[Bioc-devel] reverting to older version

[Hervé Pagès]

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,
H.

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:
> 
>     Hi,
> 
>     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".
> 
>     Cheers,
>     H.
> 
>     On 06/11/2018 09:27 AM, Samsiddhi Bhattacharjee wrote:
> 
>         Hi,
> 
>         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
>         further
>         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 3.2.
> 
>         As suggested by Nitesh, I have made the changes in devel branch
>         (basically
>         by copying the code as it was in release 3.2, and only updating the
>         DESCRIPTION file make the version 1.99.0 as this will be a major
>         change
>         (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
>         causing
>         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,
>         what
>         should the version number be bumped to?
> 
>         Thanks in advance.
> 
>         Regards,
> 
>         --
>         Samsiddhi
> 
>                  [[alternative HTML version deleted]]
> 
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> 
>     -- 
>     Hervé Pagès
> 
>     Program in Computational Biolog
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-- 
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