Question: Cannot install clusterProfiler
0
gravatar for dtatarak
14 months ago by
dtatarak0
dtatarak0 wrote:

I am using the following code to install clusterProfiler:

 

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

BiocInstaller::biocLite("clusterProfiler")

 

I get the following error:

 

Error: package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 there is no package called ‘bit’

Error : package ‘AnnotationDbi’ could not be loaded

ERROR: lazy loading failed for package ‘GO.db’
  • removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/GO.db’
The downloaded source packages are in

‘/private/var/folders/jm/lw5pqpvs0_j025smc3qkpl5c0000gn/T/RtmpnPsdF8/downloaded_packages’

Warning message:

In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘GO.db’ had non-zero exit status

 

I'm really not sure what to do here. When I search online, everyone pretty much says to do exactly what I did, and that it should install the required packages. I am new to R, and this is beyond me. Thanks for any help you can provide!

ADD COMMENTlink modified 14 months ago by Guangchuang Yu1.1k • written 14 months ago by dtatarak0
Answer: Cannot install clusterProfiler
0
gravatar for James W. MacDonald
14 months ago by
United States
James W. MacDonald50k wrote:

It looks like you have AnnotationDbi installed, but are missing dependencies. Or actually, dependencies of dependencies, as bit isn't a direct dependency of AnnotationDbi. You probably need to re-install AnnotationDbi to get all the dependencies.

ADD COMMENTlink written 14 months ago by James W. MacDonald50k

I tried that. It installs successfully, but I still get the exact same error when installing clusterProfiler.

ADD REPLYlink written 14 months ago by dtatarak0

Then install bit using biocLite

ADD REPLYlink written 14 months ago by James W. MacDonald50k
Answer: Cannot install clusterProfiler
0
gravatar for Guangchuang Yu
14 months ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:
ADD COMMENTlink written 14 months ago by Guangchuang Yu1.1k
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