Bug#1002525: r-cran-tmb: autopkgtest needs update for new version of rmatrix: Package version inconsistency detected.
Hi Nilesh, On 26 December 2021 at 00:20, Nilesh Patra wrote: | control: reassign -1 r-cran-tmb/1.7.22-1 | | Hi Dirk, | | On Thu, 23 Dec 2021 14:30:10 -0600 Dirk Eddelbuettel wrote: | > passfail | > | rmatrixfrom testing1.4-0-1 | > | r-cran-tmb from testing1.7.22-1 | > | all others from testingfrom 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. | | Interesting. OK, I did the needful and uploaded. rmatrix should migrate soonish. | | > Nothing I can do (as maintainer of r-cran-matrix built of source package | > rmatrix aka CRAN package Matrix. | | What you can do is inform people about it, by sending an email to the mailing list. | Someone would take that up soonish. | As per your words, and as per the autopkgtest problem, it needs a re-compilation, with | every new rmatrix, and that does not happen by default with buildd machines, right. It's a fairly rare case. I had it myself with Rcpp (version 1.0.7) too. What we might need _within the R ecosystem_ is the ability to push binary rebuilds through. | > | 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. | | Yep. | | > Coupled with what happens around here with our ability to not keep packages | > aligned with their CRAN versions. | | For this particular bug, tmb is already at the latest version, so it has got nothing to | do with this bug report. Yes. I guess it is the forced rebuild we need. I wonder if the TMB maintainer should have resorted to Matrix (>= 1.4.0) ? | If I talk about it otherwise then, I am usually (personally) trying to keep everything to CRAN-latest | and Andreas helps with that. There are some blockers in the process for instance introduction of new cran | dependencies that are un-packaged. So we quickly package that and upload to NEW, but then, | there is nothing we can do in those cases except waiting action for accept from the FTP-team. | Despite this, the number of cran-'non'-latest had been well below 20 (IIRC it was max 10) for past | several months. | | It has now unfortunately increased a little (but manageable) because we have less time. | At the end of the day, we are all 'volunteers' | | > | 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. | | Actually, that's sort of a templated reply that you see above which is reasonable since there are so many similar bugs, | if you see other bugs that break autopkgtests, you will find the wording to be awfully similar. For example: | | https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=996279 | | Hence, we need to re-assign and check accordingly. As I mentioned before, I cannot not help but think these autopkgtests _for CRAN packages_ add nothing (as CRAN does for all tests for us already), but create extra work (when we slip away from CRAN pairings and create our own bugs). But we're all adults and as you all feel it adds value, you keep doing it. Such is life. We're volunteers and if that is what you all do then I am still thankful for all the other work ;-) | Lastly, Merry Christmas! :) Thanks! Same to you. Dirk | Kind Regards, | Nilesh | x[DELETED ATTACHMENT signature.asc, application/pgp-signature] -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#1002525: r-cran-tmb: autopkgtest needs update for new version of rmatrix: Package version inconsistency detected.
control: reassign -1 r-cran-tmb/1.7.22-1 Hi Dirk, On Thu, 23 Dec 2021 14:30:10 -0600 Dirk Eddelbuettel wrote: > passfail > | rmatrixfrom testing1.4-0-1 > | r-cran-tmb from testing1.7.22-1 > | all others from testingfrom 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. Interesting. OK, I did the needful and uploaded. rmatrix should migrate soonish. > Nothing I can do (as maintainer of r-cran-matrix built of source package > rmatrix aka CRAN package Matrix. What you can do is inform people about it, by sending an email to the mailing list. Someone would take that up soonish. As per your words, and as per the autopkgtest problem, it needs a re-compilation, with every new rmatrix, and that does not happen by default with buildd machines, right. > | 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. Yep. > Coupled with what happens around here with our ability to not keep packages > aligned with their CRAN versions. For this particular bug, tmb is already at the latest version, so it has got nothing to do with this bug report. If I talk about it otherwise then, I am usually (personally) trying to keep everything to CRAN-latest and Andreas helps with that. There are some blockers in the process for instance introduction of new cran dependencies that are un-packaged. So we quickly package that and upload to NEW, but then, there is nothing we can do in those cases except waiting action for accept from the FTP-team. Despite this, the number of cran-'non'-latest had been well below 20 (IIRC it was max 10) for past several months. It has now unfortunately increased a little (but manageable) because we have less time. At the end of the day, we are all 'volunteers' > | 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. Actually, that's sort of a templated reply that you see above which is reasonable since there are so many similar bugs, if you see other bugs that break autopkgtests, you will find the wording to be awfully similar. For example: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=996279 Hence, we need to re-assign and check accordingly. Lastly, Merry Christmas! :) Kind Regards, Nilesh signature.asc Description: PGP signature
Bug#1002525: r-cran-tmb: autopkgtest needs update for new version of rmatrix: Package version inconsistency detected.
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...@lists.debian.org, rmat...@packages.debian.org
| Tags: sid bookworm
| User: debian...@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:
|
| passfail
| rmatrixfrom testing1.4-0-1
| r-cran-tmb from testing1.7.22-1
| all others from testingfrom 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
|
|
| R version 4.1.2 (2021-11-01) -- "Bird Hippie"
| Copyright (C) 2021 The R Foundation for Statistical Computing
| Platform: x86_64-pc-linux-gnu (64-bit)
|
| R is free software and comes with ABSOLUTELY NO WARRANTY.
| You are welcome to redistribute it under certain conditions.
| Type 'license()' or 'licence()' for distribution details.
|
| R is a collaborative project with many contributors.
| Type 'contributors()' for more information and
| 'citation()' on how to cite R or R packages in publications.
|
| Type 'demo()' for some demos, 'help()' for on-line help, or
| 'help.start()' for an HTML browser interface to help.
| Type 'q()' to quit R.
|
| > 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 | e...@debian.org
Bug#1002525: r-cran-tmb: autopkgtest needs update for new version of rmatrix: Package version inconsistency detected.
Source: r-cran-tmb
Version: 1.7.22-1
Severity: serious
X-Debbugs-CC: debian...@lists.debian.org, rmat...@packages.debian.org
Tags: sid bookworm
User: debian...@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:
passfail
rmatrixfrom testing1.4-0-1
r-cran-tmb from testing1.7.22-1
all others from testingfrom 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.
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.
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).
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
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
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
OpenPGP_signature
Description: OpenPGP digital signature
