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Question: Upgrade bioconductor 3.2 to 3.3
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gravatar for jarod_v6@libero.it
17 months ago by
Italy
jarod_v6@libero.it40 wrote:

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?

ADD COMMENTlink modified 17 months ago by Martin Morgan ♦♦ 20k • written 17 months ago by jarod_v6@libero.it40
0
gravatar for Guangchuang Yu
17 months ago by
Hong Kong
Guangchuang Yu800 wrote:

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## BiocInstaller is out of date...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

>

 

ADD COMMENTlink written 17 months ago by Guangchuang Yu800

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## BiocInstaller is out of date...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

ADD REPLYlink written 17 months ago by jarod_v6@libero.it40

just use:

 

require(rvcheck)

update_all()

 

ADD REPLYlink modified 17 months ago • written 17 months ago by Guangchuang Yu800
> 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BiocInstaller is out of date...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’

 

ADD REPLYlink written 17 months ago by jarod_v6@libero.it40

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

 

ADD REPLYlink written 17 months ago by Guangchuang Yu800
0
gravatar for Martin Morgan
17 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

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.

ADD COMMENTlink modified 17 months ago • written 17 months ago by Martin Morgan ♦♦ 20k

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

ADD REPLYlink written 17 months ago by jarod_v6@libero.it40

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

ADD REPLYlink written 17 months ago by Martin Morgan ♦♦ 20k
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