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

Thu Oct 20 16:18:09 CEST 2016

By the way, the reason why I am asking is that BiocCheck raised the
following warning, after I upgraded my system to R-3.4 and Bioc-devel:

WARNING: Update R version dependency from 3.3 to 3.4

Now that I updated the R version dependency, everything is fine on my
updated machine, but the Travis build fails because it doesn't have 3.4
installed.
But I suppose that the BioC devel-build servers have R-3.4 installed, right?

All the best, and sorry for the additional email,
Kevin

On Thu, Oct 20, 2016 at 3:07 PM, Kevin RUE <kevinrue67 at gmail.com> wrote:

> Hi all,
>
> First of all, thanks for the question and answers, it helped me a lot on
> my local machine.
>
> While we're on the topic, does anyone know when R-devel (R-3.4) will be
> available on Travis CI ? Because it is running R-3.3.1, and therefore
> produces the same error message when I instruct Travis to install packages
> from the devel branch.
>
> I suppose this is something that I need to post on the Travis GitHub isse
> tracker, right, considering the following message?
>
> R for Travis-CI is not officially supported, but is community maintained.
> Please file any issues at https://github.com/travis-ci/travis-ci/issues
> and mention @craigcitro, @hadley and @jimhester in the issue
> Best,
> Kevin
>
> On Thu, Oct 20, 2016 at 11:06 AM, Rodriguez Martinez, Andrea <
> andrea.rodriguez-martinez13 at imperial.ac.uk> 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/packa
>> ges/3.4/bioc/bin/macosx/mavericks/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
>>
>>         [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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