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

Fri Oct 21 00:18:54 CEST 2016

Hi,

Sorry for my slow response. I have just tried again and it worked, but then I was not able to install packages from the devel branch, with the warning:

>Warning: unable to access index for repository https://bioconductor.org/packages/3.5/data/experiment/bin/macosx/mavericks/contrib/3.4:
  cannot download all files

I guess this is all related with what has been discussed in this loop of emails.

Thanks,

Andrea

________________________________
From: Martin Morgan <martin.morgan at roswellpark.org>
Sent: 20 October 2016 13:31:31
To: Rodriguez Martinez, Andrea; Michael Lawrence; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

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/mavericks/contrib/3.4/PACKAGES.gz':
> status was '404 Not Found'
> Warning in install.packages :
>   URL
> 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/mavericks/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/mavericks/contrib/3.4:
>   cannot download all files
> installing the source package ‘BiocInstaller’
>
> trying URL
> 'https://bioconductor.org/packages/3.4/bioc/src/contrib/BiocInstaller_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 imperial.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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