Checking/updating package versions
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bertb • 0
@bertb-18667
Last seen 3 days ago

Hello,

I have a very simple question: how can I check my version of an installed package - in this case DiffBind? I know a simple -v in Unix achieves this, but I can't seem to figure it out in R.

Part of the reason I need to know is because I think my version is out of date now and I need to upgrade. Is there a way to do this without uninstalling and reinstalling the new one? And if I do need to uninstall/reinstall, is there a specific uninstaller, or specific procedure for uninstalling?

Thank you!

DiffBind • 113 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States
library(DiffBind)
packageDescription("DiffBind")$Version

Or more to the point

library(BiocManager)
BiocManager::valid()

After which you can do what valid says you need to do (if anything at all) to make your install valid.

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Thanks James!

When I run

library(BiocManager)
BiocManager::valid()

the output I get details all the packages I have, and at then end how I can update (I think):

Bioconductor version '3.11'

  * 9 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "backports", "colorspace", "data.table", "diffobj", "ggrepel", "jsonlite", "rlang", "V8", "vctrs"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
9 packages out-of-date; 0 packages too new

but when I run the above command, and check with BiocManager::valid() , I still receive the same packages that aren't updating. When new versions try to install, I get the following warning

Warning: cannot remove prior installation of package 'V8'
Warning: restored 'V8'

for each package

Is there something else I need to do to update these properly? Thanks again

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Well, ideally you would install R-4.0.3 and Bioconductor 3.12 because you need to update. Failing that, you should restart R and try again. Usually when you can't remove a prior installation it's because the package is loaded by R.

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I see - thanks. I was running Bioconductor 3.11, so I think that was the issue. When I installed 3.12, almost everything installed properly (latest versions of 3 packages were available with source only). However, part of the output did include:

Installation path not writeable, unable to update packages: codetools, foreign, KernSmooth, Matrix, nlme

...which is curious to me since the downloading path seems basically automated (that is, I haven't specified anything) and all the binary packages are going to \downloaded_packages. I'm just wondering why only these packages would have an issue with the installation path?

Thanks again

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Usually on Windows you install R as a privileged user, and the recommended packages (which include all those listed) are also installed in a privileged location that you as a normal user don't have write privileges. Then when you install other packages R chooses a directory that you do have write privileges (on Win10 it's in C:/<yourusername>/AppData/Roaming/R/win-library/4.0, or at least is there on my box).

So if you do this:

> .libPaths()
[1] "C:/Users/jmacdon/AppData/Roaming/R/win-library/4.0"
[2] "C:/Program Files/R/R-4.0.0/library"

You can see that there are two library paths, the first one being your 'local' path to which you have privileges, and the second one being in a place that can only be written to if you invoke admin privileges. An alternative that you sometimes hear people talking about is to run R with admin privileges so you can just have one library dir, but that in general is a horrible idea. You should always use the lowest privilege level possible so you don't inadvertently bork your machine. Or allow nefarious actors easy access to do that for you.

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Ok - I'm learning a lot. I'm the only one using R - for now - but perhaps it would be good practice to periodically run as an admin in order to update regularly.

Thanks again for taking the time with this line of questions

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