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

Thu Oct 20 19:34:42 CEST 2016

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:

> 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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>
>

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