[Bioc-devel] reverting to older version
@b@@t@tgen @ending from gm@il@com
Tue Jun 12 05:47:30 CEST 2018
OK...1.98.0 and 1.99.0 sounds good. Shall do that.
Is it necessary to convey the reasons for the change e.g. NEWS file ?
That's my last question...I hope !
On Tuesday, June 12, 2018, Hervé Pagès <hpages using fredhutch.org> wrote:
> Ah ok. Yes 1.99.0 is fine. Then the package will be released as 2.0.0
> in Fall as part of BioC 3.8.
> Not that version numbers have a strong meaning but I was thinking that
> maybe you could bump to 1.98.0 in release to sort of indicate the fact
> that the package in release is the precursor of what's going to become
> 2.0.0 in the next release. If 1.98.0 works as expected, you should
> freeze it i.e. only touch it when you absolutely need to fix something
> in it.
> Hope this helps,
> On 06/11/2018 06:33 PM, Samsiddhi Bhattacharjee wrote:
>> Thanks, I shall do that. Its OK to keep the master as 1.99.0 ? It should
>> probably have been 1.19.1 ?
>> On Monday, June 11, 2018, Hervé Pagès <hpages using fredhutch.org <mailto:
>> hpages using fredhutch.org>> wrote:
>> Having a package that is known to be broken in release is not
>> really an option.
>> How about replacing all the files in the RELEASE_3_7 branch
>> with what's in the master branch. For the version, just bump
>> z (in x.y.z) to its next version. Don't touch x or y. So the
>> version would become 1.18.1 in release. Then commit (it's going
>> to be a single commit) with a commit message that says something
>> like "Resync with master branch".
>> On 06/11/2018 09:27 AM, Samsiddhi Bhattacharjee wrote:
>> I am maintainer of package ASSET. We have recently discovered
>> some issues
>> (most importantly computational speed issues) with recent
>> versions of our
>> package and wanted to revert the code to an older version ASSET
>> v 1.8.0
>> present in Bioconductor release 3.2, before proceeding to make
>> enhancements to the package.
>> In release 3.3 , there were major changes to the package, it is
>> like a
>> branch that we now realize that we need to abandon. We had
>> introduced a new
>> feature and for that we switched from deterministic p-value
>> calculation to
>> stochastic calculation. We did not notice the issues untill now.
>> We want to
>> switch back to the deterministic one, which was present last in
>> As suggested by Nitesh, I have made the changes in devel branch
>> by copying the code as it was in release 3.2, and only updating
>> DESCRIPTION file make the version 1.99.0 as this will be a major
>> (although we are taking a few steps back, we will probably add
>> some steps
>> forward before release 3.8).
>> I wanted to put a .onAttach() message in the current version to
>> make the
>> user aware of the issues and possibly mentioning the next
>> release and/or
>> pointing to the older release. However, as Herve
>> has pointed out, people may mix up devel and release versions
>> problems. Hence Herve had suggested:
>> "It will be much better if you actually fix the release version
>> of your
>> package. This should just be a matter of porting the fixes you
>> do in devel
>> with 'git cherry-pick'."
>> Reason I am hesitating is that the changes (diff of 3.7 and 3.2)
>> are quite
>> a lot and doing selective changes as suggested will introduce
>> further bugs,
>> and even after selection these changes will be *many*. Is it ok
>> to backport
>> a "patch" to the release with a large number of changes? If yes,
>> should the version number be bumped to?
>> Thanks in advance.
>> [[alternative HTML version deleted]]
>> Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org>
>> mailing list
>> -- Hervé Pagès
>> Program in Computational Biolog
>> 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: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
> 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: hpages using fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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