Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates. With this commit, those updates have been imported and the conflicts that resulted were fixed. They were all cosmetic and had no effect on the analysis. The most significant one was about the change in the format of 'INPUTS.conf'. In the process, I also noticed that the IEEEtran LaTeX package is now called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).
author: Mohammad Akhlaghi <mohammad@akhlaghi.org> 2022-05-09 13:32:47 +0200
committer: Mohammad Akhlaghi <mohammad@akhlaghi.org> 2022-05-09 23:52:29 +0200
commit: 9fdeebaacd06d57c479cd69e9937c4bfe5d0a286 (patch)
tree: 012e6194ad6e25a81a9c99b4d0bd0852bc9a12af /reproduce/software/config
parent: 480184b3da399fab11b50e67f01d2efa6bea0e3e (diff)
parent: f51b5e2e500dd6450a5a3425e85df78245fc5c5c (diff)
10 files changed, 441 insertions, 283 deletions
diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in
index 132c3f7..a7434ea 100644
--- a/reproduce/software/config/LOCAL.conf.in
+++ b/reproduce/software/config/LOCAL.conf.in
@@ -1,9 +1,9 @@
 # Local project configuration.
 #
-# This is just a template for the `./project configure' script to fill
+# This is just a template for the './project configure' script to fill
 # in. Please don't make any change to this file.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf
index 95f12f2..94c7e5f 100644
--- a/reproduce/software/config/TARGETS.conf
+++ b/reproduce/software/config/TARGETS.conf
@@ -1,7 +1,7 @@
 # Necessary high-level software to build in this project.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -21,25 +21,29 @@
 #     reproduce/software/config/versions.conf
 #
 # Please add any software that you need for your project in the respective
-# part below (using its name in `versions.conf', but without the `-version'
+# part below (using its name in 'versions.conf', but without the '-version'
 # part). Just note that if a program/library is a dependency of another,
 # you don't need to include it here (it will be installed before the
 # higher-level software anyway).
 #
 # Note that many low-level software will be installed before those that are
 # installed in this step. They are clearly distinguished from the
-# higher-level (optional) software in `versions.conf'. These low-level
+# higher-level (optional) software in 'versions.conf'. These low-level
 # software MUST NOT be added here.
 
 
 
 
 
-# Programs and libraries.
+# Programs and libraries (for Python or R modules, use respective variable).
 #
 # Ghostscript: to build PDF paper (in particular the `ps2pdf' command).
 # XLSXI/O: to read and write XLSX files.
-top-level-programs = ghostscript xlsxio
+top-level-programs  = ghostscript xlsxio
 
 # Python libraries/modules.
-top-level-python =
+top-level-python    =
+
+# R libraries/modules
+# [For developers 2022-01-02: 'r-cran-cowplot r-cran-gridExtra' for all]
+top-level-r-cran    =
diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index 0e21912..7450e6d 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -1,7 +1,8 @@
 # sha512 checksums of all the necessary software tarballs.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C)      2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -14,54 +15,53 @@
 
 # Basic/low-level programs and libraires (installed in any case)
 # --------------------------------------------------------------
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+zip-checksum = 433eda6a27074746a960952fa3b08028d5ba43fe976a1306dbace9209be5f89aa0554b17bba5815cd00984c0f64559c5fa0b754b620f6d646a2b145a8b599acc
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@@ -71,150 +71,208 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/TARGETS.conf' will be built as part of a
-# project. To specify a software there, just remove the `-checksum' suffix
+# 'reproduce/software/config/TARGETS.conf' will be built as part of a
+# project. To specify a software there, just remove the '-checksum' suffix
 # from the list below.
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 libnsl-checksum = a3c8f674357674b7ed4b26c05adde607f39be8d6dc9ff715448e1fcc5fc23d11fbb4ce85a6e493b79bdb0bb450dc3ffb1fb480715779f738d7bc016fae91621d
-libpaper-checksum = 3bf6ebb0af89931d2f72ea4a09a7fa958b2facda5f238983ec7bac39652e08614b33f0de3af74a03457b2a4203eee4950bf18a4b726e79aa64093ace6a1fb0bc
-libpng-checksum = 59e8c1059013497ae616a14c3abbe239322d3873c6ded0912403fc62fb260561768230b6ab997e2cccc3b868c09f539fd13635616b9fa0dd6279a3f63ec7e074
-libtiff-checksum = d213e5db09fd56b8977b187c5a756f60d6e3e998be172550c2892dbdb4b2a8e8c750202bc863fe27d0d1c577ab9de1710d15e9f6ed665aadbfd857525a81eea8
+libpaper-checksum = e1f37dfbbcc467c2269e228fa71893fd6c4738e1fd6cf24ce6e2ded568cfeeed80da097e51e833aa48e4ab9e1be0a5c75f9f4cf8bf2f050214c85013e9c24043
+libpng-checksum = 8bf8aaccf4b9efe15a18f0c7a0a6a942eba7bcdbaf61313f50af7e04a237ccc12f380b53ed88e5efa2d20b13f1a0f9f365b6bd7824d32350b3b3d9c6fa63eef6
+libtiff-checksum = 628e9e6b3ff5cdf661ac4c9cbee7fc10d5555554d39e447d9a0c4e99b9a81e4ae51e990f7e3a83b607145948a57a3d1d46fae13758d844ebb3e55bb307e28ebf
 libtirpc-checksum = bcb6b5c062c1301aa1246ec93ae0a5c1d221b8421126d020863517cb814b43ed038fb6c0c2faf4e68ff133b69abefe4f4d42bfc870671da6c27ca941a30b155a
+metastore-checksum = ac1230686535a652e95024abaf6c5585bdab36f4e092bee5fa4deff2a913cd60f3a6bd8020c6887ccab97f0da3a284a0d4619fad5464a269e7b2040d6f7e6aaf
 missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795
-netpbm-checksum = 064720f8a9d0a502488e1af4daecdbf3936910996507ca6f311073a0ad842346692a148eb1ddf7b717f7b108f60500246cb4b83f4d3665f5fc285a84ae1d63d6
-openblas-checksum = 64a5f983b2f6e02cdb6e0f14433498cc5daa1ccfb49246f7a2dcd38f9982fa608f2abea069fe0e35012af8c1441c43d1f6418eaccd40795f5002fed1c36ce05d
-openmpi-checksum = aea02a66dc67820c86172fae80f5aa4c71e918525abbfaf06df8ba6898ff78ec3b0ef9638952b2c1d1a9c878fc0999d6f6d06e840679a68779d6b81f0336eb76
+netpbm-checksum = 051c05aa080e6563483053c16bc416b0e1368d6d7b130dec12a01017245a99252f80ddf7ae7322a4f8e9c90d833fc90d94324585659605d8dbb766d5fa2238c5
+openblas-checksum = 363588495451f872d4332a1c5e5ff4422202935641f490515e6f8144d3e1838ef737f39e77aaca396d23f9011b981961aa503e5d5935260231e31bb2280f890d
+openmpi-checksum = 88c73fd708dd5fe3a893d5517425a8a4c3e252fae4715df9a9b0f2311abe94cf5f71be92f153820fbaeb32c7d0ac0175d5165bdadcadc731427309102182c1bd
 openssh-checksum = e280fa2d56f550efd37c5d2477670326261aa8b94d991f9eb17aad90e0c6c9c939efa90fe87d33260d0f709485cb05c379f0fd1bd44fc0d5190298b6398c9982
 patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187dad77d1413f0eb3319b3fe4df076714615c98b29df06af052bb65960fa8b0c86bf
 pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb
-pixman-checksum = 1b0205dbe9d9185c68813ce577a889f3c83e83fbd9955c3a72d411c3b476e6be93fc246b5b6ef4ee17e2bb8eb6fb5559e01dff7feb6a6c4c6314f980e960d690
-python-checksum = 392459354b8438f76670ec2086b4618ee21f615ca4b22e5dbb366273665a470de5047a3f241925a62b60bf3cddde5984a05144a55d0c5ced43342f5b94576952
-R-checksum = b7330613ee9795f54cde3dd9f7509be83d9156fb8577c17179727ee01450db27704249f68bd48e0331e2df09c2d9833d8bb019c4f9ce9ba669df74650ff2e842
+pixman-checksum = 333732b99994f7ea636d647e0b6123075351b27601b5b6370c9bc821a1ab3921386ddb92b51e015f3fc35104ba09be1e0d7bef47f0b4f73036b01d1d70396dd9
+python-checksum = 30cc55a4ca7d65c55a967d9c43e2ebeeed2905f2fab01540140537e0384f943b6ab6699b1c2b91cb2b3834fe7d3d1976aec58ba4c5b9f209bc0ea9a0ff248332
+r-cran-checksum = 54cc07956a70c09b5a533188eb063d2a9dc67a8aa5648ec7f9c107f626220c9f6e17ab7175e65dd54a8d608a1ca4106c8ad2856709eb995ab66439b5f033e725
 rpcsvc-proto-checksum = c3011d7d7ef97a4a751f6921df1a23e1dd8ac50fb0690c759d37010ed7be27968a2130e3b8872cb48d5914216f9d539096a424f1ec38a75f7ed899748151c6f4
 scamp-checksum = 35034a367d2cd09dc51e727e0f23ef6234edc0d978fd71cda1e80391d86af160138cb57281f7f7f9047e35b1246a0de6b235414086a62524413ed423f498583f
 scons-checksum = 0477038b014674049f12899b64584d44a85283d521b2422561e42020a5ae296a5af005684087c3ff410ed3fcbdcc5ff61998bc429eb29513f2a864138ffc4945
 sextractor-checksum = 4035710f9b8a20a0bb1a3913dab2dadd8444c179bf6dee425e0e8bb66a772944ea189bfce89fd791d316a790fc4b2cb15a62633b19d1d5331b1803dec2e70af7
 swarp-checksum = 80f4ade59738df3d4c9b47bda04148b53c6ba995d523fa8d1e02fb5d952b6078a53cc7d273849a033505de127a4f318b95adf2bf5a2dc38e8cc9bdaf5658487a
-swig-checksum = 5eaa2e06d8e4197fd02194051db1e518325dbb074a4c55a91099ad9c55193874f577764afc9029409a41bd520a95154095f26e33ef5add5c102bb2c1d98d33eb
+swig-checksum = ecb1d940f584c23df036a8f77288916003f861851dfdf836ddc5bc45b95312f9259150084191c1d9f086c006e64e12a4db22f7ea382fbb71667b811b8f99995d
 tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108
-util-linux-checksum = c95d26b9037d6b877a247e6aeb58d17aa80f7e1bd6b523a4e0fde559fe07b3d924ece6d373300fefb65d1f206b3f990aeddb3a03605040e72ce6d6ee88591021
+util-linux-checksum = 2e07b4765482182112c424cbfe5af0dc9c9a50918e335bf99846f3017b291f5df23e95c77942f2265e9b0d471201a0d53d3c79d916df1c61cf044a80e37f85ee
 vim-checksum = 06ba43386fcf308520d88d7a68e9bc1fabd824b05078b8f9112500a2ad4e50a91f1a1c2925889b7c06dbce34307f12abf508e2172b05fd283f965cc06552eb6d
-wcslib-checksum = 8c98c4b575056e2d966b77a4bc951256d02ecee3a11847e140fd38d93afd0f76b3e906d590c952dc9fc58ceeb1ba062b19d8e1e676ee0032f5b7ed13a9dfa892
+wcslib-checksum = 008bb069bcc21f7944b37ca44e85aa5d343d44aeb24ad3920c2db716a984e3fb63cdad8fe05ae63b8850c5ce4ce5f81c524dfd14958ae38fcaef32f893814b45
 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c
 yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02
-zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae
 
 # Xorg related packages
-util-macros-checksum = 3f51504b27f0478c136126f15110cf3cdbba218c4d74a8e974cca1381c6e8364609bd0c444f2fb19aa86a7f4e848dfce4f4da940463b224036f75a60b3d88619
-xorgproto-checksum = 2d10533e54987f293e1c8578aa742c38cf2fac8551db1d317cf5ee4a6a9600eced50f59c57c38b35dd210fe02d350294c967512f04cb9876d6c0c1f7e89cb199
-libxau-checksum = 3ca454ba466a807ea28b0f715066d73dc76ad312697b121d43e4d5766215052e9b7ffb8fe3ed3e496fa3f2a13f164ac692ff85cc428e26731b679f0f06a1d562
+util-macros-checksum = b29c388c60b8318a478656f0552210b2194ee302c082f694e5426ac5c3f4b97fc3e377cd6a7b2b97c3da3442cfb4a5e42dbae18e151ae39f5f84554016a01155
+xorgproto-checksum = b9471ce92f2a5fee9d32710191d7df63799027214ceace60fb2ae8616c888ad142d2a131dea5acc768e86bc71719873c72c20a2863fa821790b96faef44f603f
+libxau-checksum = bdca8935aa1a52bcd2748004d26c7405725c18021a4d9a67604c98c1ec3957cc85b5d987d2fcd9fa4ae5e59b6bbd6ab75712beee2d448bd733a7e3ffeb18e62f
 libxdmcp-checksum = cb1d4650f97d66e73acd2465ec7d757b9b797cce2f85e301860a44997a461837eea845ec9bd5b639ec5ca34c804f8bdd870697a5ce3f4e270b687c9ef74f25ec
-xcb-proto-checksum = de66d568163b6da2be9d6c59984f3afa3acd119a781378638045fd68018665ef5c9af98f024e9962ba3eb7c7a4d85c27ba70ffafceb2324ccc6940f34de16690
-libxcb-checksum = b90a23204b0d2c29d8b115577edb01df0465e02d6a8876550fecd62375d24a5d5f872ddd5946772ddba077cadce75b12c7a6d218469dc30b5b92bc82188e8bc6
-fontconfig-checksum = f97f2a9db294fd72d416a7d76dd7db5934ade2cf76903764b09e7decc33e0e2eed1a1d35c5f1c7fd9ea39e2c7653b9e65365f0c6205e047e95e38ba5000dd100
-xtrans-checksum = 4fea89a3455c0e13321cbefa43340016dbb59bdd0dbdb5b796c1a6d2a6b1fd63cf1327b769ab426286b9c54b32ec764a50cd2b46228e4e43b841bda6b94de214
-libx11-checksum = fc18f0dc17ade1fc37402179f52e1f2b9c7b7d3a1a9590fea13046eb0c5193b4796289431cd99388eac01e8e59de77db45d2c9675d4f05ef8cf3ba6382c3dd31
-libxext-checksum = 09146397d95f80c04701be1cc0a9c580ab5a085842ac31d17dfb6d4c2e42b4253b89cba695e54444e520be359883a76ffd02f42484c9e2ba2c33a5a40c29df4a
-libice-checksum = 2f1ef2c32c833c71894a08fa7e7ed53f301f6c7bd22485d71c12884d8e8b36b99f362ec886349dcc84d08edc81c8b2cea035320831d64974edeba021b433c468
-libsm-checksum = 74c42e27029db78475e62025b4711dbac5e22d2f8e8a24be98a1c31b03c0fc4afe859928f851800ea0b76854f12147900dc4f27bbfd3d8ea45daaaf24b70a903
-libxt-checksum = 06248508b6fe5dfba8ceb4518475f656162351d78136eeb5d65086d680dabe9aca7bba3c94347f9c13ef03f82dab3ac19d0952ee610bc8c51c14cee7cf65f0b1
-libpthread-stubs-checksum = 5293c847f5d0c47a6956dd85b6630866f717e51e1e9c48fa10f70aa1e8268adc778eaf92504989c5df58c0dcde656f036248993b0ea5f79d4303012bfeff3c72
+xcb-proto-checksum = 385ea15eac6326b73849f1dae790619760f473f4c5471a3ccf990b01350931395e988cd83f632c94fe987eec74198f59835b8140686774710462e0019f90c168
+libxcb-checksum = c69c7e5d6c172aa0bd65d6f3ad25d9a8388194cf2281ee9c9e02baf73c351752b7c287fd04f8ee3429d5b55358806c81565046796263212379593db4e32c4287
+fontconfig-checksum = 12dfddb3b37d71555764fe97dcb439496f3fc0e6d34e4536a92eda1069cc78ceb1dda5b2c0b247f779a093a6c75c56afcac6f0cd099d897c2ce30740a9fbb183
+xtrans-checksum = 1c2fdd7cb906f012f7db5d42466734f89608bf3376b6bf4b115c2efbf71c4247587cc218ccfcfaa6d50f0cf336865d10fc604515b25bc6e95917db8acb7e3000
+libx11-checksum = 740cc5364d49cee8fd86f3dc0f43d7b358c94989717ea8991addea9b2307df6e5b2ae1f8f7aa3571f7294b8760c7aca7be9fdf5b477dec55da14e915dccafd7c
+libxext-checksum = 58f4e87f200bfde2b9a2cd85c1c39d5462b702e12274ffa5fae5bd3a08b3dfab1290b399c31224c86627d927106e4dbfcdec6152c11b169834442008228796d4
+libice-checksum = 9e3488abaff115ac919e5df85479044579802b38a10597425e13466c22c149ef56a8adba77e2adbbcccb8d2e72e23976313f4af3dcee66128b768c971c513932
+libsm-checksum = b9eec391f0438e85e32cf771afbb35bf215119ec31d9e31be40c1b653f2c3e894c2d19add0d6ff69e944d1230f681275e8abad86a8912ec37c1c41e0f1ce4d00
+libxt-checksum = 9ec0f95ae073360ea7a80ffca2dcd998c991363b79696550c4f88edf2c9cbf740caca23929660b77fffca4ca292465a101398e9e891cd00db85f8eceaa78cde0
+libpthread-stubs-checksum = a99695c007e17d81879d5c113652c5e1edab2d63aac9b2984c4f334d85e2cebc1d0b4e8134d6196ed8eea4d4da41972fca27bb8a0c76c2946460f785233a2c03
 
 # Python packages
 # ---------------
 #
 # Similar to optional programs and libraries above.
 #
-# IMPORTANT: If you intend to change the version of any of the Python
-# modules/libraries below, please fix the hash strings of the respective
-# URL in `reproduce/software/make/python.mk'.
+# The sha512sum hash strings for the Python modules/libraries below should
+# correspond to the version numbers in
+# 'reproduce/software/conf/version.conf'. If you update the version and are
+# confident that the new version is safe to use, then you can update the
+# hash here.
 asn1crypto-checksum = 44d442a6ddfa971e31e24712fe084368356deb5e1c4c3b3e813e0910931860215bc1c4f9eb2c4bd4fdef607c324086c096e9357068646efd28c97f2d4f85c62f
 asteval-checksum = 4d64900b2f7dfdd098d6c8c102f9d9fd46f9ec265a54330e7d94479ba41f0ee0698855658e18b8b32b9c255159eb9a085af5f0306eb6508663d3fea7d2e00b4a
-astropy-checksum = c32e874d208f312f894643ab5b3d71dc37630e544da0ceb5ee998d752f9a055d32f6e4319f2cb6928637aaf8573bac58d2882bd636b6a89f5501e3ac7e5ab681
+astropy-checksum = 52b7feae68308445014665e3fc80201ca82955916fbe4d065dbb1a439885befb4f669932cec6fd7d359094138fab0ca188162efab764c4591d53896cdb335426
 astroquery-checksum = 43846791d8469a26cf6bb8819db58b830cfe50a34bc0091c2e843dd7dc78b1317530855d432a3a567a9f6a6f4d2682382a32edc91ea01716246b99b3625ec521
-beautifulsoup4-checksum = 7aa77bc6008bbcbbbe91b0a850007ab237d2832b63a787fbd94b7cbf47d4276b185e0c61c134df73221406458edff2b75b6b8c2b53b543aa3bb1b0e2202dac5a
+beautifulsoup4-checksum = bf8fd3e54da63a506f294f0e5f1201fd46bf2edcc2db23e99eda995313b8a8d24db3cd2d1903853c539a9320bfb9eb4b29e311772bfddc0d125f0b4aec71e384
+beniget-checksum = 32a19d77323a0a21544ce7fbbb71cc5f4c66949dba280d81deb36f38364544d9fdfb3d24fc48a1ff6d251fb22c24357e81dd7fa4a7e6c11d8b931723e150a182
 certifi-checksum = 6a6bf1ff98caefcdbf78a8c83e11e155368bacdd806f0ae0c6afa8f513667df6598e594b3584de61acdca3d6049f4a776937f2aa8672b602bd6db7b737f6074e
-cffi-checksum = af4fe47cf5d6f1126222898365cfa21e9f11d0e71b87d869014dbb37af30dca9ddf50c989030d0f610f50e8099e8dfd08a688d8c3629abbcc4f0294f5f91b817
+cffi-checksum = 50e2b8215ddedfa8f1d569680cc0023cf061c2c52b7b86b6b26ced56e5107b362aaf6dc10a77b9dbbbfca2e5611f7cfb42c59501f9ab7da29fb3ad3ccf418cb4
 chardet-checksum = 61a03b23447a2bfe52ceed4dd1b9afdb5784da1933a623776883ee9f297e341f633e27f0ce0230bd5fdc5fdb5382105ab42736a74a417ddeb9f83af57455dba5
 corner-checksum = ebd625ab1e4591b4c21d25ec706c35d37f560b727e1e0d6a79948c4a112ee6f21d3ca30162901a27715074e1345f3bdee1a0345c63e5fec24113e495fb094127
-cryptography-checksum = f14319e24d9dca52e74548cada5b78a6235f089ef875dbff4799e862f94da8b087f1b6e03e84dcef9fc7d7693c4a349c5f0cd54b8535806da777420ce8757d39
-cycler-checksum = b7d2ba19861ffaf4dea0444bfe68b5a6264a022d7b3f02c9ff5e5859e3901de12a90f8dc7469e995e09c418515b3df55dbf05a0cfe5368d40790a2c878a74819
-cython-checksum = 6216e63996e83b887cdcee6cd912d42e7da853640336b9190f5115d687848a902ee5a8edd6bfaef645c066b89e17dcd80ca1387688eb80a527ec23a0a4636e8f
+cryptography-checksum = 051b5007512521638981a8e975c7bbcb688b1a1c384babc81ba105c7bc2a7e776a8bf46af5939627528b2b57d99aaacf215a041018c47f6d3ae6d7a0e8eafccf
+cycler-checksum = bfd1b625c785b48f9795c4ef701ce1c8fdebaa0e82530b904ed7f481f644178834a1cbcdc6a2732bd5fa3a39f7bb543ce51b710a3e4101a6ecee89a6ff270ebc
+cython-checksum = 1db604326d0cbeb7b113bd163056ba1d4e3685aa66081911a836604dcb7f3654fedc91f4686a9e6514eed1f6cc8873b2d30ffbe6663844ce5bd04dbe5c120844
 eigency-checksum = 1e7cdfc43071da5edba30a0d32cd655442b516f15c166b049a195d151dec8c20a2177ad69bed3bba4788a668fa25a4c551ef4990717ff98d5b2f407bffb214c8
 emcee-checksum = dd60aace8879525fd3fe42b747d82170b24b2ed21f538f9186ba96b9d04c084812e3303f5d2e04119dabd2f9d3286d510b4d4a5324c71dd24b1c7e5f0a9a0ac6
 entrypoints-checksum = aa1274362d3a4b00266103319ca51aa266605b4999c89a9d0673eb61bfae9e646cb0ec6b86c95544493f6fe048385a2c7641d64adca8f45815546fb1e663c858
-esutil-checksum = c1cf8e7912b16dc675fdc7195ecc2bbffcd156c1257b2df45afdf09cc487c49f2e18a66cd5520ab30c77e60abb8ca802e327075bdd0f23eb634cc4f5a7e974f3
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+
+# R-CRAN packages
+# ---------------
+#
+# Similar to optional programs and libraries above.
+#
+# The sha512sum hash strings for the R modules/libraries below should
+# correspond to the version numbers in
+# 'reproduce/software/conf/versions.conf'. If you update the version and are
+# confident that the new version is safe to use, then you can update the
+# hash here.
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diff --git a/reproduce/software/config/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg
index 3a3171e..09c1627 100644
--- a/reproduce/software/config/numpy-scipy.cfg
+++ b/reproduce/software/config/numpy-scipy.cfg
@@ -7,8 +7,8 @@
 # appropriate sections. Not all packages will use all sections so you
 # should leave out sections that your package does not use.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -18,7 +18,7 @@
 # IMPORTANT NOTE
 # --------------
 #
-# The `ALL' grouping does't apply to ATLAS!!!!!
+# The 'ALL' grouping does't apply to ATLAS!!!!!
 
  [ALL]
  library_dirs = @LIBDIR@
diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf
index 8db0ce1..64de818 100644
--- a/reproduce/software/config/servers-backup.conf
+++ b/reproduce/software/config/servers-backup.conf
@@ -3,7 +3,7 @@
 # is irrelevant). Note that this is not a to be read as a variable but will
 # be parsed as a list.
 #
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
diff --git a/reproduce/software/config/software_acknowledge_context.sh b/reproduce/software/config/software_acknowledge_context.sh
index 788ab94..f719d5e 100755
--- a/reproduce/software/config/software_acknowledge_context.sh
+++ b/reproduce/software/config/software_acknowledge_context.sh
@@ -10,8 +10,8 @@
 # your project to make a smoothly readable English text. Afterwards, please
 # feel free to modify them as you wish.
 #
-# Copyright (C) 2020-2021 Boud Roukema <boud@cosmo.torun.pl>
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This script is free software: you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by the
diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf
index d4900f1..05dd0e2 100644
--- a/reproduce/software/config/texlive-packages.conf
+++ b/reproduce/software/config/texlive-packages.conf
@@ -1,10 +1,10 @@
 # Necessary packages to install in TeX Live.
 #
 # If any extra TeX package is necessary to build your paper, just add its
-# name to this variable (you can check in `ctan.org' to find the official
+# name to this variable (you can check in 'ctan.org' to find the official
 # name).
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -12,11 +12,11 @@
 # warranty.
 
 
-# Note on `tex' and `fancyhdr': These two packages are installed along with
+# Note on 'tex' and 'fancyhdr': These two packages are installed along with
 # the basic installation scheme that we used to install tlmgr, they will be
-# ignored in the `tlmgr install' command, but will be used later when we
+# ignored in the 'tlmgr install' command, but will be used later when we
 # want their versions.
 texlive-typewriter-pkgs = courier inconsolata xkeyval upquote
-texlive-packages = times IEEEtran cite xcolor pgfplots ps2eps \
+texlive-packages = times ieeetran cite xcolor pgfplots ps2eps \
                    listings ulem etoolbox multibib \
                    $(texlive-typewriter-pkgs)
diff --git a/reproduce/software/config/texlive.conf b/reproduce/software/config/texlive.conf
index 94a4c89..950dd4f 100644
--- a/reproduce/software/config/texlive.conf
+++ b/reproduce/software/config/texlive.conf
@@ -2,7 +2,7 @@
 #
 # installdir: Install directory
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf
index a311524..7177411 100644
--- a/reproduce/software/config/urls.conf
+++ b/reproduce/software/config/urls.conf
@@ -3,8 +3,8 @@
 # If un-commented the URLs of this file will be used. Otherwise default
 # servers (primarily on 'zenodo.org') will be checked for the tarball.
 #
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2020-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -19,15 +19,15 @@
 # -------------------------------------------------------------
 #bash-url = http://akhlaghi.org/src
 #binutils-url = http://ftp.gnu.org/gnu/binutils
-#bzip2-url = http://akhlaghi.org/maneage-software
+#bzip2-url = https://sourceware.org/pub/bzip2
 #cert-url = http://akhlaghi.org/maneage-software
 #coreutils-url = http://ftp.gnu.org/gnu/coreutils
 #curl-url = https://curl.haxx.se/download
-#dash-url = http://akhlaghi.org/maneage-software
+#dash-url = http://gondor.apana.org.au/~herbert/dash/files
 #diffutils-url = http://ftp.gnu.org/gnu/diffutils
 #file-url = ftp://ftp.astron.com/pub/file
 #findutils-url = http://ftp.gnu.org/gnu/findutils
-#flock-url = http://akhlaghi.org/src
+#flock-url = https://github.com/discoteq/flock/releases
 #gawk-url = http://ftp.gnu.org/gnu/gawk
 #gcc-url = http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version)
 #gettext-url = https://ftp.gnu.org/gnu/gettext
@@ -36,8 +36,7 @@
 #grep-url = http://ftp.gnu.org/gnu/grep
 #gzip-url = http://akhlaghi.org/src
 #isl-url = ftp://gcc.gnu.org/pub/gcc/infrastructure
-less-url = http://www.greenwoodsoftware.com/less/
-#libbsd-url = http://libbsd.freedesktop.org/releases
+#less-url = http://www.greenwoodsoftware.com/less/
 #libiconv-url = https://ftp.gnu.org/pub/gnu/libiconv
 #libtool-url = http://ftp.gnu.org/gnu/libtool
 #libunistring-url = http://ftp.gnu.org/gnu/libunistring
@@ -45,15 +44,15 @@ less-url = http://www.greenwoodsoftware.com/less/
 #lzip-url = http://akhlaghi.org/src
 #m4-url = http://akhlaghi.org/maneage-software
 #make-url = http://akhlaghi.org/src
-#metastore-url = http://akhlaghi.org/maneage-software
 #mpc-url = http://ftp.gnu.org/gnu/mpc
 #mpfr-url = http://www.mpfr.org/mpfr-current
 #nano-url = https://www.nano-editor.org/dist/v$(word 1, $(subst ., ,$(nano-version)))
 #ncurses-url = http://ftp.gnu.org/gnu/ncurses
 #openssl-url = http://www.openssl.org/source
-#patchelf-url = http://nixos.org/releases/patchelf/patchelf-$(patchelf-version)
+#patchelf-url = https://github.com/NixOS/patchelf/releases/download/$(patchelf-version)
 #perl-url = $(shell echo https://www.cpan.org/src/$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}'))
 #pkgconfig-url = http://pkg-config.freedesktop.org/releases
+#podlators-url = https://www.eyrie.org/~eagle/software/podlators/
 #readline-url = http://ftp.gnu.org/gnu/readline
 #sed-url = http://ftp.gnu.org/gnu/sed
 #tar-url = http://ftp.gnu.org/gnu/tar
@@ -73,30 +72,31 @@ less-url = http://www.greenwoodsoftware.com/less/
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/TARGETS.conf' will be built as
+# 'reproduce/software/config/TARGETS.conf' will be built as
 # part of a project. To specify a software there, just remove the
-# `-url' suffix from the list below.
+# '-url' suffix from the list below.
+
 #apachelog4cxx-url = http://akhlaghi.org/maneage-software
-#apr-url = https://www-us.apache.org/dist/apr
-#apr-util-url = https://www-us.apache.org/dist/apr
+#apr-url = https://archive.apache.org/dist/apr/
+#apr-util-url = https://archive.apache.org/dist/apr/
 #astrometrynet-url = http://astrometry.net/downloads
 #atlas-url = https://sourceforge.net/projects/math-atlas/files/Stable/$(atlas-version)/atlas$(atlas-version).tar.bz2/download
 #autoconf-url = http://akhlaghi.org/maneage-software
 #automake-url = http://ftp.gnu.org/gnu/automake
 #bison-url = http://ftp.gnu.org/gnu/bison
-#boost-url = $(shell vstr=$$(echo $(boost-version) | sed -e's/\./_/g'); echo https://dl.bintray.com/boostorg/release/$(boost-version)/source)
+#boost-url = https://www.boost.org/users/download/
 #cairo-url = https://www.cairographics.org/releases
 #cdsclient-url = http://cdsarc.u-strasbg.fr/ftp/pub/sw
 #cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c
 #cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv)
-#eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz
+#eigen-url = https://eigen.tuxfamily.org
 #emacs-url = http://ftp.gnu.org/gnu/emacs
-#expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz)
-#fftw-url = ftp://ftp.fftw.org/pub/fftw
+#expat-url = https://github.com/libexpat/libexpat/releases
+#fftw-url = https://fftw.org
 #flex-url = https://github.com/westes/flex/files/981163
 #freetype-url = https://download.savannah.gnu.org/releases/freetype
 #gdb-url = http://ftp.gnu.org/gnu/gdb
-#ghostscript-url = $(shell v=$$(echo $(ghostscript-version) | sed -e's/\.//'); echo https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs$$v)
+#ghostscript-url = https://www.ghostscript.com/releases/gsdnld.html
 #gnuastro-url = http://ftp.gnu.org/gnu/gnuastro
 #gperf-url = http://ftp.gnu.org/pub/gnu/gperf
 #gs-fonts-gnu-url = https://downloads.sourceforge.net/gs-fonts
@@ -105,28 +105,33 @@ less-url = http://www.greenwoodsoftware.com/less/
 #hdf5-url = $(shell majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src)
 #healpix-url = http://akhlaghi.org/maneage-software
 #help2man-url = http://ftp.gnu.org/gnu/help2man
-#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/
-#imagemagick-url = http://akhlaghi.org/maneage-software
+#libpaper-url = http://ftp.debian.org/debian/pool/main/libp/libpaper/
+#icu-url = https://github.com/unicode-org/icu/releases
+#imagemagick-url = https://download.imagemagick.org/ImageMagick/download
 #imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit
 #lapack-url = http://www.netlib.org/lapack
-#libffi-url = ftp://sourceware.org/pub/libffi
+#libbsd-url = http://libbsd.freedesktop.org/releases
+#libffi-url = https://sourceware.org/libffi/
 #libgit2-url = http://akhlaghi.org/src
 #libidn-url = https://ftp.gnu.org/gnu/libidn
 #libjpeg-url = http://ijg.org/files
+#libmd-url = https://archive.hadrons.org/software/libmd/
 #libnsl-url = http://akhlaghi.org/maneage-software
+#libpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/
 #libpng-url = https://download.sourceforge.net/libpng
 #libtiff-url = https://download.osgeo.org/libtiff
 #libtirpc-url = https://downloads.sourceforge.net/libtirpc
+#metastore-url = http://akhlaghi.org/maneage-software
 #minizip-url =
 #missfits-url = https://www.astromatic.net/download/missfits
-#netpbm-url = http://akhlaghi.org/maneage-software
+#netpbm-url = https://sourceforge.net/projects/netpbm/files/super_stable/
 #openblas-url = https://github.com/xianyi/OpenBLAS/archive
 #openmpi-url = $(shell majorver=$$(echo $(openmpi-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://download.open-mpi.org/release/open-mpi/v$$majorver)
 #openssh-url = https://artfiles.org/openbsd/OpenSSH/portable
 #patch-url = http://ftp.gnu.org/gnu/patch
 #pixman-url = https://www.cairographics.org/releases
-#python-url = http://akhlaghi.org/src
-#R-url = $(shell majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}'); echo https://cran.r-project.org/src/base/R-$$majver)
+#python-url = https://www.python.org/downloads/
+#r-cran-url = $(shell majver=$$(echo $(r-cran-version) | sed -e's/\./ /g' | awk '{print $$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
 #scons-url = https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download
@@ -149,8 +154,10 @@ less-url = http://www.greenwoodsoftware.com/less/
 #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
+#libice-url = https://www.x.org/archive/individual/lib/
 #util-macros-url = https://www.x.org/pub/individual/util
 #xcb-proto-url = https://xorg.freedesktop.org/archive/individual/proto
+#libxcb-url = https://xcb.freedesktop.org/dist/
 #xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto
 #xtrans-url = https://www.x.org/pub/individual/lib
 
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 102ebbd..34d074c 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -1,7 +1,8 @@
 # Versions of the various dependencies
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C)      2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -15,47 +16,47 @@
 # Basic/low-level programs and libraires (installed in any case)
 # --------------------------------------------------------------
 #
-# CLASS:BASIC (important identifier, don't modify this line)
-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 = 5.39
-findutils-version = 4.7.0
-flock-version = 0.2.3
+# CLASS:BASIC (important identifier for 'awk'; don't modify this line)
+bash-version = 5.1.8
+binutils-version = 2.37
+coreutils-version = 9.1
+curl-version = 7.79.1
+dash-version = 0.5.11.5
+diffutils-version = 3.8
+file-version = 5.41
+findutils-version = 4.8.0
+flock-version = 0.4.0
 gawk-version = 5.1.0
-gcc-version = 10.2.0
+gcc-version = 11.2.0
 gettext-version = 0.21
-git-version = 2.28.0
-gmp-version = 6.2.0
-grep-version = 3.4
-gzip-version = 1.10
+git-version = 2.36.0
+gmp-version = 6.2.1
+grep-version = 3.7
+gzip-version = 1.11
 isl-version = 0.18
-less-version = 563
-libbsd-version = 0.10.0
+less-version = 590
 libiconv-version = 1.16
 libtool-version = 2.4.6
-libunistring-version = 0.9.10
-libxml2-version = 2.9.9
-lzip-version = 1.22-rc2
-m4-version = 1.4.18-patched
+libunistring-version = 1.0
+libxml2-version = 2.9.12
+lzip-version = 1.22
+m4-version = 1.4.19
 make-version = 4.3
-metastore-version = 1.1.2-23-fa9170b
-mpc-version = 1.1.0
-mpfr-version = 4.0.2
-nano-version = 5.2
-ncurses-version = 6.2
-patchelf-version = 0.10
-perl-version = 5.32.0
+mpc-version = 1.2.1
+mpfr-version = 4.1.0
+nano-version = 6.0
+ncurses-version = 6.3
+openssl-version = 3.0.0
+patchelf-version = 0.13
+perl-version = 5.34.0
 pkgconfig-version = 0.29.2
-readline-version = 8.0
+podlators-version = 4.14
+readline-version = 8.1.1
 sed-version = 4.8
-tar-version = 1.32
-texinfo-version = 6.7
+tar-version = 1.34
+texinfo-version = 6.8
 unzip-version = 6.0
-wget-version = 1.20.3
+wget-version = 1.21.2
 which-version = 2.21
 xz-version = 5.2.5
 zip-version = 3.0
@@ -67,7 +68,16 @@ zlib-version = 1.2.11
 # When updating the version of these programs/libraries, please look into
 # the build rule first: In one way or another, the version string becomes
 # necessary during their build and must be accounted for.
-bzip2-version = 1.0.6
+bzip2-version = 1.0.8
+
+# PEM Certificate File
+# --------------------
+#
+# This file should be shipped with operating systems and can be found in
+# '/etc/ssl/cert.pem' (which may be a symbolic link to its actual
+# location). The current version was taken from an up-to-date ArchLinux at
+# the date that is also equal to the version.
+certpem-version = 2021-10-15
 
 
 
@@ -77,108 +87,104 @@ bzip2-version = 1.0.6
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/TARGETS.conf' will be built as
+# 'reproduce/software/config/TARGETS.conf' will be built as
 # part of a project. To specify a software there, just remove the
-# `-version' suffix from the list below.
+# '-version' suffix from the list below.
 #
-# CLASS:HIGHLEVEL (important identifier, don't modify this line.)
-apachelog4cxx-version = 0.10.0-603-014954db
+# CLASS:HIGHLEVEL (important identifier for 'awk'; don't modify this line)
+apachelog4cxx-version = 0.12.1
 apr-version = 1.7.0
 apr-util-version = 1.6.1
-astrometrynet-version = 0.80
+astrometrynet-version = 0.85
 atlas-version = 3.10.3
-autoconf-version = 2.69.200-babc
-automake-version = 1.16.2
-bison-version = 3.7
-boost-version = 1.73.0
+autoconf-version = 2.71
+automake-version = 1.16.5
+bison-version = 3.8.2
+boost-version = 1.77.0
 cairo-version = 1.16.0
 cdsclient-version = 3.84
-cfitsio-version = 3.48
-cmake-version = 3.18.1
-eigen-version = 3.3.7
-emacs-version = 27.1
-expat-version = 2.2.9
-fftw-version = 3.3.8
-flex-version = 2.6.4-91-ga631f5d
-freetype-version = 2.10.2
-gdb-version = 9.2
-ghostscript-version = 9.52
+cfitsio-version = 4.0.0
+cmake-version = 3.21.4
+eigen-version = 3.4.0
+emacs-version = 28.1
+expat-version = 2.4.1
+fftw-version = 3.3.10
+flex-version = 2.6.4
+freetype-version = 2.11.0
+gdb-version = 11.1
+ghostscript-version = 9.55.0
 ghostscript-fonts-gnu-version = 6.0
 ghostscript-fonts-std-version = 8.11
-gnuastro-version = 0.12
+gnuastro-version = 0.16.1-e0f1
 gperf-version = 3.1
-gsl-version = 2.6
-healpix-version = 3.50
-help2man-version = 1.47.11
-imagemagick-version = 7.0.8-67
+gsl-version = 2.7
+help2man-version = 1.48.5
+icu-version = 70.1
+imagemagick-version = 7.1.0-13
 imfit-version = 1.6.1
-libffi-version = 3.2.1
-libidn-version = 1.36
-libjpeg-version = v9b
+libbsd-version = 0.11.3
+libffi-version = 3.4.2
+libidn-version = 1.38
+libjpeg-version = 9d
+libmd-version = 1.0.4
 libnsl-version = 1.2.0-4a062cf
 libpaper-version = 1.1.28
 libpng-version = 1.6.37
-libtiff-version = 4.0.10
+libtiff-version = 4.3.0
 libtirpc-version = 1.2.6
+metastore-version = 1.1.2-23-fa9170b
 missfits-version = 2.8.0
-openblas-version = 0.3.10
-openmpi-version = 4.0.4
+openblas-version = 0.3.18
+openmpi-version = 4.1.1
 openssh-version = 8.0p1
 patch-version = 2.7.6
 pcre-version = 8.44
-pixman-version = 0.38.0
-python-version = 3.8.5
-R-version = 4.0.2
+pixman-version = 0.40.0
+python-version = 3.10.0
+r-cran-version = 4.1.2
 rpcsvc-proto-version = 1.4
 scamp-version = 2.6.7
 scons-version = 3.0.5
 sextractor-version = 2.25.0
 swarp-version = 2.38.0
-swig-version = 3.0.12
+swig-version = 4.0.2
 tides-version = 2.0
-util-linux-version = 2.35
+util-linux-version = 2.37.2
+valgrind-version = 3.18.1
 vim-version = 8.2
 xlsxio-version = 0.2.21
 yaml-version = 0.2.5
 
 # Xorg packages
-util-macros-version = 1.19.2
-xorgproto-version = 2020.1
+util-macros-version = 1.19.3
+xorgproto-version = 2021.5
 libxau-version = 1.0.9
 libxdmcp-version = 1.1.3
-xcb-proto-version = 1.14
+xcb-proto-version = 1.14.1
 libxcb-version = 1.14
-fontconfig-version = 2.13.1
+fontconfig-version = 2.13.94
 xtrans-version = 1.4.0
-libx11-version = 1.6.9
+libx11-version = 1.7.2
 libxext-version = 1.3.4
 libice-version = 1.0.10
 libsm-version = 1.2.3
-libxt-version = 1.2.0
+libxt-version = 1.2.1
 libpthread-stubs-version = 0.4
 
 # Version-dependent build
 # -----------------------
 lapack-version = 3.8.0
-libgit2-version = 1.0.1
-wcslib-version = 7.3
+libgit2-version = 1.3.0
+wcslib-version = 7.7
 
 # Netpbm's questions in the configure steps maybe change with different or
 # new versions.
-netpbm-version = 10.86.99
+netpbm-version = 10.73.38
 
-# Minizip is installed with the same `zlib' tarball, and they have the same
+# Minizip is installed with the same 'zlib' tarball, and they have the same
 # version.
 minizip-version = $(zlib-version)
 
-# From version 1.2 OpenSSL may not need a manual addition, as described in
-# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
-# cause problems, put it back in the list of "Basic/low-level" tools.
-openssl-version = 1.1.1a
-
-# Version 3.15.0 needs two patches, please check if they are necessary on
-# 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.
@@ -187,6 +193,7 @@ hdf5-version = 1.10.5
 
 
 
+
 # Python packages
 # ---------------
 #
@@ -194,65 +201,147 @@ hdf5-version = 1.10.5
 #
 # IMPORTANT: If you intend to change the version of any of the Python
 # modules/libraries below, please fix the hash strings of the respective
-# URL in `reproduce/software/make/python.mk'.
+# URL in 'reproduce/software/make/python.mk'.
 #
-# CLASS:PYTHON (important identifier, don't modify this line.)
+# CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line)
 asn1crypto-version = 0.24.0
 asteval-version = 0.9.16
-astropy-version = 4.0
-astroquery-version = 0.4
-beautifulsoup4-version = 4.7.1
+astropy-version = 5.0
+beautifulsoup4-version = 4.10.0
+beniget-version = 0.4.1
 certifi-version = 2018.11.29
-cffi-version = 1.12.2
+cffi-version = 1.15.0
 chardet-version = 3.0.4
 corner-version = 2.0.1
-cryptography-version = 2.6.1
-cycler-version = 0.10.0
-cython-version = 0.29.21
+cycler-version = 0.11.0
+cython-version = 0.29.24
 eigency-version = 1.77
 emcee-version = 3.0.1
 entrypoints-version = 0.3
-esutil-version = 0.6.4
+esutil-version = 0.6.9
+extension-helpers-version = 0.1
 flake8-version = 3.7.8
 future-version = 0.18.1
-galsim-version = 2.2.1
+galsim-version = 2.3.3
+gast-version = 0.5.3
 h5py-version = 2.10.0
 html5lib-version = 1.0.1
 idna-version = 2.8
 jeepney-version = 0.4
-keyring-version = 18.0.0
+jinja2-version = 3.0.3
 kiwisolver-version = 1.0.1
 lmfit-version = 0.9.14
 lsstdesccoord-version = 1.2.0
+markupsafe-version = 2.0.1
 matplotlib-version = 3.3.0
-mpi4py-version = 3.0.3
+mpi4py-version = 3.1.3
 mpmath-version = 1.1.0
-numpy-version = 1.19.1
+numpy-version = 1.21.3
+packaging-version = 21.3
 pexpect-version = 4.7.0
+pillow-version = 8.4.0
 pip-version = 19.0.2
+ply-version = 3.11
 pycodestyle-version = 2.5.0
 pycparser-version = 2.19
+pyerfa-version = 2.0.0.1
 pyflakes-version = 2.1.1
 pybind11-version = 2.5.0
-pyparsing-version = 2.3.1
+pyparsing-version = 3.0.4
 pypkgconfig-version = 1.5.1
 python-dateutil-version = 2.8.0
+pythran-version = 0.11.0
 pyyaml-version = 5.1
 requests-version = 2.21.0
-scipy-version = 1.5.2
-secretstorage-version = 3.1.1
-setuptools-version = 41.6.0
+scipy-version = 1.7.3
+setuptools-version = 58.3.0
 setuptools_scm-version = 3.3.3
 sip_tpv-version = 1.1
-six-version = 1.12.0
+six-version = 1.16.0
 soupsieve-version = 1.8
 sympy-version = 1.4
-uncertainties-version = 3.1.2
+uncertainties-version = 3.1.6
 urllib3-version = 1.24.1
 webencodings-version = 0.5.1
+wheel-version = 0.37.0
+# CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line)
 
 # Special Python modules:
 #
 # Healpy: When any Python module is requested, healpix will also build its
 #         Python module Healpy.
-healpy-version = xxxxx
+#
+# Bug: Healpix 3.50 doesn't yet support Python 3.10, so we are commenting
+# it here. When future versions fix the problem, we'll un-comment it again.
+#healpy-version = xxxxx
+
+
+
+
+
+# Problematic software that are currently ignored:
+
+# Healpix 3.80 has different installation scheme that is not yet
+# implemented here, and unfortunately healpix 3.50 has conflicts with
+# CFITSIO's new version macro and Python 3.10. So for now, we are ignoring
+# it.
+#healpix-version = 3.50
+
+# Setuptools-rust crash (https://savannah.nongnu.org/bugs/index.php?61731),
+# so it and its dependencies are being ignored: 'cryptography', and thus
+# 'secretstorage' and thus 'keyring' and thus 'astroquery'.
+#setuptools-rust-version = 1.1.2
+#cryptography-version = 36.0.1
+#secretstorage-version = 3.1.1
+#keyring-version = 18.0.0
+#astroquery-version = 0.4
+
+
+
+
+
+# R-CRAN (i.e. 'R') packages
+# ------------------
+#
+# Similar to optional programs and libraries above.
+#
+# Notation: The R package and variables associated with it are by default
+# called 'R-CRAN' (or 'r-cran') in Maneage, because searching on a single
+# letter string 'R' is extremely inefficient.
+#
+# IMPORTANT: If you intend to change the version of any of the R-CRAN
+# modules/libraries below, please fix the hash strings of the respective
+# packages in 'reproduce/software/conf/checksums.conf'.
+#
+# CLASS:R-CRAN-START (important identifier for 'awk'; don't modify this line)
+r-cran-cli-version = 2.5.0
+r-cran-colorspace-version = 2.0-1
+r-cran-cowplot-version = 1.1.1
+r-cran-crayon-version = 1.4.1
+r-cran-digest-version = 0.6.27
+r-cran-ellipsis-version = 0.3.2
+r-cran-fansi-version = 0.5.0
+r-cran-farver-version = 2.1.0
+r-cran-ggplot2-version = 3.3.4
+r-cran-glue-version = 1.4.2
+r-cran-gridExtra-version = 2.3
+r-cran-gtable-version = 0.3.0
+r-cran-isoband-version = 0.2.4
+r-cran-labeling-version = 0.4.2
+r-cran-lifecycle-version = 1.0.0
+r-cran-magrittr-version = 2.0.1
+r-cran-MASS-version = 7.3-54
+r-cran-mgcv-version = 1.8-36
+r-cran-munsell-version = 0.5.0
+r-cran-pillar-version = 1.6.1
+r-cran-pkgconfig-version = 2.0.3
+r-cran-R6-version = 2.5.0
+r-cran-RColorBrewer-version = 1.1-2
+r-cran-rlang-version = 0.4.11
+r-cran-scales-version = 1.1.1
+r-cran-tibble-version = 3.1.2
+r-cran-utf8-version = 1.2.1
+r-cran-vctrs-version = 0.3.8
+r-cran-viridisLite-version = 0.4.0
+r-cran-withr-version = 2.4.2
+# CLASS:R-CRAN-END (important identifier for 'awk'; don't modify this line)
author	Mohammad Akhlaghi <mohammad@akhlaghi.org>	2022-05-09 13:32:47 +0200
committer	Mohammad Akhlaghi <mohammad@akhlaghi.org>	2022-05-09 23:52:29 +0200
commit	9fdeebaacd06d57c479cd69e9937c4bfe5d0a286 (patch)
tree	012e6194ad6e25a81a9c99b4d0bd0852bc9a12af /reproduce/software/config
parent	480184b3da399fab11b50e67f01d2efa6bea0e3e (diff)
parent	f51b5e2e500dd6450a5a3425e85df78245fc5c5c (diff)