[Bioc-devel] biocLite “no packages in repository” error
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 Ume? Plant Science Center Tel: +46 90 786 7989 Email: nicolas.delhomme at umu.se SLU - Ume? universitet Ume? 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
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