Cannot install clusterProfiler
2
0
Entering edit mode
dtatarak • 0
@dtatarak-15870
Last seen 3.4 years ago

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

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!

clusterprofiler biocinstaller • 2.0k views
0
Entering edit mode
@james-w-macdonald-5106
Last seen 11 hours ago
United States

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.

0
Entering edit mode

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

0
Entering edit mode

Then install bit using biocLite

0
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…