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

Kevin RUE kevinrue67 at gmail.com
Thu Oct 20 19:50:15 CEST 2016 

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]]
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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>
>

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