Upgrade bioconductor 3.2 to 3.3
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@jarod_v6liberoit-6654
Last seen 2.6 years ago
Italy

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?

bioclIte tximportData • 2.4k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…

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## BiocInstaller is out of date...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

>

 

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thanks so much!!

check_bioc('BiocInstaller')
## BiocInstaller is out of date...
## try http:// if https:// URLs are not supported
source("https://www.bioconductor.org/biocLite.R")
biocLite("BiocInstaller")
$installed_version
[1] ‘1.20.3’

$latest_version
[1] "1.22.3"

$up_to_date
[1] FALSE

How can delete and install? If use the  suggested code I'm not able to delete

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just use:

 

require(rvcheck)

update_all()

 

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> update_all()
BiocInstaller is out of date...
Upgrading 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’

 

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the error msg indicated that the re-install BiocInstaller fails. This may due to your write permissions to the .libPaths().

 

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@martin-morgan-1513
Last seen 10 weeks ago
United States

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.

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Thanks so much! The only way to resolve this was to delete all the folder of libraries (site-library) . I use alway the root user on  installation of R .  Now I was able to install the new version. of bioconductor

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Usually install only R as root. Install all other packages as normal user.

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@hauken_heyken-13992
Last seen 2 days ago
Bergen

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.

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