Dear All ,

I try to update bioconductor for txtimportData. Unfortunately I have no positive results.

I followed the troubleshoting but  no way to update

this is my session:

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.20.3

loaded via a namespace (and not attached):
[1] tools_3.3.0

remove.packages("BiocInstaller")
Removing package from ‘/home/maurizio/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
Error in find.package(pkgs, lib) :
  there is no package called ‘BiocInstaller’

any help on how to resolve?

After remove the old version of BiocInstaller, you need to use source("https://www.bioconductor.org/biocLite.R") to install it.

> require(rvcheck)
> check_bioc('BiocInstaller')
## BiocInstaller is out of date...

$installed_version
[1] ‘1.22.2’

$latest_version
[1] "1.22.3"

$up_to_date
[1] FALSE

>

Does installed.packages()["BiocInstaller", "LibPath"] indicate that the package is installed in a path that you do not have write permissions? If so, you can remove the package by running R under that account (and then exiting R and starting as your usual user before doing anything else).

Alternatively, assuming that the LibPath of BiocInstaller is the last element of the vector returned by .libPaths(),  set .libPaths() so that it excludes that directory (before loading BiocInstaller) and then

paths = .libPaths()
.libPaths(paths[-length(paths)])
source("https://bioconductor.org/biocLite.R")

This will install a second version of BiocInstaller, ahead of the invalid version and in a directory that your user account has access. Then restart R to restore .libPaths() to its original setting.

You should figure out how you got into the situation where the 3.3 version of R accessed the wrong version of BiocInstaller -- I guess the library path from a previous version of R was copied to the current version, but instead the major version of R should have been accompanied by a full re-installation of Bioconductor packages.

This will work for everyone on both servers and local, as long as you can install local user files.

1: Go to biocinstaller page, and download the .tar file:

https://bioconductor.org/packages/release/bioc/html/BiocInstaller.html

2.  in R, create a new session and do:

remove.packages("BiocInstaller", lib=.libPaths())

do this until you get a warning or error.

3. Then do: install.packages("pathTo.tar", repos = NULL)

4. lastly do:

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

There, your version is up to date.

Martins answer with using .libPaths() will not always work on servers, because some servers restrict .libPaths() to always include the admin libraries, which you might not have write access on.

Like on our server, when i do

.libPaths(paths[-length(paths)])

it can only remove user specified libpaths, not admin paths.