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3351 Commits

Author SHA1 Message Date
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
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