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

[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:

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

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