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Author SHA1 Message Date
Mario Rodas c935567de6 lean: 3.6.1 -> 3.7.0 2020-03-14 01:32:58 +00:00
wucke13 c24b9a57c4 getdp: 3.0.4 -> 3.3.0 2020-03-13 04:10:20 +00:00
R. RyanTM a58d091d8d verilator: 4.028 -> 4.030 2020-03-12 20:57:34 -05:00
Maximilian Bosch 76821e6f43
geogebra: 5-0-573-0 -> 5-0-574-0 2020-03-12 18:12:57 +01:00
Timo Kaufmann ba589e24c9 sage: patch for pari 2.11.3 2020-03-12 12:24:41 +01:00
Timo Kaufmann c4ab541443 pari: backport bug fix 
https://trac.sagemath.org/ticket/29313#comment:4
 2020-03-12 12:24:35 +01:00
xaverdh 5ac085c3cc
wxmaxima: 18.02.0 -> 20.02.4 (#82323) 
The commit description is 18.02.0 -> 20.02.4, because in the last version bump (1c6a193b3e), the version string was changed, but the hash was not.

Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
 2020-03-11 12:07:53 -04:00
Timo Kaufmann 1a6b1fb32a symmetrica: add timokau to maintainers 2020-03-10 18:10:28 +01:00
Timo Kaufmann 0c875c28c6 symmetrica: 2.0 -> 3.0.1 
This switches to the sagemath fork, since the original upstream is no
longer maintained and sagemath has effectively maintained symmetrica
through patches for a while now. The update fixes one bug in particular
that has caused failures in the sagemath test suite:

https://github.com/NixOS/nixpkgs/issues/81449
https://trac.sagemath.org/ticket/15312
https://trac.sagemath.org/ticket/29061

Regarding the licensing change:

7cf91b3800
 2020-03-10 18:10:25 +01:00
Timo Kaufmann e05e219b31
Merge pull request #82240 from timokau/sage-docutils-0.15-fix 
sage: fix test suite with docutils 0.15
 2020-03-10 15:25:22 +00:00
Timo Kaufmann 7133577405 sage: fix test suite with docutils 0.15 
The better way to fix this would be to backport the upstream sphinx
patch:

faedcc48cc

Unfortunately it doesn't apply cleanly and isn't worth the effort
of backporting. Let's hope we can switch to python3 sage and the recent
sphinx version that comes with it before this becomes a problem.
 2020-03-10 13:15:41 +01:00
Timo Kaufmann 63ed2bf3c3
Merge pull request #81950 from r-ryantm/auto-update/pari 
pari: 2.11.2 -> 2.11.3
 2020-03-09 17:31:14 +00:00
Michael Raskin bbab73266d
Merge pull request #80719 from mucaho/feature/clingcon_init 
clingcon: init at 3.3.0
 2020-03-09 07:42:38 +00:00
mucaho 202c2a8eff clingcon: init at 3.3.0 2020-03-08 19:21:55 +01:00
Maximilian Bosch 84f862ed91
Merge pull request #81796 from JohnAZoidberg/satallax-gcc9 
satallax: Fix build with GCC9
 2020-03-08 16:12:40 +01:00
Gabriel Ebner d7a68e9bce
Merge pull request #82028 from r-ryantm/auto-update/qalculate-gtk 
qalculate-gtk: 3.7.0 -> 3.8.0
 2020-03-08 13:31:00 +01:00
Frederik Rietdijk 0eb0ddc4db Merge staging-next into master 2020-03-08 08:11:01 +01:00
R. RyanTM e6f5bb8dc4 qalculate-gtk: 3.7.0 -> 3.8.0 2020-03-08 00:14:22 +00:00
Vincent Laporte dcfccdfc33
acgtk: 1.5.0 → 1.5.1 (#81539) 
Co-authored-by: Jon <jonringer@users.noreply.github.com>
 2020-03-07 09:56:18 +01:00
R. RyanTM 6528554396 pari: 2.11.2 -> 2.11.3 2020-03-07 02:43:40 +00:00
Gabriel Ebner 8428f5bb4a elan: v0.8.0 tag was force-pushed by upstream 2020-03-06 15:35:37 +01:00
Gabriel Ebner 70e5428d66 elan: 0.7.5 -> 0.8.0 2020-03-06 14:28:36 +01:00
Joachim Breitner 2d2a5a9b63
js_of_ocaml: 3.4.0 -> 3.5.2 (#75766) 
drive-by contributions, as I was playing around with this (it has better
support for the `num` library, it seems.)

js_of_ocaml: 3.4.0 -> 3.5.2
ocamlPackages.js_of_ocaml-ppx_deriving_json: use ppxlib-0.12.0
ocamlPackages.eliom: 6.8.0 → 6.10.1
ocamlPackages.ocsigen-toolkit: 2.2.0 → 2.5.0
ocamlPackages.ocsigen-start: 2.7.0 → 2.16.1

Co-authored-by: Vincent Laporte <Vincent.Laporte@gmail.com>
 2020-03-06 07:42:04 +01:00
Frederik Rietdijk 188c3a4d03 Merge staging-next into staging 2020-03-06 07:09:30 +01:00
Mario Rodas 7597bdd59b
Merge pull request #81783 from r-ryantm/auto-update/gmsh 
gmsh: 4.5.2 -> 4.5.4
 2020-03-05 08:31:38 -05:00
Mario Rodas 1196a5c7a7
Merge pull request #81722 from r-ryantm/auto-update/workcraft 
workcraft: 3.2.5 -> 3.2.6
 2020-03-05 07:42:25 -05:00
Daniel Schaefer bc56175034 satallax: Fix build with GCC9 2020-03-05 05:16:49 +01:00
R. RyanTM 9974067129 gmsh: 4.5.2 -> 4.5.4 2020-03-05 00:20:08 +00:00
R. RyanTM adcdd7b0a7 gromacs: 2020 -> 2020.1 2020-03-04 23:10:39 +00:00
Jan Tojnar 1a44e325d2
Merge branch 'staging-next' into staging 2020-03-04 21:24:05 +01:00
R. RyanTM 86e6080daf workcraft: 3.2.5 -> 3.2.6 2020-03-04 13:41:09 +00:00
Mario Rodas 5760e001ca
Merge pull request #81706 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.21.8 -> 2.22.0
 2020-03-04 07:26:05 -05:00
R. RyanTM 343ec80712 picard-tools: 2.21.8 -> 2.22.0 2020-03-04 09:58:40 +00:00
Gabriel Ebner 0d470dc5ea
Merge pull request #81692 from r-ryantm/auto-update/lean 
lean: 3.6.0 -> 3.6.1
 2020-03-04 10:32:38 +01:00
R. RyanTM 5b833c08ef lean: 3.6.0 -> 3.6.1 2020-03-04 06:26:01 +00:00
Aiken Cairncross 3db82f6fc3 python3Packages.monosat: Fix hash 
PR #81562 inadvertently broke these builds
 2020-03-03 11:02:23 -08:00
markuskowa dbb9fab27f
Merge pull request #81604 from markuskowa/upd-octopus 
octopus: 9.1 -> 9.2
 2020-03-03 12:45:16 +01:00
R. RyanTM faa5c3bde3 R: 3.6.2 -> 3.6.3 2020-03-03 11:34:22 +00:00
markuskowa 4822d61252
Merge pull request #80977 from r-ryantm/auto-update/quantum-espresso 
quantum-espresso: 6.4.1 -> 6.5
 2020-03-03 11:09:30 +01:00
Markus Kowalewski eebd6fe75a
octopus: 9.1 -> 9.2 2020-03-03 10:54:23 +01:00
Aiken Cairncross 2148a154c6 python3Packages.monosat: Fix Python 3.8 build 2020-03-03 07:40:57 +01:00
Brenton Horne b07eb54048 marvin: 20.4.0 -> 20.6.0 2020-03-02 21:50:25 +01:00
Jan Tojnar f27031f48f
Merge pull request #81063 from NixOS/netpbm 
netpbm: 10.82.01 → 10.89.1
 2020-03-02 19:26:25 +01:00
scalavision dbb4826457 truvari:1.3.2->1.3.4 2020-03-02 09:15:58 +01:00
Jan Tojnar 9555834399
netpbm: split into multiple outputs 2020-03-01 15:13:03 +01:00
Frederik Rietdijk 21b808cd76 Merge staging-next into staging 2020-02-29 15:29:45 +01:00
Benjamin Hipple ad30a30488 rustPlatform.fetchCargo: handle custom Cargo.lock patchfiles with validation 
Previously, we would asssert that the lockfiles are consistent during the
unpackPhase, but if the pkg has a patch for the lockfile itself then we must
wait until the patchPhase is complete to check.

This also removes an implicity dependency on the src attribute coming from
`fetchzip` / `fetchFromGitHub`, which happens to name the source directory
"source". Now we glob for it, so different fetchers will work consistently.
 2020-02-28 18:54:23 -08:00
Matthieu Coudron 05b6836816 torchPackages, torch-repl: remove 
See https://github.com/NixOS/nixpkgs/issues/71888
and https://github.com/NixOS/nixpkgs/issues/56398

To sump up, development has moved on to other technologies than lua:
https://github.com/torch/torch7#development-status
and the current packages are broken anyway.
 2020-02-28 20:56:42 +01:00
Austin Seipp 7e66ce29bf
mcy: init at 2020.02.05 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-02-27 21:52:15 -06:00
Austin Seipp 3d8efecda1
symbiyosys: fix calls to external programs 
48085826f broke symbiyosys when it needed to call `yosys-abc`: when
`ABCEXTERNAL` is set in the Makefile, then `yosys-abc` is not built.

But in general `sby` was just calling programs out of the ambient
environment. Fix that for most programs it can invoke: it now has a
direct dependency on boolector, aiger, abc, yosys, etc.

This also does some other minor clean up.

Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2020-02-27 21:52:15 -06:00
Mario Rodas 79f057e2eb
lean: 3.5.1 -> 3.6.0 2020-02-26 18:00:00 -05:00
Dmitry Kalinkin b9ee6cd85c
Merge pull request #80640 from smaret/gildas-20200201a 
gildas: 20200101_a -> 20200201_a
 2020-02-25 10:26:18 -05:00
R. RyanTM 56d58ecb24 quantum-espresso: 6.4.1 -> 6.5 2020-02-24 19:40:14 +00:00
R. RyanTM 4080e7976e gtkwave: 3.3.103 -> 3.3.104 2020-02-24 11:43:54 -06:00
Linus Heckemann 0cc83f884a
Merge pull request #80292 from bcdarwin/mrtrix 
mrtrix: init at 3.0_RC3_latest
 2020-02-24 13:52:38 +01:00
Timo Kaufmann f4dbf4402b
Merge pull request #80759 from Thra11/fix-r 
Fix R
 2020-02-23 23:48:21 +00:00
Tom Hall ae9e09a2e1 R: fix build on aarch64 by removing a failing test 
I believe this test is currently incorrect on aarch64 and expects a
warning about loss of precision with much smaller numbers than the
platform's long doubles can handle.
 2020-02-22 13:17:40 +00:00
Edward Tjörnhammar 9b6faedb18
shogun: 6.0.0 -> 6.1.4 
Also migrate to opencv3 to address #72739, the PR didn't build for me.
Disable testing and ccache since they were broken.

Co-authored-by: Robert Scott <code@humanleg.org.uk>
 2020-02-21 11:05:09 +01:00
Sébastien Maret 7667207f3d
gildas: 20200101_a -> 20200201_a 
- Upgrade gildas to the latest version

 - Remove a patch that has been included upstream

 - Re-enable parallel building (fixed upstream)
 2020-02-20 15:28:57 +01:00
Gabriel Ebner f098b0dd2c
Merge pull request #80576 from bhipple/u/rust-cargo-elan 
elan: upgrade cargo fetcher and cargoSha256
 2020-02-20 09:53:49 +01:00
Maximilian Bosch 7bdc103ac8
geogebra: 5-0-570-0 -> 5-0-573-0 2020-02-20 03:09:06 +01:00
Benjamin Hipple ed85c9981a elan: upgrade cargo fetcher and cargoSha256 
Infra upgrade as part of #79975; ran `nixpkgs-review wip` successfully.
 2020-02-19 18:17:27 -05:00
Tom Hall 4e5aeca90b R: Enable java support on all platforms 2020-02-19 22:57:41 +00:00
Ben Darwin 9a2cd20478 mrtrix: init at 3.0_RC3_latest 
This package consists mostly of command-line tools, but there are also two qt5-based image viewers (`mrview` and `shview`). I have provided an option `withGui = true` to allow users to disable these viewers. They work on NixOS but unlikely to work out-of-the box on non-NixOS Linux (see #62169), but I've refrained from asserting that they shouldn't be built since a user might want to fiddle with runtime GL stuff.

Some programs rely on FSL and/or ANTs backends; I have somewhat heavy-handedly wrapped all binaries to point to ANTs, while FSL is not available in Nix at the moment and has a non-commercial license so would be convenient to disable by default for Hydra builds.
 2020-02-16 22:25:25 -05:00
Daniel Schaefer 1e613230d2
Merge pull request #80122 from r-ryantm/auto-update/kallisto 
kallisto: 0.46.1 -> 0.46.2
 2020-02-15 22:41:15 +01:00
R. RyanTM 4c6c40d96a kallisto: 0.46.1 -> 0.46.2 
Co-authored-by: Daniel Schaefer <git@danielschaefer.me>
 2020-02-15 22:39:58 +01:00
Junyoung Clare Jang b71c03e483
lean: 3.4.2 -> 3.5.1 
3.4.2 is not compilable with GCC >= 9.1
 2020-02-15 02:29:12 -05:00
R. RyanTM d54a58a2cd verilator: 4.026 -> 4.028 2020-02-14 12:13:04 -06:00
Benjamin Hipple eb11feaa0b treewide: change fetchCargoTarball default to opt-out 
Changes the default fetcher in the Rust Platform to be the newer
`fetchCargoTarball`, and changes every application using the current default to
instead opt out.

This commit does not change any hashes or cause any rebuilds. Once integrated,
we will start deleting the opt-outs and recomputing hashes.

See #79975 for details.
 2020-02-13 22:41:37 -08:00
Dmitry Kalinkin 5f2a3bef33
Merge pull request #79778 from jbedo/delly 
delly: 0.8.1 -> 0.8.2
 2020-02-11 03:54:02 -05:00
Justin Bedo a8fe9e7aff
delly: 0.8.1 -> 0.8.2 
Backported patch required for htslib 1.10.2
 2020-02-11 19:21:59 +11:00
Ryan Mulligan b99e12f4fe
Merge pull request #79534 from r-ryantm/auto-update/last 
last: 1045 -> 1047
 2020-02-10 18:10:08 -08:00
Brenton Horne 567be48707 marvin: 20.3.0 -> 20.4.0 2020-02-10 19:55:13 +01:00
Evils d3a9e634bf kicad-unstable: update update.sh && update 
use /tmp instead of XDG_RUNTIME_DIR
  which is /run/user/1000, which defaults to 10% of RAM
  and kicad-packages3d needs ~6gb
 2020-02-10 19:54:38 +01:00
Evils a9942b0226 kicad: simplify component names 2020-02-10 19:54:38 +01:00
Ben Darwin 39f0e3b32b minc_tools: enable building conversion tools 2020-02-10 19:53:25 +01:00
Ben Darwin bcad453bcf minc_tools: 2017-09-11 -> unstable-2019-12-04 2020-02-10 19:53:25 +01:00
luc65r 94c60990fc cemu: init at 1.3 2020-02-10 19:26:25 +01:00
R. RyanTM e988c072be clp: 1.17.3 -> 1.17.5 2020-02-10 13:24:22 +01:00
R. RyanTM 1d4fd7f5f2 verifast: 18.02 -> 19.12 2020-02-09 14:29:31 -06:00
R. RyanTM 3a1098e3e2 pcb: 4.2.1 -> 4.2.2 2020-02-09 16:49:13 +01:00
Frederik Rietdijk 3846896084 Merge pull request #79293 from NixOS/staging-next 
Staging next (with glibc 2.30)
 2020-02-09 16:40:16 +01:00
Ryan Mulligan c9cf351871 Merge pull request #79479 from r-ryantm/auto-update/workcraft 
workcraft: 3.1.9 -> 3.2.5
 2020-02-09 06:37:47 -08:00
Frederik Rietdijk 531a48ebdb Merge master into staging-next 2020-02-09 11:00:29 +01:00
Jannik Vierling 6ea5cd21ab iprover: 2018_Jul_24_11h -> 3.1 2020-02-09 09:38:57 +01:00
Frederik Rietdijk 03755ed59a Merge master into staging-next 2020-02-09 09:17:51 +01:00
Luz 0522b3347e librepcb: 0.1.2 -> 0.1.3 (#74786) 2020-02-09 01:07:31 -05:00
Dmitry Kalinkin 1872e69450
Merge pull request #79301 from Abdillah/patch-2 
librepcb: Fix platform plugin xcb not found
 2020-02-09 00:28:49 -05:00
Emily a14a32fd75 symbiyosys: 2019.10.11 -> 2020.02.08 2020-02-08 23:00:07 -06:00
Ryan Mulligan 537f07555f Merge pull request #79557 from r-ryantm/auto-update/marvin 
marvin: 19.27.0 -> 20.3.0
 2020-02-08 12:42:18 -08:00
R. RyanTM 20f22f681f marvin: 19.27.0 -> 20.3.0 2020-02-08 19:34:35 +00:00
markuskowa 8261fc4980
Merge pull request #79511 from r-ryantm/auto-update/gmsh 
gmsh: 4.5.1 -> 4.5.2
 2020-02-08 14:21:27 +01:00
R. RyanTM dae266aa66 last: 1045 -> 1047 2020-02-08 13:04:53 +00:00
R. RyanTM 7c58b6437b gmsh: 4.5.1 -> 4.5.2 2020-02-08 07:25:27 +00:00
Ryan Mulligan 555ca166ec
Merge pull request #79467 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.21.6 -> 2.21.8
 2020-02-07 18:10:16 -08:00
R. RyanTM 5bf0de57ad workcraft: 3.1.9 -> 3.2.5 2020-02-07 21:09:41 +00:00
Frederik Rietdijk 30f0909e3a Merge master into staging-next 2020-02-07 19:27:52 +01:00
R. RyanTM d5404eebe9 picard-tools: 2.21.6 -> 2.21.8 2020-02-07 17:20:58 +00:00
R. RyanTM 78d6e74427 eagle: 9.5.1 -> 9.5.2 2020-02-06 20:17:53 +01:00
R. RyanTM ce5b0406db labelImg: 1.6.0 -> 1.8.1 2020-02-06 20:11:53 +01:00
Hernawan Faïz Abdillah 2d4ee40176
librepcb: Fix platform plugin xcb not found 2020-02-06 08:44:16 +07:00
Frederik Rietdijk 292fd97f67 Merge staging-next into staging 2020-02-05 20:48:28 +01:00
Frederik Rietdijk 419bc0a4cd Revert "Revert "Merge master into staging-next"" 
In 87a19e9048 I merged staging-next into master using the GitHub gui as intended.
In ac241fb7a5 I merged master into staging-next for the next staging cycle, however, I accidentally pushed it to master.
Thinking this may cause trouble, I reverted it in 0be87c7979. This was however wrong, as it "removed" master.

This reverts commit 0be87c7979.
 2020-02-05 19:41:25 +01:00
Frederik Rietdijk 0be87c7979 Revert "Merge master into staging-next" 
I merged master into staging-next but accidentally pushed it to master.
This should get us back to 87a19e9048.

This reverts commit ac241fb7a5, reversing
changes made to 76a439239e.
 2020-02-05 19:18:35 +01:00
Ryan Mulligan 67143ec938
Merge pull request #79231 from r-ryantm/auto-update/SPAdes 
SPAdes: 3.13.1 -> 3.14.0
 2020-02-05 06:54:45 -08:00
Vladimír Čunát 48a997cd76
Merge #66528: glibc: 2.27 -> 2.30 (into staging) 
Includes update of stdenv bootstap tools (for three main platforms)
and many package fixes with new glibc.
 2020-02-05 13:41:09 +01:00
R. RyanTM 3c54ae5679 SPAdes: 3.13.1 -> 3.14.0 2020-02-04 16:40:50 +00:00
Millian Poquet 150f4a967c simgrid: 3.24 -> 3.25 2020-02-03 10:37:03 -08:00
Maximilian Bosch ea8ae88f04
Merge branch 'staging' into glibc230 2020-02-01 17:42:03 +01:00
Florian Klink 570afbcb5b abc-verifier: passthru rev 
Some consumers of abc-verifier require certain abc versions.
For that reason, expose the exact rev via a passtrhru.
 2020-02-01 12:49:45 +01:00
Florian Klink 351f47da57 abc-verifier: 2018-07-08 -> 2020-01-11 2020-02-01 12:49:45 +01:00
markuskowa d9209250e5
Merge pull request #78981 from r-ryantm/auto-update/jmol 
jmol: 14.30.1 -> 14.30.2
 2020-02-01 11:07:38 +01:00
Mario Rodas c8af1bef6e
Merge pull request #78833 from r-ryantm/auto-update/snakemake 
snakemake: 5.8.1 -> 5.9.1
 2020-02-01 04:11:11 -05:00
Mario Rodas 611971f9a5
Merge pull request #78849 from r-ryantm/auto-update/tetgen 
tetgen: 1.5.0 -> 1.5.1
 2020-02-01 04:10:16 -05:00
R. RyanTM 097737b5a4 jmol: 14.30.1 -> 14.30.2 2020-02-01 03:50:56 +00:00
Vincent Laporte 13dd5844fd coqPackages_8_11.coq: 8.11+β1 → 8.11.0 2020-01-31 14:09:51 +01:00
Vincent Laporte 659a7ae963 coq: disable CoqIDE on Darwin for Coq ≥ 8.10 2020-01-31 14:09:51 +01:00
Luka Blaskovic fd614a8e8f saw-tools: use default llvm 2020-01-30 18:35:30 -05:00
Jörg Thalheim 6eb23e0721
verilator: 4.024 -> 4.026 (#78891) 
verilator: 4.024 -> 4.026
 2020-01-30 20:43:40 +00:00
Jörg Thalheim 37286820f2
verilator: shebangs patch is not needed anymore 2020-01-30 20:42:51 +00:00
R. RyanTM ab63f72b23
sherpa: 2.2.6 -> 2.2.8 (#78852) 2020-01-30 13:08:47 -05:00
R. RyanTM cd526d844b verilator: 4.024 -> 4.026 2020-01-30 18:06:40 +00:00
Ryan Mulligan c179ec8a64
Merge pull request #78823 from r-ryantm/auto-update/seaview 
seaview: 4.7 -> 5.0
 2020-01-30 06:59:41 -08:00
Maximilian Bosch abefd4f78a
pspp: 1.0.1 -> 1.2.0, fix build w/glibc-2.30 2020-01-30 15:19:44 +01:00
R. RyanTM 53706054ba tetgen: 1.5.0 -> 1.5.1 2020-01-30 12:47:50 +00:00
R. RyanTM a94c66bc88 snakemake: 5.8.1 -> 5.9.1 2020-01-30 09:44:26 +00:00
R. RyanTM 42fff82421 seaview: 4.7 -> 5.0 2020-01-30 08:26:52 +00:00
Mario Rodas a20b7cff7c
Merge pull request #78521 from r-ryantm/auto-update/ott 
ott: 0.29 -> 0.30
 2020-01-29 21:47:20 -05:00
Frederik Rietdijk dce0ca29d9 Merge master into staging-next 2020-01-28 10:46:13 +01:00
Silvan Mosberger 80a2740991
Merge pull request #78265 from Synthetica9/https-homepages 
treewide: fix redirected urls
 2020-01-27 15:00:53 +01:00
Gabriel Ebner 3809627321
Merge pull request #78511 from r-ryantm/auto-update/libqalculate 
libqalculate: 3.6.0 -> 3.7.0
 2020-01-26 18:47:18 +01:00
Gabriel Ebner 8161fe21e0 qalculate-gtk: 3.6.0 -> 3.7.0 2020-01-26 18:43:29 +01:00
R. RyanTM f1085d02bb ott: 0.29 -> 0.30 2020-01-26 09:43:23 +00:00
samlich 3376628557
pymol: cleanup 2020-01-25 19:58:36 +00:00
samlich 77317774ce
pymol: link desktop icon 2020-01-24 19:51:08 +00:00
samlich 3638755ff3
pymol: add samlich as maintainer 2020-01-24 19:49:38 +00:00
samlich 97410b59f3
pymol: 2.1.0 -> 2.3.0 2020-01-24 19:42:59 +00:00
Justin Bedo 7f142260d3 manta: init 1.6.0 2020-01-24 02:02:19 -08:00
Ryan Mulligan a6dc361cae
Merge pull request #78261 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.21.3 -> 2.21.6
 2020-01-22 16:18:57 -08:00
Patrick Hilhorst 593e11fd94
treewide: fix redirected urls 
According to https://repology.org/repository/nix_unstable/problems, we have a
lot of packages that have http links that redirect to https as their homepage.
This commit updates all these packages to use the https links as their
homepage.

The following script was used to make these updates:

```

curl https://repology.org/api/v1/repository/nix_unstable/problems \
    | jq '.[] | .problem' -r \
    | rg 'Homepage link "(.+)" is a permanent redirect to "(.+)" and should be updated' --replace 's@$1@$2@' \
    | sort | uniq > script.sed

find -name '*.nix' | xargs -P4 -- sed -f script.sed -i
```
 2020-01-22 11:26:22 +01:00
R. RyanTM fff7a7a862 picard-tools: 2.21.3 -> 2.21.6 2020-01-22 10:12:28 +00:00
DwarfMaster 227a3f4383 Renamed maintainer lucas8 -> dwarfmaster 2020-01-21 16:39:52 +10:00
Jonathan Ringer 4de137a77d samtools: 1.9 -> 1.10 2020-01-19 13:13:01 -08:00
Frederik Rietdijk bcd8c6b8dc Merge master into staging-next 2020-01-17 17:08:16 +01:00
Dmitry Kalinkin 430dfb8082
Merge pull request #77631 from smaret/gildas-202001a 
gildas: 20191201_a -> 20200101_a
 2020-01-17 10:23:28 -05:00
Anders Kaseorg 3cd8ce3bce treewide: Fix unsafe concatenation of $LD_LIBRARY_PATH 
Naive concatenation of $LD_LIBRARY_PATH can result in an empty
colon-delimited segment; this tells glibc to load libraries from the
current directory, which is definitely wrong, and may be a security
vulnerability if the current directory is untrusted.  (See #67234, for
example.)  Fix this throughout the tree.

Signed-off-by: Anders Kaseorg <andersk@mit.edu>
 2020-01-15 09:47:03 +01:00
Frederik Rietdijk 2a88c3c302 Merge staging-next into staging 2020-01-15 09:23:28 +01:00
Will Dietz afe905246d nota: init at 1.0 
Fixes #77590.
 2020-01-14 15:16:21 -08:00
Sébastien Maret 0956fcab16
gildas: 20191201_a -> 20200101_a 2020-01-14 11:22:53 +01:00
Luka Blaskovic 991a7e041f pcalc: build with bison3 2020-01-13 21:35:19 +00:00