Bug#1103457: Unable to boot LUKS-encrypted system

2025-04-20 Thread Aaron Rainbolt
I discussed this issue upstream and it looks like the current behavior when using `hostonly=no` may be a bug. See [1]. Setting `hostonly=yes hostonly_mode=sloppy` might be the wrong thing to do. [1] https://github.com/dracut-ng/dracut-ng/pull/1238#issuecomment-2814286818 pgpEiROfUxkQ3.pgp Descri

Bug#1103457: Unable to boot LUKS-encrypted system

2025-04-17 Thread Aaron Rainbolt
Package: dracut Version: 106-5 Severity: critical X-Debbugs-Cc: adrela...@whonix.org, arraybo...@ubuntu.com Unsure if the chosen severity is appropriate, but this bug renders affected systems unbootable and the recovery procedure is a serious headache, so I think this counts as "breaking the whole

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#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#1091096: src:picom-conf: unsatisfied build dependency in testing: liblxqt1-dev

2025-01-26 Thread Aaron Rainbolt
Somehow my email setup is b0rked and I'm only just now learning about this bug. Mohammed Bilal graciously prepped an NMU to fix it, which he sent me a debdiff of and which I reviewed and +1'd, so hopefully this won't be a problem for much longer. I guess I'll figure out what I did wrong with emails

Bug#1087059: calamares: diff for NMU version 3.3.12-1.1

2024-12-20 Thread Aaron Rainbolt
* Add Breaks/Replaces against older versions of calamares-extensions. +(Closes: #1087059) + + -- Aaron Rainbolt Wed, 18 Dec 2024 17:48:25 -0600 + calamares (3.3.12-1) unstable; urgency=medium * New upstream release diff -Nru calamares-3.3.12/debian/control calamares-3.3.12/debian/co

Bug#1087059: calamares has an undeclared file conflict

2024-12-18 Thread Aaron Rainbolt
FYI, unless anyone has objections, I intend on proposing an NMU for this later today, and will work to find a sponsor for it on Friday. pgp_sLkuhCa62.pgp Description: OpenPGP digital signature

Bug#1087059: calamares has an undeclared file conflict

2024-11-20 Thread Aaron Rainbolt
This is because of a module that moved from calamares-extensions to calamares. calamares-extensions 3.3.11 solves the issue, however a tarball of it hasn't been published yet. I've pinged the Calamares developers to see if a full release of calamares-extensions 3.3.11 can be made. Once that's done

Bug#1085165: libgrokj2k: FTBFS on armhf: ‘vreinterpret_f16_u16’ was not declared in this scope

2024-11-14 Thread Aaron Boxer
anyone on this thread is able, would you mind uploading this package ? Many Thanks, Aaron

Bug#1086017: zless: errors out with "less: not found" if less is not installed

2024-10-24 Thread Aaron Rainbolt
Package: gzip Version: 1.12-1.1 Severity: serious Justification: Policy 3.8 X-Debbugs-Cc: arraybo...@gmail.com gzip is a package with priority "essential". It currently suggests the "less" package, which has priority "important". less is a hard dependency of zless - if it is not installed, zless w

Bug#1085165: libgrokj2k: FTBFS on armhf: ‘vreinterpret_f16_u16’ was not declared in this scope

2024-10-24 Thread Aaron Boxer
Hello, Project maintainer here. I will be releasing a new package for libgrokj2k in the coming week, which should address this armhf bug. Cheers, Aaron

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#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#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#1061277: abinit: FTBFS with Python 3.12

2024-01-21 Thread Aaron Rainbolt
Source: abinit Version: 9.10.4-2 Severity: serious Tags: ftbfs upstream Justification: fails to build from source (but built successfully in the past) X-Debbugs-Cc: arraybo...@ubuntu.com When building the abinit package on a system with Python 3.12 installed, the build fails with a "ModuleNotFound

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-12-10 Thread Aaron Rainbolt
On 12/10/23 12:08, Bas Wijnen wrote: On Sun, Dec 03, 2023 at 02:18:38AM -0600, Aaron Rainbolt wrote: [Catch 2] While it is definitely possible to port the openMSX tests to use catch2 v3, we will be departing from what upstream supports, and that seems like it could lead to way more work than

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-12-07 Thread Aaron Rainbolt
ttern "Contrib/cbios" to "Contrib/cbios/*.rom" in debian/copyright. The change is minor enough I don't think it warrants a whole new debdiff attachment, though I'm happy to make one if it would make your life easier. -- Aaron Rainbolt Lubuntu Developer Matrix: @array

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-12-07 Thread Aaron Rainbolt
Is this bug something we're still actively working on? It's been a few days. If I missed something, feel free to let me know. -- Aaron Rainbolt Lubuntu Developer Matrix: @arraybolt3:matrix.org IRC: arraybolt3 on irc.libera.chat GitHub: https://github.com/ArrayBolt3

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-12-03 Thread Aaron Rainbolt
s *are* compiled from other source code. Perhaps there's some sort of heuristic there though (I've not looked at the Lintian code and I don't know Perl, so I'm not sure). > Thanks, > Bas > > On Wed, Nov 29, 2023 at 06:50:59PM -0600, Aaron Rainbolt wrote: > > Alr

Bug#1056897: [3dprinter-general] Bug#1056897: FTBFS: Plater.cpp:5313: error: call of overloaded ‘load_files?=()=?UTF-8?Q?’ is ambiguous

2023-11-30 Thread Aaron Rainbolt
On 11/30/23 16:34, Gregor Riepl wrote: Hi Aaron, Simon is uploading the new packaging to the DELAYED/1 queue. It should arrive in the archive on November 30. If you are a maintainer of slic3r-prusa, you can review the new packaging in the mean time and reject or fast-track it as you see fit

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-29 Thread Aaron Rainbolt
with me so we could come up with the best solution possible for this! The debdiff is attached. -- Aaron Rainbolt Lubuntu Developer Matrix: @arraybolt3:matrix.org IRC: arraybolt3 on irc.libera.chat GitHub: https://github.com/ArrayBolt3 Binary files /tmp/jiw28Q_kI0/openmsx-19.1/Contrib/cbios/cbios

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-29 Thread Aaron Rainbolt
On 11/29/23 14:40, Bas Wijnen wrote: On Wed, Nov 29, 2023 at 01:52:46PM -0600, Aaron Rainbolt wrote: It appears that the C-BIOS package in Debian only ships the most recent C-BIOS files. I think we can't just depend on it for this reason, since the older C-BIOS ROMs are needed to avoid

Bug#1056897: FTBFS: Plater.cpp:5313: error: call of overloaded ‘load_files()’ is ambiguous

2023-11-29 Thread Aaron Rainbolt
Simon is uploading the new packaging to the DELAYED/1 queue. It should arrive in the archive on November 30. If you are a maintainer of slic3r-prusa, you can review the new packaging in the mean time and reject or fast-track it as you see fit. -- Aaron Rainbolt Lubuntu Developer Matrix

Bug#1056897: FTBFS: Plater.cpp:5313: error: call of overloaded ‘load_files()’ is ambiguous

2023-11-29 Thread Aaron Rainbolt
o get a Debian Developer (Simon Quigley) to help me NMU Gregor's patch so we can get this fixed before December 1st. The packaging is complete and has been submitted to Simon for review. -- Aaron Rainbolt Lubuntu Developer Matrix: @arraybolt3:matrix.org IRC: arraybolt3 on irc.liber

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-29 Thread Aaron Rainbolt
It appears that the C-BIOS package in Debian only ships the most recent C-BIOS files. I think we can't just depend on it for this reason, since the older C-BIOS ROMs are needed to avoid save state breakage. See Contrib/cbios-old/README in the openMSX package. -- Aaron Rainbolt Lu

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-29 Thread Aaron Rainbolt
n't want to break people's old save states. If the C-BIOS package only ships the latest version of C-BIOS, then this solution will not work. If it ships all needed versions and has them in the right spots, then this would probably work.. > Thanks, > Bas > > On Mon, Nov 27, 2023

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-27 Thread Aaron Rainbolt
/ArrayBolt3/openmsx-packaging. -- Aaron Rainbolt Lubuntu Developer Matrix: @arraybolt3:matrix.org IRC: arraybolt3 on irc.libera.chat GitHub: https://github.com/ArrayBolt3

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-27 Thread Aaron Rainbolt
On 11/27/23 15:02, Manuel Bilderbeek wrote: On 27-11-2023 02:11, Aaron Rainbolt wrote: Alright, I have fully rebuilt the copyright file. I also ended up adding the source code for several releases of C-BIOS into the packaging. As this code is in the form of zipped files for the sake of size

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-26 Thread Aaron Rainbolt
ight file. I suspect a Lintian bug here.) -- Aaron Rainbolt Lubuntu Developer Matrix: @arraybolt3:matrix.org IRC: arraybolt3 on irc.libera.chat GitHub: https://github.com/ArrayBolt3

Bug#1056780: Fwd: Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-26 Thread Aaron Rainbolt
Failed to reply to the right address, so forwarding. -- Forwarded message - From: Aaron Rainbolt Date: Sun, Nov 26, 2023 at 1:30 PM Subject: Re: Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues) To: Manuel Bilderbeek Thanks! I was

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-26 Thread Aaron Rainbolt
Further investigation trying to rebuild the copyright file has revealed more binaries without source code (the C-BIOS ROMs for instance). So I'll have to find the sources for those also. Thanks for your patience. -- Aaron Rainbolt Lubuntu Developer Matrix: @arraybolt3:matrix.or

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-26 Thread Aaron Rainbolt
opyright file should be rebuilt from scratch by auditing the entirety of the openMSX source code licenses. I can do that if it would be helpful. -- Aaron Rainbolt Lubuntu Developer Matrix: @arraybolt3:matrix.org IRC: arraybolt3 on irc.libera.chat GitHub: https://github.com/ArrayBolt3

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-25 Thread Aaron Rainbolt
"Thank you for contacting us" emails from apple.com. -- Aaron Rainbolt Lubuntu Developer Matrix: @arraybolt3:matrix.org IRC: arraybolt3 on irc.libera.chat GitHub: https://github.com/ArrayBolt3 Binary files /tmp/phkMJNskDj/openmsx-19.1/Contrib/codec/Win32/zmbv.dll and /tmp/Cd74GNmEnl/openms

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-25 Thread Aaron Rainbolt
Lintian gripes. +  * Created debian/upstream/metadata file. +  * Switch back to using vendored catch2, the catch2 Debian package now ships +    catch2 v3 whereas openMSX uses catch2 v2. + + -- Aaron Rainbolt   Fri, 24 Nov 2023 13:47:59 -0600 +  openmsx (19.1-1) unstable; urgency=medium    * New up

Bug#1056780: openmsx: Source-less Windows binary in source package (and other packaging issues)

2023-11-25 Thread Aaron Rainbolt
Package: openmsx Version: 19.1-1 Severity: serious Justification: Policy 2.2.1 X-Debbugs-Cc: arraybo...@ubuntu.com Packages in the Debian `main` archive area *must* comply with the DFSG, of which section 2 states "The program must include source code, and must allow distribution in source code as

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#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#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#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#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#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#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#1021032: vlc: playing videos results in a black screen

2022-10-10 Thread Aaron
VAAPI works nicely now under wayland, but users need to export LIBVA_DRIVER_NAME= Cheers. Aaron. libva info: VA-API version 1.15.0 libva info: User environment variable requested driver 'radeonsi' libva info: Trying to open /usr/lib/x86_64-linux-gnu/dri/radeonsi_drv_video.solibva i

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#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#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#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#990525: closed by Adam Borowski (closing)

2021-10-27 Thread Aaron Boxer
Hi Salvatore, Yes, you are correct - commit 3191336c0708 fixed the issue. I like to use rebase to squash commits, so I must have squashed away the commit that is logged in oss-fuz. Cheers, Aaron Sent with ProtonMail Secure Email. ‐‐‐ Original Message ‐‐‐ On Wednesday, October 27th

Bug#990525: closed by Adam Borowski (closing)

2021-10-27 Thread Aaron Boxer
know if you have any other questions. Cheers, Aaron Sent with ProtonMail Secure Email. ‐‐‐ Original Message ‐‐‐ On Wednesday, October 27th, 2021 at 15:34, Salvatore Bonaccorso wrote: > Hi, > > On Wed, Oct 27, 2021 at 08:57:06AM +, Debian Bug Tracking System wrote: &

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#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#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#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? &

Bug#990741: marked as pending in ncbi-entrez-direct

2021-07-08 Thread Aaron M. Ucko
Control: tag -1 pending Hello, Bug #990741 in ncbi-entrez-direct reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/commit/1520ff4905

Bug#990741: ncbi-entrez-direct: efetch and einfo wrappers warn about some supported options

2021-07-05 Thread Aaron M. Ucko
Package: ncbi-entrez-direct Version: 14.6.20210224+dfsg-3+b2 Severity: serious Justification: maintainer prerogative In the course of checking whether https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/1934402 affects ncbi-blast+ in testing and unstable, I observed -- *only* -- a different

Bug#949767: arrayfire update fails in configure step

2021-04-27 Thread Aaron M. Ucko
(include) Please try adding a build dependency on libclfft-dev and replacing src/backend/opencl/CMakeLists.txt's inclusion of build_clFFT with a call to find_package(clFFT) > Thanks a lot for your initial hint No problem. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at

Bug#949767: arrayfire update fails in configure step

2021-04-26 Thread Aaron M. Ucko
in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE (ll. 1472-1480). -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | htt

Bug#986592: closed by Debian FTP Masters (reply to u...@debian.org (Aaron M. Ucko)) (Bug#986592: fixed in kaptive 0.7.3-2)

2021-04-16 Thread Aaron M. Ucko
broadening this workaround accordingly. Meanwhile, thanks for pinging me -- I'd optimistically skipped subscribing to this bug (but will do so now). -- 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#986592: [Help] Re: Bug#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

2021-04-09 Thread Aaron M. Ucko
.org/970344), kleborate already supports retrying in single-threaded mode under some circumstances; kaptive just needs to indicate that it should do so, which it currently does only for much older versions. I'll extend the relevant version range shortly, and am reassigning this bug accordingly. -

Bug#986592: [Help] Re: Bug#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

2021-04-09 Thread Aaron M. Ucko
ails, I wanted to make very sure I wouldn't be able to lose them. Sorry for any resulting 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#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

2021-04-08 Thread Aaron M. Ucko
u...@debian.org (Aaron M. Ucko) writes: > Andreas Tille writes: > >> do you have possibly any hint what might be wrong here? > > Thanks for calling this bug to my attention! Based on reports I've seen > upstream, I suspect the problem may lie in some relatively new &

Bug#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

2021-04-07 Thread Aaron M. Ucko
gardless, in retrospect. I'll look into 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

Bug#985116: libgrokj2k: FTBFS on i386

2021-03-16 Thread Aaron Boxer
s/Ivor/Ivo/ :) On Tue, Mar 16, 2021 at 11:04 AM Aaron Boxer wrote: > Thanks, Ivor. How would you recommend I test on i386? > > On Fri, Mar 12, 2021 at 6:33 PM Ivo De Decker wrote: > >> package: src:libgrokj2k >> version: 7.6.6-2 >> severity: serious >> ta

Bug#985116: libgrokj2k: FTBFS on i386

2021-03-16 Thread Aaron Boxer
Thanks, Ivor. How would you recommend I test on i386? On Fri, Mar 12, 2021 at 6:33 PM Ivo De Decker wrote: > package: src:libgrokj2k > version: 7.6.6-2 > severity: serious > tags: ftbfs > > Hi, > > The latest upload of libgrokj2k to unstable fails on i386: > > https://buildd.debian.org/status/pa

Bug#983775: libgrokj2k: Baseline violation on amd64/i386

2021-03-10 Thread Aaron Boxer
Hello, I have created a patch for this bug: https://mentors.debian.net/package/libgrokj2k/ Thanks, Aaron On Mon, Mar 1, 2021 at 12:21 PM Adrian Bunk wrote: > Source: libgrokj2k > Version: 7.6.6-1 > Severity: serious > Tags: patch > > > https://buildd.debian.org/status/fet

Bug#983775: Patch

2021-03-10 Thread Aaron Boxer
Hello, I have a patch for this bug on the mentors site: https://mentors.debian.net/package/libgrokj2k/ Thanks, Aaron

Bug#983775: libgrokj2k: Baseline violation on amd64/i386

2021-03-08 Thread Aaron Boxer
Hi Adrian, Thanks very much for the bug report. I will make these changes. So, is it not possible to enable AVX2 acceleration for this package ? Regards, Aaron On Mon, Mar 1, 2021 at 12:21 PM Adrian Bunk wrote: > Source: libgrokj2k > Version: 7.6.6-1 > Severity: serious >

Bug#983239: libbio-db-ncbihelper-perl: (autopkg)test failures when network is available

2021-02-21 Thread Aaron M. Ucko
e liberty to open an issue in their VCS. Thanks! gregor herrmann writes: > I still think that NO_NETWORK_TESTING=1 should be set in debian/rules > to make sure there's no internet access attempted during the build, > as that is a policy violation. Right, we're just discussing wh

Bug#981293: [Help] Re: metastudent-data breaks metastudent autopkgtest: 255

2021-02-10 Thread Aaron M. Ucko
Whoops, I had a typo in that last command; if you go that route, please make it makeblastdb -dbtype prot -in "$<" -out "$(@:.psq=)" -blastdb_version 4 (I'd first try pushing forward, though.) Thanks! -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.

Bug#981293: [Help] Re: metastudent-data breaks metastudent autopkgtest: 255

2021-02-10 Thread Aaron M. Ucko
Control: tags -1 + upstream Andreas Tille writes: > Aaron (or whoever might want to check), do you have any idea? Due to metastudent-data's unwieldiness, I haven't tested thoroughly, but AFAICT the immediate, and with any luck only, problem is more fallout from the switch to BLAS

Bug#982266: fltk1.1: ftbfs in sid

2021-02-07 Thread Aaron M. Ucko
and meanwhile listing uncompressed man (and cat!) pages in debian/not-installed. -- 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#951508: lmod: broken on all architectures except x86_64 (wrong search path)

2020-10-26 Thread Aaron Zauner
Hey, Thanks for working this out guys! I think arch:all is a good solution having the Lua paths fixed upstream. Aaron On Mon, Oct 26, 2020 at 1:45 PM Lucas Nussbaum wrote: > Hi, > > On 26/10/20 at 11:19 +0100, Baptiste Jonglez wrote: > > Hi, > > > > On Tue, 15 Sep

Bug#969608: [Debian-med-packaging] Bug#969608: makeblastdb 2.10.x on 32-bit architectures

2020-09-15 Thread Aaron M. Ucko
larification: This variable is an override, not a cap, so any unconditional settings thereof should be low enough to work on 32-bit systems. -- 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#951508: A patch file

2020-09-15 Thread Aaron Zauner (azet)
working in HPC at the moment. The bug should definitely reported upstream. Upgrading the package should be fairly simple though - the dependencies are already in place, as are simple tests/git integration etc.: https://github.com/azet/lmod-deb Thanks, Aaron > On 15.09.2020, at 09:33, Luc

Bug#969608: makeblastdb 2.10.x on 32-bit architectures

2020-09-14 Thread Aaron M. Ucko
much more than upstream'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 -- 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#969608: makeblastdb 2.10.x on 32-bit architectures

2020-09-13 Thread Aaron M. Ucko
last/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. -- 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#969608: ncbi-blast+: regressions on armhf

2020-09-05 Thread Aaron M. Ucko
d will test it out when I get a chance, probably tomorrow or Monday. -- 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#963439: ncbi-entrez-direct: FTBFS: obj-x86_64-linux-gnu/src/golang.org/x/sys/unix/syscall_unix.go:16:2: cannot find package "golang.org/x/sys/internal/unsafeheader" in any of:

2020-06-21 Thread Aaron M. Ucko
t;> >> /<>/obj-x86_64-linux-gnu/src/golang.org/x/sys/internal/unsafeheader >> (from $GOPATH) Thanks for the report! I've prepared a fix, and plan to issue an upload incorporating it (and getting closer to the latest upstream release) this evening. -- Aaron

Bug#960756: [Debian-med-packaging] Bug#960756: python-biopython FTBFS on 32bit: test_NCBI_BLAST_tools.BlastDB failures

2020-06-09 Thread Aaron M. Ucko
Étienne Mollier writes: > Thank you for the workaround! No problem; happy to have been of help (and that it in fact worked). -- 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#960756: [Debian-med-packaging] Bug#960756: python-biopython FTBFS on 32bit: test_NCBI_BLAST_tools.BlastDB failures

2020-06-09 Thread Aaron M. Ucko
t might >> exceed too easily 32 bits architectural limits. That's entirely plausible; upstream tends to assume 64-bit systems nowadays. Explicitly supplying -blastdb_version 4 (the default prior to BLAST+ 2.10.x) may help. Thanks for calling this report to my attention! -- Aaron M. U

Bug#961347: marked as pending in sra-sdk

2020-05-25 Thread Aaron M. Ucko
Control: tag -1 pending Hello, Bug #961347 in sra-sdk reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/sra-sdk/-/commit/b36b20cb22242853e29881740e1cdfc0

Bug#961347: sra-sdk: autopktest failure

2020-05-23 Thread Aaron M. Ucko
report. FTR, libncbi-vdb2 does already install the schemas; the problem is getting it to acknowledge our differences from upstream's layout preferences. I already saw this failure and am working on a proper fix. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit

Bug#961049: marked as pending in sra-sdk

2020-05-20 Thread Aaron M. Ucko
Control: tag -1 pending Hello, Bug #961049 in sra-sdk reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/sra-sdk/-/commit/8ef4c86e26989677717f8bbabf617f5f

Bug#961049: sra-sdk FTBFS with libncbi-vdb-dev 2.10.6+dfsg-1

2020-05-19 Thread Aaron M. Ucko
vdb needs a small tweak to fix installation of a semi-private header sra-sdk uses.) -- 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#959587: python-biopython: FTBFS: AssertionError: False is not true

2020-05-05 Thread Aaron M. Ucko
gt; *.nnd *.nsi -> *.nni *.psd -> *.pnd *.psi -> *.pni Thanks for checking! BTW, python-biopython's build dependency on emboss reminded me that emboss-data is still probably overkill for emboss(-lib)'s needs and could stand to be split up (#682042). -- Aaron M. Ucko, KB1C

Bug#947995: ncbi-entrez-direct: ncbi-entrez-direct FTBFS in testing/unstable

2020-02-03 Thread Aaron M. Ucko
Andreas Tille writes: >> protected branches. Could you please adjust the project's permissions? > > Done (hopefully), Andreas. I was able to push now, thanks! -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.

Bug#947995: ncbi-entrez-direct: ncbi-entrez-direct FTBFS in testing/unstable

2020-02-02 Thread Aaron M. Ucko
> If any of the commits was not helpful just rebase. Thanks! I've uploaded with your generic commits cherry-picked (and a bunch of changes of my own), but Salsa rejected my force pushes to protected branches. Could you please adjust the project's permissions? -- Aaron M. Ucko, K

Bug#947995: ncbi-entrez-direct: ncbi-entrez-direct FTBFS in testing/unstable

2020-01-31 Thread Aaron M. Ucko
off on pushing anything so I could have more freedom to rebase in case I belatedly discovered something I should have done earlier. -- 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#940210: ncbi-cn3d: missing Breaks+Replaces: ncbi-tools-x11 (<< 6.1.20170106+dfsg1-5)

2019-09-14 Thread Aaron M. Ucko
ed. I uploaded a correction just now. Thanks for the report, and sorry about that! -- 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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