Am Sun, Jan 22, 2023 at 10:35:37PM -0500 schrieb Aaron M. Ucko:
> Version 3.x of ncbi-vdb and sra-sdk are now in unstable, and looking
> good. Please do not make further uploads of either, or of skesa, until
> they migrate unless absolutely necessary.
Thanks a lot for all your work on this. I'm
Version 3.x of ncbi-vdb and sra-sdk are now in unstable, and looking
good. Please do not make further uploads of either, or of skesa, until
they migrate unless absolutely necessary.
Thanks!
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuf
Hi Aaron,
thanks for all your work on this.
Am Sun, Nov 13, 2022 at 11:08:31PM -0500 schrieb Aaron M. Ucko:
> I realized at the last minute (in the course of confirming that sra-sdk
> passes its autopkgtest) that I never merged in ngs-sdk's, which is
> likely to need formal adjustments per layout
"Aaron M. Ucko" writes:
> Meanwhile, I pushed some more tuneups, mostly related to tests; in
> particular, I arranged to label and exclude all online tests, including
> for better or worse some tests that were failing even with Internet
> access. I also made the Python binary package Architectur
Pierre Gruet writes:
> Hmm, I did not have in mind that the package is ready for amd64
> only. If this is the case, then yes, we should not use Architecture:
> all at the moment (which is otherwise the general rule for -java
> packages).
Ah, never mind, I misunderstood what you meant by "it"; so
Hi Aaron,
Le 14/10/2022 à 02:05, Aaron M. Ucko a écrit :
Pierre Gruet writes:
I have just pushed some changes. I adopted the -- I believe -- least
invasive solution by creating a new package libngs-jni which depends
on the shared lib package (not the -dev one), only ships a symlink to
the sha
Pierre Gruet writes:
> I have just pushed some changes. I adopted the -- I believe -- least
> invasive solution by creating a new package libngs-jni which depends
> on the shared lib package (not the -dev one), only ships a symlink to
> the shared lib with full version number, and on which the -j
Hi Aaron,
Le 12/10/2022 à 04:48, Aaron M. Ucko a écrit :
Pierre Gruet writes:
Indeed, this warning should be overridden, usually I do so and add a
pointer to the discussion in
https://lists.debian.org/debian-java/2018/06/msg00021.html in the
comment in the .lintian-overrides file.
Got it, t
Pierre Gruet writes:
> Indeed, this warning should be overridden, usually I do so and add a
> pointer to the discussion in
> https://lists.debian.org/debian-java/2018/06/msg00021.html in the
> comment in the .lintian-overrides file.
Got it, thanks!
> Do you have an idea of the exact way the .so
Hi Aaron and Andreas,
Le 11/10/2022 à 15:06, Aaron M. Ucko a écrit :
Andreas Tille writes:
I wanted to set you "Owner" of the Debian Med team repository since this
is the maximum power. I realised you are owner. So either someone has
beaten me and just did so or something is wrong if you ca
Hi Aaron,
Am Tue, Oct 11, 2022 at 09:06:28AM -0400 schrieb Aaron M. Ucko:
> > I wanted to set you "Owner" of the Debian Med team repository since this
> > is the maximum power. I realised you are owner. So either someone has
> > beaten me and just did so or something is wrong if you can't do wha
Andreas Tille writes:
> I wanted to set you "Owner" of the Debian Med team repository since this
> is the maximum power. I realised you are owner. So either someone has
> beaten me and just did so or something is wrong if you can't do what you
> want to do.
OK, thanks. A closer look indicated
[Pierre, please read at the end]
Hi Aaron,
Am Mon, Oct 10, 2022 at 10:48:58PM -0400 schrieb Aaron M. Ucko:
> u...@debian.org (Aaron M. Ucko) writes:
>
> > Ah, right, sra-sdk will need to go through NEW too -- the ngs-sdk code
> > it absorbed underwent an SONAME bump along the way. (All necessar
"Aaron M. Ucko" writes:
> u...@debian.org (Aaron M. Ucko) writes:
>
>> Ah, right, sra-sdk will need to go through NEW too -- the ngs-sdk code
>> it absorbed underwent an SONAME bump along the way. (All necessary
>> ncbi-vdb changes passed NEW a few weeks ago, but ncbi-vdb 3.x is sitting
>> in ex
u...@debian.org (Aaron M. Ucko) writes:
> Ah, right, sra-sdk will need to go through NEW too -- the ngs-sdk code
> it absorbed underwent an SONAME bump along the way. (All necessary
> ncbi-vdb changes passed NEW a few weeks ago, but ncbi-vdb 3.x is sitting
> in experimental until sra-sdk joins it
Andreas Tille writes:
> This would be really helpful since we are approaching the next freeze
> with an unpredictable migration time through new queue due to name
> change of the library package.
Ah, right, sra-sdk will need to go through NEW too -- the ngs-sdk code
it absorbed underwent an SON
Am Wed, Sep 28, 2022 at 04:01:41PM -0400 schrieb Aaron M. Ucko:
> Andreas Tille writes:
>
> > ping about this NCBI suite?
>
> I've continued to have a lot going on outside Debian, but will try to
> find time to get back to it soon.
This would be really helpful since we are approaching the next
Andreas Tille writes:
> ping about this NCBI suite?
I've continued to have a lot going on outside Debian, but will try to
find time to get back to it soon.
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.m
Hi Aaron,
ping about this NCBI suite?
Kind regards
Andreas.
Am Fri, Aug 26, 2022 at 08:49:23AM -0400 schrieb Aaron M. Ucko:
> Andreas Tille writes:
>
> > I noticed that another upload does not keep the position of the package
> > in the new queue but pulls it down at the end again. :-( BTW,
Andreas Tille writes:
> I noticed that another upload does not keep the position of the package
> in the new queue but pulls it down at the end again. :-( BTW, what is
Oops. I've gone ahead with 3.0.0+dfsg2-2 now, then; I'm confident in
those changes and don't want to let the position slip much
Hi Aaron,
Am Fri, Aug 26, 2022 at 12:38:39AM -0400 schrieb Aaron M. Ucko:
>
> I wasn't quite as quick as I'd hoped, but still managed to avoid a
> separate NEW cycle. I subsequently discovered the need for some
> additional tuneups, which I've pushed but not uploaded because I might
> not be ent
Andreas Tille writes:
> This would mean another trip through new. I think it would be good to
> upload this quickly sinnce the package is currently hanging in new and
> ftpmaster can inspect your changed package.
I wasn't quite as quick as I'd hoped, but still managed to avoid a
separate NEW cy
Am Sun, Aug 07, 2022 at 11:24:02PM -0400 schrieb Aaron M. Ucko:
> Andreas Tille writes:
>
> > CMake Error at test/sharq/CMakeLists.txt:42 (add_dependencies):
> > The dependency target "RE2_" of target "test-sharq-parser" does not exist.
>
> I'll try to take a look soon, but most likely your pa
Andreas Tille writes:
> CMake Error at test/sharq/CMakeLists.txt:42 (add_dependencies):
> The dependency target "RE2_" of target "test-sharq-parser" does not exist.
I'll try to take a look soon, but most likely your patch didn't go quite
far enough.
Meanwhile, I have made more (local) progres
Hi Aaron,
thanks a lot for your iterative help which enables taking one hurdle
after the other. Unfortunately there seem to be many of them. ;-)
Am Thu, Jul 28, 2022 at 11:41:18AM -0400 schrieb Aaron M. Ucko:
> Andreas Tille writes:
>
> > -- Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_A
Andreas Tille writes:
> -- Could NOT find JNI (missing: JAVA_AWT_LIBRARY JAVA_AWT_INCLUDE_PATH).
>
> (which is probably caused at the end of file
>ngs/ncbi/ngs-jni/CMakeLists.txt )
More likely the find_package(Java ...) call on line 159 of
build/env.cmake. At any rate, it looks like CMake m
Hi Aaron,
Am Wed, Jul 27, 2022 at 10:29:38PM +0200 schrieb Andreas Tille:
> No real problem - the package will sit in NEW for some time. I think I
> also stumbled upon the line-ending issue and solved it by excluding
> .gitattributes from upstream source tarball which makes the issue void
> (from
Hi Aaron,
Am Wed, Jul 27, 2022 at 02:21:11PM -0400 schrieb Aaron M. Ucko:
> Andreas Tille writes:
>
> > I think ncbi-vdb version 3.0.0 is finished in Git. I'm just uploading it to
> > experimental (needs to pass new queue due to the changed binary names). I
>
> Thanks, but I still have some u
Andreas Tille writes:
> I think ncbi-vdb version 3.0.0 is finished in Git. I'm just uploading it to
> experimental (needs to pass new queue due to the changed binary names). I
Thanks, but I still have some unpushed changes from some time back. As
noted at the time, I went to +dfsg2 to sideste
Hi Aaron,
I think ncbi-vdb version 3.0.0 is finished in Git. I'm just uploading it to
experimental (needs to pass new queue due to the changed binary names). I
tried building sra-sdk 3.0.0 against these packages but here the configure
step with cmake fails with
-- Found Java: /usr/bin/java (fo
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