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[Bioc-devel] upgrading

6 messages · Jim Hester, Bernd Klaus, Ramon Diaz-Uriarte +2 more

Original
Kasper Daniel Hansen
# 
So I have an R-devel where I have a previous (pre-bioc-3.2) installed
version of BiocInstaller.

1) I re-compile R-devel today.
2) I run
  source("http://www.bioconductor.org/biocLite.R")
which gives me BiocInstaller 1.20.0.  However, the current one for
Bioc-devel is 1.21.1.

When I try to push to a higher level version, by doing
  library(BiocInstaller)
  useDevel(TRUE)
I get
Error: 'devel' version requires a more recent R

If I now try to upgrade I get
Error: Bioconductor version 3.2 cannot be upgraded with R version 3.3.0

This all looks problematic.  How to I upgrade to Bioc-devel using R-devel?
Btw. there are no instructions anymore at
  https://www.bioconductor.org/developers/how-to/useDevel/

Best,
Kasper
Jim Hester
# 
Kasper,

The following worked for me.

```r
remove.packages("BiocInstaller")
#> Removing package from '/home/jhester/.Renv/versions/devel/lib/R/library'
#> (as 'lib' is unspecified)
#> Updating HTML index of packages in '.Library'
#> Making 'packages.html' ... done
```
Then restart R in a fresh session
```r
source("http://bioconductor.org/biocLite.R")
#> Updating HTML index of packages in '.Library'
#> Making 'packages.html' ... done
#> Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help
```

Jim

On Tue, Oct 20, 2015 at 10:55 AM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Bernd Klaus
    

    

      
      #
    

  


  

      
Hi Kasper,

I also installed a clean devel version today and had no such problems,

also 

https://www.bioconductor.org/developers/how-to/useDevel/

works for me and says that using an R-devel version is necessary
to use Bioc-devel. I also get the correct BiocInstaller version:

            

      
      
      
    

        
There is however the IRanges issue I was asking about earlier.

Maybe clean the library and try again?

Best wishes,

Bernd

        
On Di, 2015-10-20 at 10:55 -0400, Kasper Daniel Hansen wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Ramon Diaz-Uriarte
    

    

      
      #
    

  


  

      
Dear Daniel,

I was just doing the same thing, and things worked fine for me (I am on Linux):

- download and compile R-devel

- get biocLite

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

which tells me

trying URL
'https://bioconductor.org/packages/3.3/bioc/src/contrib/BiocInstaller_1.21.1.tar.gz'

(...[stuff omitted here])

Bioconductor version 3.3 (BiocInstaller 1.21.1)



- Then, I always do (since I run all of this from an automated script)

try(useDevel(devel = TRUE))

which sure enough tells me

Error : 'devel' version already in use


but things work fine, and I have installed a bunch of packages from devel.



R.

        
On Tue, 20-10-2015, at 16:55, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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Technically, prior to the release we were using R-3.2 for both release and devel. Only after the release did we 'support' R-devel, implying a new installation of BiocInstaller.

I guess you were using R-devel prior to the release and had an unsupported installation of BiocInstaller. Alternatively, you updated R over an existing library. Apparently at least one of these scenarios (probably the former) is somehow common amongst Bioc developers. I guess in general our approach has been to realize that there are many incorrect ways to skin a cat, and we cannot possibly anticipate all of them, so we will only support the approved way. 

Sorry for the frustration.

Martin

            

      
      
      
    

        

      
      
    

        
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      Kasper Daniel Hansen
    

    

      
      #
    

  


  

      
Thanks for all the help.  Indeed, removing BiocInstaller and then sourcing
biocLite made it all work.

Martin: I am updating R-devel daily by building from subversion (building
in a fresh directory, but installing on top of an existing installation),
but anything from Bioconductor comes through biocLite only.

Given that the fix is easy, it is not clear it is worth spending any energy
on this.  But it is a bit weird that running R-devel with BiocInstaller
1.20.0 installed and then sourcing biocLite.R does not detect that a newer
version can be obtained.

There also seems to be something specific to R-devel here.  I was running
  R-3.2-pached
  R-devel
both with BiocInstaller 1.19.x (pre-bioc-3.2-release).  After the Bioc 3.2
release I could run
  biocLite("BiocUpgrade")
and everything would be upgraded (and working) for R-3.2-patched (upgrading
to BiocInstaller 1.20.0 / Bioc-3.2).  For R-devel it would upgrade to
BiocInstaller 1.20.0 as well, but I could not get the last version bump
without deleting and re-installing.

Weird, but as I said, perhaps not worth spending time on since the fix is
so easy.

Best,
Kasper

On Tue, Oct 20, 2015 at 11:45 AM, Morgan, Martin <

        
Martin.Morgan at roswellpark.org> wrote: