[R-pkg-team] Bug#1002525: r-cran-tmb: autopkgtest needs update for new version of rmatrix: Package version inconsistency detected.

[Dirk Eddelbuettel]

On 23 December 2021 at 20:03, Paul Gevers wrote:
| Source: r-cran-tmb
| Version: 1.7.22-1
| Severity: serious
| X-Debbugs-CC: debian-ci at lists.debian.org, rmatrix at packages.debian.org
| Tags: sid bookworm
| User: debian-ci at lists.debian.org
| Usertags: needs-update
| Control: affects -1 src:rmatrix
| 
| Dear maintainer(s),
| 
| With a recent upload of rmatrix the autopkgtest of r-cran-tmb fails in 
| testing when that autopkgtest is run with the binary packages of rmatrix 
| from unstable. It passes when run with only packages from testing. In 
| tabular form:
| 
|                         pass            fail
| rmatrix                from testing    1.4-0-1
| r-cran-tmb             from testing    1.7.22-1
| all others             from testing    from testing
| 
| I copied some of the output at the bottom of this report. It seems the 
| binary embeds the version of rmatrix it's build against without 
| declaring proper versioned Dependencies to reflect that.

Yes. Apparently a design decision of the (R package) TMB package imposed
after the slight accidents that append with the (R package) Matrix (aka
rmatrix for us) during its last ABI/API change (at version 1.3.0 and after).

Not a lot we can do, other than to patch it out in TMB.

Nothing I can do (as maintainer of r-cran-matrix built of source package
rmatrix aka CRAN package Matrix.

| Currently this regression is blocking the migration of rmatrix to 
| testing [1]. Of course, rmatrix shouldn't just break your autopkgtest 
| (or even worse, your package), but it seems to me that the change in 
| rmatrix was intended and your package needs to update to the new situation.

None of that, AFAIK, comes from R package Matrix. It is just TMB.

Coupled with what happens around here with our ability to not keep packages
aligned with their CRAN versions.
 
| If this is a real problem in your package (and not only in your 
| autopkgtest), the right binary package(s) from rmatrix should really add 
| a versioned Breaks on the unfixed version of (one of your) package(s). 

I don't think I agree. Matrix does nothing here. You appear to be shooting a
messenger.

I.e. here it is on the Debian testing box I use for (my upstream) reverse
dependency checking:

Before reinstalling TMB:

    R> library(TMB)
    Warning message:
    In checkMatrixPackageVersion() : Package version inconsistency detected.
    TMB was built with Matrix version 1.3.4
    Current Matrix version is 1.4.0
    Please re-install 'TMB' from source using install.packages('TMB', type = \
    'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
    R>

After reinstalling:

    R> library(TMB)
    R> packageVersion("TMB")
    [1] ‘1.7.22’
    R> packageVersion("Matrix")
    [1] ‘1.4.0’
    R> 

Dirk

| Note: the Breaks is nice even if the issue is only in the autopkgtest as 
| it helps the migration software to figure out the right versions to 
| combine in the tests.
| 
| More information about this bug and the reason for filing it can be found on
| https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
| 
| Paul
| 
| [1] https://qa.debian.org/excuses.php?package=rmatrix
| 
| https://ci.debian.net/data/autopkgtest/testing/amd64/r/r-cran-tmb/17813190/log.gz
| 
| 
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| 
| > options("warn" = 2); library(TMB)
| Error: package or namespace load failed for ‘TMB’:
|   .onLoad failed in loadNamespace() for 'TMB', details:
|    call: checkMatrixPackageVersion()
|    error: (converted from warning) Package version inconsistency detected.
| TMB was built with Matrix version 1.3.4
| Current Matrix version is 1.4.0
| Please re-install 'TMB' from source using install.packages('TMB', type = 
| 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 
| 'Matrix' package
| Execution halted
| autopkgtest [16:11:05]: test r-cran-matrix_compatibility
| 
| [DELETED ATTACHMENT OpenPGP_signature, application/pgp-signature]

-- 
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org