Updating to latest Bioconductor release

Updating to latest Bioconductor release

[Roel Janssen]

Dear Guix,

Is anyone working on updating Bioconductor to the latest (3.12)
release?  If so, what's the status? :)

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

Hi Roel,

On Mon, 16 Nov 2020 at 11:49, Roel Janssen <roel@gnu.org> wrote:

> Is anyone working on updating Bioconductor to the latest (3.12)
> release?  If so, what's the status? :)

Some work is already done in the branch wip-r pulled from:

   <https://github.com/zimoun/guix>

Paretto’s principle says that 80% of the work is remaining. ;-)

Please go ahead.

All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

Hi Simon,

On Mon, 2020-11-16 at 12:27 +0100, zimoun wrote:
> Hi Roel,
> 
> On Mon, 16 Nov 2020 at 11:49, Roel Janssen <roel@gnu.org> wrote:
> 
> > Is anyone working on updating Bioconductor to the latest (3.12)
> > release?  If so, what's the status? :)
> 
> Some work is already done in the branch wip-r pulled from:
> 
>    <https://github.com/zimoun/guix>
> 
> Paretto’s principle says that 80% of the work is remaining. ;-)
> 
> Please go ahead.

Hehe. I'm building all R packages in the "wip-r" branch now to see
what's left for me to fix.

Thanks!

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

Hi Roel,

On Mon, 16 Nov 2020 at 13:10, Roel Janssen <roel@gnu.org> wrote:

> Hehe. I'm building all R packages in the "wip-r" branch now to see
> what's left for me to fix.

Cool!  I do not know if Ricardo fetched my branch to update ’wip-r’
because an error about a missing symbol was there and then I corrected
it in my branch.  Anyway.

BTW, I would like to add the type ’workflow’ in addition to ’annotation’
and ’experiment’.  Because I need:

<https://bioconductor.org/packages/3.11/workflows/html/cytofWorkflow.html>

Well, I do not know if that should go to ’wip-r’ or directly to
’master’.  WDYT?


All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

Hi Simon,

On Mon, 2020-11-16 at 13:29 +0100, zimoun wrote:
> Hi Roel,
> 
> On Mon, 16 Nov 2020 at 13:10, Roel Janssen <roel@gnu.org> wrote:
> 
> > Hehe. I'm building all R packages in the "wip-r" branch now to see
> > what's left for me to fix.
> 
> Cool!  I do not know if Ricardo fetched my branch to update ’wip-r’
> because an error about a missing symbol was there and then I
> corrected
> it in my branch.  Anyway.
> 
> BTW, I would like to add the type ’workflow’ in addition to
> ’annotation’
> and ’experiment’.  Because I need:
> 
> <https://bioconductor.org/packages/3.11/workflows/html/cytofWorkflow.html
> >
> 
> Well, I do not know if that should go to ’wip-r’ or directly to
> ’master’.  WDYT?

Well, I see we're getting R packages that fail to build because the
source cannot be downloaded (anymore), due to the outdated Bioconductor
version.  So if we can do an upgrade to 3.12 soon, and add the
'workflow' type later, that'd be my preferred route.

So to achieve that, I think we need to:
1. Update the Bioconductor version to 3.12
2. Update/build the Bioconductor packages that are already in Guix.
3. --> When all build failures have been resolved, push to master?

4. Add the bits for 'workflow' packages.
5. Add workflow packages / adjust the ones we have (do we have any?)
and build/test them.
6. --> Push to master?

WDYT?

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

Hi again, :-)

On Mon, 16 Nov 2020 at 13:38, Roel Janssen <roel@gnu.org> wrote:

> Well, I see we're getting R packages that fail to build because the
> source cannot be downloaded (anymore), due to the outdated
> Bioconductor version

Do you mean related to #39885?

   <http://issues.guix.gnu.org/issue/39885>
   

> version.  So if we can do an upgrade to 3.12 soon, and add the
> 'workflow' type later, that'd be my preferred route.
>
> So to achieve that, I think we need to:
> 1. Update the Bioconductor version to 3.12
> 2. Update/build the Bioconductor packages that are already in Guix.
> 3. --> When all build failures have been resolved, push to master?

Ok.

> 4. Add the bits for 'workflow' packages.
> 5. Add workflow packages / adjust the ones we have (do we have any?)
> and build/test them.

I do not think we have any.  But I have not checked everything neither. :-)

   <https://bioconductor.org/packages/3.11/workflows/>


All the best,
simon

Re: Updating to latest Bioconductor release

[zimoun]

Hi Roel,

Just to let you know:

  <https://ci.guix.gnu.org/eval/18656?status=failed>

I think the failure is coming from IO on the Berlin machine.

Are you building this branch too?


All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

On Tue, 2020-11-17 at 23:58 +0100, zimoun wrote:
> Hi Roel,
> 
> Just to let you know:
> 
>   <https://ci.guix.gnu.org/eval/18656?status=failed>
> 
> I think the failure is coming from IO on the Berlin machine.
> 
> Are you building this branch too?

I fixed the build issue with r-delayedarray and a couple of others on
my local machine.  I also updated the bioconductor version variable to
3.12.  Can I push these changes to the "wip-r" branch, along with
updates of the many packages involved?

I still have about 30 packages to fix the build for before we can
consider merging to master.

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

Hi Roel,

On Wed, 18 Nov 2020 at 10:31, Roel Janssen <roel@gnu.org> wrote:

> I fixed the build issue with r-delayedarray and a couple of others on
> my local machine.  I also updated the bioconductor version variable to
> 3.12.  Can I push these changes to the "wip-r" branch, along with
> updates of the many packages involved?

Please go ahead.  Then Berlin will rebuild all since it tracks the
branch wip-r.

All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

Hi Simon,

On Wed, 2020-11-18 at 12:50 +0100, zimoun wrote:
> Hi Roel,
> 
> On Wed, 18 Nov 2020 at 10:31, Roel Janssen <roel@gnu.org> wrote:
> 
> > I fixed the build issue with r-delayedarray and a couple of others
> > on
> > my local machine.  I also updated the bioconductor version variable
> > to
> > 3.12.  Can I push these changes to the "wip-r" branch, along with
> > updates of the many packages involved?
> 
> Please go ahead.  Then Berlin will rebuild all since it tracks the
> branch wip-r.

I pushed updates and fixes for various packages. Now I'm at r-
rhdf5lib. 

In 38881c9368595c5a894abe3695d98aabb1ef0029 you updated it to 1.12.0,
but it seems that building has changed quite a bit.  I wonder how it
could've built for you?

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

Hi Roel,

On Wed, 18 Nov 2020 at 17:13, Roel Janssen <roel@gnu.org> wrote:

> I pushed updates and fixes for various packages. Now I'm at r-
> rhdf5lib.

Cool!


> In 38881c9368595c5a894abe3695d98aabb1ef0029 you updated it to 1.12.0,
> but it seems that building has changed quite a bit.  I wonder how it
> could've built for you?

I have not.  The idea proposed by Ricardo was to update everything and
let Cuirass build.  BTW, I do not have enough power at hand to rebuild
all the BioConductor packages.

Thank you for working on it.

All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

On Wed, 2020-11-18 at 17:23 +0100, zimoun wrote:
> Hi Roel,
> 
> On Wed, 18 Nov 2020 at 17:13, Roel Janssen <roel@gnu.org> wrote:
> 
> > I pushed updates and fixes for various packages. Now I'm at r-
> > rhdf5lib.
> 
> Cool!
> 
> 
> > In 38881c9368595c5a894abe3695d98aabb1ef0029 you updated it to
> > 1.12.0,
> > but it seems that building has changed quite a bit.  I wonder how
> > it
> > could've built for you?
> 
> I have not.  The idea proposed by Ricardo was to update everything
> and
> let Cuirass build.  BTW, I do not have enough power at hand to
> rebuild
> all the BioConductor packages.
> 

Okay.  Then I'll look into it.  I currently have only these left as
changed in my tree:
- r-atacseqqc: Needs r-rhdf5lib.
- r-cytoml: Needs r-rhdf5lib.
- r-scater: Needs r-rhdf5lib.
- r-scuttle (new package for r-scran): Needs r-rhdf5lib.
- r-scran: Needs r-scuttle.

So it seems we are almost there.

I pushed the rest to the wip-r branch.

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

On Wed, 18 Nov 2020 at 17:33, Roel Janssen <roel@gnu.org> wrote:

> Okay.  Then I'll look into it.  I currently have only these left as
> changed in my tree:
> - r-atacseqqc: Needs r-rhdf5lib.
> - r-cytoml: Needs r-rhdf5lib.
> - r-scater: Needs r-rhdf5lib.
> - r-scuttle (new package for r-scran): Needs r-rhdf5lib.
> - r-scran: Needs r-scuttle.

Now it rings a bell and I think you missed this email (and I forgot to
point you, sorry):

# NOT DONE
r-rhdf5lib: consider removing this native input: hdf5-source
r-rhdf5lib: consider removing this propagated input: hdf5

https://lists.gnu.org/archive/html/guix-devel/2020-11/msg00047.html


> So it seems we are almost there.

Cool!


> I pushed the rest to the wip-r branch.

I will give a look on Friday.  Because of lockdown, today and
tomorrow, I have to be at the office and do some boring stuff with
physical access (plug/unplug, reboot, etc.)

Thanks,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

On Wed, 2020-11-18 at 17:59 +0100, zimoun wrote:
> On Wed, 18 Nov 2020 at 17:33, Roel Janssen <roel@gnu.org> wrote:
> 
> > Okay.  Then I'll look into it.  I currently have only these left as
> > changed in my tree:
> > - r-atacseqqc: Needs r-rhdf5lib.
> > - r-cytoml: Needs r-rhdf5lib.
> > - r-scater: Needs r-rhdf5lib.
> > - r-scuttle (new package for r-scran): Needs r-rhdf5lib.
> > - r-scran: Needs r-scuttle.
> 
> Now it rings a bell and I think you missed this email (and I forgot
> to
> point you, sorry):
> 
> # NOT DONE
> r-rhdf5lib: consider removing this native input: hdf5-source
> r-rhdf5lib: consider removing this propagated input: hdf5
> 
> https://lists.gnu.org/archive/html/guix-devel/2020-11/msg00047.html
> 

I fixed the build of r-rhfd5lib.

It seems, however, that you removed all of my changes to the wip-r
branch. Why?

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

Hi,

On Thu, 19 Nov 2020 at 16:31, Roel Janssen <roel@gnu.org> wrote:

> I fixed the build of r-rhfd5lib.

Cool!

> It seems, however, that you removed all of my changes to the wip-r
> branch. Why?

Who is "you"? ;-)
Personally, I did nothing; or I have nights that I am not aware. :-)
(Even, I do not have commit access.)
So if I did something wrong, I am sorry and could you point me to what?


All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

On Thu, 2020-11-19 at 16:36 +0100, zimoun wrote:
> Hi,
> 
> On Thu, 19 Nov 2020 at 16:31, Roel Janssen <roel@gnu.org> wrote:
> 
> > I fixed the build of r-rhfd5lib.
> 
> Cool!
> 
> > It seems, however, that you removed all of my changes to the wip-r
> > branch. Why?
> 
> Who is "you"? ;-)
> Personally, I did nothing; or I have nights that I am not aware. :-)
> (Even, I do not have commit access.)
> So if I did something wrong, I am sorry and could you point me to
> what?
> 

My bad, I jumped to a conclusion too quickly. :)

So, *something* removed my commits to the wip-r branch. Is it some kind
of automation that syncs the Github and the Savannah branches?

The good news is that in my local checkout I've fixed the build problem
with r-rhdf5lib, so I should be able to build the remaining packages
this evening.

I am hesitant to push it to the "wip-r" branch, because it seems
pointless. :)  So where can I push my updates to?

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

On Thu, 19 Nov 2020 at 16:57, Roel Janssen <roel@gnu.org> wrote:

> My bad, I jumped to a conclusion too quickly. :)

No worries. :-)


> So, *something* removed my commits to the wip-r branch. Is it some kind
> of automation that syncs the Github and the Savannah branches?

Which upstream?
I have no access on Savannah.  And I think you could should there.
My wip-r branch on my personal GitHub account, no automation.  Ricardo
did couple of days ago: fetch my branch and push it to Savannah.  Then
they reported a tiny mistake that I corrected on my branch, by
rewriting the history since it is WIP.  It was before you have started
to work on, I guess.

To be concrete, the last commit on my branch is 9 days ago.  And the
last commit on Savannah wip-r is 30th Otc.


> The good news is that in my local checkout I've fixed the build problem
> with r-rhdf5lib, so I should be able to build the remaining packages
> this evening.

Really cool!  Thank you.


> I am hesitant to push it to the "wip-r" branch, because it seems
> pointless. :)  So where can I push my updates to?

Please push your changes to wip-r on Savannah, rewriting the history
is fine with me.  Then Cuirass will rebuild everything, check.  Then
we can merge to master.


All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

On Thu, 2020-11-19 at 17:18 +0100, zimoun wrote:
> On Thu, 19 Nov 2020 at 16:57, Roel Janssen <roel@gnu.org> wrote:
> 
> > My bad, I jumped to a conclusion too quickly. :)
> 
> No worries. :-)
> 
> 
> > So, *something* removed my commits to the wip-r branch. Is it some
> > kind
> > of automation that syncs the Github and the Savannah branches?
> 
> Which upstream?
> I have no access on Savannah.  And I think you could should there.
> My wip-r branch on my personal GitHub account, no automation. 
> Ricardo
> did couple of days ago: fetch my branch and push it to Savannah. 
> Then
> they reported a tiny mistake that I corrected on my branch, by
> rewriting the history since it is WIP.  It was before you have
> started
> to work on, I guess.
> 
> To be concrete, the last commit on my branch is 9 days ago.  And the
> last commit on Savannah wip-r is 30th Otc.

Yeah, because mine got removed.

> > The good news is that in my local checkout I've fixed the build
> > problem
> > with r-rhdf5lib, so I should be able to build the remaining
> > packages
> > this evening.
> 
> Really cool!  Thank you.
> 
> 
> > I am hesitant to push it to the "wip-r" branch, because it seems
> > pointless. :)  So where can I push my updates to?
> 
> Please push your changes to wip-r on Savannah, rewriting the history
> is fine with me.  Then Cuirass will rebuild everything, check.  Then
> we can merge to master.

Well, they got removed from Savannah. Now I get this when I try to
push:
$ git push -f origin wip-r
Enumerating objects: 1599, done.
Counting objects: 100% (1599/1599), done.
Delta compression using up to 4 threads
Compressing objects: 100% (362/362), done.
Writing objects: 100% (1590/1590), 359.31 KiB | 14.37 MiB/s, done.
Total 1590 (delta 1271), reused 1545 (delta 1228), pack-reused 0
remote: error: denying non-fast-forward refs/heads/wip-r (you should
pull first)
To git.savannah.gnu.org:/srv/git/guix.git
 ! [remote rejected]       wip-r -> wip-r (non-fast-forward)
error: failed to push some refs to
'git.savannah.gnu.org:/srv/git/guix.git'

So, that's not going to work. 
Perhaps @Ricardo knows more about the setup of the "wip-r" branch.

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

Hi,

> > To be concrete, the last commit on my branch is 9 days ago.  And the
> > last commit on Savannah wip-r is 30th Otc.
>
> Yeah, because mine got removed.

Yeah, sorry.  I think Ricardo pushed.  The history is:

 - I pushed  on Tue Nov 10 16:31:17 to GitHub rewriting the history
 - Ricardo pushed that on Nov 19 13:33:49 to Savannah, rewriting the
history too.

Sorry for the mess.  And the annoyance.


> Well, they got removed from Savannah. Now I get this when I try to
> push:
> $ git push -f origin wip-r
[...]
> remote: error: denying non-fast-forward refs/heads/wip-r (you should
> pull first)
> To git.savannah.gnu.org:/srv/git/guix.git
>  ! [remote rejected]       wip-r -> wip-r (non-fast-forward)
> error: failed to push some refs to
> 'git.savannah.gnu.org:/srv/git/guix.git'
>
> So, that's not going to work.
> Perhaps @Ricardo knows more about the setup of the "wip-r" branch.

I do not know.  Weird.

All the best,
simon

Re: Updating to latest Bioconductor release

[zimoun]

Hi Roel,

Quick heads up of Ricardo from IRC.

On Thu, 19 Nov 2020 at 17:25, Roel Janssen <roel@gnu.org> wrote:

> Well, they got removed from Savannah. Now I get this when I try to
> push:

http://logs.guix.gnu.org/guix/2020-11-19.log#182429

> $ git push -f origin wip-r
> Enumerating objects: 1599, done.
> Counting objects: 100% (1599/1599), done.
> Delta compression using up to 4 threads
> Compressing objects: 100% (362/362), done.
> Writing objects: 100% (1590/1590), 359.31 KiB | 14.37 MiB/s, done.
> Total 1590 (delta 1271), reused 1545 (delta 1228), pack-reused 0
> remote: error: denying non-fast-forward refs/heads/wip-r (you should
> pull first)
> To git.savannah.gnu.org:/srv/git/guix.git
>  ! [remote rejected]       wip-r -> wip-r (non-fast-forward)
> error: failed to push some refs to
> 'git.savannah.gnu.org:/srv/git/guix.git'
>
> So, that's not going to work.
> Perhaps @Ricardo knows more about the setup of the "wip-r" branch.

http://logs.guix.gnu.org/guix/2020-11-19.log#182349

Hope that helps,

All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

Hi Simon,

On Thu, 2020-11-19 at 18:27 +0100, zimoun wrote:
> Hi Roel,
> 
> Quick heads up of Ricardo from IRC.
> 
> On Thu, 19 Nov 2020 at 17:25, Roel Janssen <roel@gnu.org> wrote:
> 
> > Well, they got removed from Savannah. Now I get this when I try to
> > push:
> 
> http://logs.guix.gnu.org/guix/2020-11-19.log#182429
> 
> > $ git push -f origin wip-r
> > Enumerating objects: 1599, done.
> > Counting objects: 100% (1599/1599), done.
> > Delta compression using up to 4 threads
> > Compressing objects: 100% (362/362), done.
> > Writing objects: 100% (1590/1590), 359.31 KiB | 14.37 MiB/s, done.
> > Total 1590 (delta 1271), reused 1545 (delta 1228), pack-reused 0
> > remote: error: denying non-fast-forward refs/heads/wip-r (you
> > should
> > pull first)
> > To git.savannah.gnu.org:/srv/git/guix.git
> >  ! [remote rejected]       wip-r -> wip-r (non-fast-forward)
> > error: failed to push some refs to
> > 'git.savannah.gnu.org:/srv/git/guix.git'
> > 
> > So, that's not going to work.
> > Perhaps @Ricardo knows more about the setup of the "wip-r" branch.
> 
> http://logs.guix.gnu.org/guix/2020-11-19.log#182349
> 
> Hope that helps,
> 

Right, so I shouldn't have pushed to "wip-r" in the first place.
Perhaps I should do it "the old way" and base my patches on the master
branch and send the gazillion patches to the mailing list. :)

Then we can discuss each line of the commit messages separately before
pushing to the master branch.

I can prepare it this evening and tomorrow evening.

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[zimoun]

Hi Roel,

On Thu, 19 Nov 2020 at 20:03, Roel Janssen <roel@gnu.org> wrote:

> > http://logs.guix.gnu.org/guix/2020-11-19.log#182349

> Right, so I shouldn't have pushed to "wip-r" in the first place.

Well, I think it is a lack of synchronisation between all of 3;
especially with this work around via external GitHub upstream.


> Perhaps I should do it "the old way" and base my patches on the master
> branch and send the gazillion patches to the mailing list. :)

What Ricardo did previously (my rewrite of history on Nov. 10 on
GitHub, and then pushed by Ricardo to Savannah today), quoting their
word: "delete origin/wip-r, reset my local copy to zimoun/wip-r,
rebased on top of origin/master, and pushed origin/wip-r".  Maybe you
could do the same.

Or if you have the super power to do that: you can delete the branch
and re-push.


> Then we can discuss each line of the commit messages separately before
> pushing to the master branch.

Well, I do not know what Ricardo thinks, but personally I would prefer
first a wip-r branch then merge.  It will avoid avoid annoyance of
possible broken packages, I mean we could detect them.


All the best,
simon

Re: Updating to latest Bioconductor release

[Ricardo Wurmus]

Hi,

>> > http://logs.guix.gnu.org/guix/2020-11-19.log#182349
>
>> Right, so I shouldn't have pushed to "wip-r" in the first place.
>
> Well, I think it is a lack of synchronisation between all of 3;
> especially with this work around via external GitHub upstream.

Yeah, sorry.  I didn’t realize wip-r was worked on by any one other than
simon and myself.  The commits are still there, they just don’t have a
named pointer (= branch) to them any longer:

https://git.savannah.gnu.org/cgit/guix.git/log/?id=8ed6a08a998d4abd58eb67c85699f38f87f76d05

If that’s the last commit (or if you have another one that was pushed) I
can simply reset the branch pointer to it and then stay out of it :)

>
>> Perhaps I should do it "the old way" and base my patches on the master
>> branch and send the gazillion patches to the mailing list. :)
>
> What Ricardo did previously (my rewrite of history on Nov. 10 on
> GitHub, and then pushed by Ricardo to Savannah today), quoting their
> word: "delete origin/wip-r, reset my local copy to zimoun/wip-r,
> rebased on top of origin/master, and pushed origin/wip-r".  Maybe you
> could do the same.
>
> Or if you have the super power to do that: you can delete the branch
> and re-push.

Deleting the branch is “git push -d origin wip-r”.

>> Then we can discuss each line of the commit messages separately before
>> pushing to the master branch.
>
> Well, I do not know what Ricardo thinks, but personally I would prefer
> first a wip-r branch then merge.  It will avoid avoid annoyance of
> possible broken packages, I mean we could detect them.

Same.  I prefer having a branch so ci.guix.gnu.org can build things and
we can keep an eye on the fall-out (if any).

Sorry again for making this harder than it should be!

-- 
Ricardo

Re: Updating to latest Bioconductor release

[Roel Janssen]

On Thu, 2020-11-19 at 22:13 +0100, Ricardo Wurmus wrote:
> Hi,
> 
> > > > http://logs.guix.gnu.org/guix/2020-11-19.log#182349
> > 
> > > Right, so I shouldn't have pushed to "wip-r" in the first place.
> > 
> > Well, I think it is a lack of synchronisation between all of 3;
> > especially with this work around via external GitHub upstream.
> 
> Yeah, sorry.  I didn’t realize wip-r was worked on by any one other than
> simon and myself.  The commits are still there, they just don’t have a
> named pointer (= branch) to them any longer:
> 
> https://git.savannah.gnu.org/cgit/guix.git/log/?id=8ed6a08a998d4abd58eb67c85699f38f87f76d05
> 
> If that’s the last commit (or if you have another one that was pushed) I
> can simply reset the branch pointer to it and then stay out of it :)
> 

This is the most recent commit I pushed:
https://git.savannah.gnu.org/cgit/guix.git/log/?id=ea92cec586893748b6de32b930117c598225c38c

It'd be great if you could reset the branch pointer! :)

> > 
> > > Perhaps I should do it "the old way" and base my patches on the master
> > > branch and send the gazillion patches to the mailing list. :)
> > 
> > What Ricardo did previously (my rewrite of history on Nov. 10 on
> > GitHub, and then pushed by Ricardo to Savannah today), quoting their
> > word: "delete origin/wip-r, reset my local copy to zimoun/wip-r,
> > rebased on top of origin/master, and pushed origin/wip-r".  Maybe you
> > could do the same.
> > 
> > Or if you have the super power to do that: you can delete the branch
> > and re-push.
> 
> Deleting the branch is “git push -d origin wip-r”.
> 
> > > Then we can discuss each line of the commit messages separately before
> > > pushing to the master branch.
> > 
> > Well, I do not know what Ricardo thinks, but personally I would prefer
> > first a wip-r branch then merge.  It will avoid avoid annoyance of
> > possible broken packages, I mean we could detect them.
> 
> Same.  I prefer having a branch so ci.guix.gnu.org can build things and
> we can keep an eye on the fall-out (if any).

On IRC you noted that the commit messages are wrong.  I interpret that as "my
commit messages are wrong", which I guess will be those where I updated the
inputs of packages.  Could you tell me how I need to format the commit messages?
Then I can perhaps rewrite the most recent history of the wip-r branch to fix my
commit messages.

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:

> On Thu, 2020-11-19 at 22:13 +0100, Ricardo Wurmus wrote:
>> Hi,
>> 
>> > > > http://logs.guix.gnu.org/guix/2020-11-19.log#182349
>> > 
>> > > Right, so I shouldn't have pushed to "wip-r" in the first place.
>> > 
>> > Well, I think it is a lack of synchronisation between all of 3;
>> > especially with this work around via external GitHub upstream.
>> 
>> Yeah, sorry.  I didn’t realize wip-r was worked on by any one other than
>> simon and myself.  The commits are still there, they just don’t have a
>> named pointer (= branch) to them any longer:
>> 
>> https://git.savannah.gnu.org/cgit/guix.git/log/?id=8ed6a08a998d4abd58eb67c85699f38f87f76d05
>> 
>> If that’s the last commit (or if you have another one that was pushed) I
>> can simply reset the branch pointer to it and then stay out of it :)
>> 
>
> This is the most recent commit I pushed:
> https://git.savannah.gnu.org/cgit/guix.git/log/?id=ea92cec586893748b6de32b930117c598225c38c
>
> It'd be great if you could reset the branch pointer! :)

Done!  I rebased onto master and pushed to r-wip.

> On IRC you noted that the commit messages are wrong.  I interpret that as "my
> commit messages are wrong", which I guess will be those where I updated the
> inputs of packages.  Could you tell me how I need to format the commit messages?
> Then I can perhaps rewrite the most recent history of the wip-r branch to fix my
> commit messages.

Many of the commit messages were incomplete (didn’t mention all changed
inputs) and used the wrong heading “gnu: Update r-foo to 1.2.3.” instead
of the more greppable “gnu: r-foo: Update to 1.2.3.”.

You can save yourself some time in the future by using
./etc/committer.scm; I strongly recommend it for R package upgrades.
(First commit all package additions manually, then run
./etc/committer.scm for all the updates.)

I have manually rewritten the commit messages.

There are some open questions: the changes to r-mutationalpatterns
invalidate the comment

   ;; These two packages are suggested packages

above r-bsgenome-hsapiens-1000genomes-hs37d5 and
r-bsgenome-hsapiens-ucsc-hg19.  Would be good to adjust the comment or
to move it down.

I also saw that r-rsubread fails to build.

-- 
Ricardo

Re: Updating to latest Bioconductor release

[Ricardo Wurmus]

Ricardo Wurmus <rekado@elephly.net> writes:

> There are some open questions: the changes to r-mutationalpatterns
> invalidate the comment
>
>    ;; These two packages are suggested packages
>
> above r-bsgenome-hsapiens-1000genomes-hs37d5 and
> r-bsgenome-hsapiens-ucsc-hg19.  Would be good to adjust the comment or
> to move it down.
>
> I also saw that r-rsubread fails to build.

And one more:

The commit that updates %bioconductor-version (“import: cran: Update the
Bioconductor version to 3.12.”) should also change “bioconductor-uri” in
(guix build-system r).  This is still at 3.11.

-- 
Ricardo

Re: Updating to latest Bioconductor release

[zimoun]

Hi,

On Fri, 20 Nov 2020 at 14:37, Ricardo Wurmus <rekado@elephly.net> wrote:

> > It'd be great if you could reset the branch pointer! :)
>
> Done!  I rebased onto master and pushed to r-wip.

Nice!  Thanks.

(You mean wip-r, right?)



> Many of the commit messages were incomplete (didn’t mention all changed
> inputs) and used the wrong heading “gnu: Update r-foo to 1.2.3.” instead
> of the more greppable “gnu: r-foo: Update to 1.2.3.”.

Just to understand for the next time: when should the commit upgrading
the %bioconductor-version be done?  First one or last one?

(I am speaking of this kind of commit: ac6a55e68a6ed675a55abc5339f776613648cb9d)


> I also saw that r-rsubread fails to build.

That's the thing where I do not understand the concept of WIP branch
if it is not possible to rewrite history.

Only one commit should do the fix. now
e57bf84eb80d6ad23710f2cad3d4fdb44ce1aca5 updates but fails.  How to
proceed without adding another commit ending to master?  Is the fix
added to wip-r and then before rebase to master, do the local rebase
(with reorder and squash) and push?  I am sorry if my question about
the Git workflow is naive, I am not used to work such way. :-)


All the best,
simon

Re: Updating to latest Bioconductor release

[zimoun]

Hi Ricardo,

On Fri, 20 Nov 2020 at 14:40, Ricardo Wurmus <rekado@elephly.net> wrote:

> The commit that updates %bioconductor-version (“import: cran: Update the
> Bioconductor version to 3.12.”) should also change “bioconductor-uri” in
> (guix build-system r).  This is still at 3.11.

When should this commit be done?  First or last of the series?

I have understood, last that's why it was not in the first first series.

All the best,
simon

Re: Updating to latest Bioconductor release

[Roel Janssen]

On Fri, 2020-11-20 at 14:42 +0100, Ricardo Wurmus wrote:
> 
> Ricardo Wurmus <rekado@elephly.net> writes:
> 
> > There are some open questions: the changes to r-mutationalpatterns
> > invalidate the comment
> > 
> >    ;; These two packages are suggested packages
> > 
> > above r-bsgenome-hsapiens-1000genomes-hs37d5 and
> > r-bsgenome-hsapiens-ucsc-hg19.  Would be good to adjust the comment or
> > to move it down.
> > 
> > I also saw that r-rsubread fails to build.
> 
> And one more:
> 
> The commit that updates %bioconductor-version (“import: cran: Update the
> Bioconductor version to 3.12.”) should also change “bioconductor-uri” in
> (guix build-system r).  This is still at 3.11.
> 

Can/may I rewrite the history of my own commits to fix these?

Kind regards,
Roel Janssen

Re: Updating to latest Bioconductor release

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:

> (You mean wip-r, right?)

Oof, yes, of course :)

>> Many of the commit messages were incomplete (didn’t mention all changed
>> inputs) and used the wrong heading “gnu: Update r-foo to 1.2.3.” instead
>> of the more greppable “gnu: r-foo: Update to 1.2.3.”.
>
> Just to understand for the next time: when should the commit upgrading
> the %bioconductor-version be done?  First one or last one?
>
> (I am speaking of this kind of commit: ac6a55e68a6ed675a55abc5339f776613648cb9d)

It doesn’t really matter; usually I do this first, so that for all
following commits the fallback URL is going to be the correct new URL.
I haven’t thought much about this, so there may be reasons involving
“guix time-machine” that are for or against that position.

It should, in my opinion, be done together with the other change to the
version string.

>> I also saw that r-rsubread fails to build.
>
> That's the thing where I do not understand the concept of WIP branch
> if it is not possible to rewrite history.
>
> Only one commit should do the fix. now
> e57bf84eb80d6ad23710f2cad3d4fdb44ce1aca5 updates but fails.  How to
> proceed without adding another commit ending to master?  Is the fix
> added to wip-r and then before rebase to master, do the local rebase
> (with reorder and squash) and push?  I am sorry if my question about
> the Git workflow is naive, I am not used to work such way. :-)

We can and should rewrite history in the wip-r branch.  So if you have a
fix you can add a new commit on top of wip-r branch and mark it so that
someone later can reorder and squash it before the merge into the master
branch.

To avoid stepping on each other’s toes we should be adding commits to
the top and then agree on a freeze to reorder and squash those commits
in the end.

-- 
Ricardo

Re: Updating to latest Bioconductor release

[zimoun]

On Fri, 20 Nov 2020 at 15:26, Ricardo Wurmus <rekado@elephly.net> wrote:

> > Just to understand for the next time: when should the commit upgrading
> > the %bioconductor-version be done?  First one or last one?
> >
> > (I am speaking of this kind of commit: ac6a55e68a6ed675a55abc5339f776613648cb9d)
>
> It doesn’t really matter; usually I do this first, so that for all
> following commits the fallback URL is going to be the correct new URL.
> I haven’t thought much about this, so there may be reasons involving
> “guix time-machine” that are for or against that position.

I will think a bit about that; especially related to #39885.

<http://issues.guix.gnu.org/issue/39885>

> It should, in my opinion, be done together with the other change to the
> version string.

Yes, for sure. :-)


> We can and should rewrite history in the wip-r branch.  So if you have a
> fix you can add a new commit on top of wip-r branch and mark it so that
> someone later can reorder and squash it before the merge into the master
> branch.
>
> To avoid stepping on each other’s toes we should be adding commits to
> the top and then agree on a freeze to reorder and squash those commits
> in the end.

Ok, that's make sense.  Thanks.


All the best,
simon