Bug#1041485: RFS: spades/3.15.5+dfsg-2.1 [NMU] [RC] -- genome assembler for single-cell and isolates data sets

Étienne Mollier <[email protected]> Wed, 19 Jul 2023 20:27:48 +0200

Newsgroups	gmane.linux.debian.devel.medical
Message-ID	<ZLgrJDnU/+MWffch__25711.8719209515$1689791434$gmane$org@fusion>

X-Debbugs-Cc: [email protected]

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 <algorithm>
 #include <string>
 #include <sysexits.h>

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:[email protected]
[2]: https://buildd.debian.org/status/package.php?p=spades

Have a nice day,  :)
-- 
  .''`.  Étienne Mollier <[email protected]>
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