Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
Hi Bo, Am Fri, Jul 21, 2023 at 12:29:24AM +0800 schrieb Bo YU: > > [1]: https://med-team.pages.debian.net/policy/ > > > > If you agree to it, please feel free to proceed, git easily > > I have read the policy and accepted it. :-) > > Sounds good, let us know once you pushed your modification. > > I have updated it here: > https://salsa.debian.org/med-team/spades > > The only thing this is uncertain about is whether the distribution > should be UNRELEASE or unstable UNRELEASED (mind the 'D' at end - probably a typo in your mail since the commit was correct. Just mentioning it for other readers.) > in changelog. In Debian python team, it was `UNRELEASE` if team upload > from non-DD/DM. So l use it there. > Could you have a look?:) This is correct and Etienne just did what was needed. ;-) Thanks a lot for your contribution Andreas. -- http://fam-tille.de
Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
Hi! On Fri, Jul 21, 2023 at 1:12 AM Étienne Mollier wrote: > > Hi, > > Bo YU, on 2023-07-21: > > On Thu, Jul 20, 2023 at 5:34 PM Étienne Mollier wrote: > > > Bo YU, on 2023-07-20: > > > > I will clean up the change for here and upstream. > > > > > > Sounds good, let us know once you pushed your modification. > > > > I have updated it here: > > https://salsa.debian.org/med-team/spades > > > > The only thing this is uncertain about is whether the distribution > > should be UNRELEASE or unstable > > in changelog. In Debian python team, it was `UNRELEASE` if team upload > > from non-DD/DM. So l use it there. > > I'm fine with both convention; having a the changelog entry > stating "unstable" at least makes it clear the last person > having touched intended to have the package ready for upload. > The state can be reverted easily to UNRELEASED if something off > is noted. > > By contrast the tag would be more problematic to remove after > being pushed to the VCS. Personally, I usually run dgit, which > does the tagging for me on upload, so always tag and push after > the actual upload of the package. > > > Could you have a look?:) > > The RC bug is appropriately addressed, well done! > > The only issues I caught were some trailing blank spaces in the > changelog, and the named log entry was a bit redundant since > your change is the only one since last spades upload. I patched > these out along setting the package to ready it for upload; see > what I mean: > > --- a/debian/changelog > +++ b/debian/changelog > @@ -1,8 +1,6 @@ > -spades (3.15.5+dfsg-3) UNRELEASED; urgency=medium > - > +spades (3.15.5+dfsg-3) unstable; urgency=medium > + >* Team upload. > - > - [Bo YU] >* Add fix-gcc13.patch to fix gcc-13 build issues. (Closes: > #1037863) > > -- Bo YU Thu, 20 Jul 2023 21:38:50 +0800 > > > Otherwise your bug fix is uploaded. > Thank you for your contribution! Thanks for your upload and fixed it for me. I will keep it mind. BR, Bo > > Have a nice day, :) > -- > .''`. Étienne Mollier > : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da > `. `' sent from /dev/pts/2, please excuse my verbosity >`-on air: Need - Entheogen
Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
Hi, Bo YU, on 2023-07-21: > On Thu, Jul 20, 2023 at 5:34 PM Étienne Mollier wrote: > > Bo YU, on 2023-07-20: > > > I will clean up the change for here and upstream. > > > > Sounds good, let us know once you pushed your modification. > > I have updated it here: > https://salsa.debian.org/med-team/spades > > The only thing this is uncertain about is whether the distribution > should be UNRELEASE or unstable > in changelog. In Debian python team, it was `UNRELEASE` if team upload > from non-DD/DM. So l use it there. I'm fine with both convention; having a the changelog entry stating "unstable" at least makes it clear the last person having touched intended to have the package ready for upload. The state can be reverted easily to UNRELEASED if something off is noted. By contrast the tag would be more problematic to remove after being pushed to the VCS. Personally, I usually run dgit, which does the tagging for me on upload, so always tag and push after the actual upload of the package. > Could you have a look?:) The RC bug is appropriately addressed, well done! The only issues I caught were some trailing blank spaces in the changelog, and the named log entry was a bit redundant since your change is the only one since last spades upload. I patched these out along setting the package to ready it for upload; see what I mean: --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,6 @@ -spades (3.15.5+dfsg-3) UNRELEASED; urgency=medium - +spades (3.15.5+dfsg-3) unstable; urgency=medium + * Team upload. - - [Bo YU] * Add fix-gcc13.patch to fix gcc-13 build issues. (Closes: #1037863) -- Bo YU Thu, 20 Jul 2023 21:38:50 +0800 Otherwise your bug fix is uploaded. Thank you for your contribution! Have a nice day, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/2, please excuse my verbosity `-on air: Need - Entheogen signature.asc Description: PGP signature
Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
X-Debbugs-Cc: debian-...@lists.debian.org Hi! On Thu, Jul 20, 2023 at 5:34 PM Étienne Mollier wrote: > > Hi Bo, > > Bo YU, on 2023-07-20: > > On Thu, Jul 20, 2023 at 2:27 AM Étienne Mollier wrote: ... > > In case your haven't come by it yet, you can have a look and > bookmark the Debian Med policy manual here[1]. These guidelines > ensure rough consistency between packages under Debian Med > umbrella; there are about one thousand and a half. > > [1]: https://med-team.pages.debian.net/policy/ > > If you agree to it, please feel free to proceed, git easily I have read the policy and accepted it. > allows reverting changes anyway; just don't force push without > discussing the matter on the mailing list first. > ... > > I will clean up the change for here and upstream. > > Sounds good, let us know once you pushed your modification. I have updated it here: https://salsa.debian.org/med-team/spades The only thing this is uncertain about is whether the distribution should be UNRELEASE or unstable in changelog. In Debian python team, it was `UNRELEASE` if team upload from non-DD/DM. So l use it there. Could you have a look?:) BR, Bo > > Have a nice day, :) > -- > .''`. Étienne Mollier > : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da > `. `' sent from /dev/pts/2, please excuse my verbosity >`-on air: Neal Morse - So Many Roads
Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
Hi, Am Thu, Jul 20, 2023 at 12:57:11PM +0800 schrieb Bo YU: > ... > Oh, thanks you told me the background so today I learned many here. > > I think it is okay i push the update to the salsa repo directly as > your suggestion. Thank you for your contribution and welcome in the team Andreas. -- http://fam-tille.de
Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
Hi Bo,
Bo YU, on 2023-07-20:
> On Thu, Jul 20, 2023 at 2:27 AM Étienne Mollier wrote:
> > Bo YU, on 2023-07-19:
> > > I am looking for a sponsor for my package "spades":
> > […]
> > > Changes since the last upload:
> > >
> > > spades (3.15.5+dfsg-2.1) unstable; urgency=medium
> > > .
> > >* Non-maintainer upload.
> >
> > If you happen to go by the Salsa login vimerbf-guest, then you
> > should have direct access to push directly to the team
> > maintained repository. Don't hesitate to work there, and ping
> > the debian-med[1] list once you are happy with your changes and
> > they are ready for "Team upload.". ;)
> >
> Yeah, it is me. I just got access at yesterday so I am not sure I can
> follow the workflow of Debian med team. But now I can try after your
> confirmation.:)
In case your haven't come by it yet, you can have a look and
bookmark the Debian Med policy manual here[1]. These guidelines
ensure rough consistency between packages under Debian Med
umbrella; there are about one thousand and a half.
[1]: https://med-team.pages.debian.net/policy/
If you agree to it, please feel free to proceed, git easily
allows reverting changes anyway; just don't force push without
discussing the matter on the mailing list first.
> > >* Fix ftbfs on gcc-13. (Closes: #1037863)
> >
> > Thanks for your help fixing that bug, and also for the forward
> > upstream. My only matter for head scratching is the following
> > hunk in your patch:
> >
> > --- a/assembler/ext/src/llvm/Signals.inc
> > +++ b/assembler/ext/src/llvm/Signals.inc
> > @@ -43,6 +43,7 @@
> > #include "llvm/Support/Program.h"
> > #include "llvm/Support/SaveAndRestore.h"
> > #include "llvm/Support/raw_ostream.h"
> > +#include "llvm/Support/Signals.h"
> > #include
> > #include
> > #include
> >
> > Including cstdint would have probably been less intrusive, and
> > solves the build failure as far as I could test. Was there a
> > specific reason to include the whole llvm/Support/Signals.h
> > instead of just cstdint?
> >
> Okay, I rebuild the package again without the change, it works.
> I recalled the background, maybe it messed up due to previous
> error I ignored. In fact, maybe I overlooked the log:
> ```
> [ 46%] Building CXX object
> ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o
> In file included from /<>/assembler/ext/src/llvm/Signals.cpp:219:
> /<>/assembler/ext/src/llvm/Signals.inc:347:50: error:
> 'void llvm::sys::CleanupOnSignal(uintptr_t)' should have been declared
> inside 'llvm::sys'
> 347 | void llvm::sys::CleanupOnSignal(uintptr_t Context) {
> ```
>
> I will clean up the change for here and upstream.
Sounds good, let us know once you pushed your modification.
Have a nice day, :)
--
.''`. Étienne Mollier
: :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/2, please excuse my verbosity
`-on air: Neal Morse - So Many Roads
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Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
X-Debbugs-Cc: debian-...@lists.debian.org
hi!
On Thu, Jul 20, 2023 at 2:27 AM Étienne Mollier wrote:
>
> X-Debbugs-Cc: debian-...@lists.debian.org
>
> Hi Bo YU,
>
> Bo YU, on 2023-07-19:
> > I am looking for a sponsor for my package "spades":
> […]
> > Changes since the last upload:
> >
> > spades (3.15.5+dfsg-2.1) unstable; urgency=medium
> > .
> >* Non-maintainer upload.
>
> If you happen to go by the Salsa login vimerbf-guest, then you
> should have direct access to push directly to the team
> maintained repository. Don't hesitate to work there, and ping
> the debian-med[1] list once you are happy with your changes and
> they are ready for "Team upload.". ;)
>
Yeah, it is me. I just got access at yesterday so I am not sure I can
follow the workflow of Debian med team. But now I can try after your
confirmation.:)
> >* Fix ftbfs on gcc-13. (Closes: #1037863)
>
> Thanks for your help fixing that bug, and also for the forward
> upstream. My only matter for head scratching is the following
> hunk in your patch:
>
> --- a/assembler/ext/src/llvm/Signals.inc
> +++ b/assembler/ext/src/llvm/Signals.inc
> @@ -43,6 +43,7 @@
> #include "llvm/Support/Program.h"
> #include "llvm/Support/SaveAndRestore.h"
> #include "llvm/Support/raw_ostream.h"
> +#include "llvm/Support/Signals.h"
> #include
> #include
> #include
>
> Including cstdint would have probably been less intrusive, and
> solves the build failure as far as I could test. Was there a
> specific reason to include the whole llvm/Support/Signals.h
> instead of just cstdint?
>
Okay, I rebuild the package again without the change, it works.
I recalled the background, maybe it messed up due to previous
error I ignored. In fact, maybe I overlooked the log:
```
[ 46%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o
In file included from /<>/assembler/ext/src/llvm/Signals.cpp:219:
/<>/assembler/ext/src/llvm/Signals.inc:347:50: error:
'void llvm::sys::CleanupOnSignal(uintptr_t)' should have been declared
inside 'llvm::sys'
347 | void llvm::sys::CleanupOnSignal(uintptr_t Context) {
```
I will clean up the change for here and upstream.
> Note the file is copied from llvm source code, so I suspect that
> whatever the right change is, it may have a non negligible
> contribution in resolving #1037760 affecting llvm-toolchain-15.
>
> > BTW, the package maybe only need to build target like x64.
>
> I guess you are referring to #976523. In case a package were to
> drop dependency amd64 specific flags and become architecture
> indepent, then this would be automatically caught by the build
> daemons network. That being said, in the specific case of
> spades, the package looks to already be exluded by the buildd
> network[2]; if that is the case, reintroducing non-amd64
> architectures will require a couple of manual steps anyway.
>
Oh, thanks you told me the background so today I learned many here.
I think it is okay i push the update to the salsa repo directly as
your suggestion.
Thanks again!
BR,
Bo
> [1]: mailto:debian-...@lists.debian.org
> [2]: https://buildd.debian.org/status/package.php?p=spades
>
> Have a nice day, :)
> --
> .''`. Étienne Mollier
> : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
> `. `' sent from /dev/pts/1, please excuse my verbosity
>`-on air: The Flower Kings - Garden Of Dreams (Part B Ed…
Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
X-Debbugs-Cc: debian-...@lists.debian.org Hi Bo YU, Bo YU, on 2023-07-19: > I am looking for a sponsor for my package "spades": […] > Changes since the last upload: > > spades (3.15.5+dfsg-2.1) unstable; urgency=medium > . >* Non-maintainer upload. If you happen to go by the Salsa login vimerbf-guest, then you should have direct access to push directly to the team maintained repository. Don't hesitate to work there, and ping the debian-med[1] list once you are happy with your changes and they are ready for "Team upload.". ;) >* Fix ftbfs on gcc-13. (Closes: #1037863) Thanks for your help fixing that bug, and also for the forward upstream. My only matter for head scratching is the following hunk in your patch: --- a/assembler/ext/src/llvm/Signals.inc +++ b/assembler/ext/src/llvm/Signals.inc @@ -43,6 +43,7 @@ #include "llvm/Support/Program.h" #include "llvm/Support/SaveAndRestore.h" #include "llvm/Support/raw_ostream.h" +#include "llvm/Support/Signals.h" #include #include #include Including cstdint would have probably been less intrusive, and solves the build failure as far as I could test. Was there a specific reason to include the whole llvm/Support/Signals.h instead of just cstdint? Note the file is copied from llvm source code, so I suspect that whatever the right change is, it may have a non negligible contribution in resolving #1037760 affecting llvm-toolchain-15. > BTW, the package maybe only need to build target like x64. I guess you are referring to #976523. In case a package were to drop dependency amd64 specific flags and become architecture indepent, then this would be automatically caught by the build daemons network. That being said, in the specific case of spades, the package looks to already be exluded by the buildd network[2]; if that is the case, reintroducing non-amd64 architectures will require a couple of manual steps anyway. [1]: mailto:debian-...@lists.debian.org [2]: https://buildd.debian.org/status/package.php?p=spades Have a nice day, :) -- .''`. Étienne Mollier : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `-on air: The Flower Kings - Garden Of Dreams (Part B Ed… signature.asc Description: PGP signature
Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets
Package: sponsorship-requests Severity: important Dear mentors, I am looking for a sponsor for my package "spades": * Package name : spades Version : 3.15.5+dfsg-2.1 Upstream contact : spades.supp...@bioinf.spbau.ru * URL : http://cab.spbu.ru/software/spades/ * License : Expat, Apache-2.0, BSD-3-clause-Akiba, GPL-2+, BSD-3-clause, BSD-2-clause, GPL-3+, LGPL-2.1+, BSD-3-clause-Google, Boost-1, UoI-NCSA, BSDlike-libbzip2, BSD-3-clause-PacBio * Vcs : https://salsa.debian.org/med-team/spades Section : science The source builds the following binary packages: spades - genome assembler for single-cell and isolates data sets To access further information about this package, please visit the following URL: https://mentors.debian.net/package/spades/ Alternatively, you can download the package with 'dget' using this command: dget -x https://mentors.debian.net/debian/pool/main/s/spades/spades_3.15.5+dfsg-2.1.dsc Changes since the last upload: spades (3.15.5+dfsg-2.1) unstable; urgency=medium . * Non-maintainer upload. * Fix ftbfs on gcc-13. (Closes: #1037863) -- BTW, the package maybe only need to build target like x64. -- Regards, -- Bo YU signature.asc Description: PGP signature
