Bug#858183: marked as done (binNMU needed for r-bioc- packages broken by R 3.3.3.)
Your message dated Wed, 22 Mar 2017 19:34:18 +0100
with message-id <20170322183415.GA24340@ugent.be>
and subject line Re: binNMU needed for r-bioc- packages broken by R 3.3.3.
has caused the Debian Bug report #858183,
regarding binNMU needed for r-bioc- packages broken by R 3.3.3.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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858183: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=858183
Debian Bug Tracking System
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--- Begin Message ---
Package: release.debian.org
Severity: grave
Hello everybody,
the update of R to version 3.3.3 unexpectedly breaks some R packages, which
need to be reinstalled from source. In Debian terms, given how we package R
packages, this can be solved by a binNMU.
A quick look at ci.debian.net shows that a large number of Bioconductor
packages (r-bioc-*) started to fail their tests at the end of February
following the upload of r-base version 3.3.2.20170227-1, which was a release
candidate of 3.3.3. Some of the failures are direct, and some may be a ripple
effect.
On Bioconductor's support forum (https://support.bioconductor.org/p/93695/#93719),
it was suggested to reinstall the packages "BiocGenerics", "S4Vectors",
"IRanges", and "GenomicRanges". I tried this on my computer (using sbuild --make-binNMU)
and their regression tests restarted to pass. These packages are very central in
Bioconductor's dependency graph.
If time remains, how about starting with these four and see if the failures in the
the other packages dissapear ?
nmu r-bioc-biocgenerics_0.20.0-1 . all . -m "Rebuild for R 3.3.3."
nmu r-bioc-s4vectors_0.12.1-2 . ANY . -m "Rebuild for R 3.3.3."
nmu r-bioc-iranges_2.8.1-1-m . ANY . "Rebuild for R 3.3.3."
nmu r-bioc-genomicranges_1.26.2-1 . ANY -m "Rebuild for R 3.3.3."
Otherwise I can prepare a more extensive list of packages to rebuild.
Cheers,
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
--- End Message ---
--- Begin Message ---
Hi,
On Sun, Mar 19, 2017 at 11:24:50PM +0900, Charles Plessy wrote:
> the update of R to version 3.3.3 unexpectedly breaks some R packages, which
> need to be reinstalled from source. In Debian terms, given how we package R
> packages, this can be solved by a binNMU.
>
> A quick look at ci.debian.net shows that a large number of Bioconductor
> packages (r-bioc-*) started to fail their tests at the end of February
> following the upload of r-base version 3.3.2.20170227-1, which was a release
> candidate of 3.3.3. Some of the failures are direct, and some may be a ripple
> effect.
>
> On Bioconductor's support forum (https://support.bioconductor.org/p/93695/#93719),
> it was suggested to reinstall the packages "BiocGenerics", "S4Vectors",
> "IRanges", and "GenomicRanges". I tried this on my computer (using sbuild --make-binNMU)
> and their regression tests restarted to pass. These packages are very central in
> Bioconductor's dependency graph.
>
> If time remains, how about starting with these four and see if the failures in the
> the other packages dissapear ?
>
> nmu r-bioc-biocgenerics_0.20.0-1 . all . -m "Rebuild for R 3.3.3."
Arch all package cannot be binNMUed.
> nmu r-bioc-s4vectors_0.12.1-2 . ANY . -m "Rebuild for R 3.3.3."
> nmu r-bioc-iranges_2.8.1-1-m . ANY . "Rebuild for R 3.3.3."
> nmu r-bioc-genomicranges_1.26.2-1 . ANY -m "Rebuild for R 3.3.3."
Scheduled.
> Otherwise I can prepare a more extensive list of packages to rebuild.
Cheers,
Ivo
--- End Message ---
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