Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Gabe Becker
On Thu, Oct 5, 2017 at 10:03 PM, Gabe Becker wrote: > Oh, and the svn/git walking knows about release branches so it will find > hot-patch versions correctly, as well. > In the Bioc case, I mean, not generally. And with that flurry of emails I'm off to bed. Best, ~G > > ~G

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Gabe Becker
Oh, and the svn/git walking knows about release branches so it will find hot-patch versions correctly, as well. ~G On Thu, Oct 5, 2017 at 10:01 PM, Gabe Becker wrote: > Correct. The actual order of checks is: > >1. did switchr already retrieve that exact version for

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Gabe Becker
Correct. The actual order of checks is: 1. did switchr already retrieve that exact version for something else and keep it around, 2. A GRANRepository object if one is specified (don't worry much about this one) 3. the manifest itself (cran and bioc source types are ignored, but it

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Henrik Bengtsson
That's really nice; I didn't know it could do all that. For my clarification, when using PkgManifest(..., type = "bioc") it'll search (i) the CRAN archives, (ii) the Bioconductor repos(es), and then (iii) the Bioconductor Git repos - is that a correct observation? (I installed from

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Gabe Becker
In point of fact, it looks like IRanges 2.6.0 is an instance of that weakness, so was probably a bad example. 2.6.1 installs correctly, or would in it's native R/base bioc environment... (it fails for me in the library I have...) Also, the version on CRAN uses the bioc SVN, so may not work for

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Gabe Becker
Henrik et al., My switchr package (on CRAN, github at: http://github.com/gmbecker/switchr, preprint of the paper here: https://arxiv.org/abs/1501.02284 ) can do this. In fact, installing (cohorts of) old versions of packages is one of it's primary purposes.

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Martin Morgan
On 10/05/2017 05:14 PM, Henrik Bengtsson wrote: On Thu, Oct 5, 2017 at 1:46 PM, Martin Morgan wrote: On 10/05/2017 01:50 PM, Henrik Bengtsson wrote: Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you

Re: [Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Martin Morgan
On 10/05/2017 01:50 PM, Henrik Bengtsson wrote: Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you can find all released versions of a package, e.g. https://cran.r-project.org/src/contrib/Archive/PSCBS/? Say I want to access the source

[Bioc-devel] Old package versions / Bioc archive of package's *.tar.gz releases?

2017-10-05 Thread Henrik Bengtsson
Is there an easily accessible archive for Bioconductor packages similar to what is provided on CRAN where you can find all released versions of a package, e.g. https://cran.r-project.org/src/contrib/Archive/PSCBS/? Say I want to access the source code for affy 1.18.0. Here are the two approaches