[Bioc-devel] A new way to manage side-by-side BioC release and Devel installs
Hey all, One of the things that has come up from the recent Release/Devel distinction thread on this list is that people don't consider there to be an easy way of handling both at the same time. I'd like to offer an alternative based on the switchr https://github.com/gmbecker/switchr package I'm developing. switchr is designed to allow seamless switching between distinct sets of installed packages. It also has build in support for the BioC release/devel distinction, like so: * library(switchr)* *switchTo(BiocDevel)* trying URL ' http://www.bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/BiocInstaller_1.15.5.zip ' Content type 'application/zip' length 109769 bytes (107 Kb) opened URL downloaded 107 Kb package 'BiocInstaller' successfully unpacked and MD5 sums checked Switched to the 'BioC_3.0' computing environment. 31 packages are currently available. Packages installed in your site library ARE suppressed. To switch back to your previous environment type switchBack() * BiocInstaller::biocVersion()* [1] '3.0' * switchBack()* Reverted to the 'original' computing environment. 40 packages are currently available. Packages installed in your site library ARE NOT suppressed. To switch back to your previous environment type switchBack() * BiocInstaller::biocVersion()* [1] '2.14' Note that this only works if you have an R version able to install the devel version of the BiocInstaller package, but that will be true of any solution using BioC Devel. I'm working on making the failure more graceful when this is not the case, and on writing/updating the documentation more generally. switchr is more widely useful than this, which I will be talking about publicly soon, but since it is so on-topic I figured I'd give this list a heads-up on this aspect of it. Please feel free to try switchr out, any feedback is appreciated. ~G -- Computational Biologist Genentech Research [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] A new way to manage side-by-side BioC release and Devel installs
Hi Gabe, Thanks for the heads up, sounds promising. Note that one major difficulty of switching between BioC release and devel is that between October and April it also requires to switch between R release and devel. How is that handled in switchr? Thanks, H. On 07/24/2014 08:42 AM, Gabe Becker wrote: Hey all, One of the things that has come up from the recent Release/Devel distinction thread on this list is that people don't consider there to be an easy way of handling both at the same time. I'd like to offer an alternative based on the switchr https://github.com/gmbecker/switchr package I'm developing. switchr is designed to allow seamless switching between distinct sets of installed packages. It also has build in support for the BioC release/devel distinction, like so: * library(switchr)* *switchTo(BiocDevel)* trying URL ' http://www.bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.1/BiocInstaller_1.15.5.zip ' Content type 'application/zip' length 109769 bytes (107 Kb) opened URL downloaded 107 Kb package 'BiocInstaller' successfully unpacked and MD5 sums checked Switched to the 'BioC_3.0' computing environment. 31 packages are currently available. Packages installed in your site library ARE suppressed. To switch back to your previous environment type switchBack() * BiocInstaller::biocVersion()* [1] '3.0' * switchBack()* Reverted to the 'original' computing environment. 40 packages are currently available. Packages installed in your site library ARE NOT suppressed. To switch back to your previous environment type switchBack() * BiocInstaller::biocVersion()* [1] '2.14' Note that this only works if you have an R version able to install the devel version of the BiocInstaller package, but that will be true of any solution using BioC Devel. I'm working on making the failure more graceful when this is not the case, and on writing/updating the documentation more generally. switchr is more widely useful than this, which I will be talking about publicly soon, but since it is so on-topic I figured I'd give this list a heads-up on this aspect of it. Please feel free to try switchr out, any feedback is appreciated. ~G -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] A new way to manage side-by-side BioC release and Devel installs
Herve, It doesn't handle that, so it is a time-saving approximation akin to devtools, rather than an exact solution. I recognize and agree with the reasons that Bioc devel targets R devel (sometimes); the question becomes how often BioC devel will actually fail if you use an R with a slightly old R. I'm hoping not often, but you know more than me about that, so maybe that will happen more often than I think. ~G On Thu, Jul 24, 2014 at 9:51 AM, Hervé Pagès hpa...@fhcrc.org wrote: Hi Gabe, Thanks for the heads up, sounds promising. Note that one major difficulty of switching between BioC release and devel is that between October and April it also requires to switch between R release and devel. How is that handled in switchr? Thanks, H. On 07/24/2014 08:42 AM, Gabe Becker wrote: Hey all, One of the things that has come up from the recent Release/Devel distinction thread on this list is that people don't consider there to be an easy way of handling both at the same time. I'd like to offer an alternative based on the switchr https://github.com/gmbecker/switchr package I'm developing. switchr is designed to allow seamless switching between distinct sets of installed packages. It also has build in support for the BioC release/devel distinction, like so: * library(switchr)* *switchTo(BiocDevel)* trying URL ' http://www.bioconductor.org/packages/3.0/bioc/bin/windows/ contrib/3.1/BiocInstaller_1.15.5.zip ' Content type 'application/zip' length 109769 bytes (107 Kb) opened URL downloaded 107 Kb package 'BiocInstaller' successfully unpacked and MD5 sums checked Switched to the 'BioC_3.0' computing environment. 31 packages are currently available. Packages installed in your site library ARE suppressed. To switch back to your previous environment type switchBack() * BiocInstaller::biocVersion()* [1] '3.0' * switchBack()* Reverted to the 'original' computing environment. 40 packages are currently available. Packages installed in your site library ARE NOT suppressed. To switch back to your previous environment type switchBack() * BiocInstaller::biocVersion()* [1] '2.14' Note that this only works if you have an R version able to install the devel version of the BiocInstaller package, but that will be true of any solution using BioC Devel. I'm working on making the failure more graceful when this is not the case, and on writing/updating the documentation more generally. switchr is more widely useful than this, which I will be talking about publicly soon, but since it is so on-topic I figured I'd give this list a heads-up on this aspect of it. Please feel free to try switchr out, any feedback is appreciated. ~G -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 -- Computational Biologist Genentech Research [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
