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[Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

13 messages · Michael Lawrence, Rodriguez Martinez, Andrea, Martin Morgan +3 more

Original
Michael Lawrence
# 
---------- Forwarded message ----------
From: Rodriguez Martinez, Andrea <andrea.rodriguez-martinez13 at imperial.ac.uk>
Date: Wed, Oct 19, 2016 at 3:33 PM
Subject: Re: [Bioc-devel] BiocInstaller::useDevel() Error: 'devel'
version requires a more recent R
To: Michael Lawrence <lawrence.michael at gene.com>


Sorry again,

I have just installed the R-devel version and now I get the following
error: "Bioconductor does not yet support R version 3.4.0"

Thanks,

Andrea
Martin Morgan
#
On 10/20/2016 12:00 AM, Michael Lawrence wrote:
Thank you, you installed BiocInstaller in R-devel (R-3.4) before 
Bioconductor officially supported R-3.4, and need to manually remove and 
re-install BiocInstaller.

I have updated the online configure, so in a new session, try to load 
the BiocInstaller package and you should now see

Bioconductor version 3.4 is too old for R version 3.4.0; see
   https://bioconductor.org/install/#troubleshoot-biocinstaller

The instructions are to remove BiocInstaller by hand

   remove.packages("BiocInstaller")
   remove.packages("BiocInstaller") # fails, if not then investigate

and install again

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

Martin
This email message may contain legally privileged and/or...{{dropped:2}}
Rodriguez Martinez, Andrea
# 
Thanks for your reply.


I have successfully removed BiocInstaller by hand, restart R, and then, installed with:
Warning in install.packages :
  URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.4/PACKAGES.gz': status was '404 Not Found'
Warning in install.packages :
  URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.4/PACKAGES': status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/contrib/3.4:
  cannot download all files
installing the source package ?BiocInstaller?

trying URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/BiocInstaller_1.24.0.tar.gz'
Content type 'application/x-gzip' length 17756 bytes (17 KB)
==================================================
downloaded 17 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 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning: Bioconductor version 3.4 is too old for R version 3.4.0; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
* DONE (BiocInstaller)

The downloaded source packages are in
?/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs80000gn/T/RtmpRmVsc5/downloaded_packages?
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Error: 'devel' version requires a more recent R


Thanks very much,

Andrea
Martin Morgan
# 
Sorry, can you try one more time? Thanks, Martin
On 10/20/2016 06:06 AM, Rodriguez Martinez, Andrea wrote:
This email message may contain legally privileged and/or...{{dropped:2}}
Kevin RUE
# 
Hi all,

First of all, thanks for the question and answers, it helped me a lot on my
local machine.

While we're on the topic, does anyone know when R-devel (R-3.4) will be
available on Travis CI ? Because it is running R-3.3.1, and therefore
produces the same error message when I instruct Travis to install packages
from the devel branch.

I suppose this is something that I need to post on the Travis GitHub isse
tracker, right, considering the following message?

R for Travis-CI is not officially supported, but is community maintained.
Please file any issues at https://github.com/travis-ci/travis-ci/issues
and mention @craigcitro, @hadley and @jimhester in the issue
Best,
Kevin

On Thu, Oct 20, 2016 at 11:06 AM, Rodriguez Martinez, Andrea <
andrea.rodriguez-martinez13 at imperial.ac.uk> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Kevin RUE
    

    

      
      #
    

  


  

      
By the way, the reason why I am asking is that BiocCheck raised the
following warning, after I upgraded my system to R-3.4 and Bioc-devel:

WARNING: Update R version dependency from 3.3 to 3.4

Now that I updated the R version dependency, everything is fine on my
updated machine, but the Travis build fails because it doesn't have 3.4
installed.
But I suppose that the BioC devel-build servers have R-3.4 installed, right?

All the best, and sorry for the additional email,
Kevin

        
On Thu, Oct 20, 2016 at 3:07 PM, Kevin RUE <kevinrue67 at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Kevin RUE
    

    

      
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Actually, nevermind, I think I solved the issue of R-devel with the
following YAML instructions:

language: r
r: devel

before_install:
    - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R
");tryCatch(useDevel(devel = TRUE), error = function(err){message(err)})'
    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then tlmgr install bera
nowidow parnotes marginfix; fi

Now the build <https://travis-ci.org/kevinrue/TVTB/builds/169246652> only
fails because S4Vectors is not available on the new devel branch, but I'm
sure that's going to resolve itself within the next couple of builds/days.

All the best,
Kevin


Just for the record, prior to the recent BioC release, I had the following
(working) configuration. I have never been sure how elegant that was (I may
have combined some redundant bioc instructions):

language: r
use_bioc: true
bioc_required: true
r: bioc-release
before_install:
    - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R
");tryCatch(useDevel(devel = TRUE), error = function(err){message(err)})'
    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then tlmgr install bera
nowidow parnotes marginfix; fi



On Thu, Oct 20, 2016 at 1:31 PM, Martin Morgan <

        
martin.morgan at roswellpark.org> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Lukas Weber
    

    

      
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Hi Kevin,

I have been using the following setup in my .travis.yml file. Travis CI
should automatically use the correct version of R for the Bioconductor
version specified in the "r: bioc-devel" line (you can replace this with
"r: bioc-release" to use the release version). There is some more
information here: https://docs.travis-ci.com/user/languages/r/ (see the
Bioconductor section).

language: r
r: bioc-devel
sudo: false
cache: packages
r_github_packages:
  - jimhester/covr
after_success:
  - Rscript -e 'covr::codecov()'

The additional "covr" lines are for checking unit test code coverage with
codecov.

Lukas

        
On Thu, Oct 20, 2016 at 4:51 PM, Kevin RUE <kevinrue67 at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Kevin RUE
    

    

      
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Thanks Lukas,

I remember trying "r: bioc-devel" and having issues with it a while ago,
but maybe I had an overall incorrect combination of YAML instructions, so
I'll try again with your config and see if that works better. Things moving
a lot during the release process, YAML files may just invalidate overnight,
but only temporarily.

At the moment, I'm still just having the issue of S4Vectors not being
available on the devel branch of BioC (apart from that, it seems my YAML
now uses the correct version of R (devel); now, I just wonder if r:
bioc-devel would get S4Vectors from the release branch if it's not
available from the devel branch). As I wrote previously, I'm sure this is
some minor issue that will disappear shortly (For S4Vectors. the R CMD
check only fails for a unit test, which might prevent the package from
being released on the devel branch, but that's another problem.)

I'll play with my YAML file and find out how to make Travis happy again,
before taking any risk pushing to Bioc, be it devel or release.

In any case, thanks for your advice !
Kevin

        
On Thu, Oct 20, 2016 at 4:49 PM, Lukas Weber <lukmweber at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Kevin RUE
    

    

      
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Hi again,

I applied your YAML config in my latest commit
<https://github.com/kevinrue/TVTB/blob/master/.travis.yml>
But in my (ongoing) Travis build
<https://travis-ci.org/kevinrue/TVTB/builds/169301723>, I can already see
that it has installed the wrong R version (3.1.1, not devel), see line 370
<https://travis-ci.org/kevinrue/TVTB/builds/169301723#L370>

$ curl -Lo /tmp/R-3.3.1.xz https://s3.amazonaws.com/rstudio-travis/R-3.3.1.xz

As opposed to the configuration I posted earlier that states:
r: devel

which did install R-devel (line 370
<https://travis-ci.org/kevinrue/TVTB/builds/169258984#L370> of the previous
build):

$curl -Lo /tmp/R-devel.xz https://s3.amazonaws.com/rstudio-travis/R-devel.xz

I honestly don't know how YAML instructions work on Travis, but maybe some
action must be taken before "bioc-devel" becomes synonym to "R-devel" ?

Thanks for your help.
Kevin

        
On Thu, Oct 20, 2016 at 4:49 PM, Lukas Weber <lukmweber at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Kasper Daniel Hansen
    

    

      
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I am not sure if the _intention_ is that bioc-devel installs r-devel.  But
note that this is a change in the last 48h. Monday, the right thing was to
use r-stable.  Some switch has to be flipped and it may not have happened
yet.

What would be nice is clear documentation as to whether bioc-devel implies
switching to r-devel every 6 months, or if the travis people wants users
(us) to make the switch by changing .travis.yml.

Kasper

        
On Thu, Oct 20, 2016 at 1:50 PM, Kevin RUE <kevinrue67 at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Lukas Weber
    

    

      
      #
    

  


  

      
I just checked by sending a commit to my package. I am also still seeing
installation of R version 3.3.1:

$ curl -Lo /tmp/R-3.3.1.xz
https://s3.amazonaws.com/rstudio-travis/R-3.3.1.xz

In fact looking at the Travis build log more closely, all packages still
seem to be coming from Bioconductor 3.4, even though I have "r: bioc-devel"
in the .travis.yml file.

This does sound like something that may be resolved in the coming days,
i.e. something needs to be updated manually. If not, we should open an
issue in the Travis CI issue tracker, as Kevin suggested:

Travis CI support for R is contributed by the community and may be removed
or altered at any time. If you run into any problems, please report them in
the Travis CI issue tracker and cc @craigcitro, @hadley, and @jimhester.

Best regards,
Lukas


On Thu, Oct 20, 2016 at 8:28 PM, Kasper Daniel Hansen <

        
kasperdanielhansen at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Rodriguez Martinez, Andrea
    

    

      
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Hi,


Sorry for my slow response. I have just tried again and it worked, but then I was not able to install packages from the devel branch, with the warning:

            

      
      
      
    

        
cannot download all files

I guess this is all related with what has been discussed in this loop of emails.

Thanks,

Andrea