R devel - Sep 2022 - Should package version requirements assume installation from sources?

[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

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

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 at 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
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

On 13/09/2022 5:45 p.m., 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.
This sounds like a bug or bad design in the S4 system, i.e. caching 
things without a way to detect or update when the cache becomes stale.

Is it really necessary to cache things as part of the binary package, or 
could they be put in place when needed using lazy loading, getting a 
copy from the loaded copy of Matrix?

Duncan Murdoch