mbox series

[bug#37988,0/6] Add flowWorkspace from BioConductor

Message ID 20191030102324.12437-1-zimon.toutoune@gmail.com
Headers show
Series Add flowWorkspace from BioConductor | expand

Message

Simon Tournier Oct. 30, 2019, 10:23 a.m. UTC 
Dear,

The aim of this serie is to add the package flowWorkspace.

It is important to notice that the package RProtobuflib [1] from BioConductor
is not packaged using the correct convention.  RProtobuflib includes its
dependency protobuf-2.6.0 as an archive tgz and compiles it using its
./configure [2].  Therefore, the file ./configure from the unarchived
protobuf-2.6.0 needs to be patched to apply the correct shebang.

It is clearly unconventional and we should distribute our own version of
RProtobuflib using the correct way i.e., packaging protobuf-2.6.0.  However,
do we want to diverge to the official BioConductor and add maintenance burden
when we are not fully able to already package all the BioConductor archive?


All the best,
simon


[1] https://bioconductor.org/packages/release/bioc/html/RProtoBufLib.html
[2] https://github.com/RGLab/RProtoBufLib/blob/trunk/configure#L2860-L2889



zimoun (6):
  gnu: Add r-idpmisc.
  gnu: Add r-flowviz.
  gnu: Add r-rprotobuflib.
  gnu: Add r-cytolib.
  gnu: Add r-ncdfflow.
  gnu: Add r-flowworkspace.

 gnu/packages/bioconductor.scm | 173 ++++++++++++++++++++++++++++++++++
 gnu/packages/cran.scm         |  30 ++++++
 2 files changed, 203 insertions(+)

Comments

Simon Tournier Feb. 21, 2020, 4:39 p.m. UTC | #1 
Hi Ricardo,

Why did you pushed your commits instead of mines?
Especially when they had not fallen in the crack.

I sent them the October 30, 2019.
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988

And you commented them the same day:
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#26

I modified one the November 5th, 2019:
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#47


And you committed and pushed the same packages on the December, 15th.


Cheers,
simon
Ricardo Wurmus Feb. 21, 2020, 6:38 p.m. UTC | #2 
Hi,

> Why did you pushed your commits instead of mines?
> Especially when they had not fallen in the crack.
>
> I sent them the October 30, 2019.
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988
>
> And you commented them the same day:
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#26
>
> I modified one the November 5th, 2019:
> https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#47

Uh, that’s odd.  I remember working with your r-flow* patches.  I did
not have my own versions of these patches.  I know this because I had
not previously encountered flow cytometry.  (I don’t specifically
remember r-rprotobuflib from this series.)

My guess is that I wasn’t able to apply them cleanly, so I copy & pasted
the diff, adjusted as needed, and then forgot to override the commit
author before pushing :-(

December is a blur.  It’s quite possible that I didn’t work on the
patches all in one go, got interrupted, and then pushed them together
with some other work (I see that there are R update commits after these
pushes).

I’m very sorry to have messed up the authorship here.  This was
definitely not intended :(

--
Ricardo
Simon Tournier Feb. 21, 2020, 7:12 p.m. UTC | #3 
Hi Ricardo,

On Fri, 21 Feb 2020 at 19:39, Ricardo Wurmus <rekado@elephly.net> wrote:

> > Why did you pushed your commits instead of mines?
> > Especially when they had not fallen in the crack.
> >
> > I sent them the October 30, 2019.
> > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988
> >
> > And you commented them the same day:
> > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#26
> >
> > I modified one the November 5th, 2019:
> > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#47
>
> Uh, that’s odd.  I remember working with your r-flow* patches.  I did
> not have my own versions of these patches.  I know this because I had
> not previously encountered flow cytometry.  (I don’t specifically
> remember r-rprotobuflib from this series.)

That's why I found weird the twist. :-)
I thought I did something unexpected and/or there was a special
motivation. And so my "why?". :-)


> My guess is that I wasn’t able to apply them cleanly, so I copy & pasted
> the diff, adjusted as needed, and then forgot to override the commit
> author before pushing :-(

> I’m very sorry to have messed up the authorship here.  This was
> definitely not intended :(

I am ok about the authorship; my salary does not depend on the number
of commits accepted. ;-)
The most important is that the packages end in Guix; who committed
them is less important.


Thanks,
simon