Problem running clusterProfiler. Says DO.db is missing even when it's installed
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16 months ago
syrez ▴ 40

I'm running Rstudio/R on Windows 10 Pro 64bit

I need to generate a bunch of figures for a poster for one of our collaborating labs. A long long time ago, I used clusterProfiler within RStudio and it worked like a charm.

Now, there's a chain of packages that are somehow always missing and manually installing them will only lead to another package missing error.

One of the recurrent problem is - missing DO.db

I spent an entire day trying to install DO.db; I don't really remember ever having to deal with DO.db when I used clusterProfiler earlier.

Installation using BiocManager::install("DO.db") seems to work but when I try to load the library, I get the following error

library(DO.db) Error in library(DO.db) : there is no package called ‘DO.db’

Installing DO.db by downloading the tar file gives the following result :

install.packages("D:/RStudio/DO.db_2.9.tar.gz", repos = NULL, type = "source", lib="C:/Program Files/R/R-3.5.0/library")

WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding: The screen cannot be set to the number of lines and columns specified. In R CMD INSTALL

If I install RTools, my RStudio fails to load the workspace and eventually Terminate/Wait confirmation box pops up which doesn't do anything and I have to use task manager to kill the instance.

I'm running the latest R(3.6.2) and Rstudio(1.2.5033)

I've tried using older versions of R(3.5.0) and R(3.5.1) to resolve the version warnings but none of that seems to help.

Am I missing something that's right in my face?

rstudio clusterprofiler do.db • 605 views
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Rtools contains the tool chain required to compile R packages under Windows. Either it's not installed or R is not finding it. There can be several reasons. One I have sometimes seen causing trouble with scientific software on Windows is antivirus programs. Another is that you may have messed up the whole set up by trying different versions (e.g. in particular BINREF and PATH environment variables may get confusing values). I would suggest starting fresh following this Guide to (Re-)Installing R and Related Software.

Entering edit mode

I've done multiple clean installs of R/RStudio/Rtools and nothing seems to be working. clusterProfiler is working absolutely fine on my other desktop - same version of OS, R, and Rstudio without any error asking for Rtools or indicating locked DLL files. I've set R/RStudio to run as administrator in case it has anything to do with user rights. I can't find any environmental differences between both systems.


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