Groups > linux.debian.bugs.dist > #1070852

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

From	Andreas Tille <andreas@an3as.eu>
Newsgroups	linux.debian.bugs.dist, linux.debian.devel.release
Subject	Bug#991919: transition: r-api-bioc-3.13
Date	2021-09-12 08:30 +0200
Message-ID	<CWra1-4VS-1@gated-at.bofh.it> (permalink)
References	(1 earlier) <CV6AG-38S-3@gated-at.bofh.it> <CW5jb-7YH-5@gated-at.bofh.it> <CWfsd-5DX-3@gated-at.bofh.it> <CILii-3Fz-3@gated-at.bofh.it> <CWfsd-5DX-3@gated-at.bofh.it>
Organization	linux.* mail to news gateway

Cross-posted to 2 groups.

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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.


-- 
http://fam-tille.de

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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

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