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Question: Problem with installation of org.Hs.eg.db
0
gravatar for sven.schuierer
13 months ago by
Switzerland
sven.schuierer0 wrote:

Hi,

I have a problem with installing org.Hs.eg.db:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("org.Hs.eg.db")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.3 (2015-12-10).
Installing package(s) 'org.Hs.eg.db'
trying URL 'http://bioconductor.org/packages/3.2/data/annotation/src/contrib/org.Hs.eg.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 68856557 bytes (65.7 MB)
==================================================
downloaded 65.7 MB

* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error in unloadNamespace(package) :
  namespace 'DBI' is imported by 'RSQLite', 'AnnotationDbi' so cannot be unloaded
Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,
  error: Package 'DBI' version 0.3.1 cannot be unloaded
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/dlab/ldrive/PHCHBS-I21605/schuisv1/R/library-3.2.3/org.Hs.eg.db'
* restoring previous '/dlab/ldrive/PHCHBS-I21605/schuisv1/R/library-3.2.3/org.Hs.eg.db'

Can you give me some pointers what I can do?

Best regards,

Sven

 

ADD COMMENTlink modified 13 months ago by Jenny Drnevich1.9k • written 13 months ago by sven.schuierer0
0
gravatar for Jenny Drnevich
13 months ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:

I believe your problem is that you already have some packages loaded in that R session. Try closing all R sessions you may have open on your computer, open a new R session and don't load any packages before calling source("https://bioconductor.org/biocLite.R").

However, you are also running an outdated R and Bioconductor version - BioC version 3.4 just came out, so the org.Hs.eg.db package you're trying to load is a year out of date. You really should install R 3.3.1 then BioC 3.4 to get the most updated annotations in the package.

Jenny

ADD COMMENTlink written 13 months ago by Jenny Drnevich1.9k
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