github.com/sagemath/homebrew-science commits | Ecosyste.ms: OpenCollective

fastx_toolkit: add 0.0.14 bottle for Linuxbrew.

947e99fd99dbdc80b5f1dd6a3358926c24973501 authored over 8 years ago

fastx_toolkit: add 0.0.14 bottle.

Closes #4474.

Signed-off-by: Shaun Jackman <[email protected]>

8c949bd816ed4675f1a868b4d81372a9f6bb039c authored over 8 years ago

fastx_toolkit: Add desc and tag bioinformatics

Closes #4474.

Signed-off-by: Shaun Jackman <[email protected]>

853dd9fe8a4d26875a6d6bf5ea3109b664e673ce authored over 8 years ago

libbi: prevent perl version conflicts

9b0ef4671c251d30482207f8f5658815eecbd4b0 authored over 8 years ago

gmt4: update 4.5.15 bottle.

2bc65a63f79a5744aeefd7255eb979b518efb091 authored over 8 years ago

gmt4 4.5.15

- fix audits
- add test

Closes #4409

Closes #4470.

Signed-off-by: Dominique Orban <dominique....

374f9704a2271c95108574861991677cf29bae7f authored over 8 years ago

diamond: update 0.8.24 bottle for Linuxbrew.

b1275ee883d55911c66299e54b6501edc0229988 authored over 8 years ago

diamond: update 0.8.24 bottle.

e7cd1c502779c7f14e1a5e93810f2bdaa525b862 authored over 8 years ago

diamond 0.8.24

Closes #4469.

Signed-off-by: ilovezfs <[email protected]>

103061d7cdd67355fd14d5494e5756414cfccc51 authored over 8 years ago

vtk: remove test dependency on cmake

Closes #4451.

Signed-off-by: Jonathan Chang <[email protected]>

699ccccf2c8ef18f7aac1b74127f548cd67cd910 authored over 8 years ago

lightstringgraph: add 0.4.0_1 bottle.

5de9585f495e7b0d0e68d70b098cc0d535f77b7c authored over 8 years ago

lightstringgraph: build with gcc on 10.11, 10.12

Closes #2544

Closes #4466.

Signed-off-by: Dominique Orban <[email protected]>

83f02979cb831dcc5c8e837cfd80aa2bccd348fb authored over 8 years ago

cube: add 4.2.2 bottle.

4708255d1617b5533901390fedc2237222b19249 authored over 8 years ago

cube: fails with clang, audit fixes

- qt not available on sierra

Closes #4465.

Signed-off-by: Dominique Orban <dominique.orban@gma...

abe972f1a05d28553991e0e504bdd3ba327ac1e0 authored over 8 years ago

sara: add 1.13 bottle.

ca1e8755f5ccd2b024e5ce7600de1c300276b29e authored over 8 years ago

sara: fix build, audits

Closes #2553

Closes #4468.

Signed-off-by: Dominique Orban <[email protected]>

914a456fcf42c2bd41f9fe75484760cd8616a99e authored over 8 years ago

travis: request Xcode 8

Closes #4462.

Signed-off-by: Dominique Orban <[email protected]>

ae3e1d6f0d01fa1c4fb8e87c64fca7cd714782a6 authored over 8 years ago

pnapi: add 4.03 bottle.

ef8dfa7a6b849a2323ed89529bb3075a7353a2cc authored over 8 years ago

pnapi: fix deps, audits

Closes #2549

Closes #4467.

Signed-off-by: Dominique Orban <[email protected]>

2dfa0c028abcaaf505d783e30508a145e6d802fa authored over 8 years ago

elph: add 1.0.1 bottle.

38b380fa484251eb02c377622b97acd4658eb0fc authored over 8 years ago

elph: still fail with clang

- audit fixes

Closes #2543

Closes #4464.

Signed-off-by: Dominique Orban <dominique.orban@gmai...

8040c47bb0908cdd8c6e70049ec35612b6ec98a9 authored over 8 years ago

datamash: update 1.1.0 bottle for Linuxbrew.

Closes Linuxbrew/homebrew-science#295.
Signed-off-by: Shaun Jackman <[email protected]>

b0557702c26561ad54a2c19a9f17abe21ec8a2fa authored over 8 years ago

velvet: update 1.2.10 bottle for Linuxbrew.

Closes Linuxbrew/homebrew-science#294.
Signed-off-by: Shaun Jackman <[email protected]>

440fc079622ab39be51841e149b700e2097eae13 authored over 8 years ago

oases: update 0.2.08 bottle for Linuxbrew.

e56168032f29b93e68d7167858bef7971e19a810 authored over 8 years ago

trilinos: update 12.8.1 bottle.

58c91243f838510c7c38206a82228bd45e071e94 authored over 8 years ago

trilinos 12.8.1

option for OpenMP support

Closes #4460.

Signed-off-by: Dominique Orban <dominique.orban@gmail....

7339a231ff27f3ab7c829789300881ecc3e91bc8 authored over 8 years ago

velvet: update 1.2.10 bottle.

bc39e3ae3361b58e504dc7c3b7ced03ce8af507c authored over 8 years ago

velvet: openmp option, audit fixes

Closes #4458.

Signed-off-by: Dominique Orban <[email protected]>

54076543dc5364d3d98f69954a7c211658ae8b6d authored over 8 years ago

tmv-cpp 0.73

- new url
- option for openmp
- audit fixes

The build currently fails with OpenMP enabled.

Clo...

0604b597155c64d03807fab51a86cd5a6e52646a authored over 8 years ago

tmv-cpp: add 0.73 bottle.

7f5aebdc707066d6a6889519af78681d12a7dd08 authored over 8 years ago

oases: update 0.2.08 bottle.

3bed551d863883c1b5882ad96099ca301d043052 authored over 8 years ago

oases: option for openmp, audit fixes

Closes #4455.

Signed-off-by: Dominique Orban <[email protected]>

09f9d17a2a56a2f92a67d1d1bcd770b3453d4200 authored over 8 years ago

idba: update 1.1.3 bottle for Linuxbrew.

Closes Linuxbrew/homebrew-science#293.
Signed-off-by: Shaun Jackman <[email protected]>

29ca7cebf65fd971098e138279acb8ec6a395102 authored over 8 years ago

harry: update 0.4.2 bottle.

520f99400f7e33b9b7a607339b81747cf67b1b1f authored over 8 years ago

harry: option for openmp, fix audits

- ENV.delete("SDKROOT") fixes the build on xcode 8

Closes #4449.

Signed-off-by: Dominique Orba...

55253b2836c0cf2743ead60eda16dbedef3d9730 authored over 8 years ago

gatk 3.6 (new formula)

Genome Analysis Toolkit
Variant Discovery in High-Throughput Sequencing Data

Closes #4426.

Sig...

0e92b9b3df4c8230e1b6ab762114435837613a45 authored over 8 years ago

abinit: update 8.0.8b bottle.

2950ea522fdbdffc6140c8e9cb0a2cf43d633506 authored over 8 years ago

abinit: openmp option

Closes #4453.

Signed-off-by: Dominique Orban <[email protected]>

ab96e0ab992f1c05a734b7c922c145a7097b8364 authored over 8 years ago

soplex: add 2.2.1 bottle.

47aa64c103a952a850fa86eccd22e2a14aee191d authored over 8 years ago

soplex 2.2.1 (new formula)

Closes #4326.

Signed-off-by: Dominique Orban <[email protected]>

870c2d0a146be72698fb3a85464077d86e74628a authored over 8 years ago

idba: update 1.1.3 bottle.

e1ff7cbceb361d1523cb0440eaa41c6247755d48 authored over 8 years ago

idba 1.1.3

- needs openmp
- improve test
- fix audits

Closes #2339
Fixes #2252

Closes #4450.

Signed-off-...

482899ddca36d96940727a82f4e5f90fb8db2b6b authored over 8 years ago

metis: update 5.1.0 bottle.

75910dd94c610eaf2379f39e46524b0352eb3928 authored over 8 years ago

metis: fix openmp option, audits

Closes #4433.

Signed-off-by: Dominique Orban <[email protected]>

d83f35553b7bc09e66a659408ae37dcfe999491e authored over 8 years ago

phlawd: update 3.4a_2 bottle for Linuxbrew.

1e174170012ff159c921f4941c9e9ec1331b186b authored over 8 years ago

phlawd: Add tag bioinformatics

b3740ce66074f58ace3e122b02ab37bd3aaa826f authored over 8 years ago

vsearch: update 2.3.0 bottle for Linuxbrew.

109d0c5a3e1c14381552fbfa8617413817abaaca authored over 8 years ago

diamond: update 0.8.23 bottle for Linuxbrew.

b001b1fa714bfaab64f2aaa8b995e447d463c115 authored over 8 years ago

sratoolkit: update 2.8.0 bottle for Linuxbrew.

24ae7c0c5135c0167500be6144075804afb01e83 authored over 8 years ago

oce: Fix undefined method >= for nil for Linuxbrew

1867602fe79f525c612804b0b102640c6db6a2a9 authored over 8 years ago

CONTRIBUTING.md: update urls

The documentation urls have changed

Closes #4447.

Signed-off-by: Dominique Orban <dominique.or...

30462fd043decb37330735aed0675bb85f11e351 authored over 8 years ago

colpack: update 1.0.10 bottle.

b142bdab9296cb117ec1efc179e460eea1d1b029 authored over 8 years ago

colpack: fix openmp option

Closes #4430.

Signed-off-by: Dominique Orban <[email protected]>

f3515cf419310806ec44b3708f02df0fc7c5ad49 authored over 8 years ago

dealii: update 8.4.2_2 bottle.

da915f6f596cb3e11f60f6cd8f81b9dcce8ee801 authored over 8 years ago

getdp: update 2.9.2_1 bottle.

f32cb582d10eeec3c77a033b31e40cdfbdd7f7c1 authored over 8 years ago

sundials: update 2.7.0_1 bottle.

8c4dc032192e169154a693e4057dd4838a428333 authored over 8 years ago

petsc: update 3.7.4 bottle.

0f1506984c711e2328eb1e1d4b5633e831c8aaa9 authored over 8 years ago

slepc: update 3.7.3 bottle.

b977bd7d9945f8a01f50e2b80cdadf749bc36c67 authored over 8 years ago

petsc 3.7.4

add custom requirement to avoid circular dependency with sundials

433a0dc5083b7bae2a4cf537195773d5830466c4 authored over 8 years ago

getdp: bump for petsc and slepc

9ddfe6de95882d95b6a83ca9ed5ba9c517d365e7 authored over 8 years ago

sundials: openmp and superlu_mt options, fixes

- fix C compiler setting
- fix BLAS/LAPACK dependency
- custom requirement to avoid circular dep...

711ee2cba7b3b2013ac32b6bcd9e25af87d5ab04 authored over 8 years ago

dealii: bump for petsc and slepc

b1a3822337b7b63e85ba7e5fd12326edbff103f2 authored over 8 years ago

slepc 3.7.3

72b6397b56a28493d78d48f1826a8f4f8c075e63 authored over 8 years ago

vtk: update 7.0.0_5 bottle.

19afd0a6f057d94e24391845d3e6a87377df7c34 authored over 8 years ago

vtk: improve python path setup

This fixes #3577
The changes are inspired from the gdcm formula

- The check for simultaneous py...

700440acc6098ad7a22287d9bd3f773e8c87b6fb authored over 8 years ago

oce: update 0.17.2_1 bottle.

9916e3a3c76b236810e7db18eb774011db66783b authored over 8 years ago

oce: patch for Xcode8

Closes #4406.

Signed-off-by: Dominique Orban <[email protected]>

df988b0a6408b6b5d5aad6efc9ea01adf2414f4e authored over 8 years ago

vips: update 8.4.2 bottle.

8ce80ffec3255ae32bcdc8bd6a3943028f995410 authored over 8 years ago

vips 8.4.2

update vips to latest

8.4.2 fixes a nasty race condition on exit after heavy threading

Closes ...

f2bdb941827dfaf1e45803058e04e1f91a6edf49 authored over 8 years ago

nextflow 0.22.3

Closes #4444.

Signed-off-by: Dominique Orban <[email protected]>

af4af7b821b496988746a27f12f7a462800169fb authored over 8 years ago

vsearch: update 2.3.0 bottle.

44930feb49f740aa54a4c77cce7b0e08bf10b652 authored over 8 years ago

vsearch 2.3.0

Closes #4441.

Signed-off-by: ilovezfs <[email protected]>

e70e805f2e61bbeb92ad8fbe15b81c7aa3a4805b authored over 8 years ago

galsim: fix openmp option, audits

Closes #4431.

Signed-off-by: Dominique Orban <[email protected]>

c8f7c13e4e86647da116a998485bee4014da3316 authored over 8 years ago

phlawd: update 3.4a_2 bottle.

46e53d949e1e048e71ac75c89d2ec08e5eeb9b71 authored over 8 years ago

phlawd: redundant fails_with

Closes #4435.

Signed-off-by: Dominique Orban <[email protected]>

b72dee0af25a83371f72c7486ca2d2167ce86495 authored over 8 years ago

mathgl: update 2.3.5.1_1 bottle.

3084b0324240b7767e7185fec3612e92ea62f1ac authored over 8 years ago

mathgl: fix openmp option

Closes #4432.

Signed-off-by: Dominique Orban <[email protected]>

9a063800f0448ac73a8a86fa41c84f7f4288dbd5 authored over 8 years ago

nfft: update 3.2.3 bottle.

fc5d8baa36d2ce501c0101f6316a3a8c1ae390ca authored over 8 years ago

nfft: fix openmp option, audits

Closes #4434.

Signed-off-by: Dominique Orban <[email protected]>

a2e8e8ceb50c532106054f30f8a0983b40e42618 authored over 8 years ago

viennarna: update 2.1.9 bottle.

07beb902159173e8ef8c44d251952e5346792be3 authored over 8 years ago

viennarna: fix openmp option, audits

Closes #4436.

Signed-off-by: Dominique Orban <[email protected]>

61b9d0d8e292433289dab0c4c9fbc4d0490fd262 authored over 8 years ago

update CONTRIBUTING.md

--without-check => --without-test

Closes #4408.

Signed-off-by: Dominique Orban <dominique.orba...

90f4685bf5190b7f038b52cafefd73bee107c09c authored over 8 years ago

adol-c: update 2.6.2 bottle.

3b0322df85f3830142b07b6a50b048592b3a77bf authored over 8 years ago

adolc 2.6.2

fix OpenMP option

Closes #4429.

Signed-off-by: Dominique Orban <[email protected]>

e8f48563b9bbf84deb8dfd95bb39013d63f9748f authored over 8 years ago

elemental: update 0.85_1 bottle.

64e82603a7b083102da848e7f5159a6e161ea4f4 authored over 8 years ago

elemental: fix build errors in {stable, devel}

* remove conflicting CMake macros in {stable, devel}
Remove the Elemental versions of conflict...

e5011ea2ab561752f71f094a9a18141fd1d2ecbd authored over 8 years ago

boost-compute: update 1.62.0 bottle.

6a35e78f0fded4b929c742143c15bf6c3cd71ed9 authored over 8 years ago

boost-compute 1.62.0

Closes #4364.

Signed-off-by: ilovezfs <[email protected]>

b6d983c69d246edb67014a3ee49060529acf3379 authored over 8 years ago

libbi: add 1.2.0 bottle.

100f1bfc51bb3daeb0d42d95f34f1909f476f4b1 authored over 8 years ago

libbi 1.2.0 (new formula)

Closes #4385.

Signed-off-by: Jonathan Chang <[email protected]>

dc6a49a4777e634e9f0b1c9c8c8cd5229bd67167 authored over 8 years ago

getdp: update 2.9.2 bottle.

978222bf6cbcb2bea327a3981ceac674fa878c32 authored over 8 years ago

getdp 2.9.2

Closes #4405.

Signed-off-by: Jonathan Chang <[email protected]>

cbbf9e93bf9d03f87fc149a57fa85abadf075e21 authored over 8 years ago

diamond: update 0.8.23 bottle.

4413fe9fc7a6512133fe176cb41e8f881d5f783d authored over 8 years ago

diamond 0.8.23

Closes #4422.

Signed-off-by: ilovezfs <[email protected]>

1c74514e65afa1e4cbd96b471bc5185bcbf53c12 authored over 8 years ago

sratoolkit: update 2.8.0 bottle.

cbd1c022e56e110ec74ce6778e1fd6696cfdbb22 authored over 8 years ago

sratoolkit 2.8.0

build in the buildpath instead of in the prefix

Closes #4421.

Signed-off-by: ilovezfs <ilovezf...

ed990d19b7356f4ec018add5497680ab7756931d authored over 8 years ago

vsearch: update 2.2.0 bottle.

f6c7925bd9b36a26a151f7c9188a4c3eb87106f4 authored over 8 years ago

vsearch 2.2.0

Closes #4420.

Signed-off-by: ilovezfs <[email protected]>

73f649ea8b8c586678570294c7d61f028e9638d4 authored over 8 years ago

beast: update 1.8.4 bottle for Linuxbrew.

4a338fc8a4745bbdb283c6efcd80b3eab24b8fb6 authored over 8 years ago

cantera: update 2.2.1_1 bottle.

3eb76714534dd4c149be9429e511597cb5a7f35e authored over 8 years ago