Question: DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
0
gravatar for goodwinjinesh
11 days ago by
goodwinjinesh0 wrote:

I have installed latest R-studio for windows7 and installed various packages like BiocManager, ReactomePA, ClusterProfiler, DOSE etc. But I could not load any of these libraries and it shows a constant erroro message "there is no package called ‘DO.db’". I have installed DO.db multiple times, the installation goes fine, updates (a) goes fine, but again I could not find DO.db in the installed packages plus, could not load ReactomePA or DOSE or ClusterProfiler. All shown the same error "there is no package called ‘DO.db’". I have posted the session info below. Please help to fix this issue. Thanks in advance.

R version 3.4.2 (2017-09-28) -- "Short Summer"
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[Workspace loaded from ~/.RData]

> library(BiocManager)
Bioconductor version 3.6 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.6' is out-of-date; BiocManager does not support R version '3.4.2'. For older installations of
  Bioconductor, use 'source("https://bioconductor.org/biocLite.R")' and refer to the 'BiocInstaller' vignette on the
  Bioconductor website
> library(ReactomePA)
Loading required package: DOSE
Error: package or namespace load failed for ‘DOSE’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘DO.db’
Error: package ‘DOSE’ could not be loaded
> library(clusterProfiler)
Loading required package: DOSE
Error: package or namespace load failed for ‘DOSE’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘DO.db’
Error: package ‘DOSE’ could not be loaded
> library(DOSE)
Error: package or namespace load failed for ‘DOSE’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘DO.db’
> library(corrplot)
corrplot 0.84 loaded
Warning message:
package ‘corrplot’ was built under R version 3.4.4
ADD COMMENTlink modified 11 days ago by Martin Morgan ♦♦ 24k • written 11 days ago by goodwinjinesh0
Answer: DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
0
gravatar for Guangchuang Yu
11 days ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

it would be better to upgrade your R to latest release 3.6.1 and try again.

ADD COMMENTlink written 11 days ago by Guangchuang Yu1.1k
Answer: DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
0
gravatar for Martin Morgan
11 days ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Focus on installing DO.db; I suspect that BiocManager::install("DO.db") fails, and that RStudio is not displaying the full reason for failure. I suspect you are on Windows and using a network share //some-share/... and that you either need to google for windows map network drive and fix that, or download and install DO.db using a location that is not on the network share, along the lines of

download.packages("DO.db", repos = BiocManager::repositories(), "c://some/path/")
install.packages("c://some/path/DO.db_....tar.gz", repos = NULL)

PLEASE NOTE that the snippet above needs to be customized for your situation.

ADD COMMENTlink written 11 days ago by Martin Morgan ♦♦ 24k
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