Bug#1080479: ncbi-blast+: failure to create blastdb v5 on riscv64

2025-04-24 Thread Aaron M. Ucko
the combination, though.) > I'm not sure what to make of it. Perhaps the issue can be > closed. I'm on board with leaving it open for now but on hold until after Trixie. -- 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

Bug#1080479: ncbi-blast+: failure to create blastdb v5 on riscv64

2025-04-21 Thread Aaron M. Ucko
its rebuild served to pick up Mbed TLS 3.x -- but none I'd expect to be pertinent here. Sorry for the delayed response -- I normally go through *-porterbox.debian.net aliases, but ricci didn't have one (and still doesn't!), so I'd missed the possibility of investigating dir

Bug#1102742: eureka: it looks like eureka could be rebuilt against fltk1.4

2025-04-15 Thread Aaron M. Ucko
ch apps can use to make it stick with the X11 backend: https://salsa.debian.org/ucko/fltk1.4/-/blob/main/README.Wayland.txt?ref_type=heads#L57 I've locally confirmed it works 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

Bug#1102671: unblock: fltk1.4/1.4.2-7

2025-04-12 Thread Aaron M. Ucko
dev I've promptly fixed both in -7 and meanwhile filed a fake RC bug on fltk1.3 [1] to ensure that my latest upload of it doesn't migrate until fltk1.4 is ready to avoid a gap in fluid's availability. [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1102893 FTR: unblock fltk1.4/1.

Bug#1102893: fltk1.3: fake RC bug to delay migration until fltk1.4 is ready

2025-04-12 Thread Aaron M. Ucko
Source: fltk1.3 Version: 1.3.11-1 Severity: serious fluid should remain continuously available in testing. -- System Information: Debian Release: trixie/sid APT prefers testing-debug APT policy: (500, 'testing-debug'), (500, 'stable-security'), (500, 'stable-debug'), (500, 'oldstable-securit

Bug#1102671: unblock: fltk1.4/1.4.2-6

2025-04-11 Thread Aaron M. Ucko
Control: retitle 1102671 unblock: fltk1.4/1.4.2-6 "Aaron M. Ucko" writes: > unblock fltk1.4/1.4.2-5 Please make that unblock fltk1.4/1.4.2-6 which I'll upload soon with a fix for https://bugs.debian.org/1102681 (and a proper m68k symbols fix while I'm at it). Tha

Bug#1102671: unblock: fltk1.4/1.4.2-5

2025-04-11 Thread Aaron M. Ucko
Package: release.debian.org Severity: normal X-Debbugs-Cc: fltk...@packages.debian.org Control: affects -1 + src:fltk1.4 User: release.debian@packages.debian.org Usertags: unblock Please unblock package fltk1.4. It implements long-awaited Wayland support [1], and its runtime libraries can coe

Bug#1099996: ITP: fltk1.4 -- Fast Light ToolKit 1.4.x

2025-03-26 Thread Aaron M. Ucko
d appreciate testing in due course, particularly if you run Wayland natively anywhere. -- 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

Bug#1099996: ITP: fltk1.4 -- Fast Light ToolKit 1.4.x

2025-03-09 Thread Aaron M. Ucko
Package: wnpp Severity: wishlist Owner: "Aaron M. Ucko" X-Debbugs-Cc: debian-de...@lists.debian.org * Package name: fltk1.4 Version : 1.4.2 Upstream Contact: f...@fltk.org * URL : https://www.fltk.org/ * License : LGPL-2+ with static linking

Bug#1098984: ncbi-entrez-direct,acedb-other: ship conflicting file

2025-02-26 Thread Aaron M. Ucko
he diverted instance or its own code, depending on usage. (Their syntax is conveniently very different.) Likewise for einfo, as also found in epub-utils. Thanks for checking, though! -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cg

Bug#1068442: [help] Re: igblast: Package igblast does not contain binary for igblast

2024-12-03 Thread Aaron M. Ucko
ackage. I'll take a look when I get a chance. -- 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

Bug#959884: hardening-runtime: max_user_namespaces breaks uuid-runtime

2024-11-22 Thread Aaron M. Ucko
At any rate, per https://github.com/systemd/systemd/issues/35311, setting the limit to 0 now also breaks the latest systemd version (257~rc2-3).  I haven't attempted to assess the minimum it needs.

Bug#1077454: [Debian-med-packaging] Bug#1077454: bioperl-run: t/SABlastPlus.t failure

2024-11-20 Thread Aaron M. Ucko
->factory->stderr =~ /No alias or index file found/); + return 0 if ($self->factory->stderr =~ /No alias or index file found|Database memory map file error/); return 1; } return; -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.

Bug#1075868: ncbi-vdb: FTBFS with MbedTLS 3.6

2024-10-21 Thread Aaron M. Ucko
; I'm glad there's nothing else I need to do here after all. Thanks for maintaining MbedTLS in Debian! -- 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

Bug#1075868: ncbi-vdb: FTBFS with MbedTLS 3.6

2024-10-20 Thread Aaron M. Ucko
Oops, arranging to use system Mbed TLS 3.6 in lieu of vendored 3.2.1 didn't work out quite as well as I'd initially thought, with builds succeeding but actual usage attempts failing. AFAICT, we need to add a call to psa_crypto_init and make other tuneups TBD. -- Aaron M. Ucko, KB1C

Bug#1085073: dpkg: please expose no-triggers mode to hooks

2024-10-14 Thread Aaron M. Ucko
argument apt (or cupt) would then pass, something like --phase={start,middle,end}. -- 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

Bug#1085073: dpkg: please expose no-triggers mode to hooks

2024-10-13 Thread Aaron M. Ucko
Package: dpkg Version: 1.22.11 Severity: normal X-Debbugs-Cc: debian-security-supp...@packages.debian.org As dpkg's man page notes, complex apt runs can yield multiple invocations of dpkg and hence also of dpkg-level hooks. As (at minimum) I and the reporters of #775503 and #931344 have found, th

Bug#1078825: src:ncbi-tools6: unsatisfied build dependency in testing: libpcre3-dev

2024-09-04 Thread Aaron M. Ucko
upload a fix when I get a chance, probably over the weekend. Sorry for the noise about slated autoremovals, meanwhile. -- 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

Bug#1077777: Bug#1077941: RM: ncbi-blast+ [s390x] -- ANAIS; BE support subtly broken

2024-08-08 Thread Aaron M. Ucko
tags 1077941 + wontfix done 1077941 thanks "Aaron M. Ucko" writes: > Removal is still on the table, but I'm taking another look at > the feasibility of instituting a proper fix in the near future after > all. I wound up finding an adequate workaround (arranging for big

Bug#1077941: RM: ncbi-blast+ [s390x] -- ANAIS; BE support subtly broken

2024-08-04 Thread Aaron M. Ucko
Package: ftp.debian.org Severity: normal X-Debbugs-Cc: ncbi-bla...@packages.debian.org Control: affects -1 + src:ncbi-blast+ User: ftp.debian@packages.debian.org Usertags: remove Per https://bugs.debian.org/107, two of ncbi-blast+'s reverse dependencies (cct and kleborate) encountered auto

Bug#1077777: ncbi-blast+: makeblastdb yields broken DBs on s390x (BE generally?)

2024-08-01 Thread Aaron M. Ucko
ng to -O on sh4 because disabling parallelism was insufficient to avoid virtual memory exhaustion. -- 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

Bug#1076983: dgit: sometimes tries to run QF linkorigs twice

2024-07-25 Thread Aaron M. Ucko
=always > Could you share the debug log ? I've attached a full - log from the above push-source invocation. > I think the linkorigs step is supposed to be idempotent. It evidently isn't. Thanks for the quick reply, at any rate! -- Aaron M. Ucko, KB1CJC (amu at alum.

Bug#1076983: dgit: sometimes tries to run QF linkorigs twice

2024-07-24 Thread Aaron M. Ucko
Package: dgit Version: 11.10 Severity: normal My attempts to run dgit push-source --collab-non-dgit for ncbi-tools6 6.1.20170106+dfsg2-3 a little while ago failed: dgit: error: (sym)link /home/amu/src/ncbi-tools6/ncbi-tools6-git/../ncbi-tools6_6.1.20170106+dfsg2.orig.tar.xz ncbi-tools6_6.

Bug#1072383: lintian: flag packages bloated by auxiliary tests/docs/examples

2024-06-01 Thread Aaron M. Ucko
Package: lintian Version: 2.117.0 Severity: normal A number of binary packages accompany their primary content by tests, examples, and/or other documentation that appreciably increase their size, in some cases by more than an order of magnitude, and as such would be very reasonable to split out.

Bug#1067957: [[maude-bugs]] [EXTERNAL] Re: Maude fails to build on armhf

2024-04-10 Thread Aaron M. Ucko
n overhead would be negligible in practice. 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

Bug#1065961: sra-sdk: Please drop dependencies on python3-distutils

2024-03-13 Thread Aaron M. Ucko
dependency, which I called out just now: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066833 Thanks for the report, though! -- 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

Bug#1066833: dh-python: depends on legacy python3-distutils

2024-03-13 Thread Aaron M. Ucko
Package: dh-python Version: 6.20240310 Severity: important I'm sure I'm not alone in having a request [1] to ensure a package builds without legacy python3-distutils. However, sra-sdk, for one, uses dh-python, which still depends on python3-distutils. As such, removing the explicit build depende

Bug#1065333: q2-types: test data heavily outweighs actual code

2024-03-02 Thread Aaron M. Ucko
Package: q2-types Version: 2024.2.0-1 Severity: minor The latest q2-types release increased its disk footprint from 800 kB or so to nearly 52 MB. AFAICT, the increase is largely due to the addition of test data, most notably two 19.5+ MB eggnog.db files, a 6.6+ MB eggnog.taxa.db.traverse.pkl acco

Bug#1063800: Should we restrict libtread-pool to 64bit only

2024-02-12 Thread Aaron M. Ucko
Andreas Tille writes: >Build-Depends libthread-pool 4.0.0 which does not build >for 32bit architectures[1] I see a fix in experimental: https://buildd.debian.org/status/package.php?p=libthread-pool&suite=experimental Why not just reupload it to unstable? -- Aaron M. Uc

Bug#1063115: fltk1.3: NMU diff for 64-bit time_t transition

2024-02-05 Thread Aaron M. Ucko
arrange for unaffected architectures' dependency templates to read e.g. libfltk1.3t64 #MINVER# | libfltk1.3 #MINVER# Sorry if I missed any relevant discussion; I must confess I haven't followed -devel in years. :-/ -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) ht

Bug#1058886: irqbalance: floods logs with ---...--- lines

2023-12-17 Thread Aaron M. Ucko
Package: irqbalance Version: 1.9.3-1 Severity: normal Since the latest irqbalance upgrade, I've been encountering log lines like 2023-12-17T10:08:10.722658-05:00 v100a irqbalance[4194303]: #012#012#012- every ten second

Bug#1055761: python3-selenium: *WebKit*/RemoteWebDriver __init__ skew

2023-11-10 Thread Aaron M. Ucko
Package: python3-selenium Version: 4.14.0+dfsg-1 Severity: normal Tags: upstream python3-selenium's WebKitGTK and WPEWebKit backends are both unusable even when supplied explicit executable paths to keep them from trying to go through the (understandably) unpackaged driver manager, because *WebKit

Bug#869510: dhtnode: please handle connection problems gracefully

2023-10-21 Thread Aaron M. Ucko
Thanks for your work here, and sorry for the earlier confusion! -- 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

Bug#1054267: RM: fltk1.1 -- RoQA; leaf library

2023-10-20 Thread Aaron M. Ucko
ndencies, so the package will still need a sourceful upload; copying its migration bug accordingly. > I am going to file a RM bug when this is autoremoved from testing. Thanks! To confirm, I don't need to do anything active here, just leave this bug open at RC severity and reencourage drawxt

Bug#1053904: location-update can take very long to restart

2023-10-13 Thread Aaron M. Ucko
Package: location Version: 0.9.16-2.1 Severity: normal I've found that restarting location-update (as needrestart prompts me to do after upgrading Python or a shared library it uses) can take ages, to the point where I generally give up and kill the systemctl process, letting the start job continu

Bug#891197: ncbi-blast+ is marked for autoremoval from testing

2023-09-05 Thread Aaron M. Ucko
Control: severity 891197 normal u...@debian.org (Aaron M. Ucko) writes: > For the time being, we can switch to an embedded copy of classic PCRE by > dropping the build dependency on libpcre3-dev; that's of course not a > proper fix, but should at least let us downgrade this bug

Bug#891197: ncbi-blast+ is marked for autoremoval from testing

2023-08-23 Thread Aaron M. Ucko
f classic PCRE by dropping the build dependency on libpcre3-dev; that's of course not a proper fix, but should at least let us downgrade this bug's severity. -- 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

Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1

2023-07-14 Thread Aaron M. Ucko
usting my workflow to DTRT. -- 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

Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1

2023-07-13 Thread Aaron M. Ucko
u...@debian.org (Aaron M. Ucko) writes: >> The fix itself looks fine, so please feel free to go ahead (with the >> Closes: removed and possibly with .gitignore restored if appropriate). > > Will do, thanks! Uploaded, final debdiff confirmed not to touch .gitignore. Thanks!

Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1

2023-07-13 Thread Aaron M. Ucko
f looks fine, so please feel free to go ahead (with the > Closes: removed and possibly with .gitignore restored if appropriate). Will do, 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

Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1

2023-07-12 Thread Aaron M. Ucko
-6~deb12u1) bookworm; urgency=medium + + * Reupload to bookworm (stable). (Closes: #10nnnnn). + + -- Aaron M. Ucko Wed, 12 Jul 2023 22:20:14 -0400 + +sra-sdk (3.0.3+dfsg-6) unstable; urgency=high + + * debian/rules: Expand $(DEB_HOST_MULTIARCH) in libngs-java.links.in. +(Closes: #1039621.)

Bug#1039089: [PATCH 1/1] correct_posix1e_v1_delimiters: provide path for error messages

2023-07-02 Thread Aaron M. Ucko
ganic" test case. Thanks for the fix! -- 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

Bug#1039621: libngs-jni: Installs shared object in wrong directory

2023-06-27 Thread Aaron M. Ucko
led. I went with a minimal fix, in part to facilitate getting it into a stable update if anyone considers that warranted. -- 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

Bug#1039089: bup: _correct_posix1e_v1_delimiters usage mismatch

2023-06-25 Thread Aaron M. Ucko
Package: bup Version: 0.33.1-1 Severity: important Tags: upstream Updating a save that had old-format ACL metadata (from e.g. /var/log/journal) fails with ... File "/usr/lib/bup/bup/metadata.py", line 864, in read result._load_posix1e_acl_rec(port, version=1) File "/usr/lib/bup/bu

Bug#1034369: C++ help needed

2023-04-14 Thread Aaron M. Ucko
andom_value here and in the other unittests/*map.hpp headers to match the corresponding containers' declarations, per the attached patch. The relevant platform difference is whether plain char is signed, as it notably is on x86 but not arm*. (There are other architectures in each camp.) --

Bug#1031853: sra-sdk: Unsatisfied dependency in libngs-java on any platform other than arm64 and amd64

2023-02-24 Thread Aaron M. Ucko
27;s dependency on VDB left me no choice. -- 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

Bug#1029987: RM: paleomix [mips64el ppc64el] -- ANAIS; indirect dep on libngs-java unsatisfiable

2023-01-29 Thread Aaron M. Ucko
mips64el and ppc64el to unblock the current libngs-* packages (and sra-sdk more broadly)? 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

Bug#1029474: closed by Scott Kitterman (Re: RM: sra-sdk [i386 x32] -- ANAIS; requires a 64-bit address space)

2023-01-23 Thread Aaron M. Ucko
ure that is not managed by the FTP Team. Ah, OK; I wasn't entirely clear on the logistical details.  Do you happen to know the SOP for getting cruft cleaned up on that front?  I know it doesn't block migration, but I still might as well flag it. -- Aaron M. Ucko, KB1CJC (amu at

Bug#1029478: RM: skesa [i386 x32] -- ANAIS; build dependencies unavailable

2023-01-22 Thread Aaron M. Ucko
Package: ftp.debian.org Severity: normal User: ftp.debian@packages.debian.org Usertags: remove X-Debbugs-Cc: sk...@packages.debian.org Control: affects -1 + src:skesa Per other recent removal requests[1][2][3], skesa's build dependencies are available only on amd64 and (now) arm64 at this poin

Bug#1029477: RM: dictionary-el -- ROM; redundant as of emacs 28

2023-01-22 Thread Aaron M. Ucko
Package: ftp.debian.org Severity: normal User: ftp.debian@packages.debian.org Usertags: remove X-Debbugs-Cc: dictionary...@packages.debian.org Control: affects -1 + src:dictionary-el Because dictionary-el uses dh-elpa these days, it integrates only with GNU Emacs, which however incorporated th

Bug#1029475: RM: ngs-sdk -- ROM; subsumed by sra-sdk 3.x

2023-01-22 Thread Aaron M. Ucko
Package: ftp.debian.org Severity: normal User: ftp.debian@packages.debian.org Usertags: remove X-Debbugs-Cc: sra-...@packages.debian.org Control: affects -1 + src:sra-sdk sra-sdk 3.x subsumed ngs-sdk, albeit with only partial overlap because the C library changed both its basename and its SO v

Bug#1029474: RM: sra-sdk [i386 x32] -- ANAIS; requires a 64-bit address space

2023-01-22 Thread Aaron M. Ucko
Package: ftp.debian.org Severity: normal User: ftp.debian@packages.debian.org Usertags: remove X-Debbugs-Cc: sra-...@packages.debian.org Control: affects -1 + src:sra-sdk Fully building sra-sdk requires a 64-bit address space these days. It might be possible to contrive to build some of its bi

Bug#1029472: RM: ncbi-vdb [i386] -- ANAIS; upstream fully dropped i386 support

2023-01-22 Thread Aaron M. Ucko
Package: ftp.debian.org Severity: normal User: ftp.debian@packages.debian.org Usertags: remove X-Debbugs-Cc: ncbi-...@packages.debian.org Control: affects -1 + src:ncbi-vdb ncbi-vdb 3.x switched to a new build system that supports only a narrow list of architectures, with specific associated s

Bug#869510: dhtnode: please handle connection problems gracefully

2023-01-15 Thread Aaron M. Ucko
total cached nodes IPv6 stats: Known nodes: 0 good, 0 dubious, 0 incoming. 0 searches, 0 total cached nodes Meanwhile, all I see in the log is dhtnode[...]: Bootstrap: bootstrap.ring.cx Thanks for asking! -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://w

Bug#1028165: libfltk1.3-dev: Missing dependency on fluid?

2023-01-07 Thread Aaron M. Ucko
r broke the logic to honor FLTK_SKIP_FLUID (which I've confirmed remains present). Thanks for the report (reminiscent of [1], FWIW), and sorry for the trouble! [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=855040 -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)

Bug#891197: Please switch to pcre2

2022-12-05 Thread Aaron M. Ucko
o moving on, albeit at low priority. -- 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

Bug#982384: [Help] Bug 982384: Warnings profile count data file not found

2022-12-04 Thread Aaron M. Ucko
ile-generate option. It may be simplest to drop the option, particularly if cross compilation is otherwise possible. -- 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

Bug#891197: Please switch to pcre2

2022-12-04 Thread Aaron M. Ucko
Andreas Tille writes: > it would be great if you could use your upstream contact to convince > them to switch to pcre2. Upstream explicitly passed on pcre2 a few years ago, but times have changed; I've opened an internal ticket to revisit the question. -- Aaron M. Ucko, KB1

Bug#1024155: Fixed in Git [Re: libngs-c++-dev: missing Breaks+Replaces: libncbi-vdb-dev (<< 3), libngs-sdk-dev (<< 3)]

2022-12-01 Thread Aaron M. Ucko
ere sra-sdk 3.x stands in terms of architecture support, which may be clearer with upgrades to 3.0.1 in place. I've been working on them, but a power outage last weekend delayed me; I'll try to wrap them up this weekend. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)

Bug#1025004: dash: errors in sourced functions reported against wrong files

2022-11-28 Thread Aaron M. Ucko
Package: dash Version: 0.5.11+git20210903+057cd650a4ed-9 Severity: normal I have found that dash defers "bad substitution" errors until actually attempting to evaluate the substitution in question. That in itself is plausibly legitimate, particularly given that bash does the same. However, when

Bug#1024155: libngs-c++-dev: missing Breaks+Replaces: libncbi-vdb-dev (<< 3), libngs-sdk-dev (<< 3)

2022-11-15 Thread Aaron M. Ucko
Andreas Beckmann writes: > during a test with piuparts I noticed your package fails to upgrade from > 'sid' to 'experimental'. Good catch, 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

Bug#1014797: FTBFS: test failures with new libgd3

2022-09-29 Thread Aaron M. Ucko
ackaging fix (for #624130) and stayed there by inertia. -- 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

Bug#1012893: [Help] anfo: ftbfs with GCC-12

2022-09-29 Thread Aaron M. Ucko
lue: std::unique_ptr&& is -- 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

Bug#1012893: [Help] anfo: ftbfs with GCC-12

2022-09-28 Thread Aaron M. Ucko
errors in the rare cases where its usage would be problematic. -- 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

Bug#1017271: zynaddsubfx: FTBFS: make[3]: *** No rule to make target 'src/UI/fluid', needed by 'src/UI/VirKeyboard.h'. Stop.

2022-09-06 Thread Aaron M. Ucko
Adrian Bunk writes: > Makes sense. Thanks. > It would also be useful if fltk1.3 would FTBFS when an input file was > not found. Don't worry, I'm already planning to put in such a safeguard at this point. Sorry for missing this possible failure mode earlier. -- Aaron M

Bug#1017271: zynaddsubfx: FTBFS: make[3]: *** No rule to make target 'src/UI/fluid', needed by 'src/UI/VirKeyboard.h'. Stop.

2022-09-06 Thread Aaron M. Ucko
xport/*/FLTK-Targets-none.cmake \ Got it, thanks, though I'm inclined to use find(1) so I'm not specifically tied to new cmake. -- 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

Bug#1017271: zynaddsubfx: FTBFS: make[3]: *** No rule to make target 'src/UI/fluid', needed by 'src/UI/VirKeyboard.h'. Stop.

2022-09-06 Thread Aaron M. Ucko
t have been to patch CMake's input, but I want to make some across-the-board tweaks that are best centralized modulo this sort of wrinkle.) I'll take a look when I get a chance. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.

Bug#1017421: fltk1.3: reproducible builds: locale-specific month embedded in fltk.pdf

2022-08-15 Thread Aaron M. Ucko
issues. I seem to recall some other wrinkles, but I'll be happy to move closer to reproducibility regardless. > ++TODAY=`date -ud'$(DEB_DATE)' +'%Y-%m-%s'`; \ ITYM '%Y-%m-%d' or '%F' -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.

Bug#1013940: New version of nfft breaks its autopkgtest (Was: nfft breaks pynfft autopkgtest on i386: Segmentation fault

2022-07-27 Thread Aaron M. Ucko
rence to `nfftf_init_1d' [...] Please try listing simple_test.c ahead of the libraries, which the linker otherwise discards as apparently unneeded. -- 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

Bug#1013608: marked as done (ncbi-entrez-direct: FTBFS: cannot find package "github.com/shirou/gopsutil/mem")

2022-06-24 Thread Aaron M. Ucko
golang-github-pbnjay-memory-dev now that the latter exists. -- 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

Bug#1010110: ncbi-blast+: terminate called after throwing an instance of 'ncbi::CIO_Exception'

2022-04-24 Thread Aaron M. Ucko
Patrice DUROUX writes: > Using the same command line with different versions of the package, Can you please give an example of a command line that reproduces the error? Thanks! -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.

Bug#1010087: waylandpp: please split out a -doc package

2022-04-23 Thread Aaron M. Ucko
Source: waylandpp Version: 0.2.10-1 Severity: minor waylandpp-dev's size increased from 843 kB to 14.4 MB between versions 0.2.8-2 and 0.2.10-1 on amd64, with other architectures presumably also encountering similar increases. AFAICT, this massive increase comes primarily from Doxygen's generated

Bug#1003631: dlocate: update-dpkg-list can deadlock

2022-01-13 Thread Aaron M. Ucko
Craig Sanders writes: > On Wed, Jan 12, 2022 at 06:06:45PM -0500, Aaron M. Ucko wrote: >> Long story short, update-dpkg-list's batched bidirectional pipe usage wound >> up deadlocking on a system with 20,000+ provided virtual packages, mostly >> from installed librust-*

Bug#1003631: dlocate: update-dpkg-list can deadlock

2022-01-12 Thread Aaron M. Ucko
Package: dlocate Version: 1.09 Severity: important Long story short, update-dpkg-list's batched bidirectional pipe usage wound up deadlocking on a system with 20,000+ provided virtual packages, mostly from installed librust-*-dev packages. Could you please take a look? Thanks! -- System Informa

Bug#1002579: libfltk1.3-dev: libfltk1.3-dev is not Multi-Arch:same

2021-12-30 Thread Aaron M. Ucko
Dima Kogan writes: > /bin/sh: 1: test: =: unexpected operator For whatever reason, I didn't run into that one; I'll look into it. Thanks for pointing it out and for confirming that all is otherwise well. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http:

Bug#1002880: signing-party: caff defaults to retired pool.sks-keyservers.net

2021-12-30 Thread Aaron M. Ucko
That's fair. In that case, though, perhaps caff should refrain from suggesting any specific server or pool until there's a sufficiently good choice again. -- 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

Bug#1002880: signing-party: caff defaults to retired pool.sks-keyservers.net

2021-12-30 Thread Aaron M. Ucko
Package: signing-party Version: 2.11-1 Severity: normal caff has historically defaulted to looking keys up on pool.sks-keyservers.net and recommending that signees upload their keys there. However, per https://sks-keyservers.net/, that pool is no longer in service. Could you please substitute so

Bug#1002579: libfltk1.3-dev: libfltk1.3-dev is not Multi-Arch:same

2021-12-29 Thread Aaron M. Ucko
u...@debian.org (Aaron M. Ucko) writes: > Only in the context of package builds; in other contexts (ad-hoc builds > against system FLTK), it's currently entirely possible to have only > libfltk1.3-dev installed. I could perhaps downgrade the dependency to a > recommendation, but

Bug#1002579: libfltk1.3-dev: libfltk1.3-dev is not Multi-Arch:same

2021-12-25 Thread Aaron M. Ucko
em FLTK), it's currently entirely possible to have only libfltk1.3-dev installed. I could perhaps downgrade the dependency to a recommendation, but I don't think it would be unreasonable to leave it as a full dependency. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.or

Bug#1002579: libfltk1.3-dev: libfltk1.3-dev is not Multi-Arch:same

2021-12-25 Thread Aaron M. Ucko
g-dev:any, but that should be straightforward and uncontroversial. -- 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

Bug#1002579: libfltk1.3-dev: libfltk1.3-dev is not Multi-Arch:same

2021-12-24 Thread Aaron M. Ucko
friendly by moving the files to architecture-specific paths and arranging to select appropriate instances dynamically. If you're up for putting together such a patch, I'll be happy to consider it; otherwise, I'll try to find time myself. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, u

Bug#1002253: Help with possibly broken ar archive

2021-12-21 Thread Aaron M. Ucko
akefile to drop the T flag from LINK.A (line 72). -- 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

Bug#1000358: ncbi-blast+: Please rebuild against MBEDTLS 2.16.11

2021-11-30 Thread Aaron M. Ucko
Andreas Tille writes: > I'd be really happy if you would consider separating changes that > require a trip to new. I'm already specifically planning NOT to make any such changes now; sorry if that was unclear. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at

Bug#1000358: ncbi-blast+: Please rebuild against MBEDTLS 2.16.11

2021-11-30 Thread Aaron M. Ucko
e to take care of it within the next day or two, holding off for now on other non-routine changes -- and particularly on implementation of #984871, which would entail a trip through NEW (and moreover has severity wishlist). -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.

Bug#1000358: ncbi-blast+: Please rebuild against MBEDTLS 2.16.11

2021-11-21 Thread Aaron M. Ucko
Stefano Rivera writes: > Critical: External MBEDTLS version mismatch: 2.16.9 headers vs. 2.16.11 > runtime Thanks for the report! FTR, the correct fix will be to disable this overstrict version check in favor of trusting dpkg-shlibdeps, as previously done for GNUTLS. -- Aaron M

Bug#984243: Help: mothur: ftbfs with GCC-11

2021-11-08 Thread Aaron M. Ucko
command line later on. > Any idea how to specify the number of object files more sensibly > to not explode the command line arguments too much? You (or upstream) could consider using internal static libraries. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http

Bug#997209: [Help needed] eegdev: FTBFS: ./doc/examples/library-usage/eegdev_acq.c:214: undefined reference to `rpl_free'

2021-11-02 Thread Aaron M. Ucko
rely for its own use.) -- 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

Bug#984243: Help: mothur: ftbfs with GCC-11

2021-10-25 Thread Aaron M. Ucko
Andreas Tille writes: > I'm wondering why the makefile stopped working just because a new compiler > version is used. :-( Along the way, you pulled in a new upstream version, whose makefile evidently wasn't quite right. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at

Bug#793549: cmake-data: Can't find fluid with FLTK 1.3.3

2021-10-22 Thread Aaron M. Ucko
sufficient for you to consider this bug done? Sure, 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

Bug#984243: Help: mothur: ftbfs with GCC-11

2021-10-22 Thread Aaron M. Ucko
p,%.o,$(wildcard source/*.cpp)) OBJECTS+=$(patsubst %.c,%.o,$(wildcard source/*.c)) to match the relevant sources' actual location; sorry if that was unclear. (The existing setup only covers subdirectories of source, missing that directory's immediate contents.) -- Aaron M. Ucko,

Bug#984243: Help: mothur: ftbfs with GCC-11

2021-10-21 Thread Aaron M. Ucko
/uchime_src/makefile to add -std=c++14 to CXXFLAGS, thereby suppressing std::byte for now. I also found massive link errors, resolvable by correcting the top-level Makefile to pick up source/*.cpp and source/*.c rather than the nonexistent *.cpp and *.c. [1] https://en.cppreference.com/w/cpp/types/byte

Bug#996794: ncbi-acc-download: autopkgtest failure with python-biopython 1.79+dfsg-1~0exp0 in experimental

2021-10-20 Thread Aaron M. Ucko
rd > to make sure it is functionally equivalent. Great, thanks! I suppose it might be slightly cleaner to factor out a helper predicate function. -- 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

Bug#996794: ncbi-acc-download: autopkgtest failure with python-biopython 1.79+dfsg-1~0exp0 in experimental

2021-10-19 Thread Aaron M. Ucko
ng full-length live data instead. -- 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

Bug#995349: ncbi-entrez-direct: FTBFS: no required module provides package github.com/fiam/gounidecode/unidecode

2021-09-30 Thread Aaron M. Ucko
ll look into doing so when I get a chance. -- 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

Bug#994714: ncbi-blast+: makeblastdb output dependent of endianness

2021-09-20 Thread Aaron M. Ucko
Étienne Mollier writes: > the pieces of the puzzle together. Thanks for your explanation, No problem; please feel free to ping me if there's anything else I can clarify. Also, sorry for the badly half-baked metadata update. > Have a nice day, :) Thanks, you too! -- Aaron M. U

Bug#994714: ncbi-blast+: makeblastdb output dependent of endianness

2021-09-19 Thread Aaron M. Ucko
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=959587 https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960756 and especially https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=981293 Thanks for checking! -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ |

Bug#992993: libapt-pkg6.0: infinite recursion in pkgDepCache::MarkPackage

2021-08-26 Thread Aaron M. Ucko
u...@debian.org (Aaron M. Ucko) writes: > David Kalnischkies writes: > >> Points at my changes in 2.3.3, especially "Mark only provides from >> protected versioned kernel packages", as the most likely culprit. I went ahead with git bisect h

Bug#992993: libapt-pkg6.0: infinite recursion in pkgDepCache::MarkPackage

2021-08-25 Thread Aaron M. Ucko
ease take a look? 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 -- apt-config dump -- APT ""; APT::Architecture "amd64"; APT::Build-Essential ""; APT::Build-Es

Bug#990741: [nore...@release.debian.org: ncbi-entrez-direct is marked for autoremoval from testing]

2021-07-14 Thread Aaron M. Ucko
Yes, 990743, already granted. It doesn't appear to have reduced the delay below what the autopkgtest already gave, though. -- Aaron On July 15, 2021 12:08:17 AM EDT, Andreas Tille wrote: >Hi Aaron, > >did you filed an unblock request to release.debian.org bug report? > >Kind regards >Andrea

Bug#990743: unblock: ncbi-entrez-direct/14.6.20210224+dfsg-4

2021-07-08 Thread Aaron M. Ucko
Paul Gevers writes: > On 08-07-2021 21:06, Aaron M. Ucko wrote: >> I should be able to upload around 22:00 UTC. (Also, I take it you're OK >> with the full version, since you didn't indicate otherwise.) Thanks much! > > Yes. Uploaded. Thanks again! --

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