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Bug#1088632: transition: hdf5

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  Bug#1088632: transition: hdf5 Gilles Filippini <pini@debian.org> - 2024-11-28 21:50 +0100
    Bug#1088632: transition: hdf5 pini@debian.org - 2024-12-08 15:50 +0100
    Bug#1088632: transition: hdf5 pini@debian.org - 2024-12-10 22:20 +0100
    Bug#1088632: transition: hdf5 pini@debian.org - 2024-12-22 00:40 +0100
    Bug#1088632: transition: hdf5 pini@debian.org - 2024-12-22 13:10 +0100
      Bug#1088632: transition: hdf5 pini@debian.org - 2024-12-22 18:00 +0100

#1222005 — Bug#1088632: transition: hdf5

Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: transition

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Hi Release Team,

I am requesting a transition slot for HDF5 1.14 currently in experimental. I've run a test rebuild of the 154 reverse dependencies. Out of them most of the FTBFS are currently not in testing and the other have patch proposals [1]. There is only issue left: #1087738 (khl). I am confident it will be solved because khl's maintainer is its upstream as well.

[1] https://udd.debian.org/cgi-bin/bts-usertags.cgi?user=pini%40debian.org&tag=ftbfs-hdf5-1.14

Please let me know in case you think other issues need attention.

Thanks in advance,
_g.


Ben file:

title = "hdf5";
is_affected = .depends ~ "libhdf5-103-1t64" | .depends ~ "libhdf5-cpp-103-1t64" | .depends ~ "libhdf5-fortran-102t64" | .depends ~ "libhdf5-hl-100t64" | .depends ~ "libhdf5-hl-cpp-100t64" | .depends ~ "libhdf5-hl-fortran-100t64" | .depends ~ "libhdf5-mpich-103-1t64" | .depends ~ "libhdf5-mpich-cpp-103-1t64" | .depends ~ "libhdf5-mpich-fortran-102t64" | .depends ~ "libhdf5-mpich-hl-100t64" | .depends ~ "libhdf5-mpich-hl-cpp-100t64" | .depends ~ "libhdf5-mpich-hl-fortran-100t64" | .depends ~ "libhdf5-openmpi-103-1t64" | .depends ~ "libhdf5-openmpi-cpp-103-1t64" | .depends ~ "libhdf5-openmpi-fortran-102t64" | .depends ~ "libhdf5-openmpi-hl-100t64" | .depends ~ "libhdf5-openmpi-hl-cpp-100t64" | .depends ~ "libhdf5-openmpi-hl-fortran-100t64" | .depends ~ "libhdf5-310" | .depends ~ "libhdf5-cpp-310" | .depends ~ "libhdf5-fortran-310" | .depends ~ "libhdf5-hl-310" | .depends ~ "libhdf5-hl-cpp-310" | .depends ~ "libhdf5-hl-fortran-310" | .depends ~ "libhdf5-mpich-310" | .depends ~ "libhdf5-mpich-cpp-310" | .depends ~ "libhdf5-mpich-fortran-310" | .depends ~ "libhdf5-mpich-hl-310" | .depends ~ "libhdf5-mpich-hl-cpp-310" | .depends ~ "libhdf5-mpich-hl-fortran-310" | .depends ~ "libhdf5-openmpi-310" | .depends ~ "libhdf5-openmpi-cpp-310" | .depends ~ "libhdf5-openmpi-fortran-310" | .depends ~ "libhdf5-openmpi-hl-310" | .depends ~ "libhdf5-openmpi-hl-cpp-310" | .depends ~ "libhdf5-openmpi-hl-fortran-310";
is_good = .depends ~ "libhdf5-310" | .depends ~ "libhdf5-cpp-310" | .depends ~ "libhdf5-fortran-310" | .depends ~ "libhdf5-hl-310" | .depends ~ "libhdf5-hl-cpp-310" | .depends ~ "libhdf5-hl-fortran-310" | .depends ~ "libhdf5-mpich-310" | .depends ~ "libhdf5-mpich-cpp-310" | .depends ~ "libhdf5-mpich-fortran-310" | .depends ~ "libhdf5-mpich-hl-310" | .depends ~ "libhdf5-mpich-hl-cpp-310" | .depends ~ "libhdf5-mpich-hl-fortran-310" | .depends ~ "libhdf5-openmpi-310" | .depends ~ "libhdf5-openmpi-cpp-310" | .depends ~ "libhdf5-openmpi-fortran-310" | .depends ~ "libhdf5-openmpi-hl-310" | .depends ~ "libhdf5-openmpi-hl-cpp-310" | .depends ~ "libhdf5-openmpi-hl-fortran-310";
is_bad = .depends ~ "libhdf5-103-1t64" | .depends ~ "libhdf5-cpp-103-1t64" | .depends ~ "libhdf5-fortran-102t64" | .depends ~ "libhdf5-hl-100t64" | .depends ~ "libhdf5-hl-cpp-100t64" | .depends ~ "libhdf5-hl-fortran-100t64" | .depends ~ "libhdf5-mpich-103-1t64" | .depends ~ "libhdf5-mpich-cpp-103-1t64" | .depends ~ "libhdf5-mpich-fortran-102t64" | .depends ~ "libhdf5-mpich-hl-100t64" | .depends ~ "libhdf5-mpich-hl-cpp-100t64" | .depends ~ "libhdf5-mpich-hl-fortran-100t64" | .depends ~ "libhdf5-openmpi-103-1t64" | .depends ~ "libhdf5-openmpi-cpp-103-1t64" | .depends ~ "libhdf5-openmpi-fortran-102t64" | .depends ~ "libhdf5-openmpi-hl-100t64" | .depends ~ "libhdf5-openmpi-hl-cpp-100t64" | .depends ~ "libhdf5-openmpi-hl-fortran-100t64";



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#1223221

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Le 2024-11-29 00:56, Emilio Pozuelo Monfort a écrit :
> On 28/11/2024 21:45, Gilles Filippini wrote:
>> Package: release.debian.org
>> Severity: normal
>> User: release.debian.org@packages.debian.org
>> Usertags: transition
>> 
>> Hi Release Team,
>> 
>> I am requesting a transition slot for HDF5 1.14 currently in 
>> experimental. I've run a test rebuild of the 154 reverse dependencies. 
>> Out of them most of the FTBFS are currently not in testing and the 
>> other have patch proposals [1]. There is only issue left: #1087738 
>> (khl). I am confident it will be solved because khl's maintainer is 
>> its upstream as well.
>> 
>> [1] 
>> https://udd.debian.org/cgi-bin/bts-usertags.cgi?user=pini%40debian.org&tag=ftbfs-hdf5-1.14
>> 
>> Please let me know in case you think other issues need attention.
> 
> This should wait until openmpi 5 is in testing.

Now that openmpi 5 is in testing is there any other blocker left?

Best,
_g.

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#1223516

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Le 2024-12-10 09:25, Emilio Pozuelo Monfort a écrit :
> Control: tags -1 confirmed
> 
> On 08/12/2024 15:37, pini@debian.org wrote:
>> Le 2024-11-29 00:56, Emilio Pozuelo Monfort a écrit :
>>> On 28/11/2024 21:45, Gilles Filippini wrote:
>>>> Package: release.debian.org
>>>> Severity: normal
>>>> User: release.debian.org@packages.debian.org
>>>> Usertags: transition
>>>> 
>>>> Hi Release Team,
>>>> 
>>>> I am requesting a transition slot for HDF5 1.14 currently in 
>>>> experimental. I've run a test rebuild of the 154 reverse 
>>>> dependencies. Out of them most of the FTBFS are currently not in 
>>>> testing and the other have patch proposals [1]. There is only issue 
>>>> left: #1087738 (khl). I am confident it will be solved because khl's 
>>>> maintainer is its upstream as well.
>>>> 
>>>> [1] https://udd.debian.org/cgi-bin/bts-usertags.cgi? 
>>>> user=pini%40debian.org&tag=ftbfs-hdf5-1.14
>>>> 
>>>> Please let me know in case you think other issues need attention.
>>> 
>>> This should wait until openmpi 5 is in testing.
>> 
>> Now that openmpi 5 is in testing is there any other blocker left?
> 
> No, go ahead.

Uploaded.

Best,
_g.

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#1225145

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Le 2024-12-16 09:12, Emilio Pozuelo Monfort a écrit :
> On 10/12/2024 22:10, pini@debian.org wrote:
>> Le 2024-12-10 09:25, Emilio Pozuelo Monfort a écrit :
>>> Control: tags -1 confirmed
>>> 
>>> On 08/12/2024 15:37, pini@debian.org wrote:
>>>> Le 2024-11-29 00:56, Emilio Pozuelo Monfort a écrit :
>>>>> On 28/11/2024 21:45, Gilles Filippini wrote:
>>>>>> Package: release.debian.org
>>>>>> Severity: normal
>>>>>> User: release.debian.org@packages.debian.org
>>>>>> Usertags: transition
>>>>>> 
>>>>>> Hi Release Team,
>>>>>> 
>>>>>> I am requesting a transition slot for HDF5 1.14 currently in 
>>>>>> experimental. I've run a test rebuild of the 154 reverse 
>>>>>> dependencies. Out of them most of the FTBFS are currently not in 
>>>>>> testing and the other have patch proposals [1]. There is only 
>>>>>> issue left: #1087738 (khl). I am confident it will be solved 
>>>>>> because khl's maintainer is its upstream as well.
>>>>>> 
>>>>>> [1] https://udd.debian.org/cgi-bin/bts-usertags.cgi? 
>>>>>> user=pini%40debian.org&tag=ftbfs-hdf5-1.14
>>>>>> 
>>>>>> Please let me know in case you think other issues need attention.
>>>>> 
>>>>> This should wait until openmpi 5 is in testing.
>>>> 
>>>> Now that openmpi 5 is in testing is there any other blocker left?
>>> 
>>> No, go ahead.
>> 
>> Uploaded.
> 
> There are a few autopkgtest regressions. I briefly looked at fast5 and 
> it looks like its examples need changes for the new API. I haven't 
> looked at the others. Can you take a look and file bugs as appropriate?

* fast5: I filed bug #1090898 and proposed a patch
* fclib: autopkgtest is successful on my box
* fenics-dolfinx: autopkgtest is successful on my box
* field3d: needs a binNMU
* gatb-core: autopkgtest is successful on my box
* petsc: autopkgtest is successful on my box

Best,
_g.

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#1225204

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Le 2024-12-22 09:07, Paul Gevers a écrit :
> On 22-12-2024 00:36, pini@debian.org wrote:
>>> There are a few autopkgtest regressions. I briefly looked at fast5 
>>> and it looks like its examples need changes for the new API. I 
>>> haven't looked at the others. Can you take a look and file bugs as 
>>> appropriate?
> 
>> * fclib: autopkgtest is successful on my box
> 
> I assume you test in a pure unstable/sid environment. Indeed on ci.d.n 
> fclib also passes on unstable. Most of the times that means we're 
> missing a *versioned* (test-) Depends or Breaks somewhere. The test 
> infrastructure tries to test in a testing/trixie environment with as 
> little as possible from unstable. Do you have any idea what that could 
> be?
> 
>> * fenics-dolfinx: autopkgtest is successful on my box
> 
> Same.
> 
>> * gatb-core: autopkgtest is successful on my box
> 
> Same.
> 
>> * petsc: autopkgtest is successful on my box
> 
> Same.

Should I upload a new HDF5 revision with versioned `Breaks:` against 
these packages?

Best,
_g.

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#1225245

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Le 2024-12-22 12:59, pini@debian.org a écrit :
> Le 2024-12-22 09:07, Paul Gevers a écrit :
>> On 22-12-2024 00:36, pini@debian.org wrote:
>>>> There are a few autopkgtest regressions. I briefly looked at fast5 
>>>> and it looks like its examples need changes for the new API. I 
>>>> haven't looked at the others. Can you take a look and file bugs as 
>>>> appropriate?
>> 
>>> * fclib: autopkgtest is successful on my box
>> 
>> I assume you test in a pure unstable/sid environment. Indeed on ci.d.n 
>> fclib also passes on unstable. Most of the times that means we're 
>> missing a *versioned* (test-) Depends or Breaks somewhere. The test 
>> infrastructure tries to test in a testing/trixie environment with as 
>> little as possible from unstable. Do you have any idea what that could 
>> be?
>> 
>>> * fenics-dolfinx: autopkgtest is successful on my box
>> 
>> Same.
>> 
>>> * gatb-core: autopkgtest is successful on my box
>> 
>> Same.
>> 
>>> * petsc: autopkgtest is successful on my box
>> 
>> Same.
> 
> Should I upload a new HDF5 revision with versioned `Breaks:` against 
> these packages?

As I understand it the failing test for fclib depends on libfclib-dev 
which brings the transitioning libhdf5-dev. This leads to an executable 
linked to both libhdf5_serial_hl.so.100 and libhdf5_serial_hl.so.310, 
causing the failure.

What is the best practice to prevent this?

I thought about adding `Breaks: libfclib-dev (<< 3.1.0+dfsg-3+b4)` to 
libhdf5-dev but it seems inappropriable because the binNMU number is not 
the same for all architectures.

Best,
_g.

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