/smile_english.html.
Perhaps these were added since you last looked at the page.
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Andreas Tille [EMAIL PROTECTED] writes:
On 12 Apr 2003, Aaron M. Ucko wrote:
http://lists.debian.org/debian-devel-changes/2003/debian-devel-changes-200304/msg00824.html
Many thanks to Mario.
Indeed.
I just ask on Debian-Med with this mail (sorry for quoting you in
a public list, but I
form
package is a/an description. I'd suggest something like
Description: tool to test a DNA sequence for sequence tagged sites [Biology]
(I realize that [Biology] has typically gone at the beginning, but
I'd have to say that that's not really the most appropriate place for
it.)
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on a given sequence.
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[EMAIL PROTECTED] (Aaron M. Ucko) writes:
Sure, no problem; I've launched a build on my home machine, and will
upload the resulting binaries when it completes.
The build completed, so I'll sign and upload the binaries when I get
home. (I don't have access to my key at present
possible to write
I'd say supports rather than encourages, as the relevant option
(mergeWithUpstream) is off by default. Some teams insist on using it
for their shared repositories, but that's a separate matter.
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Charles Plessy [EMAIL PROTECTED] writes:
Maq is likely to have to access files bigger than 2Gb sometimes, so
I probably should not remove -D_FILE_OFFSET_BITS=64.
Indeed.
Would the following patch make sense?
Yes, looks reasonable to me.
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is that I have
been using Debhelper 7 whereas it still recommends version 5. Is that
likely to be an issue? (FWIW, lenny has 7.0.15.)
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Nelson A. de Oliveira nao...@gmail.com writes:
See the package git-svn
Thanks for the suggestion! I found it already, but I wasn't sure
whether a different tool (tailor?) would be more appropriate for
one-shot conversions.
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cdbs extensively before migrating to dh.)
Thanks!
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u...@debian.org (Aaron M. Ucko) writes:
lately.) I now have a plausible-looking draft Git repository, but am
holding off on pushing it anywhere public until I get a chance to
sanity check it further.
This review ended up falling by the wayside for far longer than I
intended, for which I must
last time. ;-)
So asking for a freeze exceptions seems to make sense.
Thanks for supporting the idea.
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u...@debian.org (Aaron M. Ucko) writes:
No, I hadn't; thanks for the pointer. The new release includes BLAST
2.2.24, so that report definitely also argues in favor of trying to
get it into Squeeze.
At any rate, I've now completed and fully published my work on the new
upstream release
formatting.
* debian/control:
- bump dpkg-dev build-dep to = 1.15.7 for dpkg-buildflags.
- Standards-Version: 3.9.1 (already compliant).
- note switch to git-mediated Debian-Med team maintenance.
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In particular, please
.
Likewise, as Andreas noted. Thanks!
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+ binaries.
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, perhaps) containing such symlinks,
which users could then add to their PATHs as desired.
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Olivier Sallou olivier.sal...@irisa.fr writes:
did you had time to look at ncbi-blast+ package before pushing it ?
I'm terribly sorry, but I still haven't had time. Perhaps this weekend.
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, and would like to thank you for
taking the lead here.
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on the package; there are just a lot of details to packaging
anything.
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Index: debian/control
(800), whereas only members of
groups 40063 and 80063 can write to the repository.
Could you please take a look?
Thanks!
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for the explanation; I've kept the split.
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) rather than pretending to be
coinstallable.
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; I've asked my usual contact on the
BLAST team whether he has any concerns about such an approach.
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blast2 and ncbi-blast+ packages coexist without complications.
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,
please note that the BLAST engine is a library, and available to other
packages; for instance, I think Sequin (from the ncbi-tools-x11 package)
may support running BLAST internally. Thanks for asking!
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, the whole C++ Toolkit has proven too unwieldy to package
properly, so we've just packaged the BLAST+ subset so far. Sorry for
any resulting inconvenience.
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Hi, Olivier.
This is a false alarm, which you can safely ignore; blhc confirms that
all is well:
$ blhc --ignore-flag -g --ignore-flag -O2 ncbi-blast+_2.2.26-3_amd64.build
LDFLAGS missing (-fPIE -pie): /usr/bin/g++ -Wl,--enable-new-dtags -pthread
-Wl,-z,relro -Wl,-z,now -Wl,--as-needed -O
that to be too much of a problem. If it is, perhaps
ncbi-blast+ could divert blast2's seedtop and substitute a script that
would figure out which version to launch, depending on whether it saw
long or short option names.
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cc1plus. ncbi-blast+ will need a new
upload soon anyway to address other bugs, so there's probably no point
in requesting a give-back.
Sorry to bother you!
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Olivier Sallou olivier.sal...@irisa.fr writes:
the patch you provided for arm/mips is not enough.
Please try actually enabling it in debian/patches/series.
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with fortification, but I don't have time
to look into that option at the moment.
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, but won't be able to sign an upload until this evening.
At any rate, I will push the necessary change upstream.
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Aaron M. Ucko a...@alum.mit.edu writes:
shortly, but won't be able to sign an upload until this evening.
FTR, this upload accidentally slipped by a day, but has occurred, with
good autobuilder results.
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Package: wnpp
Severity: wishlist
Owner: "Aaron M. Ucko" <u...@debian.org>
* Package name: ncbi-entrez-direct
Version : 3.60
Upstream Author : Jonathan Kans <k...@ncbi.nlm.nih.gov>
* URL : http://www.ncbi.nlm.nih.gov/books/NBK179288
* License
ver a "build" directory in the source tree,
just in the build tree (which I think we've been naming BUILD).
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oad 2.4.0 tonight.
For the record, the immediate problem turned out to be fallout from missing
https://www.ncbi.nlm.nih.gov/viewvc/v1?view=revision=72513, which
evidently didn't make it into the 2.4.0 release branch.
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such awkward to test automatically. However, some
of their functionality is also available from programs in ncbi-tools-bin
(or sometimes blast2).
As for blast2, perhaps it would be possible to adapt the automated tests
recently added to ncbi-blast+.
Thanks for asking!
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ecreate them locally?
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(over /usr/bin/efetch)
is with acedb-other, which is also from debian-med. I've prepared local
drafts of argument-analyzing scripts and just need to test and upload
them. I have both today and Friday off from work, so should be able to
find time to take care of that this week.
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ke another look.
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e
sufficient for most purposes. That said, I did try to take care of both
packages tonight, but wound up only having time for ncbi-blast+; I plan
to follow up with ncbi-tools6 tomorrow. (I also remain confident that
it won't need to go through NEW, though ncbi-blast+ might.)
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ls6 should be fine.
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anything yet in case I need to
rework any changes first.
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"Aaron M. Ucko" <u...@debian.org> writes:
> to follow up with ncbi-tools6 tomorrow.
Done as planned, so we're now pretty much set, though I'll want to make
one more ncbi-blast+ upload to disable a strict GNU TLS version check,
as already done for ncbi-tools6:
https://anon
though Cn3D++ comes from the same overarching tree
(NCBI's C++ Toolkit) as BLAST+, it is a separate project. The packaging
work done for BLAST+ would make for a decent starting point, though.
Meanwhile, what ever happened with https://bugs.debian.org/682042 ? ;-)
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directory. What do you think about the whole test at this stage?
Great, thanks! I suppose you could check for specific output contents
(via grep, not necessarily 100% identity), but this otherwise all looks
good, and is a clear improvement over not having autopkgtests at all.
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Liubov Chuprikova <chuprikov...@gmail.com> writes:
> On Thu, 12 Apr 2018 at 17:30 Aaron M. Ucko <u...@debian.org> wrote:
>
>>
>> That said, you did catch a bug in taxblast; I'll push a fix this
>> evening. (The binary will still require a network connect
n!
That said, you did catch a bug in taxblast; I'll push a fix this
evening. (The binary will still require a network connection, just
actually be able to use it now).
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Package: wnpp
Severity: wishlist
Owner: "Aaron M. Ucko" <u...@debian.org>
* Package name: golang-github-dataence-porter2(-dev)
Version : 0.0~git20150829.0.56e4718
Upstream Author : Jian Zhen / Dataence, LLC
* URL : https://github.com/dataence/p
reached you first. I'm now openly copying both specialized
lists, and leaving -devel off.
> I am not a mod, so don't worry all too much about me.
I appreciate your feedback regardless.
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to
> sponsor the upload. If you need any additional information about *taxblast*,
> I'll be happy to provide it.
OK, thanks. I'm not sure any of these is critical to test, but some
should be relatively straightforward to work in at this point, and as
noted I'm not quite ready to upl
art of preparing
to make an upload, but redirection does certainly still work for now. I
do share your frustration that the anonscm alias didn't offer as much
permanance as promised.
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kage
> dependencies on my computer..
Thanks for adding these tests, and sorry you ran into dpkg errors along
the way! Please let me know if you have usage questions about any of
this package's tools.
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g echo statement.)
Спасибо!
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h a file by any program?
Just by a generic text editor, sorry. However, this package does
already ship a macro file you may be able to test with:
/usr/share/ncbi/data/autofix.prt.
Thanks!
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gh, since I don't have
time to split out individual patches at the moment. In the long term,
how do you feel about gbp-pq(1) as a compromise between our preferred
approaches?
BTW, I see that the repository has moved to Salsa (thanks!) Are you
planning to update the Vcs-* fields accordingly?
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> binary:ncbi-cn3d is NEW.
In retrospect, its version number should be a variant of the
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vs. 6.1.x). Will a simple reupload with this correction (and no epoch)
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ly, or via e-mail. (Rather, I use Gmane's
NNTP mirror.)
> So, now: Many thanks for all these efforts. Much appreciated!
You're quite welcome.
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package
ncbi-cn3d for consistency with other NCBI package names.
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t back up to date. I'll try to find time to
take care of ncbi-blast+ as well.
Thanks for checking!
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I've bridged this gap by adding a symlink to the latest
ncbi-data binary package, which hit Debian testing this morning and from
what I gather should automatically make it into the next Ubuntu release.
Sorry you ran into trouble here!
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don't appear to be ncbi-blast+'s fault
either, but I'll let them slide for now because they don't affect
testing migration and the latest changes should all be formalities on
those architectures.
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gotten that it was an option
nowadays, and then proceeding to overlook the brief directions on using
it. Sorry for the noise.
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u...@debian.org (Aaron M. Ucko) writes:
>> I'd be super happy if you would find some time to turn your hints into
>> code in salsa. ;-)
>
> I'll try to find time this weekend.
I didn't find as much time as I hoped, but I just pushed changes to
correct sra-sdk's accidental c
til/validate-names4.c accordingly.
Meanwhile, it looks like sra-sdk's latest "2.10.4+dfsg" upstream tree
wound up as an accidental copy of ncbi-vdb.
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)
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My thanks to both of you! Please feel free to copy me on future
requests involving ncbi-entrez-direct, since I don't follow this list
closely. (Likewise for ncbi-tools6, though that doesn't need much
attention nowadays, and ncbi-blast+, though Olivier's also familiar with
that package and has
ream
(3)
https://salsa.debian.org/med-team/sra-sdk/-/tree/bdf0081d3363e836e27474f0898a55f3ca7562f3
(2) should closely resemble (3), not (1).
> I'd be super happy if you would find some time to turn your hints into
> code in salsa. ;-)
I'll try to find time this weekend.
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that workaround in favor of specifically avoiding
ncbi-blast+ 2.10.0-1.
Meanwhile, I know 2.10.1 is out upstream, but it will need additional
patching to avoid an FTBFS on non-x86, so I held off on taking it for
now.
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y introduced a regression on 64-bit architectures;
fixed in -3 just now. (An intended formal clarification misfired.)
Thank you very much for pointing it out!
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/lib/${DEB_HOST_MULTIARCH}/amplsolver.a
in debian/ampl-netlib-solvers.links.
Making a shared version of this library might be a good idea regardless.
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OpenCL may
need different treatment, though.
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larification: This variable is an override, not a cap, so any
unconditional settings thereof should be low enough to work on 32-bit
systems.
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ream's trunk
allows on Windows:
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/include/objtools/blast/seqdb_writer/writedb_lmdb.hpp#L51
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p an eye out for it! I've found the rr tool (from the
eponymous package) very helpful in debugging this sort of
nondeterministic bug. With any luck, I'll be able to capture such a
crash under it, at which point I'll be able to replay it as often as
needed, and moreover reversibly.
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seqdb_writer/writedb_lmdb.hpp:52:59:
warning: integer overflow in expression of type ‘int’ results in ‘-647710720’
[-Woverflow]
occurs only in the logs for 2.10.0-2.
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l need to conditionalize
appropriately to avoid FTBFS errors on other architectures.
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http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
ges waiting for ghostscript, but it probably won't make much
difference in practice.
--
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.mit.edu
ilable there.
> On the great news side, the build on riscv64 went through! :)
Glad to hear it!
--
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.mit.edu
blastn performs direct nucleotide-nucleotide comparisons, it
doesn't care about genetic codes, and upstream evidently limited this
flag's use to the one tool for which it would be meaningful: tblastx.
(Likewise, only tblastn and tblastx support -db_gencode these days.)
Thanks for checking!
--
Aaro
Andreas Tille writes:
> On Fri, Oct 16, 2020 at 08:44:20AM -0400, Aaron M. Ucko wrote:
>>
>> Please try simply dropping -query_gencode (and its argument) here --
>> because blastn performs direct nucleotide-nucleotide comparisons, it
>> doesn't care about genetic co
m.nih.gov/Coffeebreak/ redirects there.)
--
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.mit.edu
u...@debian.org (Aaron M. Ucko) writes:
> issue a give-back request for python-biopython on mipsel once a suitable
> new BLAST+ build is available there.
Update: The new BLAST+ build showed up overnight (from my time zone,
anyway) as expected, and python-biopython's mipsel status change
u...@debian.org (Aaron M. Ucko) writes:
> and should be able to supply a proper patch within the next day or two.
Pushed. As noted in both my commit message and the patch's description,
though:
NB: The use of -v $settings{HITLIST_SIZE} in conjunction with the
supplied $format_type value
y installing the dynamic library (shasta.cpython-*.so) directly
to /usr/lib/python3/dist-packages/, as in (e.g.) python3-biosig.
--
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.mit.edu
"Aaron M. Ucko" writes:
> I didn't find as much time as I hoped, but I just pushed changes to
> correct sra-sdk's accidental cutover to ncbi-vdb, and will follow up
> with my tweaks to both packages when I get a chance.
I think I finally have everything in order and on t
u...@debian.org (Aaron M. Ucko) writes:
> No problem. It's too bad that unrelated changes in this release
> resulted in compilation errors on mips(64)el, but I do at least have
> ideas on how to fix them.
2.10.1-2 (uploaded a little while ago) should be good all around.
--
Aaro
stn issue with
> multi-threading!
No problem. It's too bad that unrelated changes in this release
resulted in compilation errors on mips(64)el, but I do at least have
ideas on how to fix them.
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http:/
Étienne Mollier writes:
> Said missing dependency turned out to be libtie-ixhash-perl
... which I had indeed already installed. Thanks for tracking it down!
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/fin
ogtail)
or, in the case of a Java program like jmodeltest, libjemmy2-java
(http://wiki.netbeans.org/Jemmy) here.
--
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.mit.edu
ublic domain).
Thanks for asking!
--
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.mit.edu
robably what happened; AFAICT, we have the right thing on
SALSA and the GH repository simply holds source for Magic-BLAST's
external documentation https://boratyng.github.io/magicblast .
Thanks for checking!
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/
t of the input file
> `debian/ont-fast5-api/usr/lib/python3.8/dist-packages/ont_fast5_api/vbz_plugin/libvbz_hdf_plugin_aarch64.so'
Ugh, looks like there are prebuilt binaries in ont-fast5-api/vbz_plugin
with no obvious source. Please repack this package without them.
Thanks!
--
Aaron M. Uc
ar doesn't include the
problematic jsonchecker subtree.
Thanks!
--
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.mit.edu
libncbi-vdb-dev
should indirectly take care of any other helpful lib*-dev dependencies;
I'm not sure what purpose the build dependency on sra-toolkit serves.
Thanks, and please feel free to consult me again if you have any other
questions.
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at d
u...@debian.org (Aaron M. Ucko) writes:
> override_dh_auto_test:
Oops, I accidentally left the leading - in place and omitted an
environment variable one or two tests will need to work fully offline;
please make that
override_dh_auto_test:
NCBI_CONFIG__GENBANK__PREOPEN=fa
oaders/genbank/gicache/gicache.c
ran afoul of -Werror=format-security, which this fresh upstream patch
should address:
https://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/c%2B%2B/src/objtools/data_loaders/genbank/gicache/gicache.c?r1=86537=90486=patch
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu
a false
> positive.
Right, these aren't minified, just poorly formatted in spots. Lintian
should perhaps consider average rather than maximum line length.
Thanks for checking!
--
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.mit.edu
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