From hp@ge@@on@g|thub @end|ng |rom gm@||@com  Wed Sep 14 01:11:54 2022
From: hp@ge@@on@g|thub @end|ng |rom gm@||@com (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Tue, 13 Sep 2022 16:11:54 -0700
Subject: [Rd] 
 Should package version requirements assume installation from
 sources?
In-Reply-To: <b3e53fa9-b0e0-a8c8-147a-c1c56348f3e9@gmail.com>
References: <b3e53fa9-b0e0-a8c8-147a-c1c56348f3e9@gmail.com>
Message-ID: <07ec1390-3e67-82cf-09b4-6668db099c31@gmail.com>

FWIW this happens all the time in Bioconductor, where S4 is used very 
intensively, when we make that kind of change to a core infrastructure 
package. Then a bunch of Windows and Mac binary packages need to be 
rebuilt because they contain cached stuff that is now out-of-sync with 
the new state of affairs. The way we deal with this is by bumping the 
version numbers of all the affected packages. This triggers automatic 
rebuilt and propagation of the new binaries.

Note that these problems also affect packages that were already 
installed on the user machines _prior_ to the changes to the upstream 
package. Because the caching we are talking about is actually in the 
package installation folder (and the fact that it ends up in the 
binaries is just a consequence of that). So even on a system where 
packages are installed from source, the affected packages need to be 
reinstalled. Bumping the version numbers of all the affected packages 
also solves that.

I don't see how this could be handled or mitigated via package requirements.

Best,

H.


On 13/09/2022 14:45, Mikael Jagan 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com



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