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Bug#868558: marked as done (nmu: multiple r-* packages)

Your message dated Sat, 9 Sep 2017 15:38:01 +0200
with message-id <20170909133801.m6pwpdteiex6gjsl@an3as.eu>
and subject line All affected packages are manually uloaded
has caused the Debian Bug report #868558,
regarding nmu: multiple r-* packages
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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-- 
868558: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=868558
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: release.debian.org
User: release.debian.org@packages.debian.org
Usertags: binnmu
Severity: normal

R 3.4.0, which was released in April, made one subtle breaking change
affecting how (optional) compiled code in contributed package is loaded,
affecting the older two of the three (plus one internal) available
mechanisms:  .C() and .Fortran().  Packages still load and run parts of
their code, they just can no longer access this compiled code---unless
rebuilt. 

This has been discussed in #86133 at https://bugs.debian.org/861333

I have now prepared a fine-grained set of packages requiring a NMU, narrowing
the actual set of required rebuilds down from an unconditional 514 packages
(all reverse depends of r-base-core) to 92 packages meeting all requirements.

  nmu r-bioc-makecdfenv_1.50.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-multtest_2.30.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-edger_3.14.0+dfsg-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-boolnet_2.1.3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-tikzdevice_0.10-1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-logspline_2.1.9-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-genabel_1.8-0-1+b1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-lhs_0.14-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-limma_3.30.8+dfsg-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-coin_1.1-3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-other-iwrlars_0.9-5-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-mnp_2.6-4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-msm_1.6.4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-fields_8.10-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-desolve_1.14-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-adephylo_1.1-10-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-dosefinding_0.9-15-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-deldir_0.1-12-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-rniftilib_0.0-35.r79-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-data.table_1.10.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-qtl_1.40-8-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-preprocesscore_1.36.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-contfrac_1.1-10-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-glmnet_2.0-5-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-bitops_1.0-6-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-sp_1:1.2-4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-spc_1:0.5.3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-snpstats_1.24.0+dfsg-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-tgp_2.4-14-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-brglm_0.5-9-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-cmprsk_2.2-7-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-affy_1.52.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-ncdf4_1.15-1+b2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-treescape_1.10.18-6 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-rbgl_1.50.0+dfsg1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-rtracklayer_1.34.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-hexbin_1.27.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-princurve_1.1-12-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-mapproj_1.2-4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-blockmodeling_0.1.8-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-hdf5_1.6.10-4+b1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-pscl_1.4.9-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-ade4_1.7-5-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-vgam_1.0-3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-adegenet_2.0.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-mixtools_1.0.4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-phylobase_0.8.2-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-amelia_1.7.4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-spam_1.4-0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-medadherence_1.03-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-biobase_2.34.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-surveillance_1.13.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-randomfieldsutils_0.3.15-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-deal_1:1.2-37-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-hilbertvis_1.32.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-rcurl_1.95-4.8-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-other-mott-happy.hbrem_2.4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-mcmcpack_1.3-8-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-spatstat_1.48-0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-vegan_2.4-2-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-haplo.stats_1.7.7-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-bayesm_3.0-2-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-expm_0.999-0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-dnacopy_1.48.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-phangorn_2.1.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-maptools_1:0.8-41+dfsg-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-mlbench_2.1-1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-affyio_1.44.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-graph_1.52.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-polycub_0.5-2-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-deseq2_1.14.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-pbivnorm_0.6.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-caret_6.0-73+dfsg1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-biovizbase_1.22.0-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-nnls_1.4-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-goftest_1.0-3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-igraph_1.0.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-maps_3.1.1-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-eco_3.1-7-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-catools_1.17.1-1+b1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-randomfields_3.1.36-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-erm_0.15-7-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-etm_0.6-2-3 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-randomforest_4.6-12-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-evd_2.3-2-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-raschsampler_0.8-8-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-bioc-genefilter_1.56.0-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-mcmc_0.9-4-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-spdep_0.6-9-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-gam_1.14-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-other-amsmercury_1.3.0-2 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
  nmu r-cran-gsl_1.9-10.3-1 . ANY . -m 'Rebuild against R 3.4.*, see #861333'
   
I have provided extensive details of how I derived this set in this vignette:
  
  http://eddelbuettel.github.io/rcppapt/binnmuAfterR340.html

Its code is part of the (still somewhat unpolished but fully working for a
subset of apt's functionality) package RcppAPT at

  https://github.com/eddelbuettel/rcppapt

The package interfaces `libapt-pkg`; the package sources also contain the
vignette source and should allow anyone to replicate the analysis (modulo the
one step where I take advantage of having access to fully expanded CRAN
mirror to grep through a subset of packages, see the write-up for more).

I hope the write-up in the vignette provides sufficient detail.

If you have questions please to not hesitate to contact me directly, or
follow-up at either this ticket, or the r-base-core ticket #86133, or on the
r-sig-debian mailing list.

Many thanks in advance for your help with this.

Cheers, Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

--- End Message ---
--- Begin Message --- 
Hi,

I hereby closing this bug since all affected packages were
manually uploaded.

Kind regards and thanks for your work as release team

    Andreas.

-- 
http://fam-tille.de

--- End Message ---
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