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Bug#991919: transition: r-api-bioc-3.13

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  Bug#991919: transition: r-api-bioc-3.13 Andreas Tille <tille@debian.org> - 2021-09-08 16:20 +0200
    Bug#991919: transition: r-api-bioc-3.13 Andreas Tille <andreas@an3as.eu> - 2021-09-11 09:10 +0200
      Bug#991919: transition: r-api-bioc-3.13 Nilesh Patra <nilesh@nileshpatra.info> - 2021-09-11 20:00 +0200
        Bug#991919: transition: r-api-bioc-3.13 Andreas Tille <andreas@an3as.eu> - 2021-09-12 08:30 +0200

#1070374 — Bug#991919: transition: r-api-bioc-3.13

Hi,

I'd like to give a short status update here.
I have uploaded several r-bioc-* packages.  Currently I'm facing two
blockers

  * libhdf5-dev needs an update which can be expected soon[1]
    thanks to Gilles Filippini
  + r-bioc-rtracklayer needs r-bioc-biocio and r-cran-restfulr
    which are both in new.  I've pinged #debian-ftp on IRC about
    this

Most (probably all) packages listed in the transition tracker
are affected.  I added the actual issue to d/changelog of those
packages I touched.

I'll be unable to do anything about this from 11.-13. September.

Kind regards

       Andreas.


[1] https://lists.debian.org/debian-r/2021/09/msg00037.html

-- 
http://fam-tille.de

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#1070729

Hi,

the blockers mentioned below are done now.  Those who have some
spare time might like to continue with the transition.  I will
not contribute relevant things until Tuesday.

There is one thing I would love to be solved soon:  I just cheated
with the test suite of biomformat in this patch:

   https://salsa.debian.org/r-pkg-team/r-bioc-biomformat/-/blob/master/debian/patches/fixme_disable_test_for_the_moment.patch

I would love if somebody could find a fix - may be by discussing
with upstream.

Kind regards

        Andreas.

On Wed, Sep 08, 2021 at 04:15:28PM +0200, Andreas Tille wrote:
> Hi,
> 
> I'd like to give a short status update here.
> I have uploaded several r-bioc-* packages.  Currently I'm facing two
> blockers
> 
>   * libhdf5-dev needs an update which can be expected soon[1]
>     thanks to Gilles Filippini
>   + r-bioc-rtracklayer needs r-bioc-biocio and r-cran-restfulr
>     which are both in new.  I've pinged #debian-ftp on IRC about
>     this
> 
> Most (probably all) packages listed in the transition tracker
> are affected.  I added the actual issue to d/changelog of those
> packages I touched.
> 
> I'll be unable to do anything about this from 11.-13. September.
> 
> Kind regards
> 
>        Andreas.
> 
> 
> [1] https://lists.debian.org/debian-r/2021/09/msg00037.html
> 
> -- 
> http://fam-tille.de
> 
> 

-- 
http://fam-tille.de

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#1070795

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On 9/11/21 12:27 PM, Andreas Tille wrote:
> Hi,
> 
> the blockers mentioned below are done now.  Those who have some
> spare time might like to continue with the transition.  I will
> not contribute relevant things until Tuesday.

I did few uploads to get the transition moving forward. Current blocker is
for r-bioc-biocsingular which needs r-bioc-scaledmatrix and the latter is still in NEW.
For scaledmatrix, I've asked already on the #-ftp IRC as well, hopefully it gets proc soon.

This is blocking a few packages, but I'm in the process of uploading the rest which are not directly uploaded.
Will upload a few packages tomorrow as well.

> There is one thing I would love to be solved soon:  I just cheated
> with the test suite of biomformat in this patch:
> 
>    https://salsa.debian.org/r-pkg-team/r-bioc-biomformat/-/blob/master/debian/patches/fixme_disable_test_for_the_moment.patch

Looking at the error, and also at the calls for those, they are called with `suppressWarnings(read_biom(min_sparse_hdf5))`
So probably the file was not good already, since it explicitly tries to suppress warnings.
_*Maybe*_ in this release, there were a few changes that rendered the file unusable to for analysis.
To me, it does not appear high priority.

> I would love if somebody could find a fix - may be by discussing
> with upstream.

No time, sorry :)

Cheers,

-- 
Nilesh Patra

Debian Developer, Uploading
  ⢀⣴⠾⠻⢶⣦⠀
  ⣾⠁⢠⠒⠀⣿⡁  
  ⢿⡄⠘⠷⠚⠋   nilesh@debian.org / nileshpatra.info / tchncs.de
  ⠈⠳⣄

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#1070852

Hi Nilesh,

On Sat, Sep 11, 2021 at 11:24:44PM +0530, Nilesh Patra wrote:
> 
> I did few uploads to get the transition moving forward. Current blocker is
> for r-bioc-biocsingular which needs r-bioc-scaledmatrix and the latter is still in NEW.
> For scaledmatrix, I've asked already on the #-ftp IRC as well, hopefully it gets proc soon.
> 
> This is blocking a few packages, but I'm in the process of uploading the rest which are not directly uploaded.
> Will upload a few packages tomorrow as well.

Before going offline again I quickly uploaded r-bioc-biocsingular
so this can keep on moving now.
 
> > There is one thing I would love to be solved soon:  I just cheated
> > with the test suite of biomformat in this patch:
> > 
> >    https://salsa.debian.org/r-pkg-team/r-bioc-biomformat/-/blob/master/debian/patches/fixme_disable_test_for_the_moment.patch
> 
> Looking at the error, and also at the calls for those, they are called with `suppressWarnings(read_biom(min_sparse_hdf5))`
> So probably the file was not good already, since it explicitly tries to suppress warnings.
> _*Maybe*_ in this release, there were a few changes that rendered the file unusable to for analysis.
> To me, it does not appear high priority.

I would love to see that settled anyway since it looks suspicious to me.
 
> > I would love if somebody could find a fix - may be by discussing
> > with upstream.
> 
> No time, sorry :)

It would be really cool if someone could take this task. 

Kind regards

       Andreas.


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