From b3b44798a3f472e5f5a6633de4a582d4c902b008 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Thu, 18 Jun 2020 18:01:33 +0100 Subject: IMPORTANT: New software versions (17 basic, 16 high-level and 7 Python) It was a long time that the Maneage software versions hadn't been updated. With this commit, the versions of all basic software were checked and 17 of that had newer versions were updated. Also, 16 high-level programs and libraries were updated as well as 7 Python modules. The full list is available below. Basic Software (affecting all projects) --------------------------------------- bash 5.0.11 -> 5.0.18 binutils 2.32 -> 2.35 coreutils 8.31 -> 8.32 curl 7.65.3 -> 7.71.1 file 5.36 -> 5.39 gawk 5.0.1 -> 5.1.0 gcc 9.2.0 -> 10.2.0 gettext 0.20.2 -> 0.21 git 2.26.2 -> 2.28.0 gmp 6.1.2 -> 6.2.0 grep 3.3 -> 3.4 libbsd 0.9.1 -> 0.10.0 ncurses 6.1 -> 6.2 perl 5.30.0 -> 5.32.0 sed 4.7 -> 4.8 texinfo 6.6 -> 6.7 xz 5.2.4 -> 5.2.5 Custom programs/libraries ------------------------- astrometrynet 0.77 -> 0.80 automake 0.16.1 -> 0.16.2 bison 3.6 -> 3.7 cfitsio 3.47 -> 3.48 cmake 3.17.0 -> 3.18.1 freetype 2.9 -> 2.10.2 gdb 8.3 -> 9.2 ghostscript 9.50 -> 9.52 gnuastro 0.11 -> 0.12 libgit2 0.28.2 -> 1.0.1 libidn 1.35 -> 1.36 openmpi 4.0.1 -> 4.0.4 R 3.6.2 -> 4.0.2 python 3.7.4 -> 3.8.5 wcslib 6.4 -> 7.3 yaml 0.2.2 -> 0.2.5 Python modules -------------- cython 0.29.6 -> 0.29.21 h5py 2.9.0 -> 2.10.0 matplotlib 3.1.1 -> 3.3.0 mpi4py 3.0.2 -> 3.0.3 numpy 1.17.2 -> 1.19.1 pybind11 2.4.3 -> 2.5.0 scipy 1.3.1 -> 1.5.2 --- reproduce/software/config/TARGETS.conf | 2 +- reproduce/software/config/checksums.conf | 80 +++++++++++++++--------------- reproduce/software/config/urls.conf | 31 ++++++------ reproduce/software/config/versions.conf | 85 +++++++++++++++++--------------- reproduce/software/make/basic.mk | 29 ++++++----- reproduce/software/make/build-rules.mk | 20 ++++++-- reproduce/software/make/high-level.mk | 55 +++++++++++++++++---- reproduce/software/make/python.mk | 5 +- reproduce/software/shell/configure.sh | 50 ++----------------- 9 files changed, 187 insertions(+), 170 deletions(-) (limited to 'reproduce/software') diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf index 8d3bdb0..5f10c96 100644 --- a/reproduce/software/config/TARGETS.conf +++ b/reproduce/software/config/TARGETS.conf @@ -35,7 +35,7 @@ -# Programs and libraries. +# Programs and libraries (for Python modules, add to 'top-level-python'). top-level-programs = gnuastro # Python libraries/modules. diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 62af1e1..b516a61 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -14,26 +14,26 @@ # Basic/low-level programs and libraires (installed in any case) # -------------------------------------------------------------- -bash-checksum = a93f221fe800908e335584837f63d02a350d9c8b2711f1923e946980b960fb2d4a21e4321f722c70e5faf5554991a6b9ef6722d214a1921f71030896cf134639 -binutils-checksum = a5e1f77e985d7d66e3ec6ed62a51a61c82ed0964a5108a1f318bf717f3f2af4dcd018ec3a66c10d6dc7525bad801b118f468eca07b2502c836895f4091bbeed4 +bash-checksum = e210cd63ce1241636fbb14d1a105c83e9481a0312026f746f76f7115b777707170ddfe1840fb4d3a4093613048e2d1eedf926e843ad15ffc8d66f08525e8b04b +binutils-checksum = 5ad795fab0803be83b53aa955fd5414c8408b4cf2a66eba2f8688298312934b4b1b0cbe9cf887d86de77f88adf1333d85fc9f6ab4a530e85a09b9b2dbf6aaf3f bzip2-checksum = 00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12 cert-checksum = a81dfa59c70788126a395c576e54cb8f61c1ea34da69b5cd42e2d83ee6426c2a26941360c7302793774ea98ca16846deb6e683144cc7fb6da6ef87b70447e4c8 -coreutils-checksum = ef8941dae845bbf5ae5838bc49e44554a766302930601aada6fa594e8088f0fbad74e481ee392ff89633e68b99e4da3f761fcb5d31ee3b233d540fe2a2d4e1af -curl-checksum = df8fc6b2cccf100f7479e25cad743964a84066b587da19585b36a788b0041925e33944986d636a451d6bb95a452d5ac6812b2d5fa6631a10e0ac82a2c7821c75 +coreutils-checksum = 1c8f3584efd61b4b02e7ac5db8e103b63cfb2063432caaf1e64cb2dcc56d8c657d1133bbf10bd41468d6a1f31142e6caa81d16ae68fa3e6e84075c253613a145 +curl-checksum = 614f8d67e6ee942cb5e57f2da1a3faaf84ebff549ffe383aaf3751a4de3c8874ff482076afa27a52e910a137dec9b0f6e98265dc7d4ad7c95845b63f39236fd4 dash-checksum = 9d55090115ac04f505d70e6790179331178950f96fe713b33fd698fa8bfa60d4eff1b68cb7b8a2f099d29c587d36034a17dccd6658ba1623ff0a625ac1fb9620 diffutils-checksum = 7b12cf8aea1b9844773748f72272d9c6a38adae9c3c3a8c62048f91fb56c60b76035fa5f51665dceaf2cfbf1d1f4a3efdcc24bf47a5a16ff4350543314b12c9c -file-checksum = 3ec5e51ffb7a82defa74845a90fbc983f6e169fc116606049bc01ff6e720d340c8abf6eb7a08b9ac1099162a5c02deac3633b07b039d486344c8abd9052ca751 +file-checksum = 9cf1a7b769c56eb6f5b25c66ce85fa1300128396e445b2e53dbbd8951e5da973a7a07c4ef9f7ebd1fe945d47bdaf2cd9ef09bd2be6c217a0bcb907d9449835e6 findutils-checksum = 650a24507f8f4ebff83ad28dd27daa4785b4038dcaadc4fe00823b976e848527074cce3f9ec34065b7f037436d2aa6e9ec099bc05d7472c29864ac2c69de7f2e flock-checksum = ddb997174c0653bc3d29410a5a16b6290e737aa40fbf4b746e2d1db1e88e5acb08ec11a25c27c8a5a5fbf5a00fcac17abeaa245e7df27bd975ae86364d400b86 -gawk-checksum = 3734740b7406ddfec9e04bb7774e76c6446cba76642a6180266e7b1822de20aab824c29c4e417256d877762ef04ef3f9df855cd4a3ca414a9225323b49d79195 -gcc-checksum = a12dff52af876aee0fd89a8d09cdc455f35ec46845e154023202392adc164848faf8ee881b59b681b696e27c69fd143a214014db4214db62f9891a1c8365c040 -gettext-checksum = 08d20c659004a77e607af17df15f5ce9bd4fc0feca9436aa206b0cbd2516f9f0c98c7ee1faacf7ff429f9b0dd9de219947b300216887a60727602a688acabc82 -git-checksum = 5d92d07b171c5cd6e89a29c1211c73c1c900cd51c74d690aebfb4a3d0e93b541b09b42b6d6a1a82f5c3d953096771f9a8605c63be139f559f58698c1a0eabcfc -gmp-checksum = 8aea94f867174eacac44f395ceb9212530c208e8de69d0bb53056f52360317230fc84ac177fd3ffc9fdb19a07c7549305dcc34c83c34821ccfab9dc63a16e67e -grep-checksum = e4805dbddf7cd0f0faf412557d408509650c1ccf703bc450f10a3f727c690dbfaa1235aa81939a0e4b7ac6190f88c15ea1fcc562b343d4b4c7550f967aeb15db +gawk-checksum = 682fadd3630d51d13d19443a9a93d4cba1bd6802dd078f1366f17f39d3fa5800f47037b103d742be9254475fdc251d90626f95a2e04b5ace117cfaecebca2281 +gcc-checksum = 42ae38928bd2e8183af445da34220964eb690b675b1892bbeb7cd5bb62be499011ec9a93397dba5e2fb681afadfc6f2767d03b9035b44ba9be807187ae6dc65e +gettext-checksum = f3083af79341bfdc849118333c1598812c12bc225d998181694648187088050160deb4777c252f72a7158e914c2967416489bc6167ef8505664497f2fb94ecbf +git-checksum = a6159c0a15e3c5f9603157d4010664a6d74e7d65b9fe97a03b36fac12607248ed57980d96565841e88eae343001c167222232737d3af812608c8db011941df1a +gmp-checksum = 9975e8766e62a1d48c0b6d7bbdd2fccb5b22243819102ca6c8d91f0edd2d3a1cef21c526d647c2159bb29dd2a7dcbd0d621391b2e4b48662cf63a8e6749561cd +grep-checksum = 0f1506bd19971fbdcb47a111277ca63e8ad045456f096980852fd0a61c860f29f4b369bbaaa5cbce4b0a81718e3e3274d9a078b491f2109baa9a02ce600ee206 gzip-checksum = 753fbcf5eb104bfc8a8eb81b69b8701f757b5158e6333b17438574169a4662642a122e1fdbd920a536edbcb77253d65fa571e4f507dbe72a70fee5eb161d6324 isl-checksum = 85d0b40f4dbf14cb99d17aa07048cdcab2dc3eb527d2fbb1e84c41b2de5f351025370e57448b63b2b8a8cf8a0843a089c3263f9baee1542d5c2e1cb37ed39d94 -libbsd-checksum = 435822b8f2495a5e2705e5ab5c834a4f0f3a177b3e5c46a7c6162924507ca984e957e94a512b5ebd0067ecb413bac458fade357709ef199e9b75edf0315de91c +libbsd-checksum = b75529785b16c93d31401187f8a58258fbebe565dac071c8311775c913af989f62cd29d5ce2651af3ea6221cffd31cf04826577d3e546ab9ca14340f297777b9 libiconv-checksum = 365dac0b34b4255a0066e8033a8b3db4bdb94b9b57a9dca17ebf2d779139fe935caf51a465d17fd8ae229ec4b926f3f7025264f37243432075e5583925bb77b7 libtool-checksum = a6eef35f3cbccf2c9e2667f44a476ebc80ab888725eb768e91a3a6c33b8c931afc46eb23efaee76c8696d3e4eed74ab1c71157bcb924f38ee912c8a90a6521a4 libunistring-checksum = 01dcab6e05ea4c33572bf96cc0558bcffbfc0e62fc86410cef06c1597a0073d5750525fe2dee4fdb39c9bd704557fcbab864f9645958108a2e07950bc539fe54 @@ -44,20 +44,20 @@ make-checksum = ddf0fdcb9ee1b182ef294c5da70c1275288c99bef60e63a25c0abed2ddd44aba metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628 mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88 -ncurses-checksum = e308af43f8b7e01e98a55f4f6c4ee4d1c39ce09d95399fa555b3f0cdf5fd0db0f4c4d820b4af78a63f6cf6d8627587114a40af48cfc066134b600520808a77ee +ncurses-checksum = 4c1333dcc30e858e8a9525d4b9aefb60000cfc727bc4a1062bace06ffc4639ad9f6e54f6bdda0e3a0e5ea14de995f96b52b3327d9ec633608792c99a1e8d840d openssl-checksum = 1523985ba90f38aa91aa6c2d57652f4e243cb2a095ce6336bf34b39b5a9b5b876804299a6825c758b65990e57948da532cca761aa12b10958c97478d04dd6d34 patchelf-checksum = 39745662651cf0a9915685b2767a611ceab4286f8fa57eace342b3f44248431616e8563d4ac6709c97d8534229c73c05470239e462b7e74b36bf629a876dfbad -perl-checksum = b0db58699dfbe1bab10a7b0472cc377ed215668c89d13c7ca693e6b75ab6a6593a9cf137adbd6096063ee8200d83b389e745bb96b7c6bf4cf4588ac587a446ae +perl-checksum = b00f3482f6961be043349a09445227e99472a8ae804919bfa0641de5bbd683249deb607f3b5c6c44ccfcf916408eac125132f9660191d574de0a9d1f17892bc1 pkgconfig-checksum = 4861ec6428fead416f5cbbbb0bbad10b9152967e481d4b0ff2eb396a9f297f552984c9bb72f6864a37dcd8fca1d9ccceda3ef18d8f121938dbe4fdf2b870fe75 readline-checksum = 41759d27bc3a258fefd7f4ff3277fa6ab9c21abb7b160e1a75aa8eba547bd90b288514e76264bd94fb0172da8a4faa54aab2c07b68a0356918ecf7f1969e866f -sed-checksum = e0be5db4cdf8226b34aaa9071bc5ae0eafde1c52227cee3512eea7fe2520d6c5cebf15266aa5c4adffbb51bf125c140a15644e28d57759893c12823ea9bbf4fb +sed-checksum = 7de25d9bc2981c63321c2223f3fbcab61d7b0df4fcf7d4394b72400b91993e1288d8bf53948ed5fffcf5a98c75265726a68ad4fb98e1d571bf768603a108c1c8 tar-checksum = 4be18afeac54aec4af074cf2358cfade5aaebe2041c5075c5764a81114df4d002e90b28f4444bd1430783e7d6bed82abd0440ef5cb244695f2e56a9a41b42fbc -texinfo-checksum = 96e0764d0808152d3662e65c3287fb0f86ed918912cdc036380637dbadaacd6a489b516543c07b08105686575e8d495a945f73e23ff0909d5a0f12026e4131e0 +texinfo-checksum = da55a0d0a760914386393c5e8e864540265d8550dc576f784781a6d72501918e8afce716ff343e5c2a0ce09cf921bfaf0a48ecb49f6182a7d10e920ae3ea17e7 unzip-checksum = 0694e403ebc57b37218e00ec1a406cae5cc9c5b52b6798e0d4590840b6cdbf9ddc0d9471f67af783e960f8fa2e620394d51384257dca23d06bcd90224a80ce5d valgrind-checksum = 5695d1355226fb63b0c80809ed43bb077b6eed4d427792d9d7ed944c38b557a84fe3c783517b921e32f161228e10e4625bea0550faa4685872bb4454450cfa7f wget-checksum = 95fb064f0d79b0a3178a83322f58a85a3a036fb300ed759eb67a538f0bbacdd552f6cbeb60d63b4f0113e8467d923a5ce7ac5570b7a4ce1733b3dfd559bb33b2 which-checksum = d2f04a5c5291f2d7d1226982da7cf999d36cfe24d3f7bda145508efcfb359511251d3c68b860c0ddcedd66b15a0587b648a35ab6d1f173707565305c506dfc61 -xz-checksum = e5bf6eb88365d2dbdc774db49261fb9fae0544ed297891fc20f1ed223f4072cb0357cbd98146ac35b6d29410a12b6739bbd111cd57d4a225bef255ed46988578 +xz-checksum = 7443674247deda2935220fbc4dfc7665e5bb5a260be8ad858c8bd7d7b9f0f868f04ea45e62eb17c0a5e6a2de7c7500ad2d201e2d668c48ca29bd9eea5a73a3ce zip-checksum = c1c3d62bf1426476c0f9919b568013d6d7b03514912035f09ee283226d94c978791ad2af5310021e96c4c2bf320bfc9d0b8f4045c48e4667e034d98197e1a9b3 zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae @@ -75,26 +75,26 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff apachelog4cxx-checksum = aa59ce549c2c5cbeec031361dfce09cdfc3e62ee3bc9ecbc809507b7ec878c14409b98536b7d13c27690809c8e9d5ebafc3589c9fb5e4aecd5cc064943ae7d6b apr-checksum = daa140c83c7e2c45c3980d9dc81d34fa662bebd050653562c39572d0ddf2eaedb71767c518a59d77f59db9b32e00221ef48b9f72ec3666c4521dd511969f3706 apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536 -astrometrynet-checksum = 35c268bf0a7068e01323b9bfccdf255c993df83c24b2e6026a00084c4ab87d031f1024205d0ed3aecc7e2a495d4bc0b0e67270d66679020b7cc2e4b2f30f5c4a +astrometrynet-checksum = 1ee3a3490fb687dc580e660a05ec21dc65972e6c1c97b9a5f648b9e4ac39bbb6b783b351d9b3fd8a4721ce01bb891166c18809f24144f6fc0d436955f0bc435e atlas-checksum = bf17306f09f2aa973cb776e2c9eacfb2409ad4d95d19802e1c4e0597d0a099fccdb5eaafe273c2682a41e41a3c6fabc8bbba4ce03180cffea40ede5df1d1f56e autoconf-checksum = c25e834251bfc2befe822614caf1c80d7e1314a83e7173304abc235fd15a958b8db9fbc801e8ad98328dfd6d9dbc425bfbbefec500fa268992ae7bbf4fa5bc35 -automake-checksum = 47b0120a59e3e020529a6ce750297d7de1156fd2be38db5d101e50120f11b40c28741ecd5eacf2790a9e25386713dcf7717339cfa5d7943d0dbf47c417383448 -bison-checksum = 968bbcfd1dffd10fb46ea4b3d49486d31b605f79ca88b8e2aa45fbafdb2fca3e1b0ac38564a9101681c8831cf423ea6a366f55d9497d21c05ddb3c7d66acb042 +automake-checksum = 8bd5b1d698eeb1d969ca0a32184ad46014b3ec334e3b8a0caf0e462ea5e100fe4ccaa7dcc2224c5db6c87e215d594593db0bf4431649186afb821b0a711c1a82 +bison-checksum = 8763e7b08fbcdeea3200fcb8d65a2589a12b17988d088ace58d19ea09e44d32e73a34ab1d6c4a2106e7147149997aaeabaada22b07159a5a0055cf60a9db162b boost-checksum = 2844dddd3357e76909f2f3d008f686949f8b54aed29e1c650e18becd0b50701a273bb3754f1a4e56c0c056693b27c354c9ba54ddbec92599e192c2f6736fe3be cairo-checksum = 9eb27c4cf01c0b8b56f2e15e651f6d4e52c99d0005875546405b64f1132aed12fbf84727273f493d84056a13105e065009d89e94a8bfaf2be2649e232b82377f cdsclient-checksum = 2d7abf0079189b9dd19cb8919061445fd19ea9f7dfd54e8ceee26b743218cf62ab00eba0147abe82d9294223927f04b4cc3328620dfc9184a7049f8d515b29e4 -cfitsio-checksum = c0502699e266928dd25abe57730dc4b357ccc9023789fe745324ae01aa688516aceaf37321ee578f0430111d9718f0fec0dc5b54c07f935529560f00b32ce1e3 -cmake-checksum = f09440681e0c414f5ca669f3aeba6666d09e0642f30a2e12c3199e7fb3da95a7dd17994fc54475c49638c37f0502ea0a2d8da0f9098805f11088ba7b299bf72a +cfitsio-checksum = 08a13931726b0ee15bd4e2ad6dd4debb8268f3b0bc33adadec5c6a29295dd536bcccb3cc949721c6cebac6f43b6118e5e38332ac0ba8a07a43553416d8debae5 +cmake-checksum = e0591d5fb234f3e7b74d6d2aad44fbf3e19e69547bd428681ba6ad0461d4f3d2a154605808b4733531d2c66f0e91eb39a179ae0d89a37e92a3f20e9cae691468 eigen-checksum = 34cf600914cce719d61511577ef9cd26fbdcb7a6fad1d0ab8396f98b887fac6a5577d3967e84a8f56225cc50de38f3b91f34f447d14312028383e32b34ea1972 expat-checksum = 514ff2ef3c93af0b1715b7a08732db33c13a113c4c72422716a22ee26c09235deed71ec55510cee24c33bcd6b2347602bd71ce70a432d5583fb63765ff9e0e09 fftw-checksum = ab918b742a7c7dcb56390a0a0014f517a6dff9a2e4b4591060deeb2c652bf3c6868aa74559a422a276b853289b4b701bdcbd3d4d8c08943acf29167a7be81a38 flex-checksum = b4ef58d4a1d66b213e2f59df06959decf46d26b253cdc3f51cd26e2e2b505461ef23dafa974dd2005b1f0cafa5a83fe9258baf78004b2fdae6dfc299bc17bfd1 -freetype-checksum = 02f0f4211f9cee5b5e46ebe61190482fca5b41bc26be06fcf0d2d717e9fb119229308398c420eeea476fa2511ca2d52948f1a3242efad30ca82ed0b07cd50e3a -gdb-checksum = b4161df5adfce3eb51b3b3fc6072b2ef9f612f5e0f95b25bc57382812854836e9d1b24807c68cc8987e37e90112c6d75ffc1de3ea67a9f92858b4ce1af85c479 -ghostscript-checksum = acee64fae78771bffa19b0b2bfaba3c345b420f93ceb4fc9df5fb705f785c8ed720fde2aef53546fac6aca2f7366c64c68a6e373a71999a42dc71aadc9aa782f +freetype-checksum = cbb1b6bb7f99f6ecb473ce6027ec5f2868af939f793dd7b083b23e9823e18c4bcbac0b92483ebe70804ad7f4ef5bf4ea5c6b476e7f631a3e6a1b3e904a41e1a5 +gdb-checksum = 0ccd3a2a24963c848976848ba890f99a458569ff10da4d2bb6dd4782852662ab2df7fb9b3525dd4fd04f95070cea07e1bae6dbe2969e321cbb4004a033845d1c +ghostscript-checksum = 32fb2a3d4e81ac9e281202aaed2f7811e80c939cbce3ffef7ec7cf78213e5da8a2f6c13d15f0c6c8fd24566579ba8b69364d4c66f4e4b7851f6df9209d0ff046 ghostscript-fonts-gnu-checksum = 222cb81e6956d9724e746f5f4d5c7b47b04bfd75b889f437f946c29a5bf16b5ed57b7584cf7fb0d8561287ef9f2e1ac53e4d231b6eaf23cba2612b47e8a5f919 ghostscript-fonts-std-checksum = d4fe6b097a3bdd9694dc704a2d986e22d649fbb7ca8302f872dff573525596a3f38246bd6dd166a5970a4fbca8cce6ebfb9a7030806b4662630afdf243438e1f -gnuastro-checksum = 718b391cc59e8f6b57afc963fb27161ecc9f32b18dcef1cf9c24c88f61d264d8d1154e59a74c36f6ac3a970e1a6f77eee288ec881899beb57e51cc55b56c089b +gnuastro-checksum = e236814001c1740355cfb1490926c667d14c026c8e93249afb25c1fc934a8ef8c52178276b7ab5cdbeb819117f962a4c7f65df74f0fc35bf512388cbe3b26d39 gperf-checksum = 855ebce5ff36753238a44f14c95be7afdc3990b085960345ca2caf1a2db884f7db74d406ce9eec2f4a52abb8a063d4ed000a36b317c9a353ef4e25e2cca9a3f4 gsl-checksum = 0be8240715f0b86aba2c63d9f12da4dba4719d4e350e9308d279e0dd3b2f0519ea26fd2e38a17f3e8cf43aacbaa2455207a7ca0d6c305f3b8725e8ece2250a74 hdf5-checksum = f828ee9d63533effe1ad358230e5ce7b64c5016e49291d9533575f713cbfba496290fc0151fd9617898bdf36785984ddb38a9207f529d7702d4e23838fe050d8 @@ -104,8 +104,8 @@ imagemagick-checksum = ad4325df57769f9c4edf8ac71370cb9bb19e090e588d47eb0311e3f48 imfit-checksum = 15edd2349232c1c8e611b31d3a46b0700112d274515f54d0a0085bb4bfa6d3d5f8a15cd926516e043a29ce841accf3534ae58dbfb952d858dc9445199c957096 lapack-checksum = 17786cb7306fccdc9b4a242de7f64fc261ebe6a10b6ec55f519deb4cb673cb137e8742aa5698fd2dc52f1cd56d3bd116af3f593a01dcf6770c4dcc86c50b2a7f libffi-checksum = 980ca30a8d76f963fca722432b1fe5af77d7a4e4d2eac5144fbc5374d4c596609a293440573f4294207e1bdd9fda80ad1e1cafb2ffb543df5a275bc3bd546483 -libidn-checksum = 782260f73b1fd8ebea8a40e2b3a6866c4f67494b2b3df03748daa9c0f842a9578932e746eb4bbf2547fccb1d65d7fc99a7977759dbe58f87f2fdd26d0fe45a09 -libgit2-checksum = 0879c162e2e1dc00eadfbda22cd1f9d3a95b4ec2b653c108983f37c2f695140882de4d50d7cbc04ced247125a4e9fe6df16130e1267891aecdb2411d920db5c6 +libidn-checksum = 0d66e10bf7a8de4b27f692a427d2c8e901b8bed73b0a36268d8f939205df81f6a30f0634fd3b87370d4e81c1327c0b10391fa122a0a5459c32a3541b8a2149ad +libgit2-checksum = 7c307822b22e3771e5e908b115600310f7901b3250287532c498003b25a5b1e007bfa23592f16ec4d83c1567a9213710526f78cab7c120316e9a8fc74c5e57a9 libjpeg-checksum = 74ea5af3545657d4ac03f8f7933913112cc2d982f0e379d0e5647f1acac21931468e53806297c30ebe180c7bcf84919a0ac20a4195afb03db03060d57904ef6c libnsl-checksum = a3c8f674357674b7ed4b26c05adde607f39be8d6dc9ff715448e1fcc5fc23d11fbb4ce85a6e493b79bdb0bb450dc3ffb1fb480715779f738d7bc016fae91621d libpaper-checksum = 3bf6ebb0af89931d2f72ea4a09a7fa958b2facda5f238983ec7bac39652e08614b33f0de3af74a03457b2a4203eee4950bf18a4b726e79aa64093ace6a1fb0bc @@ -115,13 +115,13 @@ libtirpc-checksum = bcb6b5c062c1301aa1246ec93ae0a5c1d221b8421126d020863517cb814b missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795 netpbm-checksum = 064720f8a9d0a502488e1af4daecdbf3936910996507ca6f311073a0ad842346692a148eb1ddf7b717f7b108f60500246cb4b83f4d3665f5fc285a84ae1d63d6 openblas-checksum = 64a5f983b2f6e02cdb6e0f14433498cc5daa1ccfb49246f7a2dcd38f9982fa608f2abea069fe0e35012af8c1441c43d1f6418eaccd40795f5002fed1c36ce05d -openmpi-checksum = 760716974cb6b25ad820184622e1ee7926bc6fda87db6b574f76792bc1ca99522e52195866c14b7cb2df5a4981efdaf9f71d2c5533cc0e8e45c2c4b3b74cbacc +openmpi-checksum = aea02a66dc67820c86172fae80f5aa4c71e918525abbfaf06df8ba6898ff78ec3b0ef9638952b2c1d1a9c878fc0999d6f6d06e840679a68779d6b81f0336eb76 openssh-checksum = e280fa2d56f550efd37c5d2477670326261aa8b94d991f9eb17aad90e0c6c9c939efa90fe87d33260d0f709485cb05c379f0fd1bd44fc0d5190298b6398c9982 patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187dad77d1413f0eb3319b3fe4df076714615c98b29df06af052bb65960fa8b0c86bf pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb pixman-checksum = 1b0205dbe9d9185c68813ce577a889f3c83e83fbd9955c3a72d411c3b476e6be93fc246b5b6ef4ee17e2bb8eb6fb5559e01dff7feb6a6c4c6314f980e960d690 -python-checksum = c25a72ad792f7c1b4c2f79faebbe9608d04b04b2fe58ab804cb4732cdaa75ea93d175f5e52b38e91cb6ae0559ea6b645d802c8b6a869584e8bb9b5018367ce3d -R-checksum = 17513e9f4dd27c61c11f7aa45227aeeeefb375bf5d4e193b471724f379a1b2da33e127cbe91aa175cbbbb048b892047e2f610280585c8159242a6c94790b07f9 +python-checksum = 392459354b8438f76670ec2086b4618ee21f615ca4b22e5dbb366273665a470de5047a3f241925a62b60bf3cddde5984a05144a55d0c5ced43342f5b94576952 +R-checksum = b7330613ee9795f54cde3dd9f7509be83d9156fb8577c17179727ee01450db27704249f68bd48e0331e2df09c2d9833d8bb019c4f9ce9ba669df74650ff2e842 rpcsvc-proto-checksum = c3011d7d7ef97a4a751f6921df1a23e1dd8ac50fb0690c759d37010ed7be27968a2130e3b8872cb48d5914216f9d539096a424f1ec38a75f7ed899748151c6f4 scamp-checksum = 35034a367d2cd09dc51e727e0f23ef6234edc0d978fd71cda1e80391d86af160138cb57281f7f7f9047e35b1246a0de6b235414086a62524413ed423f498583f scons-checksum = 0477038b014674049f12899b64584d44a85283d521b2422561e42020a5ae296a5af005684087c3ff410ed3fcbdcc5ff61998bc429eb29513f2a864138ffc4945 @@ -130,9 +130,9 @@ swarp-checksum = 80f4ade59738df3d4c9b47bda04148b53c6ba995d523fa8d1e02fb5d952b607 swig-checksum = 5eaa2e06d8e4197fd02194051db1e518325dbb074a4c55a91099ad9c55193874f577764afc9029409a41bd520a95154095f26e33ef5add5c102bb2c1d98d33eb tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108 util-linux-checksum = c95d26b9037d6b877a247e6aeb58d17aa80f7e1bd6b523a4e0fde559fe07b3d924ece6d373300fefb65d1f206b3f990aeddb3a03605040e72ce6d6ee88591021 -wcslib-checksum = fed47771defb2a93fb50aa2e701c46f8ce35773dd3de91eeaed311b5a0474c096c7f9be6996fe95f82faa30b1d5c0aba892bca5da80bc32b15919dfaf551aeb7 +wcslib-checksum = 8c98c4b575056e2d966b77a4bc951256d02ecee3a11847e140fd38d93afd0f76b3e906d590c952dc9fc58ceeb1ba062b19d8e1e676ee0032f5b7ed13a9dfa892 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c -yaml-checksum = 13d2197135946204323dbfccafa0ac7b3d05437e920545a56f46811fd7319c01419a58083090ce85fccd4d6901a620ceb9f1190078cc0830bc0ce769bb024f51 +yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02 zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae # Xorg related packages @@ -170,7 +170,7 @@ chardet-checksum = 61a03b23447a2bfe52ceed4dd1b9afdb5784da1933a623776883ee9f297e3 corner-checksum = ebd625ab1e4591b4c21d25ec706c35d37f560b727e1e0d6a79948c4a112ee6f21d3ca30162901a27715074e1345f3bdee1a0345c63e5fec24113e495fb094127 cryptography-checksum = f14319e24d9dca52e74548cada5b78a6235f089ef875dbff4799e862f94da8b087f1b6e03e84dcef9fc7d7693c4a349c5f0cd54b8535806da777420ce8757d39 cycler-checksum = b7d2ba19861ffaf4dea0444bfe68b5a6264a022d7b3f02c9ff5e5859e3901de12a90f8dc7469e995e09c418515b3df55dbf05a0cfe5368d40790a2c878a74819 -cython-checksum = bb8095b438a7d2567b8b831628fbb32c02299c866e41113da62fb5a5d4982dc0df947a9f723a82c52086806435d8f3518e78a803166149d476f81e042a12494e +cython-checksum = 6216e63996e83b887cdcee6cd912d42e7da853640336b9190f5115d687848a902ee5a8edd6bfaef645c066b89e17dcd80ca1387688eb80a527ec23a0a4636e8f eigency-checksum = 1e7cdfc43071da5edba30a0d32cd655442b516f15c166b049a195d151dec8c20a2177ad69bed3bba4788a668fa25a4c551ef4990717ff98d5b2f407bffb214c8 emcee-checksum = dd60aace8879525fd3fe42b747d82170b24b2ed21f538f9186ba96b9d04c084812e3303f5d2e04119dabd2f9d3286d510b4d4a5324c71dd24b1c7e5f0a9a0ac6 entrypoints-checksum = aa1274362d3a4b00266103319ca51aa266605b4999c89a9d0673eb61bfae9e646cb0ec6b86c95544493f6fe048385a2c7641d64adca8f45815546fb1e663c858 @@ -178,7 +178,7 @@ esutil-checksum = c1cf8e7912b16dc675fdc7195ecc2bbffcd156c1257b2df45afdf09cc487c4 flake8-checksum = a25076bb7f978ca23af0f2016b30bf5fe4680371b4c0939361a6f8c496f3c846cf98ecadee35fc2dedd588116c8cd982529972dd2411ab139621912b69132a1e future-checksum = c70565a660cf87c5e7e994bae0d4eb0b2b8b607ecb5ce65521c027bf0a39ce5699f0578413bd3c7edd5d01aeb1617de48dcea098a9e9021d8487a73007573030 galsim-checksum = 11ecbfb9628cf85a4c25024c6f3a34bbdadf522f64e4e93e6428b545c65a48906a05eb7774d0faaacf52a48dddfd599bfc7cc7252ca854a18c3930f116533a3c -h5py-checksum = 73b1f59e3e2b3eceebf7b97e49bd8f5199afafd7ef29917af05ff8415c2f2129a5c59db9658944370c9bcf8fc04ab26948ee27fc6fd948a22d19cace1ce8c853 +h5py-checksum = c49b04f7dcddf03f36d4f063d79ecbe544e0b1daee432d4a76cfa83dac3a1f2cb144f40a74fb85ea17cb5b778f57f709969ea5d1a2afc5bdd5aecbc9d732898d healpy-checksum = installed-with-healpix html5lib-checksum = 35939b4450893864da04e735ee5e0addacf1dd34bae6a6909c76572abf6bfded446a78a713dfde91c1485ba45867d7abeb6a45cf0545c16ea968707be7de5dd2 idna-checksum = 8ca5cfe6350c51250bafdac7c6e4ddd54c4a5d6bf7acbcef896760a759868c8e9df1fdf550121d8512fa3eb316dcf031ec6058e03b4f66eadee21b63e2187d33 @@ -187,13 +187,13 @@ keyring-checksum = 3863f2cd89131d7e927e55691b4eb4b7c2599af189525293d0948aef5215e kiwisolver-checksum = 80ed3d7429a2ed4944aa09766bebac2709a3a0e0a184ff414f04bf3c7ec3034ea7d0f70dff319922b870dedaf13d64fc87eff86a82e720ec93a2510885ad738d lmfit-checksum = 8435328fd8baf92b424299c341aafb995dc45245e17b1774e9eaabdd994dd6ec3b2e70f7506d67b587631cebd2dc584fcd1a9902286925a61e2135b7e11ece21 lsstdesccoord-checksum = a66b8b702cd8122f0c8aee05abe0fc0c6299f8bdb99b151f54bd7ad7430d6bc9f843f7294a7f08f3ce9f8606ea0ced0796a63b79cc8a53ae73068b691e2e6871 -matplotlib-checksum = d44729028b91523c7ed2659e7ce7e9c2022ff322c3804e1ca16c9f64038f21d63ebf74a4da4239605cfb9c65729bf519360ac7f2a25dc70daa6fdcfa9c610c31 -mpi4py-checksum = 0a18332fd45e8e80b8dab0761fbaa30444a0d55776af7a2333be17ade827e92d04ac5bb8619ce26937142f344f75de0e5ef6dcb7502f33389716aa9482ddf5ab +matplotlib-checksum = 2ffd9e79e300a37092ab4b5a7156c2f57e408975818abd413c74477ad622030c7636695467aab821c9996564cddec57e26ba6a8004f6639070964fcb7a510a75 +mpi4py-checksum = 041768f753c8188b2560fe92711861780f0d77eda3281433520c98bb1e9b4da6a89c364f2d1c4623868ffbbcfde34ef556198b1bef6fc1c4a9c19cd5e71b546c mpmath-checksum = 58c69a801f65d73cc0eeb0d2c79277ed638568c656e7213d06ab4709c218aac908b2752377139010bed0e91bbfff01d129c60835ff0a928ba1185aded6de7c0a -numpy-checksum = 3f7691de2b3c5423b9bf55f51ba961bf9931b13c59da80f406a1b50fcf1aa4174db948eb7e450c851c98eb7406f8b7da373df48fb07b0e577638360affad40ee +numpy-checksum = ddc5f5e262d6f7f6e1a8879165860427baa237b6aad5b09d5b943a36bb0d5922424aac4c0e32a2cc3e14087bf6eb671988b6ff6df0d9ab8c89724e093220eead pexpect-checksum = 4cea4229332c1f3de26dfcad596877665b3c02e91d51ca3c45c1f9b44462adb7c82abc7b76eb09a73822c2d1ccc9d812574cf79bf6bc8fb0b7d2f1093962cc3f pip-checksum = c6e13da3a57462371d32982c80575c5181592f5c6a8e70d60ec879e689442f4ad468e7aef97eb58c9da50a5a770385aa35e701eefd713a8e9fafeb12e11d956b -pybind11-checksum = 97b6ffb38dbda8021e8265c2052df65785d532dbcd94a2b711306f806eab1a9e2aaf31ea466f13eb5784856ac69e0f4c1dc6d742aa70e5a10ce9ce338e5e9d84 +pybind11-checksum = a863b92a03a23395ba67f6e4916c479ba800060e89a6d80e586533a23603df111b5cba9fd03b3ed500956169edfd8cb1b32a0bc05c42f928740beeea5bd63352 pycodestyle-checksum = 84e751a7d00048393b02ca743de5d71d1641e948ee1b4daebbdf2d07e0cd8f087ca4e81f826061114b40ef41920bbcd680c9f479e7cc1a159a70188425717208 pycparser-checksum = 7f830e1c9066ee2d297a55e2bf6db4bf6447b6d9da0145d11a88c3bb98505755fb7986eafa6e06ae0b7680838f5e5d6a6d188245ca5ad45c2a727587bac93ab5 pyflakes-checksum = 7ebf5843b38146305c1063e070480fea8ec3b47fa1be546b1fafaeb242a688a5a001f978e7257fd71d5905b9a338b466ef17c7330725191587e9c40ba632c3f8 @@ -202,7 +202,7 @@ pypkgconfig-checksum = 1fd9aa973bd20a8fab864722598f1d19b94c23c7f2b522556b3182b19 python-dateutil-checksum = ec7da86203572582f883a4686acf8a732a2de4f396d809057eb51b2c60dbca5623a7fa90c2c0618c281a2282c60841739bd837731a51cc876f4ff369297f2f81 pyyaml-checksum = 8f27f92bdfa310a99dd6d83947332cc033fa18f0011998bb585ad5c4340a2da20d8c20bfdb53beaae15651198d1240c986818379b0a05b230f74d1f30f53e7fd requests-checksum = 385e1d80993a21c09e7c4682500ca8c24155962ba41ecd8e73612722b2ff6618b736e827fc48ad1683b0d2bc7a420cfe680f5107860aca52656ef777f1d60104 -scipy-checksum = 672915da782f5a439a3920ad1a200937b8415aeb4f1db2451cf0b5a90ba6e18c69e17e9ff8433f6a7760bbef2434d7b0f6447319faec9bb96fa6841794bfa538 +scipy-checksum = 45463df30a0f6270d9f4cf52235f31607904a6ae1375e12600e7f1ab2d27b1dc25a6211b49dceb71506be22c756890adaf9f81d9e6be7455def86c9caf0dc923 secretstorage-checksum = 295e0f75c772edf153480730dc20051f06e60e040a18f169620cb4aaa37b8c1a254a496464d3794a38cf49fa884a7b561fe364816f0d12a5b2622c77259f03cf setuptools-checksum = 1bed75e7173ea0399f078c96cf5c1818dada7a4b86a93e61ff72da6a25694e321b9047e024617aa775b71a25fe8cb0848323902e1fb9c8c8a1f39434f0de6434 setuptools_scm-checksum = 196d4785a1802875d89b9e54ae788e791a9c5cb685109784059955b691242984e42b96d77075116790935f56be82259bc2588d95d65ecbb101261d76daddb83c diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index 945537d..34c4d89 100644 --- a/reproduce/software/config/urls.conf +++ b/reproduce/software/config/urls.conf @@ -16,8 +16,8 @@ # Basic/low-level programs and libraires (installed in any case) -# -------------------------------------------------------------- -#bash-url = http://akhlaghi.org/maneage-software +# ------------------------------------------------------------- +#bash-url = http://akhlaghi.org/src #binutils-url = http://ftp.gnu.org/gnu/binutils #bzip2-url = http://akhlaghi.org/maneage-software #cert-url = http://akhlaghi.org/maneage-software @@ -86,7 +86,7 @@ #cairo-url = https://www.cairographics.org/releases #cdsclient-url = http://cdsarc.u-strasbg.fr/ftp/pub/sw #cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c -#cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv/cmake-$(cmake-version).tar.gz) +#cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv) #eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz #expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz) #fftw-url = ftp://ftp.fftw.org/pub/fftw @@ -94,22 +94,23 @@ #freetype-url = https://download.savannah.gnu.org/releases/freetype #gdb-url = http://ftp.gnu.org/gnu/gdb #ghostscript-url = $(shell v=$$(echo $(ghostscript-version) | sed -e's/\.//'); echo https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs$$v) -#gs-fonts-std-url = https://downloads.sourceforge.net/gs-fonts -#gs-fonts-gnu-url = https://downloads.sourceforge.net/gs-fonts #gnuastro-url = http://ftp.gnu.org/gnu/gnuastro +#gperf-url = http://ftp.gnu.org/pub/gnu/gperf +#gs-fonts-gnu-url = https://downloads.sourceforge.net/gs-fonts +#gs-fonts-std-url = https://downloads.sourceforge.net/gs-fonts #gsl-url = http://ftp.gnu.org/gnu/gsl #hdf5-url = $(shell majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src) #healpix-url = http://akhlaghi.org/maneage-software #help2man-url = http://ftp.gnu.org/gnu/help2man +#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/ #imagemagick-url = http://akhlaghi.org/maneage-software #imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit #lapack-url = http://www.netlib.org/lapack #libffi-url = ftp://sourceware.org/pub/libffi +#libgit2-url = http://akhlaghi.org/src #libidn-url = https://ftp.gnu.org/gnu/libidn -#libgit2-url = https://github.com/libgit2/libgit2/archive #libjpeg-url = http://ijg.org/files #libnsl-url = http://akhlaghi.org/maneage-software -#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/ #libpng-url = https://download.sourceforge.net/libpng #libtiff-url = https://download.osgeo.org/libtiff #libtirpc-url = https://downloads.sourceforge.net/libtirpc @@ -121,7 +122,7 @@ #openssh-url = https://artfiles.org/openbsd/OpenSSH/portable #patch-url = http://ftp.gnu.org/gnu/patch #pixman-url = https://www.cairographics.org/releases -#python-url = https://www.python.org/ftp/python/$(python-version) +#python-url = http://akhlaghi.org/src #R-url = $(shell majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}'); echo https://cran.r-project.org/src/base/R-$$majver) #rpcsvc-proto-url = https://github.com/thkukuk/rpcsvc-proto/releases/download #scamp-url = http://akhlaghi.org/maneage-software @@ -138,16 +139,16 @@ # Xorg packages # ------------- -#util-macros-url = https://www.x.org/pub/individual/util -#xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto +#fontconfig-url = https://www.freedesktop.org/software/fontconfig/release +#libpthread-stubs-url = https://xcb.freedesktop.org/dist +#libx11-url = https://www.x.org/pub/individual/lib #libxau-url = https://www.x.org/pub/individual/lib #libxdmcp-url = https://www.x.org/pub/individual/lib +#libxext-url = https://www.x.org/pub/individual/lib +#util-macros-url = https://www.x.org/pub/individual/util #xcb-proto-url = https://xorg.freedesktop.org/archive/individual/proto -#fontconfig-url = https://www.freedesktop.org/software/fontconfig/release +#xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto #xtrans-url = https://www.x.org/pub/individual/lib -#libx11-url = https://www.x.org/pub/individual/lib -#libxext-url = https://www.x.org/pub/individual/lib -#libpthread-stubs-url = https://xcb.freedesktop.org/dist @@ -167,7 +168,7 @@ # files" menu, you can download the source '.zip' file. For version 1.18.5, # (with full filename of 'numpy-1.18.5.zip') the link will be like this. # -# numpy-url = https://files.pythonhosted.org/packages/01/1b/d3ddcabd5817be02df0e6ee20d64f77ff6d0d97f83b77f65e98c8a651981/numpy-1.18.5.zip +# numpy-url = https://files.pythonhosted.org/packages/01/1b/d3ddcabd5817be02df0e6ee20d64f77ff6d0d97f83b77f65e98c8a651981 # # Hence, if the version changes, the checksum, and its two top host # directories also change. This is why we aren't putting any URL here by diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 7998345..0a9e21e 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -16,24 +16,24 @@ # -------------------------------------------------------------- # # CLASS:BASIC (important identifier, don't modify this line) -bash-version = 5.0.11 -binutils-version = 2.32 -coreutils-version = 8.31 -curl-version = 7.65.3 +bash-version = 5.0.18 +binutils-version = 2.35 +coreutils-version = 8.32 +curl-version = 7.71.1 dash-version = 0.5.10.2 diffutils-version = 3.7 -file-version = 5.36 +file-version = 5.39 findutils-version = 4.7.0 flock-version = 0.2.3 -gawk-version = 5.0.1 -gcc-version = 9.2.0 -gettext-version = 0.20.2 -git-version = 2.26.2 -gmp-version = 6.1.2 -grep-version = 3.3 +gawk-version = 5.1.0 +gcc-version = 10.2.0 +gettext-version = 0.21 +git-version = 2.28.0 +gmp-version = 6.2.0 +grep-version = 3.4 gzip-version = 1.10 isl-version = 0.18 -libbsd-version = 0.9.1 +libbsd-version = 0.10.0 libiconv-version = 1.16 libtool-version = 2.4.6 libunistring-version = 0.9.10 @@ -44,18 +44,18 @@ make-version = 4.3 metastore-version = 1.1.2-23-fa9170b mpc-version = 1.1.0 mpfr-version = 4.0.2 -ncurses-version = 6.1 +ncurses-version = 6.2 patchelf-version = 0.10 -perl-version = 5.30.0 +perl-version = 5.32.0 pkgconfig-version = 0.29.2 readline-version = 8.0 -sed-version = 4.7 +sed-version = 4.8 tar-version = 1.32 -texinfo-version = 6.6 +texinfo-version = 6.7 unzip-version = 6.0 wget-version = 1.20.3 which-version = 2.21 -xz-version = 5.2.4 +xz-version = 5.2.5 zip-version = 3.0 zlib-version = 1.2.11 @@ -83,35 +83,34 @@ bzip2-version = 1.0.6 apachelog4cxx-version = 0.10.0-603-014954db apr-version = 1.7.0 apr-util-version = 1.6.1 -astrometrynet-version = 0.77 +astrometrynet-version = 0.80 atlas-version = 3.10.3 autoconf-version = 2.69.200-babc -automake-version = 1.16.1 -bison-version = 3.6 +automake-version = 1.16.2 +bison-version = 3.7 boost-version = 1.73.0 cairo-version = 1.16.0 cdsclient-version = 3.84 -cfitsio-version = 3.47 -cmake-version = 3.17.0 +cfitsio-version = 3.48 +cmake-version = 3.18.1 eigen-version = 3.3.7 expat-version = 2.2.9 fftw-version = 3.3.8 flex-version = 2.6.4-91-ga631f5d -freetype-version = 2.9 -gdb-version = 8.3 -ghostscript-version = 9.50 +freetype-version = 2.10.2 +gdb-version = 9.2 +ghostscript-version = 9.52 ghostscript-fonts-gnu-version = 6.0 ghostscript-fonts-std-version = 8.11 -gnuastro-version = 0.11 +gnuastro-version = 0.12 gperf-version = 3.1 gsl-version = 2.6 -hdf5-version = 1.10.5 healpix-version = 3.50 help2man-version = 1.47.11 imagemagick-version = 7.0.8-67 imfit-version = 1.6.1 libffi-version = 3.2.1 -libidn-version = 1.35 +libidn-version = 1.36 libjpeg-version = v9b libnsl-version = 1.2.0-4a062cf libpaper-version = 1.1.28 @@ -120,13 +119,13 @@ libtiff-version = 4.0.10 libtirpc-version = 1.2.6 missfits-version = 2.8.0 openblas-version = 0.3.10 -openmpi-version = 4.0.1 +openmpi-version = 4.0.4 openssh-version = 8.0p1 patch-version = 2.7.6 pcre-version = 8.44 pixman-version = 0.38.0 -python-version = 3.7.4 -R-version = 3.6.2 +python-version = 3.8.5 +R-version = 4.0.2 rpcsvc-proto-version = 1.4 scamp-version = 2.6.7 scons-version = 3.0.5 @@ -136,7 +135,7 @@ swig-version = 3.0.12 tides-version = 2.0 util-linux-version = 2.35 xlsxio-version = 0.2.21 -yaml-version = 0.2.2 +yaml-version = 0.2.5 # Xorg packages util-macros-version = 1.19.2 @@ -157,8 +156,8 @@ libpthread-stubs-version = 0.4 # Version-dependent build # ----------------------- lapack-version = 3.8.0 -libgit2-version = 0.28.2 -wcslib-version = 6.4 +libgit2-version = 1.0.1 +wcslib-version = 7.3 # Netpbm's questions in the configure steps maybe change with different or # new versions. @@ -177,6 +176,9 @@ openssl-version = 1.1.1a # any future release. valgrind-version = 3.15.0 +# Be careful with updateing hdf5 because h5py 2.10.0 doesn't work with +# version 1.12.0. +hdf5-version = 1.10.5 @@ -202,7 +204,7 @@ chardet-version = 3.0.4 corner-version = 2.0.1 cryptography-version = 2.6.1 cycler-version = 0.10.0 -cython-version = 0.29.6 +cython-version = 0.29.21 eigency-version = 1.77 emcee-version = 3.0.1 entrypoints-version = 0.3 @@ -210,7 +212,7 @@ esutil-version = 0.6.4 flake8-version = 3.7.8 future-version = 0.18.1 galsim-version = 2.2.1 -h5py-version = 2.9.0 +h5py-version = 2.10.0 html5lib-version = 1.0.1 idna-version = 2.8 jeepney-version = 0.4 @@ -218,22 +220,22 @@ keyring-version = 18.0.0 kiwisolver-version = 1.0.1 lmfit-version = 0.9.14 lsstdesccoord-version = 1.2.0 -matplotlib-version = 3.1.1 -mpi4py-version = 3.0.2 +matplotlib-version = 3.3.0 +mpi4py-version = 3.0.3 mpmath-version = 1.1.0 -numpy-version = 1.17.2 +numpy-version = 1.19.1 pexpect-version = 4.7.0 pip-version = 19.0.2 pycodestyle-version = 2.5.0 pycparser-version = 2.19 pyflakes-version = 2.1.1 -pybind11-version = 2.4.3 +pybind11-version = 2.5.0 pyparsing-version = 2.3.1 pypkgconfig-version = 1.5.1 python-dateutil-version = 2.8.0 pyyaml-version = 5.1 requests-version = 2.21.0 -scipy-version = 1.3.1 +scipy-version = 1.5.2 secretstorage-version = 3.1.1 setuptools-version = 41.6.0 setuptools_scm-version = 3.3.3 @@ -249,3 +251,4 @@ webencodings-version = 0.5.1 # # Healpy: When any Python module is requested, healpix will also build its # Python module Healpy. +healpy-version = xxxxx diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index b9678d0..0b672d8 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -183,6 +183,10 @@ $(ibdir) $(ildir):; mkdir $@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \ | $(ibdir) $(ildir) + # Hardware specific + $(call makelink,lp) # For printing, necessary for R. + $(call makelink,lpr) # For printing, necessary for R. + # Mac OS specific $(call makelink,mig) $(call makelink,xcrun) @@ -922,7 +926,7 @@ $(ibidir)/gettext-$(gettext-version): \ $(ibidir)/ncurses-$(ncurses-version) \ $(ibidir)/libiconv-$(libiconv-version) \ $(ibidir)/libunistring-$(libunistring-version) - tarball=gettext-$(gettext-version).tar.xz + tarball=gettext-$(gettext-version).tar.lz $(call import-source, $(gettext-url), $(gettext-checksum)) $(call gbuild, gettext-$(gettext-version), static,, \ V=1 -j$(numthreads)) @@ -959,7 +963,7 @@ $(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version) $(call import-source, $(libtool-url), $(libtool-checksum)) $(call gbuild, libtool-$(libtool-version), static, \ --program-prefix=g, V=1 -j$(numthreads)) - ln -s $(ibdir)/glibtoolize $(ibdir)/libtoolize + ln -sf $(ibdir)/glibtoolize $(ibdir)/libtoolize echo "GNU Libtool $(libtool-version)" > $@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) @@ -1211,6 +1215,7 @@ $(ibidir)/binutils-$(binutils-version): \ $(call makelink,ld) $(call makelink,nm) $(call makelink,ps) + $(call makelink,strip) $(call makelink,ranlib) echo "" > $@ else @@ -1220,14 +1225,15 @@ $(ibidir)/binutils-$(binutils-version): \ --with-lib-path=$(sys_library_path), \ -j$(numthreads) ) - # The `ld' linker of Binutils needs several `*crt*.o' file to - # run. On some systems these object files aren't installed in - # standard places. We defined `LIBRARY_PATH' and that fixed the - # problem for many systems. However, some software (for example - # ImageMagick) over-write `LIBRARY_PATH', therefore there is no - # other way than to put a link to these necessary files in our - # local build directory. IMPORTANT NOTE: later, when we build the - # GNU C Library in the project, we should remove this step. + # The `ld' linker of Binutils needs several `*crt*.o' files from + # the host's GNU C Library to run. On some systems these object + # files aren't installed in standard places. We defined + # `LIBRARY_PATH' and that fixed the problem for many + # systems. However, some software (for example ImageMagick) + # over-write `LIBRARY_PATH', therefore there is no other way than + # to put a link to these necessary files in our local build + # directory. IMPORTANT NOTE: later, when we build the GNU C + # Library in the project, we should remove this step. if ! [ x"$(sys_library_path)" = x ]; then for f in $(sys_library_path)/*crt*.o; do b=$$($(ibdir)/basename $$f) @@ -1284,9 +1290,9 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # built/existing compilers in this project. Note that GCC also # installs several executables like this 'x86_64-pc-linux-gnu-gcc', # 'x86_64-pc-linux-gnu-gcc-ar' or 'x86_64-pc-linux-gnu-g++'. + rm -f $(ibdir)/*g++ $(ibdir)/cpp $(ibdir)/gfortran rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc* rm -f $(ibdir)/*gcc* $(ibdir)/gcov* $(ibdir)/cc $(ibdir)/c++ - rm -f $(ibdir)/*g++ $(ibdir)/cpp $(ibdir)/gfortran $(ibdir)/strip rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64* # GCC builds is own libraries in '$(idir)/lib64'. But all other @@ -1315,7 +1321,6 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # having GNU CPP in the project build directory is known to cause # problems with 'libX11'. $(call makelink,gfortran) - $(call makelink,strip,mandatory) if [ x$(on_mac_os) = xyes ]; then $(call makelink,clang) $(call makelink,clang++) diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk index 7471e5b..86370ab 100644 --- a/reproduce/software/make/build-rules.mk +++ b/reproduce/software/make/build-rules.mk @@ -170,11 +170,21 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \ \ echo; echo "Using '$$confscript' to configure:"; echo; \ echo "$$confscript $(3) $$configop"; echo; \ - $$confscript $(3) $$configop; \ - make "$$shellop" $(4); \ - $$check; \ - make "$$shellop" install $(7); \ - cd ..; \ + if [ x$$configure_in_different_directory = x1 ]; then \ + mkdir build; \ + cd build; \ + ../$$confscript $(3) $$configop; \ + make "$$shellop" $(4); \ + $$check; \ + make "$$shellop" install $(7); \ + cd ../..; \ + else \ + $$confscript $(3) $$configop; \ + make "$$shellop" $(4); \ + $$check; \ + make "$$shellop" install $(7); \ + cd ..; \ + fi; \ rm -rf $(1) diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 4052ed4..9f434bc 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -763,8 +763,8 @@ $(ibidir)/libgit2-$(libgit2-version): $(ibidir)/cmake-$(cmake-version) -DUSE_SSH=OFF -DBUILD_CLAR=OFF \ -DTHREADSAFE=ON -DUSE_ICONV=OFF ) if [ x$(on_mac_os) = xyes ]; then - install_name_tool -id $(ildir)/libgit2.28.dylib \ - $(ildir)/libgit2.28.dylib + install_name_tool -id $(ildir)/libgit2.1.0.dylib \ + $(ildir)/libgit2.1.0.dylib fi echo "Libgit2 $(libgit2-version)" > $@ @@ -785,8 +785,8 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version) --with-cfitsioinc=$(idir)/include \ --without-pgplot $$fortranopt) if [ x$(on_mac_os) = xyes ]; then - install_name_tool -id $(ildir)/libwcs.6.4.dylib \ - $(ildir)/libwcs.6.4.dylib + install_name_tool -id $(ildir)/libwcs.7.3.dylib \ + $(ildir)/libwcs.7.3.dylib fi echo "WCSLIB $(wcslib-version)" > $@ @@ -853,7 +853,7 @@ $(ibidir)/automake-$(automake-version): $(ibidir)/autoconf-$(autoconf-version) echo "GNU Automake $(automake-version)" > $@ $(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version) - tarball=bison-$(bison-version).tar.xz + tarball=bison-$(bison-version).tar.lz $(call import-source, $(bison-url), $(bison-checksum)) $(call gbuild, bison-$(bison-version), static, ,V=1 -j$(numthreads)) echo "GNU Bison $(bison-version)" > $@ @@ -916,6 +916,7 @@ $(ibidir)/flex-$(flex-version): $(ibidir)/bison-$(bison-version) $(ibidir)/gdb-$(gdb-version): $(ibidir)/python-$(python-version) tarball=gdb-$(gdb-version).tar.gz + export configure_in_different_directory=1; $(call import-source, $(gdb-url), $(gdb-checksum)) $(call gbuild, gdb-$(gdb-version),,,V=1 -j$(numthreads)) echo "GNU Project Debugger (GDB) $(gdb-version)" > $@ @@ -1096,10 +1097,17 @@ $(ibidir)/minizip-$(minizip-version): $(ibidir)/automake-$(automake-version) rm -rf $$unpackdir echo "Minizip $(minizip-version)" > $@ +# The Astromatic software packages (including missfits, sextractor, swarp +# and others) need the '-fcommon' flag to compile properly on GCC 10 and +# after. Previous to GCC 10, it was the default, but from GCC 10, the +# default is '-fno-common'. This is known by the author (as SExtractor +# issue 12: https://github.com/astromatic/sextractor/issues/12) and will +# hopefully be fixed in the future. $(ibidir)/missfits-$(missfits-version): tarball=missfits-$(missfits-version).tar.gz $(call import-source, $(missfits-url), $(missfits-checksum)) - $(call gbuild, missfits-$(missfits-version), static) + $(call gbuild, missfits-$(missfits-version), static, \ + CFLAGS="-fcommon") cp $(dtexdir)/missfits.tex $(ictdir)/ echo "MissFITS $(missfits-version) \citep{missfits}" > $@ @@ -1163,11 +1171,25 @@ $(ibidir)/R-$(R-version): \ $(ibidir)/libpaper-$(libpaper-version) tarball=R-$(R-version).tar.gz $(call import-source, $(R-url), $(R-checksum)) + cd $(ddir) + tar xf $(tdir)/$$tarball + cd R-$(R-version) + # We need to manually remove the lines with '~autodetect~', they + # cause the configure script to crash in version 4.0.2. They are + # used in relation to Java, and we don't use Java anyway. + sed -i -e '/\~autodetect\~/ s/^/#/g' configure export R_SHELL=$(SHELL) - $(call gbuild, R-$(R-version), static, \ - --without-x --with-readline \ - --disable-openmp, -j$(numthreads)) + ./configure --prefix=$(idir) \ + --without-x \ + --with-pcre1 \ + --disable-java \ + --with-readline \ + --disable-openmp + make -j$(numthreads) + make install + cd .. + rm -rf R-$(R-version) echo "R $(R-version)" > $@ # SCAMP documentation says ATLAS is a mandatory prerequisite for using @@ -1181,7 +1203,10 @@ $(ibidir)/scamp-$(scamp-version): \ $(ibidir)/cdsclient-$(cdsclient-version) tarball=scamp-$(scamp-version).tar.lz $(call import-source, $(scamp-url), $(scamp-checksum)) + + # See comment above 'missfits' for '-fcommon'. $(call gbuild, scamp-$(scamp-version), static, \ + CFLAGS="-fcommon" \ --enable-threads \ --enable-openblas \ --enable-plplot=no \ @@ -1209,13 +1234,20 @@ $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version) # libraries. But we can override this issue since we have Openblas # installed, it is just necessary to explicity tell sextractor to use it in # the configuration step. +# +# The '-fcommon' is a necessary C compilation flag for GCC 10 and above. It +# is necessary for astromatic libraries, otherwise their build will crash. $(ibidir)/sextractor-$(sextractor-version): \ $(ibidir)/fftw-$(fftw-version) \ $(ibidir)/openblas-$(openblas-version) tarball=sextractor-$(sextractor-version).tar.lz $(call import-source, $(sextractor-url), $(sextractor-checksum)) + + # See comment above 'missfits' for '-fcommon'. $(call gbuild, sextractor-$(sextractor-version), static, \ - --enable-threads --enable-openblas \ + CFLAGS="-fcommon" \ + --enable-threads \ + --enable-openblas \ --with-openblas-libdir=$(ildir) \ --with-openblas-incdir=$(idir)/include) ln -fs $(ibdir)/sex $(ibdir)/sextractor @@ -1225,7 +1257,10 @@ $(ibidir)/sextractor-$(sextractor-version): \ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version) tarball=swarp-$(swarp-version).tar.gz $(call import-source, $(swarp-url), $(swarp-checksum)) + + # See comment above 'missfits' for '-fcommon'. $(call gbuild, swarp-$(swarp-version), static, \ + CFLAGS="-fcommon" \ --enable-threads) cp $(dtexdir)/swarp.tex $(ictdir)/ echo "SWarp $(swarp-version) \citep{swarp}" > $@ diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index 2fede35..d39208f 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -431,6 +431,7 @@ $(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version) $(ipydir)/numpy-$(numpy-version): \ $(ibidir)/unzip-$(unzip-version) \ + $(ipydir)/cython-$(cython-version) \ $(ibidir)/openblas-$(openblas-version) \ $(ipydir)/setuptools-$(setuptools-version) tarball=numpy-$(numpy-version).zip @@ -528,7 +529,9 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \ $(call pybuild, tar xf, requests-$(requests-version), , \ Requests $(requests-version)) -$(ipydir)/scipy-$(scipy-version): $(ipydir)/numpy-$(numpy-version) +$(ipydir)/scipy-$(scipy-version): \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/pybind11-$(pybind11-version) tarball=scipy-$(scipy-version).tar.gz $(call import-source, $(scipy-url), $(scipy-checksum)) if [ x$(on_mac_os) = xyes ]; then diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index b11992e..593b1d9 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -58,9 +58,6 @@ ptconf=$cdir/LOCAL_tmp.conf poconf=$cdir/LOCAL_old.conf depverfile=$cdir/versions.conf depshafile=$cdir/checksums.conf -# --------- Delete for no Gnuastro --------- -glconf=$adir/gnuastro/gnuastro-local.conf -# ------------------------------------------ @@ -634,12 +631,10 @@ EOF # (for example the user might have ran `./project configure' by mistake). printnotice=yes rewritepconfig=yes -rewritegconfig=yes -if [ -f $pconf ] || [ -f $glconf ]; then +if [ -f $pconf ]; then if [ $existing_conf = 1 ]; then printnotice=no if [ -f $pconf ]; then rewritepconfig=no; fi - if [ -f $glconf ]; then rewritegconfig=no; fi fi fi @@ -1010,44 +1005,6 @@ fi -# --------- Delete for no Gnuastro --------- -# Get the version of Gnuastro that must be used. -gversion=$(awk '$1=="gnuastro-version" {print $NF}' $depverfile) - -# Gnuastro's local configuration settings -if [ $rewritegconfig = yes ]; then - create_file_with_notice $glconf - echo "# Minimum number of bytes to use HDD/SSD instead of RAM." >> $glconf - echo " minmapsize $minmapsize" >> $glconf - echo >> $glconf - echo "# Version of Gnuastro that must be used." >> $glconf - echo " onlyversion $gversion" >> $glconf -else - ingversion=$(awk '$1=="onlyversion" {print $NF}' $glconf) - if [ x$ingversion != x$gversion ]; then - cat <