[R-pkg-team] Bug#994286: r-bioc-destiny: Orphaned upstream, marked for removal in next BioConductor release

[Andreas Tille]

Package: r-bioc-destiny
Severity: critical
Justification: breaks unrelated software
X-Debbugs-Cc: 991919 at bugs.debian.org, debian-r at lists.debian.org

Hi,

as it was discussed on the debian-r mailing list[1] r-bioc-destiny
should not block the BioConductor transition.  The relevant statement
from upstream is:

  On Tue, Sep 14, 2021 at 7:28 AM Kern, Lori <Lori.Shepherd at roswellpark.org> wrote:

  Destiny is currently marked as deprecated and scheduled to be
  removed in the next Bioconductor release as the maintainers were
  unresponsive to our requests to fix their package.  The package is
  failing in both release and devel version of Bioconductor and we tried
  numerous times to reach the maintainer. If you know the maintainer we
  encourage you to reach out to them to fix the package.  

  Lori Shepherd
  Bioconductor Core Team

This bug should remove r-bioc-destiny from testing to enable the
transition of all other r-bioc-* packages.

Kind regards

    Andreas.

[1] https://lists.debian.org/debian-r/2021/09/msg00065.html
    https://lists.debian.org/debian-r/2021/09/msg00067.html

-- System Information:
Debian Release: 11.0
  APT prefers testing
  APT policy: (501, 'testing'), (50, 'buildd-unstable'), (50, 'unstable'), (5, 'experimental'), (1, 'buildd-experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 5.10.0-8-amd64 (SMP w/4 CPU threads)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE=de_DE:de
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages r-bioc-destiny depends on:
ii  libc6                        2.31-13
ii  libgcc-s1                    10.2.1-6
ii  libstdc++6                   10.2.1-6
pn  r-api-bioc-3.12              <none>
ii  r-base-core [r-api-4.0]      4.1.1-2
pn  r-bioc-biobase               <none>
pn  r-bioc-biocgenerics          <none>
pn  r-bioc-pcamethods            <none>
pn  r-bioc-singlecellexperiment  <none>
pn  r-bioc-summarizedexperiment  <none>
pn  r-cran-ggplot.multistats     <none>
ii  r-cran-ggplot2               3.3.3+dfsg-1
pn  r-cran-ggthemes              <none>
pn  r-cran-irlba                 <none>
pn  r-cran-knn.covertree         <none>
ii  r-cran-matrix                1.3-2-1
pn  r-cran-proxy                 <none>
ii  r-cran-rcpp                  1.0.6-1
pn  r-cran-rcppeigen             <none>
pn  r-cran-rcpphnsw              <none>
pn  r-cran-rspectra              <none>
ii  r-cran-scales                1.1.1-1
pn  r-cran-scatterplot3d         <none>
pn  r-cran-smoother              <none>
ii  r-cran-tidyr                 1.1.2-1
ii  r-cran-tidyselect            1.1.0+dfsg-1
pn  r-cran-vim                   <none>

Versions of packages r-bioc-destiny recommends:
ii  r-cran-testthat  3.0.1-1

Versions of packages r-bioc-destiny suggests:
ii  r-cran-fnn     1.1.3-2
pn  r-cran-igraph  <none>