[Rd] Should package version requirements assume installation from sources?

[Simon Urbanek]

Mikael,

first about the macOS part of the issue: the first step is that you can tell me and I can trigger a full re-build. For performance reasons the macOS build system does not do full reverse builds, because they take too long as small updates in popular packages can trigger large portions of CRAN needing a re-build - in most cases with no benefit.

Now, that still only addresses one part where the users can upgrade to re-built versions __if they are aware__. However, they would have to know and do it explicitly, because a regular update.packages() would not re-install such reverse-dependent packages since their version has not changed. Therefore I would strongly suggest making sure that updates are backward-compatible, because there is simply no way around that problem as users have no way of knowing that an upgrade of Matrix requires re-installation of many other packages. In fact for Matrix I would argue that such breaking changes should only be allowed with major R release since at that point all packages have to be reinstalled by definition anyway.  So to answer your second part of the question: until next major (=annual) release.

Note that this problem can exist in both directions - even if you upgrade Matrix, if a dependent package is build against newer Matrix __but does not require the newer version__ then the user doesn't know that the installed version is incompatible, so you have to guard in both directions.

Cheers,
Simon


> On 14/09/2022, at 9:45 AM, Mikael Jagan <jaganmn2 using gmail.com> wrote:
> 
> [Arguably also appropriate for R-package-devel, but posted to R-devel
>    as the discussion is aimed primarily at "experts" ... ]
> 
> We, the authors of Matrix, have encountered a somewhat subtle issue
> induced by caching of S4 classes and methods in package namespaces.
> 
> The namespaces of three reverse dependent packages (SeuratObject, conText,
> mcmcsae) cache the formal definition of our virtual class Matrix (and some
> subclasses).  For example:
> 
> > ns <- asNamespace("SeuratObject")
> > grep("^[.]__C__.*Matrix$", names(ns), value = TRUE)
> [1] ".__C__dMatrix"       ".__C__compMatrix"    ".__C__AnyMatrix"
> [4] ".__C__generalMatrix" ".__C__CsparseMatrix" ".__C__sparseMatrix"
> [7] ".__C__dsparseMatrix" ".__C__Matrix"
> 
> The cached definition (which includes a _validity method_) is obtained from
> the version of Matrix available when the reverse dependent package was built
> from sources.  For example, if SeuratObject was built under Matrix 1.4-1,
> then we get:
> 
> > getValidity(ns$.__C__Matrix)
> function (object)
> {
>    if (!isTRUE(r <- .Call(Dim_validate, object, "Matrix")))
>        r
>    else .Call(dimNames_validate, object)
> }
> <bytecode: 0x11e7ca508>
> <environment: namespace:Matrix>
> 
> whereas if SeuratObject was built under Matrix >= 1.5-0, then we get:
> 
> > getValidity(ns$.__C__Matrix)
> function (object)
> .Call(Matrix_validate, object)
> <bytecode: 0x107dc1698>
> <environment: namespace:Matrix>
> 
> There are two "questions" here:
> 
> 1.  The symbol 'Matrix_validate' is not defined until Matrix 1.5-0.
>    Is it necessary, for this reason alone, for SeuratObject to have
>    'Imports: Matrix (>= 1.5-0)'?  Or can SeuratObject continue using
>    'Imports: Matrix (>= 1.3-3)', at the risk of errors like
> 
>    > Error: object 'Matrix_validate' not found
> 
>    (as already seen here: https://stackoverflow.com/questions/73700130)?
> 
>    Note that this error would not occur for anyone installing SeuratObject
>    from sources, unless they decide to _downgrade_ Matrix after doing so.
>    Hence this primarily concerns Windows and macOS where R users would
>    typically install a binary built by CRAN (i.e., not on their system).
> 
>    We are aware that package TMB tests in .onLoad() that the current Matrix
>    version is equal to or greater than the version available at build time,
>    thus avoiding a "strict" version requirement, but do not want this practice
>    to spread ...
> 
> 2.  For how long should Matrix retain the superceded 'Dim_validate' and
>    'dimNames_validate', in order to ensure that "stale" cached validity
>    methods continue to work?
> 
> We hope that this discussion will highlight the potential ramifications
> of importing classes and methods from other packages, and having one's
> classes and methods imported _by_ other packages, especially for version
> requirements.
> 
> Mikael, Martin, and Doug
> 
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