On 23 March 2024 at 07:25, Dirk Eddelbuettel wrote: | | On 22 March 2024 at 11:12, Dirk Eddelbuettel wrote: | | | | On 27 February 2024 at 19:01, Dirk Eddelbuettel wrote: | | | A couple of days ago, the (effective) Maintainer and rather active developer | | | of the Matrix package Mikael Jagan (CC'ed) posted on the r-package-devel list | | | (the primary list for R package development) that the upcoming change of | | | Matrix 1.7-0, planned for March 11, will be _very midly disruptive_ but only | | | to the very small subset of Matrix dependents that _actually use its | | | headers_. See the full mail at [1]. The gory detail is that Matrix embeds and | | | uses an advanced sparse matrix library (called SuiteSparse) which it updates, | | | and the change in headers affects those (and only those!) who compile against | | | these headers. | | | | | | Now, Matrix currently has 1333 packages at CRAN using it [2]. But he lists 15 | | | (fifteen) of possibly breaking because these are the packages having a | | | 'LinkingTo: Matrix' [3]. That 1.113 per cent. | | | | | | It is similar for us. Running a simple `apt-cache rdepends r-cran-matrix | wc -l` | | | gets us 145 lines (including headers and meta packages). Call it 140 that a | | | transition would cover. | | | | | | But among the 15 affected only five are in Debian: | | | | | | irlba r-cran-irlba | | | lme4 r-cran-lme4 | | | OpenMx r-cran-openmx | | | TMP r-cran-tmp | | | bcSeq r-bioc-bcseq | | | | | | One of these is mine (lme4), I can easily produce a sequenced update. I | | | suggested we deal with the other _four packages_ by standard bug reports and | | | NMUs as needed instead of forcing likely 140 packages through a transition. | | | | | | Note that is in fact truly different from the past two hickups with Matrix | | | transition which happened at the R-only level of caching elements of its OO | | | resolution and whatnot hence affecting more package. This time it really is | | | compilation, and packages NOT touching the SuiteSparse headers (ie roughly | | | 135 or so of the 140 Debian packages using Matrix) will not be affected. | | | | | | That said, I of course defer to the release team. If the feeling is 'eff | | | this, transition it is' that is what we do. Whether I think is overkill or | | | not is moot. | | | | | | Feel free to CC me as I am not longer a regular on debian-devel. | | | | The new Matrix release is now on CRAN so I plan to proceed as outlined with a | | first upload experimental, likely later today or this evening (my timezone). | | My bad. That was another release in the 1.6-* series, namely 1.6-5. No | special action needed. 1.7-0 is still pending.
Gaaa. Wrong *again*. 1.7-0 *was* released (see my CRANberries log [1]) but has since been withdrawn (!!) at CRAN. We continue to monitor. Dirk [1] https://dirk.eddelbuettel.com/cranberries/2024/03/22/#Matrix_1.7-0 | Dirk | | | Dirk | | | | | | | | Cheers, Dirk | | | | | | | | | [1] https://stat.ethz.ch/pipermail/r-package-devel/2024q1/010463.html | | | [2] In R: | | | > db <- tools::CRAN_package_db() | | | > matrixrevdep <- tools::package_dependencies("Matrix", reverse=TRUE, db=db)[[1]] | | | > length(matrixrevdep) # the vector 'matrixrevdep' list all | | | [1] 1333 | | | > | | | [3] LinkingTo:, despite its name, is the directive to include the package C | | | headers in the compilation. The 'db' object above allows to us to subset | | | which of the 1333 packages using Matrix also have a LinkingTo | | | | | | | | | -- | | | dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | | | | -- | | dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | | -- | dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
