• Planning to remove team-based R packages from 32-bit and big-endian arc

    From Charles Plessy@21:1/5 to All on Wed Apr 16 16:10:01 2025
    Hi all,

    let's be realistic, the r-cran-* packages team-maintained by me and
    others are not in a good shape. And given their complex net of cross-dependencies, there is the risk of removing a large number of them
    from Trixie before the release.

    When I check the UDD maintainer dasboard to set my priorities, I am
    distracted by issues related to the i386 and s390x platforms. For the
    first, I am not convinced that we have users that need us to ship
    r-cran-* packages in Trixie. For s390x, well, the popcon score is just
    10…

    I do not believe that we will be able to fix everything on time, and I
    want to move the less important issues out of the way. We have a script (routine-update) that clones the source package repo from Salsa, updates debian/control, builds the package, prepares a source-only upload and a
    command to push the changes to Salsa. It has a --64 option that injects architecture-is-64-bit in the build depends and I will add a
    --little-endian one that will inject architecture-is-little-endian.

    After uploading the changes, I will then ask the FTP team to remove the team-maintained r-cran-* packages and all their reverse-dependencies
    from the excluded architectures. I have added a DD list that tries to
    predict the potentially affected packages. Please note that there are
    false positives, as I generated it with dak rm -Rn r-base for
    simplicity, but I am not proposing to touch r-base or the r-cran
    packages managed by Dirk. The vast majority of the affected
    dependencies are maintained by the Debian Med and Debian Science lists,
    which I have CCed.

    If you need one of the team-maintained r-cran-* packages on a 32-bit or
    on a big endian architectures, which are not supported upstream, please
    contact me on the debian-r list and let's see how we can share the
    workload. Otherwise I will start the process next week, assuming silent approval. The alternative is to lose a lot of r-cran-* packages from
    amd64 as well.

    Have a nice day,

    Charles

    --
    Charles Plessy Nagahama, Yomitan, Okinawa, Japan
    Debian Med packaging team http://www.debian.org/devel/debian-med Tooting from work, https://fediscience.org/@charles_plessy Tooting from home, https://framapiaf.org/@charles_plessy

    Alba Crespi <crespialba+debian@gmail.com>
    r-cran-data.table (U)
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    r-cran-rngtools (U)

    Andreas Tille <tille@debian.org>
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    r-cran-plogr (U)
    r-cran-plot3d (U)
    r-cran-plotly (U)
    r-cran-plotmo (U)
    r-cran-plotrix (U)
    r-cran-pls (U)
    r-cran-plumber (U)
    r-cran-plyr (U)
    r-cran-png (U)
    r-cran-polyclip (U)
    r-cran-polycor (U)
    r-cran-polycub (U)
    r-cran-polynom (U)
    r-cran-poorman (U)
    r-cran-popepi (U)
    r-cran-posterior (U)
    r-cran-postlogic (U)
    r-cran-powerlaw (U)
    r-cran-prabclus (U)
    r-cran-pracma (U)
    r-cran-praise (U)
    r-cran-prediction (U)
    r-cran-prettycode (U)
    r-cran-prettyunits (U)
    r-cran-prevalence (U)
    r-cran-princurve (U)
    r-cran-processx (U)
    r-cran-prodlim (U)
    r-cran-profilemodel (U)
    r-cran-profvis (U)
    r-cran-progress (U)
    r-cran-progressr (U)
    r-cran-projpred (U)
    r-cran-promises (U)
    r-cran-prophet (U)
    r-cran-proto (U)
    r-cran-proxy (U)
    r-cran-ps (U)
    r-cran-psy (U)
    r-cran-psych (U)
    r-cran-psychometric (U)
    r-cran-psychotools (U)
    r-cran-psychotree (U)
    r-cran-psychtools (U)
    r-cran-psyphy (U)
    r-cran-publish (U)
    r-cran-purrr (U)
    r-cran-purrrlyr (U)
    r-cran-pvclust (U)
    r-cran-pwr (U)
    r-cran-qap (U)
    r-cran-qgraph (U)
    r-cran-qlcmatrix (U)
    r-cran-qpdf (U)
    r-cran-qqconf (U)
    r-cran-qtl (U)
    r-cran-quickjsr (U)
    r-cran-qvcalc (U)
    r-cran-r.methodss3 (U)
    r-cran-r.oo (U)
    r-cran-r.utils (U)
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    r-cran-rcdk (U)
    r-cran-rcdklibs (U)
    r-cran-rcppannoy (U)
    r-cran-rcppml (U)
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    r-cran-restfulr (U)
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    r-cran-rhpcblasctl (U)
    r-cran-riskregression (U)
    r-cran-ritis (U)
    r-cran-rlang (U)
    r-cran-rle (U)
    r-cran-rlist (U)
    r-cran-rlrsim (U)
    r-cran-rlumshiny (U)
    r-cran-rmarkdown (U)
    r-cran-rmutil (U)
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    r-cran-sampling (U)
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    r-cran-sf (U)
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    r-cran-shape (U)
    r-cran-shiny (U)
    r-cran-shinybs (U)
    r-cran-shinycssloaders (U)
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    r-cran-testit (U)
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    r-cran-threejs (U)
    r-cran-tibble (U)
    r-cran-tidygraph (U)
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    r-cran-tidytext (U)
    r-cran-tikzdevice (U)
    r-cran-timereg (U)
    r-cran-tinytex (U)
    r-cran-tm (U)
    r-cran-tmb (U)
    r-cran-tmvtnorm (U)
    r-cran-tokenizers (U)
    r-cran-transformr (U)
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    r-cran-triebeard (U)
    r-cran-trimcluster (U)
    r-cran-truncnorm (U)
    r-cran-tsp (U)
    r-cran-tweenr (U)
    r-cran-ucminf (U)
    r-cran-udunits2 (U)
    r-cran-unbalanced (U)
    r-cran-unitizer (U)
    r-cran-units (U)
    r-cran-urlchecker (U)
    r-cran-urltools (U)
    r-cran-uroot (U)
    r-cran-utf8 (U)
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    r-cran-vegan (U)
    r-cran-vim (U)
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    r-cran-wavethresh (U)
    r-cran-webfakes (U)
    r-cran-webmockr (U)
    r-cran-webshot (U)
    r-cran-webutils (U)
    r-cran-whatif (U)
    r-cran-whisker (U)
    r-cran-whoami (U)
    r-cran-wikidataqueryservicer (U)
    r-cran-wikidatar (U)
    r-cran-wikipedir (U)
    r-cran-wikitaxa (U)
    r-cran-withr (U)
    r-cran-wk (U)
    r-cran-wkutils (U)
    r-cran-wordcloud (U)
    r-cran-worrms (U)
    r-cran-xfun (U)
    r-cran-xml2 (U)
    r-cran-xslt (U)
    r-cran-xts (U)
    r-cran-yulab.utils (U)
    r-cran-zeallot (U)
    r-other-amsmercury (U)
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    r-other-chbutils (U)
    r-other-curvefdp (U)
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    r-other-wasabi (U)
    r-other-x4r (U)
    ray (U)
    rsem (U)
    surankco (U)
    transdecoder (U)

    Andrius Merkys <merkys@debian.org>
    r-cran-cyclocomp (U)
    r-cran-lintr (U)
    r-cran-rlinsolve (U)
    r-cran-xmlparsedata (U)

    Anton Gladky <gladk@debian.org>
    vtk9 (U)

    Antoni Villalonga <antoni@friki.cat>
    vt (U)

    Aurélien COUDERC <coucouf@debian.org>
    cantor (U)

    Benjamin Eikel <debian@eikel.org>
    r-cran-ggplot2 (U)
    r-cran-munsell (U)
    r-cran-scales (U)

    Carlos Borroto <carlos.borroto@gmail.com>
    r-cran-plyr (U)

    Charles Plessy <plessy@debian.org>
    picard-tools (U)
    r-bioc-genomeinfodb (U)
    r-bioc-genomeinfodbdata (U)
    r-bioc-genomicalignments (U)
    r-bioc-hdf5array (U)
    r-bioc-iranges (U)
    r-bioc-matrixgenerics (U)
    r-bioc-rtracklayer (U)
    r-bioc-s4arrays (U)
    r-bioc-s4vectors (U)
    r-bioc-summarizedexperiment (U)
    r-bioc-xvector (U)
    r-bioc-zlibbioc (U)
    r-cran-biocmanager (U)
    r-cran-cftime (U)
    r-cran-epitools (U)
    r-cran-genetics (U)
    r-cran-spacefillr (U)
    r-cran-sparsevctrs (U)
    r-cran-spatstat.univar (U)

    Chris Lamb <lamby@debian.org>
    diffoscope (U)

    Chris Lawrence <lawrencc@debian.org>
    r-cran-aer (U)
    r-cran-amelia (U)
    r-cran-bayesm (U)
    r-cran-coda (U)
    r-cran-gam (U)
    r-cran-geepack (U)
    r-cran-gmaps (U)
    r-cran-jsonlite (U)
    r-cran-mapdata (U)
    r-cran-mapproj (U)
    r-cran-maps (U)
    r-cran-matchit (U)
    r-cran-mcmc (U)
    r-cran-mcmcpack (U)
    r-cran-mnp (U)
    r-cran-pscl (U)
    r-cran-psy (U)
    r-cran-rjags (U)
    r-cran-vgam (U)
    r-cran-zelig (U)

    Christoph Berg <myon@debian.org>
    plr (U)

    Christopher Hoskin <christopher.hoskin@gmail.com>
    r-bioc-rbgl (U)

    Debian Emacsen team <debian-emacsen@lists.debian.org>
    ess

    Debian KDE Extras Team <pkg-kde-extras@lists.alioth.debian.org>
    rkward

    Debian Math Team <team+math@tracker.debian.org>
    macaulay2
    sagemath

    Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
    assemblytics
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    roary
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    transdecoder
    trinityrnaseq
    vt

    Debian Perl Group <pkg-perl-maintainers@lists.alioth.debian.org>
    libstatistics-r-perl

    Debian PostgreSQL Maintainers <team+postgresql@tracker.debian.org>
    plr

    Debian Python Team <team+python@tracker.debian.org>
    jupyter-kernel-test

    Debian Qt/KDE Maintainers <debian-qt-kde@lists.debian.org>
    cantor

    Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
    dh-r
    r-bioc-affxparser
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    r-bioc-genomeinfodbdata
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    r-bioc-qtlizer
    r-bioc-qusage
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    r-bioc-rgsepd
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    r-bioc-rhdf5lib
    r-bioc-rhtslib
    r-bioc-rots
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    r-bioc-tcgabiolinks
    r-bioc-tcgabiolinksgui.data
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    r-bioc-titancna
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    r-bioc-tximportdata
    r-bioc-ucsc.utils
    r-bioc-variantannotation
    r-bioc-wrench
    r-bioc-xvector
    r-bioc-zlibbioc
    r-cran-actuar
    r-cran-ade4
    r-cran-adegenet
    r-cran-adegraphics
    r-cran-adephylo
    r-cran-admisc
    r-cran-aer
    r-cran-afex
    r-cran-airr
    r-cran-alakazam
    r-cran-amap
    r-cran-amelia
    r-cran-amore
    r-cran-animation
    r-cran-apcluster
    r-cran-ape
    r-cran-aplpack
    r-cran-areal
    r-cran-argparse
    r-cran-argparser
    r-cran-arm
    r-cran-arsenal
    r-cran-askpass
    r-cran-assertive.base
    r-cran-assertthat
    r-cran-av
    r-cran-aweek
    r-cran-backports
    r-cran-base64enc
    r-cran-base64url
    r-cran-batchjobs
    r-cran-batchtools
    r-cran-bayesfactor
    r-cran-bayesfm
    r-cran-bayesm
    r-cran-bayesplot
    r-cran-bayestestr
    r-cran-bbmisc
    r-cran-bbmle
    r-cran-bdgraph
    r-cran-bdsmatrix
    r-cran-beeswarm
    r-cran-bench
    r-cran-benchmarkme
    r-cran-benchmarkmedata
    r-cran-biasedurn
    r-cran-bibtex
    r-cran-bigmemory
    r-cran-bigmemory.sri
    r-cran-bindr
    r-cran-bindrcpp
    r-cran-bio3d
    r-cran-biocmanager
    r-cran-bios2cor
    r-cran-bit
    r-cran-bit64
    r-cran-bitops
    r-cran-biwt
    r-cran-blme
    r-cran-blob
    r-cran-blockmodeling
    r-cran-bms
    r-cran-bold
    r-cran-bookdown
    r-cran-boolnet
    r-cran-bradleyterry2
    r-cran-brew
    r-cran-brglm
    r-cran-brglm2
    r-cran-bridgesampling
    r-cran-brio
    r-cran-brms
    r-cran-brobdingnag
    r-cran-broom
    r-cran-broom.helpers
    r-cran-broom.mixed
    r-cran-bslib
    r-cran-ca
    r-cran-cachem
    r-cran-caic4
    r-cran-cairo
    r-cran-calibrate
    r-cran-calibratr
    r-cran-callr
    r-cran-cards
    r-cran-caret
    r-cran-catools
    r-cran-cba
    r-cran-cftime
    r-cran-checkmate
    r-cran-chk
    r-cran-circlize
    r-cran-circular
    r-cran-classint
    r-cran-cli
    r-cran-cliapp
    r-cran-clipr
    r-cran-clisymbols
    r-cran-clock
    r-cran-clubsandwich
    r-cran-clue
    r-cran-clustergeneration
    r-cran-cmdfun
    r-cran-cmprsk
    r-cran-cmstatr
    r-cran-coarsedatatools
    r-cran-coda
    r-cran-coin
    r-cran-collapse
    r-cran-colorspace
    r-cran-colourpicker
    r-cran-combinat
    r-cran-commonmark
    r-cran-conditionz
    r-cran-conflicted
    r-cran-contfrac
    r-cran-corpcor
    r-cran-corrplot
    r-cran-covid19us
    r-cran-covr
    r-cran-cowplot
    r-cran-cpp11
    r-cran-crayon
    r-cran-credentials
    r-cran-crosstalk
    r-cran-crul
    r-cran-ctmcd
    r-cran-cubelyr
    r-cran-curl
    r-cran-cutpointr
    r-cran-cvst
    r-cran-cyclocomp
    r-cran-d3network
    r-cran-data.table
    r-cran-datawizard
    r-cran-dbitest
    r-cran-dbplyr
    r-cran-dbscan
    r-cran-ddalpha
    r-cran-ddrtree
    r-cran-deal
    r-cran-decor
    r-cran-deldir
    r-cran-dendextend
    r-cran-dendsort
    r-cran-densityclust
    r-cran-deoptim
    r-cran-desc
    r-cran-desolve
    r-cran-devtools
    r-cran-dfoptim
    r-cran-dharma
    r-cran-diagnosismed
    r-cran-diagram
    r-cran-diagrammer
    r-cran-dials
    r-cran-dicedesign
    r-cran-dichromat
    r-cran-diffobj
    r-cran-dimred
    r-cran-diptest
    r-cran-dirmult
    r-cran-discriminer
    r-cran-distory
    r-cran-distr
    r-cran-distributional
    r-cran-docopt
    r-cran-doparallel
    r-cran-dorng
    r-cran-dosefinding
    r-cran-dotcall64
    r-cran-downlit
    r-cran-downloader
    r-cran-dplyr
    r-cran-dqrng
    r-cran-drr
    r-cran-dslabs
    r-cran-dt
    r-cran-dtplyr
    r-cran-dygraphs
    r-cran-dynamictreecut
    r-cran-dynlm
    r-cran-eaf
    r-cran-earth
    r-cran-ecosolver
    r-cran-effectsize
    r-cran-egg
    r-cran-ei
    r-cran-eipack
    r-cran-ellipse
    r-cran-elliptic
    r-cran-emayili
    r-cran-emdbook
    r-cran-emmeans
    r-cran-emoa
    r-cran-enrichwith
    r-cran-epi
    r-cran-epibasix
    r-cran-epicalc
    r-cran-epiestim
    r-cran-epir
    r-cran-epitools
    r-cran-erm
    r-cran-estimability
    r-cran-estimatr
    r-cran-etm
    r-cran-evaluate
    r-cran-evd
    r-cran-exactextractr
    r-cran-exactranktests
    r-cran-expint
    r-cran-expm
    r-cran-extradistr
    r-cran-factoextra
    r-cran-factominer
    r-cran-fadist

    [continued in next message]

    --- SoupGate-Win32 v1.05
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  • From Simon McVittie@21:1/5 to Charles Plessy on Wed Apr 16 17:20:01 2025
    On Wed, 16 Apr 2025 at 23:04:47 +0900, Charles Plessy wrote:
    If you need one of the team-maintained r-cran-* packages on a 32-bit or
    on a big endian architectures, which are not supported upstream, please >contact me on the debian-r list and let's see how we can share the
    workload.

    It might be best to re-send this to debian-arm (representing the two
    32-bit release architectures with a porter mailing list) and debian-s390 (representing the only big-endian release architecture). Possibly also debian-powerpc, although the big-endian versions of that are -ports
    anyway.

    (I don't expect that you will realistically get contributions from those architectures, but it seems polite to let them know.)

    smcv

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Paul Gevers@21:1/5 to All on Wed Apr 16 18:40:01 2025
    To: debian-r@lists.debian.org
    To: debian-med@lists.debian.org
    To: debian-science@lists.debian.org

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    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Dirk Eddelbuettel@21:1/5 to Paul Gevers on Wed Apr 16 19:00:01 2025
    On 16 April 2025 at 18:31, Paul Gevers wrote:
    | I haven't checked why they are there, but there are several packages in
    | the key package set [1]. I would be good to check beforehand what
    | happens if they are removed on those architectures. I think it's best to
    | assume for now that you can't remove them at this stage of the release.
    |
    | [1] https://udd.debian.org/cgi-bin/key_packages.yaml.cgi

    That appears to be a different set of packages. It is comprised entirely of packages that the meta package "r-recommended" depends upon. [ The R 'engine' is provided by package "r-base-core" which can run on its own, the wider package "r-base" also depends on "r-recommended" bringing these in. It is a
    set of packages commonly used with R and curatedby upstream, that is by the upstream R Core team. ] These packages are all maintained by me, and they build fine under i386 etc. So no issue there as far as I can tell.

    Cheers, Dirk

    --
    dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Paul Gevers@21:1/5 to All on Wed Apr 16 19:30:01 2025
    To: debian-r@lists.debian.org
    To: debian-med@lists.debian.org
    To: debian-science@lists.debian.org

    This is an OpenPGP/MIME signed message (RFC 4880 and 3156) --------------ymJ4OKSH988ugTKKHG5mmpjA
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    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Dirk Eddelbuettel@21:1/5 to Paul Gevers on Wed Apr 16 20:20:01 2025
    On 16 April 2025 at 19:24, Paul Gevers wrote:
    | Hi Dirk,
    |
    | On 16-04-2025 18:55, Dirk Eddelbuettel wrote:
    | > | [1] https://udd.debian.org/cgi-bin/key_packages.yaml.cgi
    | >
    | > That appears to be a different set of packages.
    |
    |
    | The packages spotted in the original list, I assume you're talking about
    | all of them except maybe cantor and vtk9?
    | boot: r-recommended depends r-cran-boot
    | cantor: kdeedu depends cantor
    | cluster: r-recommended depends r-cran-cluster
    | codetools: r-recommended depends r-cran-codetools
    | dh-r: boot build-depends dh-r
    | foreign: r-recommended depends r-cran-foreign
    | kernsmooth: r-recommended depends r-cran-kernsmooth
    | lattice: r-recommended depends r-cran-lattice
    | mgcv: r-recommended depends r-cran-mgcv
    | nlme: r-recommended depends r-cran-nlme
    | r-cran-class: r-recommended depends r-cran-class
    | r-cran-mass: r-recommended depends r-cran-mass
    | r-cran-nnet: r-recommended depends r-cran-nnet
    | r-cran-spatial: r-recommended depends r-cran-spatial
    | rmatrix: r-recommended depends r-cran-matrix
    | rpart: r-recommended depends r-cran-rpart
    | survival: r-recommended depends r-cran-survival
    | vtk9: opencv build-depends libvtk9-dev

    Corret. Also, dh-r is only needed at build-time.

    Dirk

    --
    dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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