Package: release.debian.org User: release.debian....@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 | e...@debian.org
