Question

Why I can load the packages I had detached?

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2426986765 ▴ 10

@2426986765-22234

Last seen 5.0 years ago

source: remove.packages("AnnotationDbi") library("AnnotationDbi")

console: detach("package:AnnotationDbi", unload = TRUE) library("AnnotationDbi")

software error • 731 views

ADD COMMENT • link updated 5.0 years ago by Martin Morgan 25k • written 5.0 years ago by 2426986765 ▴ 10

score 0 · Answer 1 · 2019-11-03

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Martin Morgan 25k

@martin-morgan-1513

Last seen 3 months ago

United States

detach() detaches the package from the search() path; it does not remove the package from the library where it is installed.

Usually, removing a package is accomplished with remove.packages("AnnotationDbi"). One common reason for failure is if the package is installed in more than one library location.

pkgs <- installed.packages()
idx <- pkgs[, "Package"] %in% "AnnotationDbi"
sum(idx) # more than 1?
pkgs[idx,]

These might be removed with more than one call to remove.packages().

It might be that some of the library locations are not writeable by the user (e.g., an 'Administrator' installed the package). The administrator must then remove the package.

AnnotationDbi does not contain any compiled (C) source code, so the following is not an explanation for your specific question. It might be (on Windows) that the library was in use by another R session, or that in the current session a compiled 'dll' is in use in the current session that depends or imports AnnotationDbi. remove.packages() will then fail, silently, leaving a corrupt installation. All R sessions should be closed, and the corrupt package installation location directory removed 'by hand' through the operating system.

ADD COMMENT • link 5.0 years ago Martin Morgan 25k

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Thank you, but how can I remove it from library?

ADD REPLY • link 5.0 years ago 2426986765 ▴ 10

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I updated my answer. You should please update your question to copy and paste the commands that you use in your session, and the output of sessionInfo(). Here's mine...

> pkgs <- installed.packages()
> idx <- pkgs[, "Package"] %in% "AnnotationDbi"
> sum(idx) # more than 1?
[1] 1
> remove.packages("AnnotationDbi")
Removing package from '/Users/ma38727/Library/R/3.6/Bioc/3.10'
(as 'lib' is unspecified)
> remove.packages("AnnotationDbi")
Removing package from '/Users/ma38727/Library/R/3.6/Bioc/3.10'
(as 'lib' is unspecified)
Error in find.package(pkgs, lib) :
  there is no package called 'AnnotationDbi'
> library(AnnotationDbi)
Error in library(AnnotationDbi) :
  there is no package called 'AnnotationDbi'
> sessionInfo()
R version 3.6.1 Patched (2019-10-25 r77333)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Users/ma38727/bin/R-3-6-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-3-6-branch/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1

ADD REPLY • link 5.0 years ago Martin Morgan 25k