Re: [Bioc-devel] Resetting to previous commits

[Pages, Herve]

On 8/14/19 10:19, Kasper Daniel Hansen wrote:
...
> 
> Pro-tip: In general, you will be well served not to get too attached to
> version numbers. Bump it frequently even without new functionality or bug
> fixes and just live with the frequent bumping.

+1 for Best Advice Of The Week.


-- 
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...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Resetting to previous commits

[Kasper Daniel Hansen]

Yes, it will build the most recent version

If the previous build failed it will even build the most recent code, even
if the code is not bumped. The exception is the following
  you update package A to version X, build succeeds
  you commit code to package A, but does not bump the version
This will not trigger.a rebuild and your latest commits will not be
reflected in the tarballs available to the community. This is why you -- in
general -- need to bump versions when you commit code.

Pro-tip: In general, you will be well served not to get too attached to
version numbers. Bump it frequently even without new functionality or bug
fixes and just live with the frequent bumping.

On Wed, Aug 14, 2019 at 12:43 PM Mike Smith  wrote:

> Yes, the Bioconductor build system will only try to build the most recent
> version in the git repository.  If it never managed to successfully build a
> particular version then that version should not appear anywhere on the Bioc
> site.  For example biomaRt is now on release 2.40.3, but version 2.40.2
> never passed all the checks, and so is absent from the archive at
> https://bioconductor.org/packages/3.9/bioc/src/contrib/Archive/biomaRt/
> In
> theory someone could get hold of it via git, anyone doing so it probably
> experienced enough to look after themselves.
>
> Best,
> Mike
>
> On Wed, 14 Aug 2019 at 18:12, Erik Fasterius 
> wrote:
>
> > Thank you for the prompt response! I will just add more versions on top
> of
> > what I have already added. Would it be correct to assume that
> Bioconductor
> > will try to build the most recent version available, even though it
> failed
> > builds for previous versions?
> >
> > Regarding the change, it was indeed a breaking change, and I thus
> believed
> > that it would have been counted as a bug-fix for the release branch.
> >
> > All the best,
> > Erik
> >
> > On 14 Aug 2019, at 17:15, Kasper Daniel Hansen <
> > kasperdanielhan...@gmail.com>
> wrote:
> >
> > Also, it is not clear to me if this qualifies for a update to the release
> > branch. Updates to release should be restricted to critical bug fixes
> > (although if tidyr updates will break your package, that sounds like a
> > critical bug fix to me)
> >
> > Note to others: this (again) emphasizes that we may need to "copy" a
> > snapshot of CRAN into release.
> >
> > Best,
> > Kasper
> >
> > On Wed, Aug 14, 2019 at 11:13 AM Kasper Daniel Hansen <
> > kasperdanielhan...@gmail.com>
> wrote:
> > You cannot revert. By pushing those updates, you released a version into
> > the wild. It is true that as long as it doesn't build on the build
> servers,
> > it would have been hard to obtain for anyone, but it is still possible
> > through git. You need to update the version.
> >
> > Best,
> > Kasper
> >
> > On Wed, Aug 14, 2019 at 11:05 AM Erik Fasterius <
> > erik.faster...@outlook.com> wrote:
> > I made some changes to my seqCAT package the last few days in order to
> > prepare for version 1.0.0 of tidyr, which was apparently harder than I
> > initially thought. I was also a bit too quick with pushing to
> Bioconductor
> > (both the release and devel branches), and now I’ve got several updates
> and
> > versions that don’t work - very stupid of me, I know. I do seem to have a
> > working version now, though, and I finally learnt my lesson and have NOT
> > pushed this to Bioconductor yet. Now I want to reset to the previously
> > working versions of my package (1.6.0 for release and 1.7.2 for devel)
> >
> > I did try to make (temporary) hard resets and force push these to
> > Bioconductor (as per the “reset to a previous commit” in the “abandon
> > changes” developer section), but these did not work: all I got was errors
> > say I cannot move from a higher version (e.g. 1.6.2) back to a lower one
> > (1.6.0). Is there a way to bypass this? If not, I assume I’ll just have
> to
> > make a new version for each branch (1.6.3 and 1.7.5, as it were) and push
> > those, leaving several non-functional versions at Bioconductor? If at all
> > possible I’d like to avoid this.
> >
> > Again, I realise these problems are because of errors on my part, and
> > would like to know if I can solve them somehow or if I’ll just have to
> live
> > with them.
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> > --
> > Best,
> > Kasper
> >
> >
> > --
> > Best,
> > Kasper
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> 

Re: [Bioc-devel] Resetting to previous commits

[Mike Smith]

Yes, the Bioconductor build system will only try to build the most recent
version in the git repository.  If it never managed to successfully build a
particular version then that version should not appear anywhere on the Bioc
site.  For example biomaRt is now on release 2.40.3, but version 2.40.2
never passed all the checks, and so is absent from the archive at
https://bioconductor.org/packages/3.9/bioc/src/contrib/Archive/biomaRt/  In
theory someone could get hold of it via git, anyone doing so it probably
experienced enough to look after themselves.

Best,
Mike

On Wed, 14 Aug 2019 at 18:12, Erik Fasterius 
wrote:

> Thank you for the prompt response! I will just add more versions on top of
> what I have already added. Would it be correct to assume that Bioconductor
> will try to build the most recent version available, even though it failed
> builds for previous versions?
>
> Regarding the change, it was indeed a breaking change, and I thus believed
> that it would have been counted as a bug-fix for the release branch.
>
> All the best,
> Erik
>
> On 14 Aug 2019, at 17:15, Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
>
> Also, it is not clear to me if this qualifies for a update to the release
> branch. Updates to release should be restricted to critical bug fixes
> (although if tidyr updates will break your package, that sounds like a
> critical bug fix to me)
>
> Note to others: this (again) emphasizes that we may need to "copy" a
> snapshot of CRAN into release.
>
> Best,
> Kasper
>
> On Wed, Aug 14, 2019 at 11:13 AM Kasper Daniel Hansen <
> kasperdanielhan...@gmail.com> wrote:
> You cannot revert. By pushing those updates, you released a version into
> the wild. It is true that as long as it doesn't build on the build servers,
> it would have been hard to obtain for anyone, but it is still possible
> through git. You need to update the version.
>
> Best,
> Kasper
>
> On Wed, Aug 14, 2019 at 11:05 AM Erik Fasterius <
> erik.faster...@outlook.com> wrote:
> I made some changes to my seqCAT package the last few days in order to
> prepare for version 1.0.0 of tidyr, which was apparently harder than I
> initially thought. I was also a bit too quick with pushing to Bioconductor
> (both the release and devel branches), and now I’ve got several updates and
> versions that don’t work - very stupid of me, I know. I do seem to have a
> working version now, though, and I finally learnt my lesson and have NOT
> pushed this to Bioconductor yet. Now I want to reset to the previously
> working versions of my package (1.6.0 for release and 1.7.2 for devel)
>
> I did try to make (temporary) hard resets and force push these to
> Bioconductor (as per the “reset to a previous commit” in the “abandon
> changes” developer section), but these did not work: all I got was errors
> say I cannot move from a higher version (e.g. 1.6.2) back to a lower one
> (1.6.0). Is there a way to bypass this? If not, I assume I’ll just have to
> make a new version for each branch (1.6.3 and 1.7.5, as it were) and push
> those, leaving several non-functional versions at Bioconductor? If at all
> possible I’d like to avoid this.
>
> Again, I realise these problems are because of errors on my part, and
> would like to know if I can solve them somehow or if I’ll just have to live
> with them.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> --
> Best,
> Kasper
>
>
> --
> Best,
> Kasper
>
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Resetting to previous commits

[Erik Fasterius]

Thank you for the prompt response! I will just add more versions on top of what 
I have already added. Would it be correct to assume that Bioconductor will try 
to build the most recent version available, even though it failed builds for 
previous versions?

Regarding the change, it was indeed a breaking change, and I thus believed that 
it would have been counted as a bug-fix for the release branch.

All the best,
Erik

On 14 Aug 2019, at 17:15, Kasper Daniel Hansen 
mailto:kasperdanielhan...@gmail.com>> wrote:

Also, it is not clear to me if this qualifies for a update to the release 
branch. Updates to release should be restricted to critical bug fixes (although 
if tidyr updates will break your package, that sounds like a critical bug fix 
to me)

Note to others: this (again) emphasizes that we may need to "copy" a snapshot 
of CRAN into release.

Best,
Kasper

On Wed, Aug 14, 2019 at 11:13 AM Kasper Daniel Hansen 
mailto:kasperdanielhan...@gmail.com>> wrote:
You cannot revert. By pushing those updates, you released a version into the 
wild. It is true that as long as it doesn't build on the build servers, it 
would have been hard to obtain for anyone, but it is still possible through 
git. You need to update the version.

Best,
Kasper

On Wed, Aug 14, 2019 at 11:05 AM Erik Fasterius 
mailto:erik.faster...@outlook.com>> wrote:
I made some changes to my seqCAT package the last few days in order to prepare 
for version 1.0.0 of tidyr, which was apparently harder than I initially 
thought. I was also a bit too quick with pushing to Bioconductor (both the 
release and devel branches), and now I’ve got several updates and versions that 
don’t work - very stupid of me, I know. I do seem to have a working version 
now, though, and I finally learnt my lesson and have NOT pushed this to 
Bioconductor yet. Now I want to reset to the previously working versions of my 
package (1.6.0 for release and 1.7.2 for devel)

I did try to make (temporary) hard resets and force push these to Bioconductor 
(as per the “reset to a previous commit” in the “abandon changes” developer 
section), but these did not work: all I got was errors say I cannot move from a 
higher version (e.g. 1.6.2) back to a lower one (1.6.0). Is there a way to 
bypass this? If not, I assume I’ll just have to make a new version for each 
branch (1.6.3 and 1.7.5, as it were) and push those, leaving several 
non-functional versions at Bioconductor? If at all possible I’d like to avoid 
this.

Again, I realise these problems are because of errors on my part, and would 
like to know if I can solve them somehow or if I’ll just have to live with them.
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--
Best,
Kasper


--
Best,
Kasper


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Re: [Bioc-devel] Resetting to previous commits

[Kasper Daniel Hansen]

You cannot revert. By pushing those updates, you released a version into
the wild. It is true that as long as it doesn't build on the build servers,
it would have been hard to obtain for anyone, but it is still possible
through git. You need to update the version.

Best,
Kasper

On Wed, Aug 14, 2019 at 11:05 AM Erik Fasterius 
wrote:

> I made some changes to my seqCAT package the last few days in order to
> prepare for version 1.0.0 of tidyr, which was apparently harder than I
> initially thought. I was also a bit too quick with pushing to Bioconductor
> (both the release and devel branches), and now I’ve got several updates and
> versions that don’t work - very stupid of me, I know. I do seem to have a
> working version now, though, and I finally learnt my lesson and have NOT
> pushed this to Bioconductor yet. Now I want to reset to the previously
> working versions of my package (1.6.0 for release and 1.7.2 for devel)
>
> I did try to make (temporary) hard resets and force push these to
> Bioconductor (as per the “reset to a previous commit” in the “abandon
> changes” developer section), but these did not work: all I got was errors
> say I cannot move from a higher version (e.g. 1.6.2) back to a lower one
> (1.6.0). Is there a way to bypass this? If not, I assume I’ll just have to
> make a new version for each branch (1.6.3 and 1.7.5, as it were) and push
> those, leaving several non-functional versions at Bioconductor? If at all
> possible I’d like to avoid this.
>
> Again, I realise these problems are because of errors on my part, and
> would like to know if I can solve them somehow or if I’ll just have to live
> with them.
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Best,
Kasper

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Re: [Bioc-devel] Resetting to previous commits

[Kasper Daniel Hansen]

Also, it is not clear to me if this qualifies for a update to the release
branch. Updates to release should be restricted to critical bug fixes
(although if tidyr updates will break your package, that sounds like a
critical bug fix to me)

Note to others: this (again) emphasizes that we may need to "copy" a
snapshot of CRAN into release.

Best,
Kasper

On Wed, Aug 14, 2019 at 11:13 AM Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> You cannot revert. By pushing those updates, you released a version into
> the wild. It is true that as long as it doesn't build on the build servers,
> it would have been hard to obtain for anyone, but it is still possible
> through git. You need to update the version.
>
> Best,
> Kasper
>
> On Wed, Aug 14, 2019 at 11:05 AM Erik Fasterius <
> erik.faster...@outlook.com> wrote:
>
>> I made some changes to my seqCAT package the last few days in order to
>> prepare for version 1.0.0 of tidyr, which was apparently harder than I
>> initially thought. I was also a bit too quick with pushing to Bioconductor
>> (both the release and devel branches), and now I’ve got several updates and
>> versions that don’t work - very stupid of me, I know. I do seem to have a
>> working version now, though, and I finally learnt my lesson and have NOT
>> pushed this to Bioconductor yet. Now I want to reset to the previously
>> working versions of my package (1.6.0 for release and 1.7.2 for devel)
>>
>> I did try to make (temporary) hard resets and force push these to
>> Bioconductor (as per the “reset to a previous commit” in the “abandon
>> changes” developer section), but these did not work: all I got was errors
>> say I cannot move from a higher version (e.g. 1.6.2) back to a lower one
>> (1.6.0). Is there a way to bypass this? If not, I assume I’ll just have to
>> make a new version for each branch (1.6.3 and 1.7.5, as it were) and push
>> those, leaving several non-functional versions at Bioconductor? If at all
>> possible I’d like to avoid this.
>>
>> Again, I realise these problems are because of errors on my part, and
>> would like to know if I can solve them somehow or if I’ll just have to live
>> with them.
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> Best,
> Kasper
>


-- 
Best,
Kasper

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[Bioc-devel] Resetting to previous commits

[Erik Fasterius]

I made some changes to my seqCAT package the last few days in order to prepare 
for version 1.0.0 of tidyr, which was apparently harder than I initially 
thought. I was also a bit too quick with pushing to Bioconductor (both the 
release and devel branches), and now I’ve got several updates and versions that 
don’t work - very stupid of me, I know. I do seem to have a working version 
now, though, and I finally learnt my lesson and have NOT pushed this to 
Bioconductor yet. Now I want to reset to the previously working versions of my 
package (1.6.0 for release and 1.7.2 for devel)

I did try to make (temporary) hard resets and force push these to Bioconductor 
(as per the “reset to a previous commit” in the “abandon changes” developer 
section), but these did not work: all I got was errors say I cannot move from a 
higher version (e.g. 1.6.2) back to a lower one (1.6.0). Is there a way to 
bypass this? If not, I assume I’ll just have to make a new version for each 
branch (1.6.3 and 1.7.5, as it were) and push those, leaving several 
non-functional versions at Bioconductor? If at all possible I’d like to avoid 
this.

Again, I realise these problems are because of errors on my part, and would 
like to know if I can solve them somehow or if I’ll just have to live with them.
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