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Question: Upgrade to 3.1 error
1
gravatar for Luobin
2.5 years ago by
Luobin10
United States
Luobin10 wrote:

Dear Bioconductor team, 

I am trying to upgrade my Bioconductor from version 3.0 to 3.1, but I've got an error, any suggestions?

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.4), R version 3.2.0.
> biocLite("BiocUpgrade")
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] BiocInstaller_1.16.4
loaded via a namespace (and not attached):
[1] tools_3.2.0

Thanks,

Luobin

ADD COMMENTlink modified 2.4 years ago by Bogdan470 • written 2.5 years ago by Luobin10

That definitely shouldn't be happening. We'll take a look and try to fix it. In the meantime, try removing BiocInstaller.

remove.packages("BiocInstaller")

Quit R then start a new R session with R --vanilla and then do:

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

Then update all your pacakges with:

biocLite()

 

ADD REPLYlink modified 2.5 years ago by Martin Morgan ♦♦ 20k • written 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k

I'd like to report the same problem as Liobin- I upgraded to R 3.2 yet when I try to upgrade I get the following:

> source("http://bioconductor.org/biocLite.R")

> biocLite("BiocUpgrade")

Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0

Here's some more info:

> sessionInfo()

R version 3.2.0 (2015-04-16)

Platform: x86_64-redhat-linux-gnu (64-bit)

Running under: Fedora 21 (Twenty One)

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] BiocInstaller_1.16.4

loaded via a namespace (and not attached):

[1] tools_3.2.0

Any suggestions you might have would be greatly appreciated- I'm looking forward to upgrading to Bioconductor 3.2.

ADD REPLYlink written 2.5 years ago by rtraborn0

Did you try Dan's solution (which I've updated to make it clearer that you need to explicitly remove BiocInstaller)?

ADD REPLYlink written 2.5 years ago by Martin Morgan ♦♦ 20k

I did remove BiocInstaller() just prior to the entering the commands I listed. 

ADD REPLYlink written 2.5 years ago by rtraborn0

Please show your entire commands. Please make sure that there are no additional 'BiocInstaller' packages installed. Here's what happens for me. Again, please provide the complete transcript

In the first R session:

> remove.packages("BiocInstaller")
Removing package from '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2'
(as 'lib' is unspecified)
> remove.packages("BiocInstaller")
Removing package from '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2'
(as 'lib' is unspecified)
Error in find.package(pkgs, lib) : 
  there is no package called 'BiocInstaller'
> ## good, no more BiocInstaller!
> q()

In the next R session

> remove.packages("BiocInstaller")   # make sure I'm using the same R!
Removing package from '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2'
(as 'lib' is unspecified)
Error in find.package(pkgs, lib) : 
  there is no package called 'BiocInstaller'
> source("http://bioconductor.org/biocLite.R")
Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.2'
(as 'lib' is unspecified)
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.18.2.tar.gz'
Content type 'application/x-gzip' length 14945 bytes (14 KB)
==================================================
downloaded 14 KB

* installing *source* package 'BiocInstaller' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help
* DONE (BiocInstaller)

The downloaded source packages are in
    '/tmp/RtmpjvlDY0/downloaded_packages'
Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help
> packageVersion("BiocInstaller")
[1] '1.18.2'

 

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Martin Morgan ♦♦ 20k

Hi Martin:

Thank you for your response, which helped me find the problem. This was an issue of having another BiocInstaller/ lurking in a second R library. Once I deleted the offending second package the above instructions worked like a charm, and now I'm running Bioconductor v 3.2.

> source("http://www.bioconductor.org/biocLite.R")

Bioconductor version 3.2 (BiocInstaller 1.19.5), ?biocLite for help

Thanks again,

Taylor 

ADD REPLYlink written 2.5 years ago by rtraborn0
0
gravatar for dhwani.dholakia
2.5 years ago by
INDIA
dhwani.dholakia0 wrote:

 

Just run the below script to get latest version of R

However before installing the R it is advisable to remove the installed r

To run the script you have to make the script executable

type the command

chmod +x script name

then run in terminal ./script

 

### Script to update R
### -----------------------------------------

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install g++-4.9

## Copy the below link to
#sudo gedit /etc/apt/sources.list
sudo echo "deb http://cran.stat.nus.edu.sg/bin/linux/ubuntu trusty/">>/etc/apt/sources.list

sudo apt-get update
sudo apt-get install r-base
sudo apt-get install r-base-dev
ADD COMMENTlink modified 2.5 years ago by Martin Morgan ♦♦ 20k • written 2.5 years ago by dhwani.dholakia0
0
gravatar for Bogdan
2.4 years ago by
Bogdan470
Palo Alto, CA, USA
Bogdan470 wrote:

I am getting a similar error, after attempting to upgrade to BioC 3.1. Please could I have any help or any insights ? Thanks !

 

bogdan@bogdan:~/R/x86_64-pc-linux-gnu-library$ R --vanilla

R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> remove.packages("BiocInstaller")
Removing package from ‘/home/bogdan/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help
BiocInstaller version 3.0 is too old for R version 3.2.1;
  remove.packages("BiocInstaller") then
  source("http://bioconductor.org/biocLite.R")
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.1.

ADD COMMENTlink written 2.4 years ago by Bogdan470

Are there multiple installed versions of BiocInstaller (repeat remove.packages("BiocInstaller") several times, until R reports that there are no additional copies. If you would like to use google hangout and invite me (mtmorgan at fredhutch dot org) in the next 30 minutes then we can work through this together.

ADD REPLYlink written 2.4 years ago by Martin Morgan ♦♦ 20k
2

Bogdan and I worked through this. Bogdan's .libPaths() contained a personal directory, and several  system-wide directories

> .libPaths()
[1] "/home/bogdan/R/x86_64-pc-linux-gnu-library/3.2"
[2] "/usr/local/lib/R/site-library"                 
[3] "/usr/lib/R/site-library"                       
[4] "/usr/lib/R/library"

remove.packages("BiocInstaller") remove the package from the personal directory, but failed (silently) to remove the package from the site-wide directory, where Bogdan does not have write permissions. So next time Bogdan tried source("http://bioconductor.org/biocLite.R"), the script found the (old) version of the package in the site-wide directory. The solution was to remove the package from Bogdan's directory, and then force an installation of the correct version of BiocInstaller. We did this using

install.packages("BiocInstaller", repos="http://bioconductor.org/packages/3.1/bioc")

where '3.1' is the version of Bioconductor we wanted to install. This installed BiocInstaller in Bogdan's personal directory.

Probably Bogdan's system administrator should update BiocInstaller to match the version of R in use, or remove BiocInstaller from the system library so that users can choose to use either of the two versions of Bioconductor that will eventually be compatible with R-3.2.* (Both the current version of Bioconductor, version 3.1, and the version to be released in October, version 3.2, are compatible with the R-3.2.* series).

ADD REPLYlink written 2.4 years ago by Martin Morgan ♦♦ 20k

very comprehensive ! thanks again Martin ! it saved time and work !

ADD REPLYlink written 2.4 years ago by Bogdan470
1

Hi Bogdan,

Don't forget to upvote Martin's comment above. ;-)

Thanks,

H.

ADD REPLYlink written 2.4 years ago by Hervé Pagès ♦♦ 13k

Thank you again  gentlemen ! it really helped a lot !

ADD REPLYlink written 2.4 years ago by Bogdan470
0
gravatar for Bogdan
2.4 years ago by
Bogdan470
Palo Alto, CA, USA
Bogdan470 wrote:

Moreover, trying to reinstall Gviz, I am getting lots of errors  .... Would appreciate any help ! thanks !

 

> biocLite("Gviz")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.1.
Installing package(s) 'Gviz'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/Gviz_1.10.11.tar.gz'
Content type 'application/x-gzip' length 3338224 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

* installing *source* package ‘Gviz’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'Gviz', details:
  call: ".GvizSchemes" %in% ls(globalenv(), all.names = TRUE)
  error: error in evaluating the argument 'table' in selecting a method for function '%in%': Error in ls(globalenv(), all.names = TRUE) :
  2 arguments passed to .Internal(ls) which requires 3
Calls: ls -> ls

Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/bogdan/R/x86_64-pc-linux-gnu-library/3.2/Gviz’

The downloaded source packages are in
    ‘/tmp/Rtmp0tKEse/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘Gviz’ had non-zero exit status

 

 

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

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

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

other attached packages:
[1] BiocInstaller_1.16.5

loaded via a namespace (and not attached):
[1] tools_3.2.1

 

ADD COMMENTlink written 2.4 years ago by Bogdan470
0
gravatar for Bogdan
2.4 years ago by
Bogdan470
Palo Alto, CA, USA
Bogdan470 wrote:

Hi Martin, that would  be awesome ! thanks a lot ! let's connect please via Google Hangout !

ADD COMMENTlink written 2.4 years ago by Bogdan470
0
gravatar for Bogdan
2.4 years ago by
Bogdan470
Palo Alto, CA, USA
Bogdan470 wrote:

Thank you Martin for the chat and video call ! So,  it is working !!! for those that are interested, please do :

remove.packages("BiocInstaller")
source("http://bioconductor.org/biocLite.R")

biocLite("BiocInstaller", repos="http://bioconductor.org/packages/3.1/bioc/")

Martin, please edit if it needs corrections ! thanks very much again !

 

ADD COMMENTlink written 2.4 years ago by Bogdan470
0
gravatar for Bogdan
2.4 years ago by
Bogdan470
Palo Alto, CA, USA
Bogdan470 wrote:

Dear Martin, thanks again for conversation and kind help yesterday ! it helped tremendously ! happy weekend !

ADD COMMENTlink written 2.4 years ago by Bogdan470
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