I can't seem to get R 2.1.0a to install BioC packages using the packages & data > package installer command. The packages appear under both source and binary, but when I click to install a package, nothing happens. Has anyone else had this problem? I even tried the nightly build of the GUI, but nothing. --Jake
R 2.1.0a w/ Tiger: can't install BioC packages
3 messages · Jake Michaelson, Seth Falcon, stefano iacus
Hi Jake, Jacob Michaelson <jjmichael@comcast.net> writes:
I can't seem to get R 2.1.0a to install BioC packages using the packages & data > package installer command. The packages appear under both source and binary, but when I click to install a package, nothing happens. Has anyone else had this problem? I even tried the nightly build of the GUI, but nothing.
We've just posted the OS X binary packages to the Bioconductor website (Stefano has been hard at work to create these packages). And they have not yet been announced as we haven't had a chance to fully test them yet. I believe that I experienced the same issue you are reporting: The Bioc binary packages are visible, but selecting one or more packages and clicking the Install button does not result in an installation attempt. I assure you this will be resolved in short order. In the meantime, I found the following to work and you can give it a try if you are impatient to get the Bioc packages loaded ;-)
From the drop-down box where Bioconductor binary repos is selected,
select the Other repository option where you enter your own URL of a repository. Then enter: http://www.bioconductor.org. Check the binary package checkbox and then get list. You should see the same list of packages, only now they should be installable. YMMV. Best, + seth
This is not related to Tiger but to R.app. It seems like for BioC binaries browse.pkgs is called by R.app instead of install.packages ! Until we fix this in R.app (I need to check the sources) the trick is to use "other repository" + binary format using http://www.bioconductor.org as URL. apologizes stefano
On 26/mag/05, at 05:36, Seth Falcon wrote:
Hi Jake, Jacob Michaelson <jjmichael@comcast.net> writes:
I can't seem to get R 2.1.0a to install BioC packages using the packages & data > package installer command. The packages appear under both source and binary, but when I click to install a package, nothing happens. Has anyone else had this problem? I even tried the nightly build of the GUI, but nothing.
We've just posted the OS X binary packages to the Bioconductor website (Stefano has been hard at work to create these packages). And they have not yet been announced as we haven't had a chance to fully test them yet. I believe that I experienced the same issue you are reporting: The Bioc binary packages are visible, but selecting one or more packages and clicking the Install button does not result in an installation attempt. I assure you this will be resolved in short order. In the meantime, I found the following to work and you can give it a try if you are impatient to get the Bioc packages loaded ;-)
From the drop-down box where Bioconductor binary repos is selected,
select the Other repository option where you enter your own URL of a repository. Then enter: http://www.bioconductor.org. Check the binary package checkbox and then get list. You should see the same list of packages, only now they should be installable. YMMV. Best, + seth
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