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

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Oct 20 20:28:55 CEST 2016 

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:

> 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):
>
> $curl -Lo /tmp/R-devel.xz https://s3.amazonaws.com/
> rstudio-travis/R-devel.xz
>
> I honestly don't know how YAML instructions work on Travis, but maybe some
> action must be taken before "bioc-devel" becomes synonym to "R-devel" ?
>
> Thanks for your help.
> Kevin
>
>
> On Thu, Oct 20, 2016 at 4:49 PM, Lukas Weber <lukmweber at gmail.com> wrote:
>
> > Hi Kevin,
> >
> > I have been using the following setup in my .travis.yml file. Travis CI
> > should automatically use the correct version of R for the Bioconductor
> > version specified in the "r: bioc-devel" line (you can replace this with
> > "r: bioc-release" to use the release version). There is some more
> > information here: https://docs.travis-ci.com/user/languages/r/ (see the
> > Bioconductor section).
> >
> > language: r
> > r: bioc-devel
> > sudo: false
> > cache: packages
> > r_github_packages:
> >   - jimhester/covr
> > after_success:
> >   - Rscript -e 'covr::codecov()'
> >
> > The additional "covr" lines are for checking unit test code coverage with
> > codecov.
> >
> > Lukas
> >
> >
> > On Thu, Oct 20, 2016 at 4:51 PM, Kevin RUE <kevinrue67 at gmail.com> wrote:
> >
> >> Actually, nevermind, I think I solved the issue of R-devel with the
> >> following YAML instructions:
> >>
> >> language: r
> >> r: devel
> >>
> >> before_install:
> >>     - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R
> >> ");tryCatch(useDevel(devel = TRUE), error =
> function(err){message(err)})'
> >>     - if [[ "$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]]
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
>
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>
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