but it's easily possible to get this messed up. You could try installing RSQLite manually using BiocManager::install('RSQLite'), however there's a fair chance some other package will be missing.

I would suggest running BiocManager::valid() and then looking at the output sections that says:

create a valid installation with 

  BiocManager::install(c( 
  ...

Copying the code in this output should install any packages that are either missing or outdated.

Regarding running R as an administrator, you really don't need to do that. R will automatically create a folder you do have permission to write to and use that to install new package. On windows it's probably something like C:\Users\winst\Documents\R\win-library\3.6\ It's just that I will try to use the one created during installation first. This guide gives a little more detail and shows you how to set the default if you're using RStudio https://www.accelebrate.com/library/how-to-articles/r-rstudio-library

ADD REPLY • link 5.4 years ago Mike Smith ★ 6.6k