[Bioc-devel] biocLite “no packages in repository” error

[Dan Tenenbaum]

Hi Nico,

----- Original Message -----
> From: "Nicolas Delhomme" <nicolas.delhomme at umu.se>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "Ashley Ng" <ang at wehi.edu.au>, bioc-devel at r-project.org
> Sent: Tuesday, April 15, 2014 7:39:00 AM
> Subject: Re: [Bioc-devel]	biocLite “no packages in repository” error
> 
> Hej Dan!
> 
> With regards to this, do you have any timeline - since you got
> Maverick machines now :-) - as to when Maverick will be supported?
> 

We have ordered the machines. I have just asked for an update on the order status. As soon as the machines arrive, are configured, and start building, we'll be able to support binary Mavericks packages. We'll make an announcement on this list. 

Note that even CRAN's builds of Mavericks packages are not complete and this may impact Bioconductor's builds, but we'll work with CRAN to resolve this.

> As a feedback, compiling R and installing from source on Maverick has
> been fairly stable for me - just recently encountered a problem with
> compiling mzR but got a workaround from the package developers - and
> this since Maverick is out (October last year).
> 

Yes, it's mostly a (lack of) hardware problem, not a technical one.

Dan


> Cheers,
> 
> Nico
> 
> ---------------------------------------------------------------
> Nicolas Delhomme
> 
> The Street Lab
> Department of Plant Physiology
> Umeå Plant Science Center
> 
> Tel: +46 90 786 7989
> Email: nicolas.delhomme at umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> ---------------------------------------------------------------
> 
> On 15 Apr 2014, at 16:28, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 
> > Never mind,
> > 
> > The problem is that you are using the Mavericks build which is not
> > yet supported. Please use the Snow Leopard build of R.
> > 
> > See this link for more information:
> > 
> > https://stat.ethz.ch/pipermail/bioc-devel/2014-April/005497.html
> > 
> > Dan
> > 
> > 
> > ----- Original Message -----
> >> From: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> >> To: "Ashley Ng" <ang at wehi.EDU.AU>
> >> Cc: bioc-devel at r-project.org
> >> Sent: Tuesday, April 15, 2014 7:26:11 AM
> >> Subject: Re: biocLite “no packages in repository” error
> >> 
> >> Hi Ashley,
> >> 
> >> ----- Original Message -----
> >>> From: "Ashley Ng" <ang at wehi.EDU.AU>
> >>> To: dtenenba at fhcrc.org
> >>> Cc: bioc-devel at r-project.org
> >>> Sent: Tuesday, April 15, 2014 3:04:23 AM
> >>> Subject: biocLite “no packages in repository” error
> >>> 
> >>> Hi Dan
> >>> 
> >>> I seem to getting a “no packages in repository” biocLite error
> >>> after
> >>> installing R 3.10 and trying to upgrade packages:
> >>> 
> >>>> source("http://bioconductor.org/biocLite.R")
> >>> Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for
> >>> help
> >>>> biocLite()
> >>> Error: 'no packages in repository (no internet connection?)'
> >>> while
> >>> trying
> >>>  http://bioconductor.org/packages/2.14/bioc
> >>> 
> >>>> sessionInfo()
> >>> R version 3.1.0 (2014-04-10)
> >>> Platform: x86_64-apple-darwin13.1.0 (64-bit)
> >>> 
> >>> locale:
> >>> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
> >>> 
> >>> attached base packages:
> >>> [1] stats     graphics  grDevices utils     datasets  methods
> >>>  base
> >>> 
> >>> other attached packages:
> >>> [1] BiocInstaller_1.13.3
> >>> 
> >>> loaded via a namespace (and not attached):
> >>> [1] tools_3.1.0
> >>>> 
> >>> 
> >> 
> >> What is the result of the following command:
> >> 
> >> library(BiocInstaller)
> >> biocinstallRepos()
> >> 
> >> 
> >> ?
> >> 
> >> Dan
> >> 
> >> 
> >> 
> >>> Cheers
> >>> 
> >>> Ashley Ng
> >>> 
> >>> Clinical Haematologist and Post Doctoral Fellow
> >>> The Royal Melbourne Hospital
> >>> The Walter and Eliza Hall Institute of Medical Research, Cancer
> >>> and
> >>> Haematology Division
> >>> 1G Royal Parade
> >>> Parkville, 3050
> >>> Melbourne, Australia
> >>> 
> >>> 
> >>> 
> >>> ______________________________________________________________________
> >>> The information in this email is confidential and intended solely
> >>> for
> >>> the addressee.
> >>> You must not disclose, forward, print or use it without the
> >>> permission of the sender.
> >>> ______________________________________________________________________
> >>> 
> >> 
> > 
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
>