Bug#868558: nmu: multiple r-* packages
Dear release team,
On 16 July 2017 at 10:40, Dirk Eddelbuettel wrote:
|
| 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.
Any comment or update from your end on this bug report? The r-base package
is still blocked from migration to testing because of #861333, and this will
address this.
Cheers, Dirk
|
| Cheers, Dirk
|
| --
| http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org
Reply to: