From j@g@nmn2 @end|ng |rom gm@||@com  Tue Sep 13 23:45:13 2022
From: j@g@nmn2 @end|ng |rom gm@||@com (Mikael Jagan)
Date: Tue, 13 Sep 2022 17:45:13 -0400
Subject: [Rd] Should package version requirements assume installation from
 sources?
Message-ID: <b3e53fa9-b0e0-a8c8-147a-c1c56348f3e9@gmail.com>

[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



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