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

[Kevin RUE]

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
>>>
>>>
>>
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>>
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>>
>
>
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>
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