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

Thu Oct 20 17:49:16 CEST 2016

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:

> 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:
>
> > Sorry, can you try one more time? Thanks, Martin
> >
> >
> > On 10/20/2016 06:06 AM, Rodriguez Martinez, Andrea wrote:
> >
> >> Thanks for your reply.
> >>
> >>
> >> I have successfully removed BiocInstaller by hand, restart R, and then,
> >> installed with:
> >>
> >>
> >> source("https://bioconductor.org/biocLite.R")
> >>>
> >> Warning in install.packages :
> >>   URL
> >> 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/maver
> >> icks/contrib/3.4/PACKAGES.gz':
> >> status was '404 Not Found'
> >> Warning in install.packages :
> >>   URL
> >> 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/maver
> >> icks/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/maveri
> >> cks/contrib/3.4:
> >>   cannot download all files
> >> installing the source package ‘BiocInstaller’
> >>
> >> trying URL
> >> 'https://bioconductor.org/packages/3.4/bioc/src/contrib/Bioc
> >> Installer_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
> >>
> >> BiocInstaller::useDevel()
> >>>
> >> Error: 'devel' version requires a more recent R
> >>
> >
> >
> >>
> >> Thanks very much,
> >>
> >> Andrea
> >>
> >>
> >>
> >> ------------------------------------------------------------
> ------------
> >> *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
> >> Martin Morgan <martin.morgan at roswellpark.org>
> >> *Sent:* 20 October 2016 10:28:34
> >> *To:* Michael Lawrence; bioc-devel at r-project.org
> >> *Subject:* Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error:
> >>
> >> 'devel' version requires a more recent R
> >>
> >> On 10/20/2016 12:00 AM, Michael Lawrence wrote:
> >>
> >>> ---------- Forwarded message ----------
> >>> From: Rodriguez Martinez, Andrea <andrea.rodriguez-martinez13 at i
> >>> mperial.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"
> >>>
> >>
> >> 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
> >>
> >>
> >>> Thanks,
> >>>
> >>> Andrea
> >>>
> >>> ________________________________
> >>> From: Rodriguez Martinez, Andrea
> >>> Sent: 19 October 2016 23:13:06
> >>> To: Michael Lawrence
> >>> Subject: Re: [Bioc-devel] BiocInstaller::useDevel() Error: 'devel'
> >>> version requires a more recent R
> >>>
> >>>
> >>> Thanks!
> >>>
> >>> ________________________________
> >>> From: Michael Lawrence <lawrence.michael at gene.com>
> >>> Sent: 19 October 2016 23:02:17
> >>> To: Rodriguez Martinez, Andrea
> >>> Cc: bioc-devel at r-project.org
> >>> Subject: Re: [Bioc-devel] BiocInstaller::useDevel() Error: 'devel'
> >>> version requires a more recent R
> >>>
> >>> Bioconductor 3.5 requires R-devel.
> >>>
> >>> On Wed, Oct 19, 2016 at 2:57 PM, Rodriguez Martinez, Andrea
> >>> <andrea.rodriguez-martinez13 at imperial.ac.uk> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>>
> >>>> I was just trying to use the devel branch, but I get this error
> message
> >>>> (using R.3.3.1)
> >>>>
> >>>>
> >>>> BiocInstaller::useDevel()
> >>>>>
> >>>>
> >>>> Error: 'devel' version requires a more recent R
> >>>>>
> >>>>
> >>>>
> >>>> Any help with this?
> >>>>
> >>>> Thanks very much in advance,
> >>>>
> >>>> Andrea
> >>>>
> >>>>         [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-devel at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>>
> >>
> >> This email message may contain legally privileged and/or...{{dropped:2}}
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:2}}
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>         [[alternative HTML version deleted]]
>
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