IMPORTANT: Updates to almost all software

This commit primarily affects the configuration step of Maneage'd projects, and in particular, updated versions of the many of the software (see P.S.). So it shouldn't affect your high-level analysis other than the version bumps of the software you use (and the software's possibly improve/changed behavior). The following software (and thus their dependencies) couldn't be updated as described below: - Cryptography: isn't building because it depends on a new setuptools-rust package that has problems (https://savannah.nongnu.org/bugs/index.php?61731), so it has been commented in 'versions.conf'. - SecretStorage: because it depends on Cryptography. - Keyring: because it depends on SecretStorage. - Astroquery: because it depends on Keyring. This is a "squashed" commit after rebasing a development branch of 60 commits corresponding to a roughly two-month time interval. The following people contributed to this branch. - Boudewijn Roukema added all the R software infrastructure and the R packages, as well as greatly helping in fixing many bugs during the update. - Raul Infante-Sainz helped in testing and debugging the build. - Pedram Ashofteh Ardakani found and fixed a bug. - Zahra Sharbaf helped in testing and found several bugs. Below a description of the most noteworthy points is given. - Software tarballs: all updated software now have a unified format tarball (ustar; if not possible, pax) and unified compression (Lzip) in Maneage's software repository in Zenodo (https://doi.org/10.5281/zenodo.3883409). For more on this See https://savannah.nongnu.org/task/?15699 . This won't affect any extra software you would like to add; you can use any format recognized by GNU Tar, and all common compression algorithms. This new requirement is only for software that get merged to the core Maneage branch. - Metastore (and thus libbsd and libmd) moved to highlevel: Metastore (and the packages it depends on) is a high-level product that is only relevant during the project development (like Emacs!): when the user wants the file meta data (like dates) to be unchanged after checking out branches. So it should be considered a high-level software, not basic. Metastore also usually causes many more headaches and error messages, so personally, I have stopped using it! Instead I simply merge my branches in a separate clone, then pull the merge commit: in this way, the files of my project aren't re-written during the checkout phase and therefore their dates are untouched (which can conflict with Make's dates on configuration files). - The un-official cloned version of Flex (2.6.4-91 until this commit) was causing problems in the building of Netpbm, so with this commit, it has been moved back to version 2.6.4. - Netpbm's official page had version 10.73.38 as the latest stable tarball that was just released in late 2021. But I couldn't find our previously-used version 10.86.99 anywhere (to see when it was released and why we used it! Its at last more than one year old!). So the official stable version is being used now. - Improved instructions in 'README.md' for building software environment in a Docker container (while having project source and output data products on the local system; including the usage of the host's '/dev/shm' to speed up temporary operations). - Until now, the convention in Maneage was to put eight SPACE characters before the comment lines within recipes. This was done because by default GNU Emacs (also many other editors) show a TAB as eight characters. However, in other text editors, online browsers, or even the Git diff, a TAB can correspond to a different number of characters. In such cases, the Maneage recipes wouldn't look too interesting (the comments and the recipe commands would show a different indentation!). With this commit, all the comment lines in the Makefiles within the core Maneage branch have a hash ('#') as their first character and a TAB as the second. This allows the comment lines in recipes to have the same indentation as code; making the code much more easier to read in a general scenario including a 'git diff' (editor agnostic!). P.S. List of updated software with their old and new versions - Software with no version update are not mentioned. - The old version of newly added software are shown with '--'. Name (Basic) Old version New version ------------ ----------- ----------- Bzip2 1.0.6 1.0.8 CURL 7.71.1 7.79.1 Dash 0.5.10.2 0.5.11.5 File 5.39 5.41 Flock 0.2.3 0.4.0 GNU Bash 5.0.18 5.1.8 GNU Binutils 2.35 2.37 GNU Coreutils 8.32 9.0 GNU GCC 10.2.0 11.2.0 GNU M4 1.4.18 1.4.19 GNU Readline 8.0 8.1.1 GNU Tar 1.32 1.34 GNU Texinfo 6.7 6.8 GNU diffutils 3.7 3.8 GNU findutils 4.7.0 4.8.0 GNU gmp 6.2.0 6.2.1 GNU grep 3.4 3.7 GNU gzip 1.10 1.11 GNU libunistring 0.9.10 1.0 GNU mpc 1.1.0 1.2.1 GNU mpfr 4.0.2 4.1.0 GNU nano 5.2 6.0 GNU ncurses 6.2 6.3 GNU wget 1.20.3 1.21.2 Git 2.28.0 2.34.0 Less 563 590 Libxml2 2.9.9 2.9.12 Lzip 1.22-rc2 1.22 OpenSLL 1.1.1a 3.0.0 Patchelf 0.10 0.13 Perl 5.32.0 5.34.0 Podlators -- 4.14 Name (Highlevel) Old version New version ---------------- ----------- ----------- Apachelog4cxx 0.10.0-603 0.12.1 Astrometry.net 0.80 0.85 Boost 1.73.0 1.77.0 CFITSIO 3.48 4.0.0 Cmake 3.18.1 3.21.4 Eigen 3.3.7 3.4.0 Expat 2.2.9 2.4.1 FFTW 3.3.8 3.3.10 Flex 2.6.4-91 2.6.4 Fontconfig 2.13.1 2.13.94 Freetype 2.10.2 2.11.0 GNU Astronomy Utilities 0.12 0.16.1-e0f1 GNU Autoconf 2.69.200-babc 2.71 GNU Automake 1.16.2 1.16.5 GNU Bison 3.7 3.8.2 GNU Emacs 27.1 27.2 GNU GDB 9.2 11.1 GNU GSL 2.6 2.7 GNU Help2man 1.47.11 1.48.5 Ghostscript 9.52 9.55.0 ICU -- 70.1 ImageMagick 7.0.8-67 7.1.0-13 Libbsd 0.10.0 0.11.3 Libffi 3.2.1 3.4.2 Libgit2 1.0.1 1.3.0 Libidn 1.36 1.38 Libjpeg 9b 9d Libmd -- 1.0.4 Libtiff 4.0.10 4.3.0 Libx11 1.6.9 1.7.2 Libxt 1.2.0 1.2.1 Netpbm 10.86.99 10.73.38 OpenBLAS 0.3.10 0.3.18 OpenMPI 4.0.4 4.1.1 Pixman 0.38.0 0.40.0 Python 3.8.5 3.10.0 R 4.0.2 4.1.2 SWIG 3.0.12 4.0.2 Util-linux 2.35 2.37.2 Util-macros 1.19.2 1.19.3 Valgrind 3.15.0 3.18.1 WCSLIB 7.3 7.7 Xcb-proto 1.14 1.14.1 Xorgproto 2020.1 2021.5 Name (Python) Old version New version ------------- ----------- ----------- Astropy 4.0 5.0 Beautifulsoup4 4.7.1 4.10.0 Beniget -- 0.4.1 Cffi 1.12.2 1.15.0 Cryptography 2.6.1 36.0.1 Cycler 0.10.0 0.11.0+} Cython 0.29.21 0.29.24 Esutil 0.6.4 0.6.9 Extension-helpers -- 0.1 Galsim 2.2.1 2.3.3 Gast -- 0.5.3 Jinja2 -- 3.0.3 MPI4py 3.0.3 3.1.3 Markupsafe -- 2.0.1 Numpy 1.19.1 1.21.3 Packaging -- 21.3 Pillow -- 8.4.0 Ply -- 3.11 Pyerfa -- 2.0.0.1 Pyparsing 2.3.1 3.0.4 Pythran -- 0.11.0 Scipy 1.5.2 1.7.3 Setuptools 41.6.0 58.3.0 Six 1.12.0 1.16.0 Uncertainties 3.1.2 3.1.6 Wheel -- 0.37.0 Name (R) Old version New version -------- ----------- ----------- Cli -- 2.5.0 Colorspace -- 2.0-1 Cowplot -- 1.1.1 Crayon -- 1.4.1 Digest -- 0.6.27 Ellipsis -- 0.3.2 Fansi -- 0.5.0 Farver -- 2.1.0 Ggplot2 -- 3.3.4 Glue -- 1.4.2 GridExtra -- 2.3 Gtable -- 0.3.0 Isoband -- 0.2.4 Labeling -- 0.4.2 Lifecycle -- 1.0.0 Magrittr -- 2.0.1 MASS -- 7.3-54 Mgcv -- 1.8-36 Munsell -- 0.5.0 Pillar -- 1.6.1 R-Pkgconfig -- 2.0.3 R6 -- 2.5.0 RColorBrewer -- 1.1-2 Rlang -- 0.4.11 Scales -- 1.1.1 Tibble -- 3.1.2 Utf8 -- 1.2.1 Vctrs -- 0.3.8 ViridisLite -- 0.4.0 Withr -- 2.4.2
author: Mohammad Akhlaghi <mohammad@akhlaghi.org> 2021-10-04 02:51:45 +0200
committer: Mohammad Akhlaghi <mohammad@akhlaghi.org> 2022-01-21 01:15:24 +0100
commit: 8463df97c6f26ec4d22cd5828bb0574fd5e450d2 (patch)
tree: dbaa2e7c2fc44856eb98555b79c6814f210a6c17 /reproduce/software
parent: 775fc036e0091f05ff56e41b855bc416b9ed36c8 (diff)
49 files changed, 2219 insertions, 1404 deletions
diff --git a/reproduce/software/bibtex/astrometrynet.tex b/reproduce/software/bibtex/astrometrynet.tex
index 15d4829..26d211b 100644
--- a/reproduce/software/bibtex/astrometrynet.tex
+++ b/reproduce/software/bibtex/astrometrynet.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/astropy.tex b/reproduce/software/bibtex/astropy.tex
index c25803b..2041fc3 100644
--- a/reproduce/software/bibtex/astropy.tex
+++ b/reproduce/software/bibtex/astropy.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 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
diff --git a/reproduce/software/bibtex/corner.tex b/reproduce/software/bibtex/corner.tex
index b2e0e25..f6b4f22 100644
--- a/reproduce/software/bibtex/corner.tex
+++ b/reproduce/software/bibtex/corner.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 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
diff --git a/reproduce/software/bibtex/cython.tex b/reproduce/software/bibtex/cython.tex
index 88a5c4e..30a0713 100644
--- a/reproduce/software/bibtex/cython.tex
+++ b/reproduce/software/bibtex/cython.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/fftw.tex b/reproduce/software/bibtex/fftw.tex
index 7f525c9..1186efa 100644
--- a/reproduce/software/bibtex/fftw.tex
+++ b/reproduce/software/bibtex/fftw.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 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
diff --git a/reproduce/software/bibtex/galsim.tex b/reproduce/software/bibtex/galsim.tex
index 3646639..8fceda8 100644
--- a/reproduce/software/bibtex/galsim.tex
+++ b/reproduce/software/bibtex/galsim.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 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
diff --git a/reproduce/software/bibtex/gnuastro.tex b/reproduce/software/bibtex/gnuastro.tex
index 1470a00..018a35b 100644
--- a/reproduce/software/bibtex/gnuastro.tex
+++ b/reproduce/software/bibtex/gnuastro.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 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
diff --git a/reproduce/software/bibtex/healpix.tex b/reproduce/software/bibtex/healpix.tex
index 08bef90..77471c5 100644
--- a/reproduce/software/bibtex/healpix.tex
+++ b/reproduce/software/bibtex/healpix.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 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
diff --git a/reproduce/software/bibtex/imfit.tex b/reproduce/software/bibtex/imfit.tex
index 3822fd4..167586d 100644
--- a/reproduce/software/bibtex/imfit.tex
+++ b/reproduce/software/bibtex/imfit.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/matplotlib.tex b/reproduce/software/bibtex/matplotlib.tex
index c35f682..aab2c04 100644
--- a/reproduce/software/bibtex/matplotlib.tex
+++ b/reproduce/software/bibtex/matplotlib.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex
index 9fb0f54..470cf8a 100644
--- a/reproduce/software/bibtex/missfits.tex
+++ b/reproduce/software/bibtex/missfits.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2020-2021 Surena Fatemi <surena.fatemi@ipm.ir>
+%% Copyright (C) 2020-2022 Surena Fatemi <surena.fatemi@ipm.ir>
 %%
 %% Copying and distribution of this file, with or without modification,
 %% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/mpi4py.tex b/reproduce/software/bibtex/mpi4py.tex
index 9a99803..598bbda 100644
--- a/reproduce/software/bibtex/mpi4py.tex
+++ b/reproduce/software/bibtex/mpi4py.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/numpy.tex b/reproduce/software/bibtex/numpy.tex
index 07101cf..0dee489 100644
--- a/reproduce/software/bibtex/numpy.tex
+++ b/reproduce/software/bibtex/numpy.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/r-cran.tex b/reproduce/software/bibtex/r-cran.tex
new file mode 100644
index 0000000..cf74a8e
--- /dev/null
+++ b/reproduce/software/bibtex/r-cran.tex
@@ -0,0 +1,19 @@
+%% Copyright (C) 2022 Boud Roukema <boud@cosmo.torun.pl>
+%% Copyright (C) 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 this notice are preserved.  This file is offered as-is,
+%% without any warranty.
+
+@ARTICLE{RIhakaGentleman1996,
+      author = {{Ihaka}, Ross and {Gentleman}, Robert},
+       title = "{R: A language for data analysis and graphics}",
+     journal = {J.Comput.Graph.Stat.},
+        year = {1996},
+      volume = {5},
+      number = {3},
+       pages = {299-314},
+         DOI = {10.1080/10618600.1996.10474713},
+        ISSN = {10618600},
+}
diff --git a/reproduce/software/bibtex/scamp.tex b/reproduce/software/bibtex/scamp.tex
index ab68dd6..62e910c 100644
--- a/reproduce/software/bibtex/scamp.tex
+++ b/reproduce/software/bibtex/scamp.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/scipy.tex b/reproduce/software/bibtex/scipy.tex
index 71b0caa..4b1292d 100644
--- a/reproduce/software/bibtex/scipy.tex
+++ b/reproduce/software/bibtex/scipy.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/sextractor.tex b/reproduce/software/bibtex/sextractor.tex
index 0c91a3d..8905be8 100644
--- a/reproduce/software/bibtex/sextractor.tex
+++ b/reproduce/software/bibtex/sextractor.tex
@@ -1,5 +1,5 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 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
diff --git a/reproduce/software/bibtex/sip_tpv.tex b/reproduce/software/bibtex/sip_tpv.tex
index 02dfec0..2a5b68b 100644
--- a/reproduce/software/bibtex/sip_tpv.tex
+++ b/reproduce/software/bibtex/sip_tpv.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/swarp.tex b/reproduce/software/bibtex/swarp.tex
index 7636f1c..f645bb3 100644
--- a/reproduce/software/bibtex/swarp.tex
+++ b/reproduce/software/bibtex/swarp.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/sympy.tex b/reproduce/software/bibtex/sympy.tex
index 1d07846..3ce064a 100644
--- a/reproduce/software/bibtex/sympy.tex
+++ b/reproduce/software/bibtex/sympy.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% 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
diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex
index f3b5490..b97762a 100644
--- a/reproduce/software/bibtex/tides.tex
+++ b/reproduce/software/bibtex/tides.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 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
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 bec3adb..ef95f57 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
@@ -21,22 +21,26 @@
 #     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 (for Python modules, add to 'top-level-python').
+# Programs and libraries (for Python or R modules, use respective variable).
 top-level-programs  = gnuastro
 
 # Python libraries/modules.
 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..d8b3a96 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -1,7 +1,7 @@
 # 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>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -14,54 +14,53 @@
 
 # Basic/low-level programs and libraires (installed in any case)
 # --------------------------------------------------------------
-bash-checksum = e210cd63ce1241636fbb14d1a105c83e9481a0312026f746f76f7115b777707170ddfe1840fb4d3a4093613048e2d1eedf926e843ad15ffc8d66f08525e8b04b
-binutils-checksum = 5ad795fab0803be83b53aa955fd5414c8408b4cf2a66eba2f8688298312934b4b1b0cbe9cf887d86de77f88adf1333d85fc9f6ab4a530e85a09b9b2dbf6aaf3f
-bzip2-checksum = 00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12
-cert-checksum = a81dfa59c70788126a395c576e54cb8f61c1ea34da69b5cd42e2d83ee6426c2a26941360c7302793774ea98ca16846deb6e683144cc7fb6da6ef87b70447e4c8
-coreutils-checksum = 1c8f3584efd61b4b02e7ac5db8e103b63cfb2063432caaf1e64cb2dcc56d8c657d1133bbf10bd41468d6a1f31142e6caa81d16ae68fa3e6e84075c253613a145
-curl-checksum = 614f8d67e6ee942cb5e57f2da1a3faaf84ebff549ffe383aaf3751a4de3c8874ff482076afa27a52e910a137dec9b0f6e98265dc7d4ad7c95845b63f39236fd4
-dash-checksum = 9d55090115ac04f505d70e6790179331178950f96fe713b33fd698fa8bfa60d4eff1b68cb7b8a2f099d29c587d36034a17dccd6658ba1623ff0a625ac1fb9620
-diffutils-checksum = 7b12cf8aea1b9844773748f72272d9c6a38adae9c3c3a8c62048f91fb56c60b76035fa5f51665dceaf2cfbf1d1f4a3efdcc24bf47a5a16ff4350543314b12c9c
-file-checksum = 9cf1a7b769c56eb6f5b25c66ce85fa1300128396e445b2e53dbbd8951e5da973a7a07c4ef9f7ebd1fe945d47bdaf2cd9ef09bd2be6c217a0bcb907d9449835e6
-findutils-checksum = 650a24507f8f4ebff83ad28dd27daa4785b4038dcaadc4fe00823b976e848527074cce3f9ec34065b7f037436d2aa6e9ec099bc05d7472c29864ac2c69de7f2e
-flock-checksum = ddb997174c0653bc3d29410a5a16b6290e737aa40fbf4b746e2d1db1e88e5acb08ec11a25c27c8a5a5fbf5a00fcac17abeaa245e7df27bd975ae86364d400b86
+bash-checksum = 409843172032fbe7ef50004ddc30934e12d864e30935fa501dd8a2792c0c12c9c00e1108c05a95ba84b5ab4dd146d92e793b684df1f49ba51eba40f39d47f14d
+binutils-checksum = f3c10d8aeb50872278ece6ad31f7369bf12b2d09618812322b35e6750024b45f77fc32d498a9c579df3c152ce3da382f480281743eb5b53639aa287b7166aba3
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+coreutils-checksum = efdffdeec139e4a7e4033472197145d25400c4cbf6380cb63b18a748934021a977e613a75f018fff23bf506ebdb876b1d79166ba8d3b6077dd1c0a338ef5bff6
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+diffutils-checksum = 597cd0a14087722b78469e2238fcee25e78108f53ca43fbff1194d87625b4c7498a205f68c7bb44fcd437b8d642bba263ac40170780aede006076b11956fd06e
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+flock-checksum = f711815035e21b46572bf80e730a55822e5abf4cb29749e476ee6cf4d5027e9a7deeacf5f6b8c37f18f17a0cc7a6d98fb0be3936e97b122707f1cb2306d1e1d9
 gawk-checksum = 682fadd3630d51d13d19443a9a93d4cba1bd6802dd078f1366f17f39d3fa5800f47037b103d742be9254475fdc251d90626f95a2e04b5ace117cfaecebca2281
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+gcc-checksum = 7f9605b9527799f92b3251968f63e53bd0b74880952f0cbc58ade9b4eee60bac4990ad408c1a6067f7aa36225709061106f0d93bc581ec97711fc5ff6ae15127
 gettext-checksum = f3083af79341bfdc849118333c1598812c12bc225d998181694648187088050160deb4777c252f72a7158e914c2967416489bc6167ef8505664497f2fb94ecbf
-git-checksum = a6159c0a15e3c5f9603157d4010664a6d74e7d65b9fe97a03b36fac12607248ed57980d96565841e88eae343001c167222232737d3af812608c8db011941df1a
-gmp-checksum = 9975e8766e62a1d48c0b6d7bbdd2fccb5b22243819102ca6c8d91f0edd2d3a1cef21c526d647c2159bb29dd2a7dcbd0d621391b2e4b48662cf63a8e6749561cd
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-gzip-checksum = 753fbcf5eb104bfc8a8eb81b69b8701f757b5158e6333b17438574169a4662642a122e1fdbd920a536edbcb77253d65fa571e4f507dbe72a70fee5eb161d6324
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+gmp-checksum = 2bec8840bceaeac542ce1f7870d5b971b631b055b49751ba4f78f98229d7eb9cd97c0a668f6d7cf81a53bf0b3d5d70e682af523f8f0eee0d7390727ff2bbb271
+grep-checksum = e8c28da23fcef11825c54794b3eebffd0eaf84b7ebf5e187fd06b5d4aeff2af1ac097f0166151b3f11f332dc72abf6097188d578f549496f4c7c96ccf479a61e
+gzip-checksum = 48db13116543ffff39ce03a058e5ca279d93581b8aead3b857c41b0aa3028aa787d5bb21ee18d002565ba3e016fed60d55062b3fd91c41a9877f9f7febc6ae27
+isl-checksum = 00821ccdde36540869b47b1f68837183dfc8eb0ae580a36ba92c25308618a25680adc8de7b9df4d93851b300d7e457c931e7ff3a40fa90e336c74bcab3504e41
+less-checksum = 31f733ecf4170b4f5dcf467b902d0753833f852739b03bf611137aea3672c03e00e9418fd5e289e82624c2dd42b0de06cb65a7a637dae78e7647e5c6ecf9fb57
+libiconv-checksum = 396be5305f899619596b72ccc8a192c5fcc8e12163fd23376833c957ee44dbf3d39461360bf7e32a049f9f12a851da7836bfc8a62842114fc10717ac92762987
+libtool-checksum = 379a16baf2123d3cdd28cf8e35e4bb1e0326ae7f431c42ab2a3bd42ccac99a622e5ff0a68703b81614c147bc02178612a5cecb105b8943937a05c0b3ec91fea0
+libunistring-checksum = f1e92717fc043c2d7c454e44700559b0bd75457fdf3da5e803d9d58d8ebdff261bc73f380f6350bb04ce04071687c0317d09b4e8615003187948be1cd4d0bab3
+libxml2-checksum = 0fdc16aa7536adfe1deaadd19cdc20101dd3b081bd0a2e59d8ecc2965b2ef4c30d2e2447ab5b0cdb861c57ddb89ace1bd4ce120d9436b751b37724a90981ba8c
+lzip-checksum = 8d063a5f0609caa4d568f7bad4c67fcdee70a16c37e67b9d3cccbae53f09c14fa8590816aeb37a3fe0bc71a642c55e9fb4b371c0f68585be9564af22584d5c99
+m4-checksum = 7f8845f99e64d6a45859b9d80b03352a5526b3de0311ca4d6dd6850e504d26dfc90cd21d1640b10382f786213f8fdf20183bff424b3c41ea11432315993ab829
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-metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a
-mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628
-mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88
-nano-checksum = d101e7f4802c079254e79340b433749dcd699fa9adec3f96e4218ec12f066a1f6b0954c27254bb6f019bc370ee2116817717870f4e2bc782c552442f2cc75195
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-openssl-checksum = 1523985ba90f38aa91aa6c2d57652f4e243cb2a095ce6336bf34b39b5a9b5b876804299a6825c758b65990e57948da532cca761aa12b10958c97478d04dd6d34
-patchelf-checksum = 39745662651cf0a9915685b2767a611ceab4286f8fa57eace342b3f44248431616e8563d4ac6709c97d8534229c73c05470239e462b7e74b36bf629a876dfbad
-perl-checksum = b00f3482f6961be043349a09445227e99472a8ae804919bfa0641de5bbd683249deb607f3b5c6c44ccfcf916408eac125132f9660191d574de0a9d1f17892bc1
-pkgconfig-checksum = 4861ec6428fead416f5cbbbb0bbad10b9152967e481d4b0ff2eb396a9f297f552984c9bb72f6864a37dcd8fca1d9ccceda3ef18d8f121938dbe4fdf2b870fe75
-readline-checksum = 41759d27bc3a258fefd7f4ff3277fa6ab9c21abb7b160e1a75aa8eba547bd90b288514e76264bd94fb0172da8a4faa54aab2c07b68a0356918ecf7f1969e866f
-sed-checksum = 7de25d9bc2981c63321c2223f3fbcab61d7b0df4fcf7d4394b72400b91993e1288d8bf53948ed5fffcf5a98c75265726a68ad4fb98e1d571bf768603a108c1c8
-tar-checksum = 4be18afeac54aec4af074cf2358cfade5aaebe2041c5075c5764a81114df4d002e90b28f4444bd1430783e7d6bed82abd0440ef5cb244695f2e56a9a41b42fbc
-texinfo-checksum = da55a0d0a760914386393c5e8e864540265d8550dc576f784781a6d72501918e8afce716ff343e5c2a0ce09cf921bfaf0a48ecb49f6182a7d10e920ae3ea17e7
-unzip-checksum = 0694e403ebc57b37218e00ec1a406cae5cc9c5b52b6798e0d4590840b6cdbf9ddc0d9471f67af783e960f8fa2e620394d51384257dca23d06bcd90224a80ce5d
-valgrind-checksum = 5695d1355226fb63b0c80809ed43bb077b6eed4d427792d9d7ed944c38b557a84fe3c783517b921e32f161228e10e4625bea0550faa4685872bb4454450cfa7f
-wget-checksum = 95fb064f0d79b0a3178a83322f58a85a3a036fb300ed759eb67a538f0bbacdd552f6cbeb60d63b4f0113e8467d923a5ce7ac5570b7a4ce1733b3dfd559bb33b2
-which-checksum = d2f04a5c5291f2d7d1226982da7cf999d36cfe24d3f7bda145508efcfb359511251d3c68b860c0ddcedd66b15a0587b648a35ab6d1f173707565305c506dfc61
-xz-checksum = 7443674247deda2935220fbc4dfc7665e5bb5a260be8ad858c8bd7d7b9f0f868f04ea45e62eb17c0a5e6a2de7c7500ad2d201e2d668c48ca29bd9eea5a73a3ce
-zip-checksum = c1c3d62bf1426476c0f9919b568013d6d7b03514912035f09ee283226d94c978791ad2af5310021e96c4c2bf320bfc9d0b8f4045c48e4667e034d98197e1a9b3
-zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae
+mpc-checksum = 85e044749c2a001a70af2c11fc4bac58709ca7df11bf6da3b03cca852ef336eb37c4fb1dafdffde2d13df35caa7c296a7cba19a4625b82dc3cccc5066ac95774
+mpfr-checksum = 23a30040511809b6a8ed33d5ef83f903e987f0e4b8e87c9bfa627fdf0ca6400330bda4fd727cf1d37f04f7804c77663ed983c6b5ed26f5d5bd772bf13f1f9eb5
+nano-checksum = e1ae28710ce05ef9c73357b9fb556fa6a7e670ae6fd786339677cb8a154446029dd9c4ead4eeab014691e941211a2d2c9faefc7695d1b97c2b8b445ba77ff067
+ncurses-checksum = 68b7c0388304791ce82ab86ea5c5725357f07bbae0c230af3e4722f75617778b6e28d1f0c1d65871379670e54fcc96ecd54f529a3462d207f3d930e6dad5a2dd
+openssl-checksum = f913eb1f654f702161e524a02ccdd028e26d418f26e334069d77ee0134f094809d5c86bfd65e8d05c9bf3d4f10d58a9f3c4452c8d6120741a90541114d82d5b6
+patchelf-checksum = f74409c00e7e50a88590267fa0c173f71239f1471985792f7bcdab750d202a9a25383c015987608bbcd6ace5b3642645d46dba63199ba54fabbcb51ae7fca8f6
+perl-checksum = 47c37f2698d7f46d2bd8a19abfd329ed58509a9eeb6c9ddb32e435434fcacd5b70419c01d0fa10d1c599cf43248ebc1538076e6bdedc56624fac887d480b8b8d
+pkgconfig-checksum = c37ab9336ac15a73bf5a23101f3fd8a04810f39b0679634e420e5d7bbd60a80cfc919122694cf83965beb071d2780681efc8d954ce99d77eb235a4dc7497e250
+podlators-checksum = c653205fd1e8e570750584cdb3a813a1250ae6f66d4e654b3521b80052867a3a6ba15ad3d7c8a22065f1febc36175257f9b5685570fcf0a87908c2dc9d42cb3d
+readline-checksum = 90d9571609b90f07573f831878f5131df17f1baabc064398c95915f13d44ea0907e41218be089377523751ca5b02a8486b5306ef6d0245432a0c224b7aa7fb94
+sed-checksum = 90d8fa16b2570baee061c128d6db688a3354796a6499014f12dc4c5966b34cbb8a04a47914e4ff8dc1815444ad0235565efef2a327b67c485e3324c2a1d07d78
+tar-checksum = 98d938d76a55dca1d1ba9a13f1aa2a3e8ae25ea422843e93daab98d373f4a72eebf052c88c87122ac16ed629863dc3fdb86dddf18d3ab5a2565b06f49b7d02bd
+texinfo-checksum = 6a706bd0f973b9bbe4fdbc3bfd475cc9699eb410d276cbc19a73255924313006e1b80a87803fa30f7245e3fcb610c829da31e38c91e791e19f11ca8b998914c4
+unzip-checksum = 5c1f3c417d5feed64b8c5dbc26b51dd84130b9ea43d77e810cc9e82cee6e965fa76e2636e5ba11a029eae3454a815a6081cc2828079fa3994c511d555b82f12c
+valgrind-checksum = a99e09e6d957ce435e64f4ce7b1a14e7e266282578171ce4e3bb3f405ce304e4df3b43d2fca59a6024c176f60c2ac82b3992afc810386e8de03c72f262b32702
+wget-checksum = cbce817981864d4dc424b330126b0d06231907004f1fcfc8d105ffc043bab59e93421738d36cf95013cc03b5b9f9813b1c242a3ef3926a907889ca78dfb336d4
+which-checksum = f886f5828359584b204f20a3b712d29c14879288e6255ab612784fce167bc9467c246bf48f9c52780069a95fe25761c3edda358428893967f4a1a1e5e874b2d5
+xz-checksum = a92bc2619f668a9e462945423035a090bc91c010d0788db8fb300851a3f93c04af2d433bc545195979d51312f59667c5814e46dd711b67fa8f89c0864873b81c
+zip-checksum = 433eda6a27074746a960952fa3b08028d5ba43fe976a1306dbace9209be5f89aa0554b17bba5815cd00984c0f64559c5fa0b754b620f6d646a2b145a8b599acc
+zlib-checksum = 97493906504451830655b300b4144deeeb9f41bdb9b3f3a3d5635c2b16bf90d543841dc70d028f1cee6b52ad1c604fdc18b18f559d1e4ed6523e6b3ce76fd8c5
 
 
 
@@ -71,150 +70,208 @@ 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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-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
+esutil-checksum = 7f1f22b0a05855819e3bd9bc2eee14942c2f536fb99f4af03575eb41d3d3fd1d2e6091ad076bfab4d51a8f30e213b607af35ed00d063fb2895b58f7a57cde5ae
+extension-helpers-checksum = ea62d537d0f76af9f975ad577d3a679e027fe0dd21f8a125ccb34bff1e4cfb69ecc15c8bceb406744033e91827fc8b78477e30e8f3cc45396bb6ed8102159b08
 flake8-checksum = a25076bb7f978ca23af0f2016b30bf5fe4680371b4c0939361a6f8c496f3c846cf98ecadee35fc2dedd588116c8cd982529972dd2411ab139621912b69132a1e
 future-checksum = c70565a660cf87c5e7e994bae0d4eb0b2b8b607ecb5ce65521c027bf0a39ce5699f0578413bd3c7edd5d01aeb1617de48dcea098a9e9021d8487a73007573030
-galsim-checksum = 11ecbfb9628cf85a4c25024c6f3a34bbdadf522f64e4e93e6428b545c65a48906a05eb7774d0faaacf52a48dddfd599bfc7cc7252ca854a18c3930f116533a3c
+galsim-checksum = d7e354778de87cf5c8964a7f252025eeeabc04ef2fb673c35adc536b449442aca261e2bd96befaaa872065376ac79cbe23d1ee7d034bcab5916f74b98112b8b8
+gast-checksum = 8311f48788daf060bee54ad8986eae054c2a426adcf97f1503cde37c4da2827cd0f664188e51f5c2f932a0a4ded78166a8466465595a640106060c8b6c7072a5
 h5py-checksum = c49b04f7dcddf03f36d4f063d79ecbe544e0b1daee432d4a76cfa83dac3a1f2cb144f40a74fb85ea17cb5b778f57f709969ea5d1a2afc5bdd5aecbc9d732898d
 healpy-checksum = installed-with-healpix
 html5lib-checksum = 35939b4450893864da04e735ee5e0addacf1dd34bae6a6909c76572abf6bfded446a78a713dfde91c1485ba45867d7abeb6a45cf0545c16ea968707be7de5dd2
 idna-checksum = 8ca5cfe6350c51250bafdac7c6e4ddd54c4a5d6bf7acbcef896760a759868c8e9df1fdf550121d8512fa3eb316dcf031ec6058e03b4f66eadee21b63e2187d33
 jeepney-checksum = 43083994a7c6af84a5a68d3ff8f6dc4d9129ce9fa55517838fb62d9f62bb78bdf52067649d0b95d08d689b7d7475cb9b2a956662e265a776ad42dcf4ccc0ab63
+jinja2-checksum = db19498dbc9bd6419b474fbb465ce8c689b96f72d33ed1a31cee3c42e2c545dfd0fd5bfca610075e2e126fbdd27300a73efd76fb7ea449727ed61a6127806dcd
 keyring-checksum = 3863f2cd89131d7e927e55691b4eb4b7c2599af189525293d0948aef5215efbbbd74d45db3cd4885ba5b18a79f0fa0b0edc3783a020a6702f6a6fb7ed86b2cf2
-kiwisolver-checksum = 80ed3d7429a2ed4944aa09766bebac2709a3a0e0a184ff414f04bf3c7ec3034ea7d0f70dff319922b870dedaf13d64fc87eff86a82e720ec93a2510885ad738d
+kiwisolver-checksum = d5aec6da0a5038f969227eb6320bf6ccdae2668b5730fe3e94ea1be5a2e64d121516abea16764c4659e05d821d044e76d97054385c0bc62780c3b0cd82468aed
 lmfit-checksum = 8435328fd8baf92b424299c341aafb995dc45245e17b1774e9eaabdd994dd6ec3b2e70f7506d67b587631cebd2dc584fcd1a9902286925a61e2135b7e11ece21
 lsstdesccoord-checksum = a66b8b702cd8122f0c8aee05abe0fc0c6299f8bdb99b151f54bd7ad7430d6bc9f843f7294a7f08f3ce9f8606ea0ced0796a63b79cc8a53ae73068b691e2e6871
-matplotlib-checksum = 2ffd9e79e300a37092ab4b5a7156c2f57e408975818abd413c74477ad622030c7636695467aab821c9996564cddec57e26ba6a8004f6639070964fcb7a510a75
-mpi4py-checksum = 041768f753c8188b2560fe92711861780f0d77eda3281433520c98bb1e9b4da6a89c364f2d1c4623868ffbbcfde34ef556198b1bef6fc1c4a9c19cd5e71b546c
+markupsafe-checksum = 4bc1171f1dc86516d6002d6dc3df2ccf78481480812025114b3a1511779b152a605904f0dc3aa0a6c8c282111a74564891a2b02650f90c44b667e5e0622c62c0
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 setuptools_scm-checksum = 196d4785a1802875d89b9e54ae788e791a9c5cb685109784059955b691242984e42b96d77075116790935f56be82259bc2588d95d65ecbb101261d76daddb83c
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 sympy-checksum = 6ae09be7260b1624b4f92d39c68d5cdf54e6e33010d9215f46d62d989c04cdbee6f9f9c8b11ebeda53257d154954fb926b3ab7335b738e33ad248764875b6ddb
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 virtualenv-checksum = 3306f59bbcb48ceec225c07083e0b6831379b3e632e4a23c376849559449de1a04db66e0e7ceabb40ddcd3ae984a2a18dfdc4f1c38777d4bc04537f85a0137ac
 webencodings-checksum = b727b01bac6ec79bca517960d27b4c0668b295f25559471b9641c2c33dab55db6dac9c990952177964c6418382c22831b14d57df5e632d51d7abf97b61f24326
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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.
+r-cran-cli-checksum = 29782b4cb00a94536c871276835a5f762f3deca8355c35b9366434cd2873604ea20f2746ef624eb4e6ec1514cb9079e8c101e50ace85fb1336f3befcf77be244
+r-cran-colorspace-checksum = b6c24e1dd104d444e09049df61fcaac680aafc1f530bcff07fc8ce5f2bcfc9a3521aac032a506b61dd10de885a914ed82c4095ee95113e407ffd0cd43662f098
+r-cran-cowplot-checksum = 39e3b29078ffa67e03911c21b4cc09a8dcfe0bf38fb180691e82f2ff87c993e78f89173a750dcf08424fa1e0ab39ae5d07fc59af792ac0333ef02cd9ea8afc03
+r-cran-crayon-checksum = 7034a7ac446361c90088d53f2079144a561e2d62095884edb85700512decf4dab9fb4a85fa6d0fcdddf3d5d8a3d219d56384d1d1af9c6351d81abb5778147cde
+r-cran-digest-checksum = 44a2978be00b7a90f88f05ad8ec114fb07a8e3816fa263749d44aa61f7706c3f802feaa7b7e9267cce1d0dd5c49e7f7ae3ccd9f968a7025aeef16181f7c0d70f
+r-cran-ellipsis-checksum = b82fab404c3e1bb9df2f7ee5ae6e62b237c15c661a417adabbd86f984a2128970e0ad5581e9a8b7541b9f9b07418de469398e6bc06775bd4a3c8bc1472947f62
+r-cran-fansi-checksum = 50a7a8e597b89b49fa33fa93861a906c38508a42980072027a5f2746f047b82333074248e5c7724faf4559eb6a4cdfe7a8ccfd2dc5b637a8f3d5a8584afdbc75
+r-cran-farver-checksum = 66918ddd268b3044625d9b691fa0a2251301400026bdd12524927ccd9f3976ae55189a11ecbbc042ceef0c61e7692577cbf630f3a45fee455a4f3bd5e19e6937
+r-cran-ggplot2-checksum = f515a4710c13f69d3ed8a8d59195aa3d2b52c345ed94a5f36ebe04e1bb621e07d0b5b79290ea42c81a764fc94b17573041a27c1fb06e11b08834ea9e3e89b39a
+r-cran-glue-checksum = 5e679884f45a00a011e284f59370cabc2d470515351324ba2748b06ec780d65b6f64901eb5589713e9b122b103e58cd040eb342c88d7d4a3734a6e23064552d1
+r-cran-gridExtra-checksum = c92c9cb46312300ad9477cfe849c11a9d79fcce1f909c5bdc76e46a6741a636f598a457883fd278e0b00a47eb385bce4489ad04d3cf93ce7def9ae8771dffc71
+r-cran-gtable-checksum = e3cc4328bbb42a59ff1b315f0b030a9fe240bc6b6844f460835c25497179c3a5d9ea10fa2af1aec4b7384e78a564eb99eb4c51067f98a57ef919f2e11f6fbafe
+r-cran-isoband-checksum = 253d0b768492b64d5c32ab20f3b896cfe206305b8a53b31055813bc6957069eb76ea94a403b931fdada06ab33ee91f7105ef080fcd88af0c05860865950d99d1
+r-cran-labeling-checksum = 0ba0cb33863f79868ec6f2289f29ddc742cc620b7ed85364099448d39d71a51cce45028097100aeeaf8a8a7e4ad0982b459ef20a15faed9c5c7db79e9f9b01fe
+r-cran-lifecycle-checksum = 1ac7aafb41925d19abfd78f454d1acd5102a72ee7017840f14cf54d035cf3999d5b6dc2979b00214358e3c26dfac3407c8b525b434e8882c123a92a132bb07df
+r-cran-magrittr-checksum = b0bca6000602b90c996efc3681799a8a965a5bb90eb5e3436b7a26be15e5a219ef6300f4086f0b6efda734272775688a8ca77a4094eda429926a9179125b87c7
+r-cran-MASS-checksum = 0d22ff69cff1414bf52d11aefd75b442c9c8fecb343fe3733c7b28a6b881f3c87ac8b6e4b0d76709c36e612523ef386d207d403c2292881c083e03d21b3709ec
+r-cran-mgcv-checksum = 83df262152d9ee5081b3d16711b5cae3860f7dd879f97db014b987edd6b110b11219bac0e07f8ca04169181291aea76399d465b9bf0e96a1b6aaf83692fdf5bc
+r-cran-munsell-checksum = 59536096c637d84b80f097bf400bcbb9fcb7ddf6267ce6b026e3c7b3cbcf548caef118439a1928dd8833359a18b14e49f38fe90ea7919c28c215b3b297c036a3
+r-cran-pillar-checksum = dd2bc53539ec6838cb8d5bb5ddf30cff9c43c5de0f8d148374d5a394385429a06243db48e7cf6bdb463bad7a130fb47b172ceaac8d04ca3205b4c4210ab672ff
+r-cran-pkgconfig-checksum = 0b636d9b1233a00974ac93eb2a1e0ad6b552fa043bfe9743ec74ef884c1d01a73c372586516abca8772a836c50dcd9eed4d10c50f6883fc68ba2494e79872aaf
+r-cran-R6-checksum = 5986510ff19c1e0129bb0b88d72020d30255e26d6da9a40c123b7b0c42c3e121188c8de34b79ad5eb0e0390eb4d59f2b7f0224b58679459bec0c4d677dec6ea9
+r-cran-RColorBrewer-checksum = 62aae85a0cf349a58ff51922886f71e2a9dc7b9548b061390f3b370f240bcec72340b3ebc03077a0374ce18ccf16121247e0500eca875ef2ab2f755c809e8f28
+r-cran-rlang-checksum = 8dc647e59dc767471345f9cfda7b77316215b0bf5a96e28f63e216d80f239ba9ed260b90926d175080e256d645f9a1b621d7602bfe27c32d0151758753b6cac8
+r-cran-scales-checksum = a1c693f993010613a33b9a165d5f853ad5f4fbbd790deae2bd5b19adc6ea0adbf27962e0f56807297ec56a71a6a5f57e3aa0ef78c266e74dc600da34c24d16e8
+r-cran-tibble-checksum = 4a4953b9083064ba10e240e304617f0b2c65039eb188f56761cfac228e99186054b543aef045607b63e5ebf9da2d20255f0ae724fd974c497507706d21a92864
+r-cran-utf8-checksum = 51b98a3fd07dd82fba249ff78f6e8b1318592151be49f1fe98c061051dca4d4506f7c7c8f1ebccadab4312cef7e01f700b39f4d5a6ba0b7227acd27e028f515d
+r-cran-vctrs-checksum = 23cde893f027f876f37b704a5074fafbbc376b85a053ccdc2862a3e6dc0b68ae2ac3511e2c61ad7a0a0d55524d3f3b724f39a4eeaf1a855ace62634ddea04b4f
+r-cran-viridisLite-checksum = f59a771b4cdca74df641c936812a008bdec99578cd1c82ee8f3119087dbdc72e307b2f3093df971ee7166c010a246fb5ef6c05cec4e51f7cfe721f3343e0fd6a
+r-cran-withr-checksum = 97877fa1ec21244285366818ad51dbe9c5086b377c1217d4ffc250a1f83cd142cc28d35f9aac0527f26bb2e3f0b399537b386a27de2fe546c301029f59614f65
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 f1454c0..4dfb407 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) 2021 Boud Roukema <boud@cosmo.torun.pl>
-# Copyright (C) 2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2022 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2021-2022 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 2cca87a..ff3dad0 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
@@ -12,13 +12,15 @@
 # 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.
+#
+# fancyvrb: Needed by R.
 texlive-packages = tex fancyhdr ec newtx fontaxes xkeyval etoolbox xstring \
                    xcolor setspace caption footmisc datetime fmtcount \
                    titlesec preprint ulem biblatex biber logreq pgf pgfplots \
                    fp courier tex-gyre txfonts times csquotes kastrup \
                    trimspaces pdftexcmds pdfescape letltxmacro bitset \
-                   mweights
+                   mweights fancyvrb
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..575cdd6 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -1,7 +1,7 @@
 # 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>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -15,47 +15,47 @@
 # 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 = 9.0
+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 = 2.34.0
+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 +67,16 @@ 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 +86,103 @@ 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 = 27.2
+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 +191,7 @@ hdf5-version = 1.10.5
 
 
 
+
 # Python packages
 # ---------------
 #
@@ -194,65 +199,151 @@ 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
+
+# XLSX I/O (until version 0.2.29) crashes during compilation with GCC
+# 11.1.0, so we are temporarily commenting it.
+#xlsxio-version = 0.2.21
+
+# 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)
diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md
index 8d12d7a..76ab5c1 100644
--- a/reproduce/software/make/README.md
+++ b/reproduce/software/make/README.md
@@ -1,7 +1,7 @@
 Software building instructions
 ------------------------------
 
-Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
+Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
 See the end of the file for license conditions.
 
 This directory contains Makefiles that are called by the high-level
diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk
index e782578..b92fbfc 100644
--- a/reproduce/software/make/atlas-multiple.mk
+++ b/reproduce/software/make/atlas-multiple.mk
@@ -3,12 +3,12 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run during the initial `./project configure'
+# This Makefile will be run during the initial './project configure'
 # script. It is not included into the reproduction pipe after that.
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
diff --git a/reproduce/software/make/atlas-single.mk b/reproduce/software/make/atlas-single.mk
index 0934b66..720bad6 100644
--- a/reproduce/software/make/atlas-single.mk
+++ b/reproduce/software/make/atlas-single.mk
@@ -3,12 +3,12 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run during the initial `./project configure'
+# This Makefile will be run during the initial './project configure'
 # script. It is not included into the reproduction pipe after that.
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 6910593..1c96b3f 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -4,7 +4,7 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run by the initial `./project configure' script. It
+# This Makefile will be run by the initial './project configure' script. It
 # is not included into the project afterwards.
 #
 # This Makefile builds low-level and basic tools that are necessary in any
@@ -21,8 +21,9 @@
 #
 # ------------------------------------------------------------------------
 #
-# 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>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -90,17 +91,20 @@ export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) \
                    -Wno-nullability-completeness
 export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
 
+# Disable built-in rules (which are not needed here!)
+.SUFFIXES:
+
 # This is the "basic" tools where we are relying on the host operating
 # system, but are slowly populating our basic software envirnoment. To run
-# (system or template) programs, `LD_LIBRARY_PATH' is necessary, so here,
+# (system or template) programs, 'LD_LIBRARY_PATH' is necessary, so here,
 # we'll first tell the programs to look into any possible pre-defined
-# `LD_LIBRARY_PATH', then we'll add our own newly installed libraries.  We
+# 'LD_LIBRARY_PATH', then we'll add our own newly installed libraries.  We
 # will also make sure that there is no "current directory" in it (by
-# removing a starting or trailing `:' and any occurance of `::'.
+# removing a starting or trailing ':' and any occurance of '::'.
 export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \
                                   | sed -e's/::/:/g' -e's/^://' -e's/:$$//')
 
-# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
+# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
 # ultimately redundant. But on some systems, even having a single value
 # causes crashs (see bug #56682). So we'll just give it no value at all.
 export DYLD_LIBRARY_PATH :=
@@ -150,10 +154,10 @@ backupservers = $(filter-out $(topbackupserver),$(backupservers_all))
 #
 # About ccache: ccache acts like a wrapper over the C compiler and is made
 # to avoid/speed-up compiling of identical files in a system (it is
-# commonly used on large servers). It actually makes `gcc' or `g++' a
+# commonly used on large servers). It actually makes 'gcc' or 'g++' a
 # symbolic link to itself so it can control them internally. So, for our
 # purpose here, it is very annoying and can cause many complications. We
-# thus remove any part of PATH of that has `ccache' in it before making
+# thus remove any part of PATH of that has 'ccache' in it before making
 # symbolic links to the programs we are not building ourselves.
 #
 # The double quotations after the starting 'export PATH' are necessary in
@@ -172,9 +176,9 @@ makelink = origpath="$$PATH"; \
 	                     | tr '\n' :)"; \
 	if type $(1) > /dev/null 2> /dev/null; then \
 	  if [ x$(3) = x ]; then \
-	    ln -sf "$$(realpath $$(which $(1)))" $(ibdir)/$(1); \
+	    ln -sf "$$(realpath $$(command -v $(1)))" $(ibdir)/$(1); \
 	  else \
-	    ln -sf "$$(realpath $$(which $(1)))" $(ibdir)/$(3); \
+	    ln -sf "$$(realpath $$(command -v $(1)))" $(ibdir)/$(3); \
 	  fi; \
 	else \
 	  if [ "x$(strip $(2))" = xmandatory ]; then \
@@ -189,11 +193,11 @@ $(ibdir) $(ildir):; mkdir $@
 $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
                            | $(ibdir) $(ildir)
 
-        # Hardware specific
+#	Hardware specific
 	$(call makelink,lp)    # For printing, necessary for R.
 	$(call makelink,lpr)   # For printing, necessary for R.
 
-        # Mac OS specific
+#	Mac OS specific
 	$(call makelink,mig)
 	$(call makelink,xcrun)
 	$(call makelink,sysctl)
@@ -201,14 +205,14 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
 	$(call makelink,dsymutil)
 	$(call makelink,install_name_tool)
 
-        # On Mac OS, libtool is different compared to GNU Libtool. The
-        # libtool we'll build in the high-level dependencies has the
-        # executable name `glibtool'.
+#	On Mac OS, libtool is different compared to GNU Libtool. The
+#	libtool we'll build in the high-level dependencies has the
+#	executable name 'glibtool'.
 	$(call makelink,libtool)
 
-        # Necessary libraries:
-        #   Libdl (for dynamic loading libraries at runtime)
-        #   POSIX Threads library for multi-threaded programs.
+#	Necessary libraries:
+#	    Libdl (for dynamic loading libraries at runtime)
+#	    POSIX Threads library for multi-threaded programs.
 	for l in dl pthread; do
 	  if [ -f /usr/lib/lib$$l.a ]; then
 	    for f in /usr/lib/lib$$l.*; do
@@ -218,8 +222,8 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
 	  fi
 	done
 
-        # We want this to be empty (so it doesn't interefere with the other
-        # files in `ibidir'.
+#	We want this to be empty (so it doesn't interefere with the other
+#	files in 'ibidir'.
 	touch $@
 
 
@@ -249,26 +253,26 @@ $(ibidir)/gzip-$(gzip-version): | $(ibdir) $(ildir) $(lockdir)
 	echo "GNU Gzip $(gzip-version)" > $@
 
 $(ibidir)/xz-$(xz-version): $(ibidir)/gzip-$(gzip-version)
-	tarball=xz-$(xz-version).tar.gz
+	tarball=xz-$(xz-version).tar.lz
 	$(call import-source, $(xz-url), $(xz-checksum))
 	$(call gbuild, xz-$(xz-version), static)
 	echo "XZ Utils $(xz-version)" > $@
 
 $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
 
-        # Download the tarball.
-	tarball=bzip2-$(bzip2-version).tar.gz
+#	Download the tarball.
+	tarball=bzip2-$(bzip2-version).tar.lz
 	$(call import-source, $(bzip2-url), $(bzip2-checksum))
 
-        # Bzip2 doesn't have a `./configure' script, and its Makefile
-        # doesn't build a shared library. So we can't use the `gbuild'
-        # function here and we need to take some extra steps (inspired
-        # from the GNU/Linux from Scratch (LFS) guide for Bzip2):
-        #   1) The `sed' call is for relative installed symbolic links.
-        #   2) The special Makefile-libbz2_so builds shared libraries.
-        #
-        # NOTE: the major version number appears in the final symbolic
-        # link.
+#	Bzip2 doesn't have a './configure' script, and its Makefile doesn't
+#	build a shared library. So we can't use the 'gbuild' function here
+#	and we need to take some extra steps (inspired from the GNU/Linux
+#	from Scratch (LFS) guide for Bzip2):
+#
+#	    1) The 'sed' call is for relative installed symbolic links.
+#	    2) The special Makefile-libbz2_so builds shared libraries.
+#
+#	NOTE: the major version number appears in the final symbolic link.
 	tdir=bzip2-$(bzip2-version)
 	if [ $(static_build) = yes ]; then
 	  makecommand="make LDFLAGS=-static"
@@ -283,7 +287,7 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
 	fi
 	cd $(ddir)
 	rm -rf $$tdir
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd $$tdir
 	sed -e 's@\(ln -s -f \)$$(PREFIX)/bin/@\1@' Makefile \
 	    > Makefile.sed
@@ -296,14 +300,13 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
 	cd ..
 	rm -rf $$tdir
 	cd $(ildir)
-	ln -fs libbz2.so.1.0 libbz2.so
+	ln -fs libbz2.so.$(bzip2-version) libbz2.so
 	echo "Bzip2 $(bzip2-version)" > $@
 
 $(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
-	tarball=unzip-$(unzip-version).tar.gz
-	v=$$(echo $(unzip-version) | sed -e's/\.//')
+	tarball=unzip-$(unzip-version).tar.lz
 	$(call import-source, $(unzip-url), $(unzip-checksum))
-	$(call gbuild, unzip$$v, static,, \
+	$(call gbuild, unzip-$(unzip-version), static,, \
 	               -f unix/Makefile generic \
 	               CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
 	               -f unix/Makefile generic \
@@ -311,10 +314,9 @@ $(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
 	echo "Unzip $(unzip-version)" > $@
 
 $(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
-	tarball=zip-$(zip-version).tar.gz
-	v=$$(echo $(zip-version) | sed -e's/\.//')
+	tarball=zip-$(zip-version).tar.lz
 	$(call import-source, $(zip-url), $(zip-checksum))
-	$(call gbuild, zip$$v, static,, \
+	$(call gbuild, zip-$(zip-version), static,, \
 	               -f unix/Makefile generic \
 	               CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
 	               -f unix/Makefile generic \
@@ -324,10 +326,10 @@ $(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
 # Some programs (like Wget and CMake) that use zlib need it to be dynamic
 # so they use our custom build. So we won't force a static-only build.
 #
-# Note for a static-only build: Zlib's `./configure' doesn't use Autoconf's
-# configure script, it just accepts a direct `--static' option.
+# Note for a static-only build: Zlib's './configure' doesn't use Autoconf's
+# configure script, it just accepts a direct '--static' option.
 $(ibidir)/zlib-$(zlib-version): $(ibidir)/gzip-$(gzip-version)
-	tarball=zlib-$(zlib-version).tar.gz
+	tarball=zlib-$(zlib-version).tar.lz
 	$(call import-source, $(zlib-url), $(zlib-checksum))
 	$(call gbuild, zlib-$(zlib-version))
 	echo "Zlib $(zlib-version)" > $@
@@ -344,11 +346,12 @@ $(ibidir)/tar-$(tar-version): \
               $(ibidir)/zlib-$(zlib-version) \
               $(ibidir)/bzip2-$(bzip2-version) \
               $(ibidir)/unzip-$(unzip-version)
-        # Since all later programs depend on Tar, the configuration will be
-        # stuck here, only making Tar. So its more efficient to built it on
-        # multiple threads (when the user's Make doesn't pass down the
-        # number of threads).
-	tarball=tar-$(tar-version).tar.gz
+
+#	Since all later programs depend on Tar, the configuration will hit
+#	a bottleneck here: only making Tar. So its more efficient to built
+#	it on multiple threads (even when the user's Make doesn't pass down
+#	the number of threads).
+	tarball=tar-$(tar-version).tar.lz
 	$(call import-source, $(tar-url), $(tar-checksum))
 	$(call gbuild, tar-$(tar-version), , , -j$(numthreads) V=1)
 	echo "GNU Tar $(tar-version)" > $@
@@ -370,7 +373,7 @@ $(ibidir)/tar-$(tar-version): \
 # a prerequisite (and forgetting in others causing bugs), we'll put it as a
 # dependancy of 'tar'.
 $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version)
-	tarball=patchelf-$(patchelf-version).tar.gz
+	tarball=patchelf-$(patchelf-version).tar.lz
 	$(call import-source, $(patchelf-url), $(patchelf-checksum))
 	if [ x$(on_mac_os) = xyes ]; then
 	  echo "" > $@
@@ -395,69 +398,69 @@ $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version)
 # basic dependencies.
 #
 # Unfortunately Make needs dynamic linking in two instances: when loading
-# objects (dynamically linked libraries), or when using the `getpwnam'
+# objects (dynamically linked libraries), or when using the 'getpwnam'
 # function (for tilde expansion). The first can be disabled with
-# `--disable-load', but unfortunately I don't know any way to fix the
+# '--disable-load', but unfortunately I don't know any way to fix the
 # second. So, we'll have to build it dynamically for now.
 $(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version)
-	tarball=ncurses-$(ncurses-version).tar.gz
+	tarball=ncurses-$(ncurses-version).tar.lz
 	$(call import-source, $(ncurses-url), $(ncurses-checksum))
 
-        # Delete the library that will be installed (so we can make sure
-        # the build process completed afterwards and reset the links).
+#	Delete the library that will be installed (so we can make sure the
+#	build process completed afterwards and reset the links).
 	rm -f $(ildir)/libncursesw*
 
-        # Delete the (possibly existing) low-level programs that depend on
-        # `readline', and thus `ncurses'. Since these programs are actually
-        # used during the building of `ncurses', we need to delete them so
-        # the build process doesn't use the project's Bash and AWK, but the
-        # host's.
+#	Delete the (possibly existing) low-level programs that depend on
+#	'readline', and thus 'ncurses'. Since these programs are actually
+#	used during the building of 'ncurses', we need to delete them so
+#	the build process doesn't use the project's Bash and AWK, but the
+#	host's.
 	rm -f $(ibdir)/bash* $(ibdir)/awk* $(ibdir)/gawk*
 
-        # Standard build process.
+#	Standard build process.
 	$(call gbuild, ncurses-$(ncurses-version), static, \
 	               --with-shared --enable-rpath --without-normal \
 	               --without-debug --with-cxx-binding \
 	               --with-cxx-shared --enable-widec --enable-pc-files \
 	               --with-pkg-config=$(ildir)/pkgconfig, -j$(numthreads))
 
-        # Unfortunately there are many problems with `ncurses' using
-        # "normal" (or 8-bit) characters. The standard way that will work
-        # is to build it with wide character mode as you see above in the
-        # configuration (or the `w' prefix you see below). Also, most
-        # programs (and in particular Bash and AWK), first look for other
-        # (mostly obsolete) libraries like tinfo, which define the same
-        # symbols. The links below address both situations: we need to fool
-        # higher-level packages to find this library even if they aren't
-        # explicitly mentioning its name correctly (as a value to `-l' at
-        # link time in their configure scripts).
-        #
-        # This part is taken from the Arch GNU/Linux build script[1], then
-        # extended to Mac thanks to Homebrew's script [2].
-        #
-        # [1] https://git.archlinux.org/svntogit/packages.git/tree/trunk/PKGBUILD?h=packages/ncurses
-        # [2] https://github.com/Homebrew/homebrew-core/blob/master/Formula/ncurses.rb
-        #
-        # Since we can't have comments, in the connected script, here is a
-        # summary:
-        #
-        #   1. We find the actual suffix of the library, from the file that
-        #      is not a symbolic link (starting with `-' in the output of
-        #      `ls -l').
-        #
-        #   2. We make symbolic links to all the "ncurses", "ncurses++",
-        #      "form", "panel" and "menu" libraries to point to their
-        #      "wide" (character) library.
-        #
-        #   3. We make symbolic links to the "tic" and "tinfo" libraries to
-        #      point to the same `libncursesw' library.
-        #
-        #   4. Some programs link with "curses" (not "ncurses", notice the
-        #      starting "n"), so we'll also make links for these to point
-        #      to the `libncursesw' library.
-        #
-        #   5. A link is made to also be able to include files from the
-        #      `ncurses' headers.
+#	Unfortunately there are many problems with 'ncurses' using "normal"
+#	(or 8-bit) characters. The standard way that will work is to build
+#	it with wide character mode as you see above in the configuration
+#	(or the 'w' prefix you see below). Also, most programs (and in
+#	particular Bash and AWK), first look for other (mostly obsolete)
+#	libraries like tinfo, which define the same symbols. The links
+#	below address both situations: we need to fool higher-level
+#	packages to find this library even if they aren't explicitly
+#	mentioning its name correctly (as a value to '-l' at link time in
+#	their configure scripts).
+#
+#	This part is taken from the Arch GNU/Linux build script[1], then
+#	extended to Mac thanks to Homebrew's script [2].
+#
+#	   [1] https://git.archlinux.org/svntogit/packages.git/tree/trunk/PKGBUILD?h=packages/ncurses
+#	   [2] https://github.com/Homebrew/homebrew-core/blob/master/Formula/ncurses.rb
+#
+#	Since we can't have comments, in the connected script, here is a
+#	summary:
+#
+#	  1. We find the actual suffix of the library, from the file that
+#	     is not a symbolic link (starting with '-' in the output of 'ls
+#	     -l').
+#
+#	  2. We make symbolic links to all the "ncurses", "ncurses++",
+#	     "form", "panel" and "menu" libraries to point to their "wide"
+#	     (character) library.
+#
+#	  3. We make symbolic links to the "tic" and "tinfo" libraries to
+#	     point to the same 'libncursesw' library.
+#
+#	  4. Some programs link with "curses" (not "ncurses", notice the
+#	     starting "n"), so we'll also make links for these to point to
+#	     the 'libncursesw' library.
+#
+#	  5. A link is made to also be able to include files from the
+#            'ncurses' headers.
 	if [ x$(on_mac_os) = xyes ]; then so="dylib"; else so="so"; fi
 	if [ -f $(ildir)/libncursesw.$$so ]; then
 
@@ -489,7 +492,7 @@ $(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version)
 
 $(ibidir)/readline-$(readline-version): \
                    $(ibidir)/ncurses-$(ncurses-version)
-	tarball=readline-$(readline-version).tar.gz
+	tarball=readline-$(readline-version).tar.lz
 	$(call import-source, $(readline-url), $(readline-checksum))
 	$(call gbuild, readline-$(readline-version), static, \
 	               --with-curses --disable-install-examples, \
@@ -497,12 +500,12 @@ $(ibidir)/readline-$(readline-version): \
 	echo "GNU Readline $(readline-version)" > $@
 
 
-# IMPORTANT: Even though we have enabled `rpath', Bash doesn't write the
+# IMPORTANT: Even though we have enabled 'rpath', Bash doesn't write the
 # absolute adddress of the libraries it depends on! Therefore, if we
-# configure Bash with `--with-installed-readline' (so the installed version
+# configure Bash with '--with-installed-readline' (so the installed version
 # of Readline, that we build below as a prerequisite or AWK, is used) and
-# you run `ldd $(ibdir)/bash' on the resulting binary, it will say that it
-# is linking with the system's `readline'. But if you run that same command
+# you run 'ldd $(ibdir)/bash' on the resulting binary, it will say that it
+# is linking with the system's 'readline'. But if you run that same command
 # within a rule in this project, you'll see that it is indeed linking with
 # our own built readline.
 #
@@ -510,11 +513,11 @@ $(ibidir)/readline-$(readline-version): \
 # released as patches. Therefore we'll need to make our own fully-working
 # and updated tarball to build the proper version of Bash. You download and
 # apply them to the original tarball and make a new one with the following
-# series of commands (just replace `NUMBER' with the total number of
+# series of commands (just replace 'NUMBER' with the total number of
 # patches that you want to apply).
 #
 #   $ number=NUMBER
-#   $ tar xf bash-5.0.tar.gz
+#   $ tar -xf bash-5.0.tar.gz
 #   $ cd bash-5.0
 #   $ for i in $(seq 1 $number); do \
 #       pname=bash50-$(printf "%03d" $i); \
@@ -530,18 +533,18 @@ $(ibidir)/bash-$(bash-version): \
                $(ibidir)/gettext-$(gettext-version) \
                $(ibidir)/readline-$(readline-version)
 
-        # Download the tarball.
+#	Download the tarball.
 	tarball=bash-$(bash-version).tar.lz
 	$(call import-source, $(bash-url), $(bash-checksum))
 
-        # Delete the (possibly) existing Bash executable in the project,
-        # let it use the default shell of the host.
+#	Delete the (possibly) existing Bash executable in the project,
+#	let it use the default shell of the host.
 	rm -f $(ibdir)/bash
 
-        # Bash has many `--enable' features which are already enabled by
-        # default. As described in the manual, they are mainly useful when
-        # you disable them all with `--enable-minimal-config' and enable a
-        # subset using the `--enable' options.
+#	Bash has many '--enable' features which are already enabled by
+#	default. As described in the manual, they are mainly useful when
+#	you disable them all with '--enable-minimal-config' and enable a
+#	subset using the '--enable' options.
 	if [ "x$(static_build)" = xyes ]; then stopt="--enable-static-link"
 	else                                   stopt=""
 	fi;
@@ -554,22 +557,20 @@ $(ibidir)/bash-$(bash-version): \
 	               --with-curses=yes, \
 	               -j$(numthreads))
 
-        # Atleast on GNU/Linux systems, Bash doesn't include RPATH by
-        # default. So, we have to manually include it, currently we are
-        # only doing this on GNU/Linux systems (using the `patchelf'
-        # program).
+#	Atleast on GNU/Linux systems, Bash doesn't include RPATH by
+#	default. So, we have to manually include it, currently we are only
+#	doing this on GNU/Linux systems (using the 'patchelf' program).
 	if [ -f $(ibdir)/patchelf ]; then
 	  $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/bash;
 	fi
 
-        # To be generic, some systems use the `sh' command to call the
-        # shell. By convention, `sh' is just a symbolic link to the
-        # preferred shell executable. So we'll define `$(ibdir)/sh' as a
-        # symbolic link to the Bash that we just built and installed.
-        #
-        # Just to be sure that the installation step above went well,
-        # before making the link, we'll see if the file actually exists
-        # there.
+#	To be generic, some systems use the 'sh' command to call the
+#	shell. By convention, 'sh' is just a symbolic link to the preferred
+#	shell executable. So we'll define '$(ibdir)/sh' as a symbolic link
+#	to the Bash that we just built and installed.
+#
+#	Just to be sure that the installation step above went well, before
+#	making the link, we'll see if the file actually exists there.
 	ln -fs $(ibdir)/bash $(ibdir)/sh
 	echo "GNU Bash $(bash-version)" > $@
 
@@ -585,9 +586,9 @@ $(ibidir)/bash-$(bash-version): \
 # Level 4: Most other programs
 # ----------------------------
 
-# In Perl, The `-shared' flag will cause problems while building on macOS,
+# In Perl, The '-shared' flag will cause problems while building on macOS,
 # so we'll only use this configuration option when we are GNU/Linux
-# systems. However, since the whole option must be used (which includes `='
+# systems. However, since the whole option must be used (which includes '='
 # and empty space), its easier to define the variable as a Make variable
 # outside the recipe, not as a shell variable inside it.
 ifeq ($(on_mac_os),yes)
@@ -596,7 +597,7 @@ else
 perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS"
 endif
 $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
-	tarball=perl-$(perl-version).tar.gz
+	tarball=perl-$(perl-version).tar.lz
 	$(call import-source, $(perl-url), $(perl-checksum))
 	major_version=$$(echo $(perl-version) \
 	                     | sed -e's/\./ /g' \
@@ -606,7 +607,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
 	                     | awk '{printf("%d.%d", $$1, $$2)}')
 	cd $(ddir)
 	rm -rf perl-$(perl-version)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd perl-$(perl-version)
 	./Configure -des \
 	            -Dusethreads \
@@ -616,7 +617,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
 	            -Dprivlib=$(idir)/share/perl$$major_version/core_perl \
 	            -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \
 	            -Dsitelib=$(idir)/share/perl$$major_version/site_perl \
-	            -Dsitearch=$(idir)/lib/perl$$major_version/$$basever/site_perl \
+	            -Dsitearch=$(idir)/lib/perl$$major_version/$$base_version/site_perl \
 	            -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \
 	            -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \
 	            -Dscriptdir=$(idir)/bin/core_perl \
@@ -642,17 +643,17 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
 # Coreutils
 # ---------
 #
-# For some reason, Coreutils doesn't include `rpath' in its installed
+# For some reason, Coreutils doesn't include 'rpath' in its installed
 # executables (even though it says that by default its included and that
-# even when calling `--enable-rpath=yes'). So we have to manually add
-# `rpath' to Coreutils' executables after the standard build is
+# even when calling '--enable-rpath=yes'). So we have to manually add
+# 'rpath' to Coreutils' executables after the standard build is
 # complete.
 #
 # One problem is that Coreutils installs many very basic executables which
 # might be in used by other programs. So we must make sure that when
 # Coreutils is being built, no other program is being built in
 # parallel. The solution to the many executables it installs is to make a
-# fake installation (with `DESTDIR'), and get a list of the contents of the
+# fake installation (with 'DESTDIR'), and get a list of the contents of the
 # directory to find the names.
 #
 # The echo after the PatchELF loop is to avoid a crash if the last
@@ -665,30 +666,30 @@ $(ibidir)/coreutils-$(coreutils-version): \
                     $(ibidir)/perl-$(perl-version) \
                     $(ibidir)/openssl-$(openssl-version)
 
-        # Import, unpack and enter the source directory.
-	tarball=coreutils-$(coreutils-version).tar.xz
+#	Import, unpack and enter the source directory.
+	tarball=coreutils-$(coreutils-version).tar.lz
 	$(call import-source, $(coreutils-url), $(coreutils-checksum))
 	cd $(ddir)
 	rm -rf coreutils-$(coreutils-version)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd coreutils-$(coreutils-version)
 
-        # Set the configure script to use our shell, note that we can't
-        # assume GNU SED here yet (it installs after Coreutils).
+#	Set the configure script to use our shell, note that we can't
+#	assume GNU SED here yet (it installs after Coreutils).
 	sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \
 	    -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \
 	    configure > configure-tmp
 	mv configure-tmp configure
 	chmod +x configure
 
-        # Configure, build and install Coreutils.
+#	Configure, build and install Coreutils.
 	./configure --prefix=$(idir) SHELL=$(ibdir)/bash  \
 	            LDFLAGS="$(LDFLAGS)" CPPFLAGS="$(CPPFLAGS)" \
 	            --disable-silent-rules --with-openssl=yes
 	make SHELL=$(ibdir)/bash -j$(numthreads)
 	make SHELL=$(ibdir)/bash install
 
-        # Fix RPATH if necessary.
+#	Fix RPATH if necessary.
 	if [ -f $(ibdir)/patchelf ]; then
 	  make SHELL=$(ibdir)/bash install DESTDIR=junkinst
 	  unalias ls || true # avoid decorated 'ls' commands with extra characters
@@ -699,12 +700,34 @@ $(ibidir)/coreutils-$(coreutils-version): \
 	  echo "PatchELF applied to all programs."
 	fi
 
-        # Come back up to the unpacking directory, delete the source
-        # directory and write the final target.
+#	Come back up to the unpacking directory, delete the source
+#	directory and write the final target.
 	cd ..
 	rm -rf coreutils-$(coreutils-version)
 	echo "GNU Coreutils $(coreutils-version)" > $@
 
+# Podlators
+#
+# POD is short for "Plain Old Documentation", that is the format used in
+# Perl's documentation. Podlators provies two executables pod2man and
+# pod2text convert this into the roff format (used in man pages) or pod2 It
+# is used by some software like OpenSSL to create their man pages.
+$(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version)
+	tarball=podlators-$(podlators-version).tar.lz
+	$(call import-source, $(podlators-url), $(podlators-checksum))
+	cd $(ddir)
+	rm -rf podlators-$(podlators-version)
+	tar -xf $(tdir)/$$tarball
+	cd podlators-$(podlators-version)
+	perl Makefile.PL
+	make
+	make install
+	ln -sf $(ibdir)/site_perl/pod2man $(ibdir)/pod2man
+	ln -sf $(ibdir)/site_perl/pod2text $(ibdir)/pod2text
+	cd ..
+	rm -rf podlators-$(podlators-version)
+	echo "podlators $(podlators-version)" > $@
+
 # OpenSSL
 #
 # Until we find a nice and generic way to create an updated CA file in the
@@ -712,26 +735,26 @@ $(ibidir)/coreutils-$(coreutils-version): \
 # along with the other tarballs.
 $(idir)/etc:; mkdir $@
 $(idir)/etc/ssl: | $(idir)/etc; mkdir $@
-$(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \
+$(ibidir)/openssl-$(openssl-version): $(ibidir)/podlators-$(podlators-version) \
                   | $(idir)/etc/ssl
 
-        # First download the certificates and copy them into the
-        # installation directory.
-	tarball=cert.pem
+#	First download the certificates and copy them into the
+#	installation directory.
+	tarball=cert.pem-$(certpem-version)
 	$(call import-source, $(cert-url), $(cert-checksum))
-	cp $(tdir)/cert.pem $(idir)/etc/ssl/cert.pem
+	cp $(tdir)/cert.pem-$(certpem-version) $(idir)/etc/ssl/cert.pem
 
-        # Now download the OpenSSL tarball.
-	tarball=openssl-$(openssl-version).tar.gz
+#	Now download the OpenSSL tarball.
+	tarball=openssl-$(openssl-version).tar.lz
 	$(call import-source, $(openssl-url), $(openssl-checksum))
 
-        # According to OpenSSL's Wiki (link bellow), it can't automatically
-        # detect Mac OS's structure. It will need some help. So we'll use
-        # the `on_mac_os' Make variable that we defined in the configure
-        # script and help it with some extra configuration options and an
-        # environment variable.
-        #
-        # https://wiki.openssl.org/index.php/Compilation_and_Installation
+#	According to OpenSSL's Wiki (link bellow), it can't automatically
+#	detect Mac OS's structure. It will need some help. So we'll use the
+#	'on_mac_os' Make variable that we defined in the configure script
+#	and help it with some extra configuration options and an
+#	environment variable.
+#
+#	https://wiki.openssl.org/index.php/Compilation_and_Installation
 	if [ x$(on_mac_os) = xyes ]; then
 	  export KERNEL_BITS=64
 	  copt="shared no-ssl2 no-ssl3 enable-ec_nistp_64_gcc_128"
@@ -745,29 +768,19 @@ $(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \
 	               --with-zlib-include=$(idir)/include, \
 	               -j$(numthreads), , ./config )
 
-        # Manually insert RPATH inside the two created libraries.
+#	Manually insert RPATH inside the two created libraries.
 	if [ -f $(ibdir)/patchelf ]; then
 	   patchelf --set-rpath $(ildir) $(ildir)/libssl.so
 	   patchelf --set-rpath $(ildir) $(ildir)/libcrypto.so
 	fi
 
-        # Bug 58263 (https://savannah.nongnu.org/bugs/?58263): In OpenSSL
-        # Version 1.1.1a (also checked in 1.1.1g), `openssl/ec.h' fails to
-        # include `openssl/openconf.h' on some OSs. The SED hack below
-        # inserts a hardwired element of `openssl/openconf.h' that is
-        # needed to include sections of code `f` that are deprecated in
-        # 1.2.0, but not yet in 1.1.1. This problem may be solved in
-        # version 1.2.x, so please check again in that bug.
-	mv -v $(idir)/include/openssl/ec.h $(idir)/include/openssl/ec.h.orig
-	sed -e 's,\(# include .openssl/opensslconf\.h.\),\1\n#ifndef DEPRECATEDIN_1_2_0\n#define DEPRECATEDIN_1_2_0(f)   f;\n#endif\n,' \
-	   $(idir)/include/openssl/ec.h.orig > $(idir)/include/openssl/ec.h
-
-        # Build the final target.
+#	Build the final target.
 	echo "OpenSSL $(openssl-version)" > $@
 
 
 
 
+
 # Downloaders
 # -----------
 
@@ -776,13 +789,13 @@ $(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \
 # cURL can optionally link with many different network-related libraries on
 # the host system that we are not yet building in the template. Many of
 # these are not relevant to most science projects, so we are explicitly
-# using `--without-XXX' or `--disable-XXX' so cURL doesn't link with
+# using '--without-XXX' or '--disable-XXX' so cURL doesn't link with
 # them. Note that if it does link with them, the configuration will crash
 # when the library is updated/changed by the host, and the whole purpose of
 # this project is avoid dependency on the host as much as possible.
 $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
 
-	tarball=curl-$(curl-version).tar.gz
+	tarball=curl-$(curl-version).tar.lz
 	$(call import-source, $(curl-url), $(curl-checksum))
 
 	$(call gbuild, curl-$(curl-version), , \
@@ -812,8 +825,8 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
 # GNU Wget
 #
 # Note that on some systems (for example GNU/Linux) Wget needs to explicity
-# link with `libdl', but on others (for example Mac OS) it doesn't. We
-# check this at configure time and define the `needs_ldl' variable.
+# link with 'libdl', but on others (for example Mac OS) it doesn't. We
+# check this at configure time and define the 'needs_ldl' variable.
 #
 # Also note that since Wget needs to load outside libraries dynamically, it
 # gives a segmentation fault when built statically.
@@ -826,12 +839,12 @@ $(ibidir)/wget-$(wget-version): \
                $(ibidir)/libiconv-$(libiconv-version) \
                $(ibidir)/coreutils-$(coreutils-version)
 
-        # Download the tarball.
+#	Download the tarball.
 	tarball=wget-$(wget-version).tar.lz
 	$(call import-source, $(wget-url), $(wget-checksum))
 
-        # We need to explicitly disable `libiconv', because of the
-        # `pkg-config' and `libiconv' problem.
+#	We need to explicitly disable 'libiconv', because of the
+#	'pkg-config' and 'libiconv' problem.
 	libs="-pthread"
 	if [ x$(needs_ldl) = xyes ]; then libs="$$libs -ldl"; fi
 	$(call gbuild, wget-$(wget-version), , \
@@ -864,13 +877,13 @@ $(ibidir)/wget-$(wget-version): \
 # there is no access to the system's PATH.
 $(ibidir)/diffutils-$(diffutils-version): \
                     $(ibidir)/coreutils-$(coreutils-version)
-	tarball=diffutils-$(diffutils-version).tar.xz
+	tarball=diffutils-$(diffutils-version).tar.lz
 	$(call import-source, $(diffutils-url), $(diffutils-checksum))
 	$(call gbuild, diffutils-$(diffutils-version), static,,V=1)
 	echo "GNU Diffutils $(diffutils-version)" > $@
 
 $(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version)
-	tarball=file-$(file-version).tar.gz
+	tarball=file-$(file-version).tar.lz
 	$(call import-source, $(file-url), $(file-checksum))
 	$(call gbuild, file-$(file-version), static, \
 	               --disable-libseccomp, V=1)
@@ -878,7 +891,7 @@ $(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version)
 
 $(ibidir)/findutils-$(findutils-version): \
                     $(ibidir)/coreutils-$(coreutils-version)
-	tarball=findutils-$(findutils-version).tar.xz
+	tarball=findutils-$(findutils-version).tar.lz
 	$(call import-source, $(findutils-url), $(findutils-checksum))
 	$(call gbuild, findutils-$(findutils-version), static,,V=1)
 	echo "GNU Findutils $(findutils-version)" > $@
@@ -888,19 +901,19 @@ $(ibidir)/gawk-$(gawk-version): \
                $(ibidir)/mpfr-$(mpfr-version) \
                $(ibidir)/coreutils-$(coreutils-version)
 
-        # Download the tarball.
+#	Download the tarball.
 	tarball=gawk-$(gawk-version).tar.lz
 	$(call import-source, $(gawk-url), $(gawk-checksum))
 
-        # AWK doesn't include RPATH by default, so we'll have to manually
-        # include it using the `patchelf' program (which was a dependency
-        # of Bash). Just note that AWK produces two executables (for
-        # example `gawk-4.2.1' and `gawk') and a symbolic link `awk' to one
-        # of those executables.
+#	AWK doesn't include RPATH by default, so we'll have to manually
+#	include it using the 'patchelf' program (which was a dependency of
+#	Bash). Just note that AWK produces two executables (for example
+#	'gawk-4.2.1' and 'gawk') and a symbolic link 'awk' to one of those
+#	executables.
 	$(call gbuild, gawk-$(gawk-version), static, \
 	               --with-readline=$(idir))
 
-        # Correct the RPATH on systems that have installed patchelf.
+#	Correct the RPATH on systems that have installed patchelf.
 	if [ -f $(ibdir)/patchelf ]; then
 	  if [ -f $(ibdir)/gawk ]; then
 	    $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/gawk
@@ -911,31 +924,31 @@ $(ibidir)/gawk-$(gawk-version): \
 	  fi
 	fi
 
-        # Build final target.
+#	Build final target.
 	echo "GNU AWK $(gawk-version)" > $@
 
 $(ibidir)/libiconv-$(libiconv-version): \
                    $(ibidir)/pkg-config-$(pkgconfig-version)
-	tarball=libiconv-$(libiconv-version).tar.gz
+	tarball=libiconv-$(libiconv-version).tar.lz
 	$(call import-source, $(libiconv-url), $(libiconv-checksum))
 	$(call gbuild, libiconv-$(libiconv-version), static)
 	echo "GNU libiconv $(libiconv-version)" > $@
 
 $(ibidir)/libunistring-$(libunistring-version): \
                        $(ibidir)/libiconv-$(libiconv-version)
-	tarball=libunistring-$(libunistring-version).tar.xz
+	tarball=libunistring-$(libunistring-version).tar.lz
 	$(call import-source, $(libunistring-url), $(libunistring-checksum))
 	$(call gbuild, libunistring-$(libunistring-version), static,, \
 	               -j$(numthreads))
 	echo "GNU libunistring $(libunistring-version)" > $@
 
 $(ibidir)/libxml2-$(libxml2-version): $(ibidir)/patchelf-$(patchelf-version)
-        # The libxml2 tarball also contains Python bindings which are built
-        # and installed to a system directory by default. If you don't need
-        # the Python bindings, the easiest solution is to compile without
-        # Python support: `./configure --without-python'. If you really need
-        # the Python bindings, use `--with-python-install-dir=DIR' instead.
-	tarball=libxml2-$(libxml2-version).tar.gz
+#	The libxml2 tarball also contains Python bindings which are built
+#	and installed to a system directory by default. If you don't need
+#	the Python bindings, the easiest solution is to compile without
+#	Python support: './configure --without-python'. If you really need
+#	the Python bindings, use '--with-python-install-dir=DIR' instead.
+	tarball=libxml2-$(libxml2-version).tar.lz
 	$(call import-source, $(libxml2-url), $(libxml2-checksum))
 	$(call gbuild, libxml2-$(libxml2-version), static, \
 	               --without-python, V=1)
@@ -958,7 +971,7 @@ $(ibidir)/git-$(git-version): \
               $(ibidir)/curl-$(curl-version) \
               $(ibidir)/gettext-$(gettext-version) \
               $(ibidir)/libiconv-$(libiconv-version)
-	tarball=git-$(git-version).tar.xz
+	tarball=git-$(git-version).tar.lz
 	if [ x$(on_mac_os) = xyes ]; then
 	  export LDFLAGS="$$LDFLAGS -lcharset"
 	fi
@@ -982,7 +995,7 @@ $(ibidir)/gmp-$(gmp-version): \
 # and generally to view large files easily when the project is built in a
 # container with a minimal OS.
 $(ibidir)/less-$(less-version): $(ibidir)/ncurses-$(ncurses-version)
-	tarball=less-$(less-version).tar.gz
+	tarball=less-$(less-version).tar.lz
 	$(call import-source, $(less-url), $(less-checksum))
 	$(call gbuild, less-$(less-version), static,,-j$(numthreads))
 	if [ -f $(ibdir)/patchelf ]; then
@@ -991,9 +1004,9 @@ $(ibidir)/less-$(less-version): $(ibidir)/ncurses-$(ncurses-version)
 	echo "Less $(less-version)" > $@
 
 # On Mac OS, libtool does different things, so to avoid confusion, we'll
-# prefix GNU's libtool executables with `glibtool'.
+# prefix GNU's libtool executables with 'glibtool'.
 $(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version)
-	tarball=libtool-$(libtool-version).tar.xz
+	tarball=libtool-$(libtool-version).tar.lz
 	$(call import-source, $(libtool-url), $(libtool-checksum))
 	$(call gbuild, libtool-$(libtool-version), static, \
                        --program-prefix=g, V=1 -j$(numthreads))
@@ -1001,162 +1014,44 @@ $(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version)
 	echo "GNU Libtool $(libtool-version)" > $@
 
 $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version)
-	tarball=grep-$(grep-version).tar.xz
+	tarball=grep-$(grep-version).tar.lz
 	$(call import-source, $(grep-url), $(grep-checksum))
 	$(call gbuild, grep-$(grep-version), static,,V=1)
 	echo "GNU Grep $(grep-version)" > $@
 
-$(ibidir)/libbsd-$(libbsd-version): $(ibidir)/coreutils-$(coreutils-version)
-	tarball=libbsd-$(libbsd-version).tar.xz
-	$(call import-source, $(libbsd-url), $(libbsd-checksum))
-	if [ x$(on_mac_os) = xyes ]; then
-	  echo "" > $@
-	else
-	  $(call gbuild, libbsd-$(libbsd-version), static,,V=1)
-	  echo "Libbsd $(libbsd-version)" > $@
-	fi
-
-# We need to apply a patch to the M4 source to be used properly on macOS.
-# The patch [1] was inspired by Homebrew's build instructions [1].
-#
-# [1] https://raw.githubusercontent.com/macports/macports-ports/edf0ee1e2cf/devel/m4/files/secure_snprintf.patch
-# [2] https://github.com/Homebrew/homebrew-core/blob/master/Formula/m4.rb
-#
 # M4 doesn't depend on PatchELF, but just to be consistent with the
 # levels/phases introduced here (where the compressors are level 1,
 # PatchELF is level 2, and ...), we'll set it as a dependency.
 $(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version)
-	tarball=m4-$(m4-version).tar.gz
+	tarball=m4-$(m4-version).tar.lz
 	$(call import-source, $(m4-url), $(m4-checksum))
-	cd $(ddir)
-	unpackdir=m4-$(m4-version)
-	rm -rf $$unpackdir
-	tar xf $(tdir)/$$tarball
-	mv m4-* $$unpackdir
-	cd $$unpackdir
-	if [ x$(on_mac_os) = xyes ]; then
-	   sed 's|if !(((__GLIBC__ > 2|if !defined(__APPLE__) \&\& !(((__GLIBC__ > 2|' \
-	       lib/vasnprintf.c > lib/vasnprintf_edited.c
-	   mv lib/vasnprintf_edited.c lib/vasnprintf.c
-	fi
-	./configure --prefix=$(idir) LDFLAGS="$(LDFLAGS)" \
-	            CPPFLAGS="$(CPPFLAGS)"
-	make V=1 -j$(numthreads)
-	make V=1 install
-	cd ..
-	rm -rf $$unpackdir
+	$(call gbuild, m4-$(m4-version), static,,V=1)
 	echo "GNU M4 $(m4-version)" > $@
 
-# Metastore is used (through a Git hook) to restore the source modification
-# dates of files after a Git checkout. Another Git hook saves all file
-# metadata just before a commit (to allow restoration after a
-# checkout). Since this project is managed in Makefiles, file modification
-# dates are critical to not having to redo the whole analysis after
-# checking out between branches.
-#
-# Note that we aren't using the standard version of Metastore, but a fork
-# of it that is maintained in this repository:
-#    https://gitlab.com/makhlaghi/metastore-fork
-#
-# Note that the prerequisites `coreutils', `gawk' and `sed' are not
-# metastore oficial dependencies, but they are necessaries to run our steps
-# before and after the installation.
-#
-# Libbsd is not necessary on macOS systems, because macOS is already a
-# BSD-based distribution. But on GNU/Linux systems, it is necessary.
-$(ibidir)/metastore-$(metastore-version): \
-                    $(ibidir)/sed-$(sed-version) \
-                    $(ibidir)/git-$(git-version) \
-                    $(ibidir)/gawk-$(gawk-version) \
-                    $(ibidir)/libbsd-$(libbsd-version) \
-                    $(ibidir)/coreutils-$(coreutils-version)
-
-        # Download the tarball.
-	tarball=metastore-$(metastore-version).tar.gz
-	$(call import-source, $(metastore-url), $(metastore-checksum))
-
-        # Metastore doesn't have any `./configure' script. So we'll just
-        # call `pwd' as a place-holder for the `./configure' command.
-        #
-        # File attributes are also not available on some systems, since the
-        # main purpose here is modification dates (and not attributes),
-        # we'll also set the `NO_XATTR' flag.
-        #
-        # After installing Metastore, write the relevant hooks into this
-        # system's Git hooks, while setting the system-specific
-        # directories/files.
-        #
-        # Note that the metastore -O and -G options used in this template
-        # are currently only available in a fork of `metastore' hosted at:
-        # https://github.com/mohammad-akhlaghi/metastore
-        #
-        # Checking for presence of `.git'. When the project source is
-        # downloaded from a non-Git source (for example from arXiv), there
-        # is no `.git' directory to work with. So until we find a better
-        # solution, avoid the step to to add the Git hooks.
-	current_dir=$$(pwd); \
-	$(call gbuild, metastore-$(metastore-version), static,, \
-	               NO_XATTR=1 V=1,,pwd,PREFIX=$(idir))
-
-        # Correct RPATH when necessary.
-	if [ -f $(ibdir)/patchelf ]; then
-	  $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/metastore
-	fi
-
-        # If this project is being built in a directory version controlled
-        # by Git, copy the hooks into the Git configuation.
-	if [ -f $(ibdir)/metastore ]; then
-	  if [ -d .git ]; then
-	    user=$$(whoami)
-	    group=$$(groups | awk '{print $$1}')
-	    cd $$current_dir
-	    for f in pre-commit post-checkout; do
-	       sed -e's|@USER[@]|'$$user'|g' \
-	           -e's|@GROUP[@]|'$$group'|g' \
-	           -e's|@BINDIR[@]|$(ibdir)|g' \
-	           -e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \
-	           reproduce/software/shell/git-$$f > .git/hooks/$$f
-	       chmod +x .git/hooks/$$f
-	    done
-	  fi
-	  echo "Metastore (forked) $(metastore-version)" > $@
-	else
-	  echo; echo; echo
-	  echo "*****************"
-	  echo "metastore couldn't be installed!"
-	  echo
-	  echo "Its used for preserving timestamps on Git commits."
-	  echo "Its useful for development, not simple running of "
-	  echo "the project. So we won't stop the configuration "
-	  echo "because it wasn't built."
-	  echo "*****************"
-	  echo "" > $@
-	fi
-
 $(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version)
-	tarball=mpfr-$(mpfr-version).tar.xz
+	tarball=mpfr-$(mpfr-version).tar.lz
 	$(call import-source, $(mpfr-url), $(mpfr-checksum))
 	$(call gbuild, mpfr-$(mpfr-version), static, , , make check)
 	echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@
 
 $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version)
 
-        # Download the tarball.
-	tarball=pkg-config-$(pkgconfig-version).tar.gz
+#	Download the tarball.
+	tarball=pkg-config-$(pkgconfig-version).tar.lz
 	$(call import-source, $(pkgconfig-url), $(pkgconfig-checksum))
 
-        # An existing `libiconv' can cause a conflict with `pkg-config',
-        # this is why `libiconv' depends on `pkg-config'. On a clean build,
-        # `pkg-config' is built first. But when we don't have a clean build
-        # (and `libiconv' exists) there will be a problem. So before
-        # re-building `pkg-config', we'll remove any installation of
-        # `libiconv'.
+#	An existing 'libiconv' can cause a conflict with 'pkg-config', this
+#	is why 'libiconv' depends on 'pkg-config'. On a clean build,
+#	'pkg-config' is built first. But when we don't have a clean build
+#	(and 'libiconv' exists) there will be a problem. So before
+#	re-building 'pkg-config', we'll remove any installation of
+#	'libiconv'.
 	rm -f $(ildir)/libiconv* $(idir)/include/iconv.h
 
-        # Some Mac OS systems may have a version of the GNU C Compiler
-        # (GCC) installed that doesn't support some necessary features of
-        # building Glib (as part of pkg-config). So to be safe, for Mac
-        # systems, we'll make sure it will use LLVM's Clang.
+#	Some Mac OS systems may have a version of the GNU C Compiler (GCC)
+#	installed that doesn't support some necessary features of building
+#	Glib (as part of pkg-config). So to be safe, for Mac systems, we'll
+#	make sure it will use LLVM's Clang.
 	if [ x$(on_mac_os) = xyes ]; then export compiler="CC=clang"
 	else                              export compiler=""
 	fi
@@ -1166,7 +1061,7 @@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version
 	echo "pkg-config $(pkgconfig-version)" > $@
 
 $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version)
-	tarball=sed-$(sed-version).tar.xz
+	tarball=sed-$(sed-version).tar.lz
 	$(call import-source, $(sed-url), $(sed-checksum))
 	$(call gbuild, sed-$(sed-version), static,,V=1)
 	echo "GNU Sed $(sed-version)" > $@
@@ -1174,7 +1069,7 @@ $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version)
 $(ibidir)/texinfo-$(texinfo-version): \
                   $(ibidir)/perl-$(perl-version) \
                   $(ibidir)/gettext-$(gettext-version)
-	tarball=texinfo-$(texinfo-version).tar.xz
+	tarball=texinfo-$(texinfo-version).tar.lz
 	$(call import-source, $(texinfo-url), $(texinfo-checksum))
 	$(call gbuild, texinfo-$(texinfo-version), static)
 	if [ -f $(ibdir)/patchelf ]; then
@@ -1184,14 +1079,14 @@ $(ibidir)/texinfo-$(texinfo-version): \
 	echo "GNU Texinfo $(texinfo-version)" > $@
 
 $(ibidir)/which-$(which-version): $(ibidir)/coreutils-$(coreutils-version)
-	tarball=which-$(which-version).tar.gz
+	tarball=which-$(which-version).tar.lz
 	$(call import-source, $(which-url), $(which-checksum))
 	$(call gbuild, which-$(which-version), static)
 	echo "GNU Which $(which-version)" > $@
 
 # GNU ISL is necessary to build GCC.
 $(ibidir)/isl-$(isl-version): $(ibidir)/gmp-$(gmp-version)
-	tarball=isl-$(isl-version).tar.bz2
+	tarball=isl-$(isl-version).tar.lz
 	$(call import-source, $(isl-url), $(isl-checksum))
 	if [ $(host_cc) = 1 ]; then
 	  echo "" > $@
@@ -1203,7 +1098,7 @@ $(ibidir)/isl-$(isl-version): $(ibidir)/gmp-$(gmp-version)
 
 # GNU MPC is necessary to build GCC.
 $(ibidir)/mpc-$(mpc-version): $(ibidir)/mpfr-$(mpfr-version)
-	tarball=mpc-$(mpc-version).tar.gz
+	tarball=mpc-$(mpc-version).tar.lz
 	$(call import-source, $(mpc-url), $(mpc-checksum))
 	if [ $(host_cc) = 1 ]; then
 	  echo "" > $@
@@ -1226,33 +1121,34 @@ $(ibidir)/mpc-$(mpc-version): $(ibidir)/mpfr-$(mpfr-version)
 # -----------------------
 #
 # The installation of Binutils can cause problems during the build of other
-# programs (http://savannah.nongnu.org/bugs/?56294), but its necessary for
+# programs since it provides the linker that is used to build them
+# (http://savannah.nongnu.org/bugs/?56294). However, it is necessary for
 # GCC. Therefore, we'll set all other basic programs as Binutils
-# prerequisite and GCC (the final basic target) ultimately just depends on
-# Binutils.
+# prerequisites, so GCC (the almost-final basic target) ultimately just
+# depends on Binutils.
 $(ibidir)/binutils-$(binutils-version): \
-                   $(ibidir)/sed-$(sed-version) \
+                   $(ibidir)/git-$(git-version) \
                    $(ibidir)/isl-$(isl-version) \
                    $(ibidir)/mpc-$(mpc-version) \
-                   $(ibidir)/wget-$(wget-version) \
-                   $(ibidir)/grep-$(grep-version) \
+                   $(ibidir)/sed-$(sed-version) \
                    $(ibidir)/file-$(file-version) \
                    $(ibidir)/gawk-$(gawk-version) \
+                   $(ibidir)/grep-$(grep-version) \
+                   $(ibidir)/wget-$(wget-version) \
                    $(ibidir)/which-$(which-version) \
-                   $(ibidir)/texinfo-$(texinfo-version) \
                    $(ibidir)/libtool-$(libtool-version) \
-                   $(ibidir)/metastore-$(metastore-version) \
-                   $(ibidir)/findutils-$(findutils-version) \
+                   $(ibidir)/texinfo-$(texinfo-version) \
+                   $(ibidir)/coreutils-$(coreutils-version) \
                    $(ibidir)/diffutils-$(diffutils-version) \
-                   $(ibidir)/coreutils-$(coreutils-version)
+                   $(ibidir)/findutils-$(findutils-version)
 
-        # Download the tarball.
+#	Download the tarball.
 	tarball=binutils-$(binutils-version).tar.lz
 	$(call import-source, $(binutils-url), $(binutils-checksum))
 
-        # Binutils' assembler (`as') and linker (`ld') will conflict with
-        # other compilers. So if we don't build our own compiler, we'll use
-        # the host opertating system's equivalents by just making links.
+#	Binutils' assembler ('as') and linker ('ld') will conflict with
+#	other compilers. So if we don't build our own compiler, we'll use
+#	the host opertating system's equivalents by just making links.
 	if [ x$(on_mac_os) = xyes ]; then
 	  $(call makelink,as)
 	  $(call makelink,ar)
@@ -1264,20 +1160,20 @@ $(ibidir)/binutils-$(binutils-version): \
 	  echo "" > $@
 	else
 
-          # Build binutils with the standard 'gbuild' function.
+#	  Build binutils with the standard 'gbuild' function.
 	  $(call gbuild, binutils-$(binutils-version), static, \
 	                 --with-lib-path=$(sys_library_path), \
 	                 -j$(numthreads) )
 
-          # 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.
+#	  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)
@@ -1285,11 +1181,11 @@ $(ibidir)/binutils-$(binutils-version): \
 	    done
 	  fi
 
-          # Write the final target.
+#	  Write the final target.
 	  echo "GNU Binutils $(binutils-version)" > $@
 	fi
 
-# We are having issues with `libiberty' (part of GCC) on Mac. So for now,
+# We are having issues with 'libiberty' (part of GCC) on Mac. So for now,
 # GCC won't be built there. Since almost no natural science paper's
 # processing depends so strongly on the compiler used, for now, this isn't
 # a bad assumption, but we are indeed searching for a solution.
@@ -1298,7 +1194,7 @@ $(ibidir)/binutils-$(binutils-version): \
 # environment. So, we'll build GCC after building all the basic tools that
 # are often used in a configure and build scripts of GCC components.
 #
-# Objective C and Objective C++ is necessary for installing `matplotlib'.
+# Objective C and Objective C++ is necessary for installing 'matplotlib'.
 #
 # We are currently having problems installing GCC on macOS, so for the time
 # being, if the project is being run on a macOS, we'll just set a link.
@@ -1325,45 +1221,41 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	    echo; exit 1
 	}
 
-        # Download the tarball.
-	tarball=gcc-$(gcc-version).tar.xz
+#	Download the tarball.
+	tarball=gcc-$(gcc-version).tar.lz
 	$(call import-source, $(gcc-url), $(gcc-checksum))
 
-        # To avoid any previous build in '.local/bin' causing problems in
-        # this build/links of this GCC, we'll first delete all the possibly
-        # 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++'.
+#	To avoid any previous build in '.local/bin' causing problems in
+#	this build/links of this GCC, we'll first delete all the possibly
+#	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 -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*
 
-        # GCC builds is own libraries in '$(idir)/lib64'. But all other
-        # libraries are in '$(idir)/lib'. Since this project is only for a
-        # single architecture, we can trick GCC into building its libraries
-        # in '$(idir)/lib' by defining the '$(idir)/lib64' as a symbolic
-        # link to '$(idir)/lib'.
+#	Build (or set links) to GCC.
 	if [ $(host_cc) = 1 ]; then
 
-          # Put links to the host's tools in '.local/bin'. Note that some
-          # macOS systems have both a native clang *and* a GNU C Compiler
-          # (note that this is different from the "normal" macOS situation
-          # where 'gcc' actually points to clang, here we mean when 'gcc'
-          # is actually the GNU C Compiler).
-          #
-          # In such cases, the GCC isn't complete and using it will cause
-          # problems when building high-level tools (for example openBLAS,
-          # rpcsvc-proto, CMake, xlsxio, Python or Matplotlib among
-          # others). To avoid such situations macOSs are configured like
-          # this: we'll simply set 'gcc' to point to 'clang' and won't set
-          # 'gcc' to point to the system's 'gcc'.
-          #
-          # Also, note that LLVM's clang doesn't have a C Pre-Processor. So
-          # we will only put a link to the host's 'cpp' if the system is
-          # not macOS. On macOS systems that have a real GCC installed,
-          # having GNU CPP in the project build directory is known to cause
-          # problems with 'libX11'.
+#	  Put links to the host's tools in '.local/bin'. Note that some
+#	  macOS systems have both a native clang *and* a GNU C Compiler
+#	  (note that this is different from the "normal" macOS situation
+#	  where 'gcc' actually points to clang, here we mean when 'gcc' is
+#	  actually the GNU C Compiler).
+#
+#	  In such cases, the GCC isn't complete and using it will cause
+#	  problems when building high-level tools (for example openBLAS,
+#	  rpcsvc-proto, CMake, xlsxio, Python or Matplotlib among
+#	  others). To avoid such situations macOSs are configured like
+#	  this: we'll simply set 'gcc' to point to 'clang' and won't set
+#	  'gcc' to point to the system's 'gcc'.
+#
+#	  Also, note that LLVM's clang doesn't have a C Pre-Processor. So
+#	  we will only put a link to the host's 'cpp' if the system is not
+#	  macOS. On macOS systems that have a real GCC installed, having
+#	  GNU CPP in the project build directory is known to cause problems
+#	  with 'libX11'.
 	  $(call makelink,gfortran)
 	  if [ x$(on_mac_os) = xyes ]; then
 	    $(call makelink,clang)
@@ -1376,59 +1268,61 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	    $(call makelink,g++)
 	  fi
 
-          # We also want to have the two 'cc' and 'c++' in the build
-          # directory that point to the selected compiler. With the checks
-          # above, 'gcc' and 'g++' will point to the proper compiler, so
-          # we'll use them to define 'cc' and 'c++'.
+#	  We also want to have the two 'cc' and 'c++' in the build
+#	  directory that point to the selected compiler. With the checks
+#	  above, 'gcc' and 'g++' will point to the proper compiler, so
+#	  we'll use them to define 'cc' and 'c++'.
 	  $(call makelink,gcc,,cc)
 	  $(call makelink,g++,,c++)
 
-          # Get the first line of the compiler's '--version' output and put
-          # that into the target (so we know want compiler was used).
+#	  Get the first line of the compiler's '--version' output and put
+#	  that into the target (so we know want compiler was used).
 	  ccinfo=$$(gcc --version | awk 'NR==1')
 	  echo "C compiler (""$$ccinfo"")" > $@
 
 	else
 
-          # Mark the current directory.
+#	  Mark the current directory.
 	  current_dir=$$(pwd)
 
-          # We don't want '.local/lib' and '.local/lib64' to be separate.
-	  ln -fs $(ildir) $(idir)/lib64
-
-          # By default we'll build GCC in the RAM to avoid building so many
-          # files and possibly harming the hard-drive or SSD. But if the
-          # RAM doesn't have enough space, we can't use it.
+#	  By default 'ddir' (where GCC is decompressed and built) is in the
+#	  RAM (on systems that support '/dev/shm'). This is done to avoid
+#	  building so many small/temporary files and possibly harming the
+#	  hard-drive or SSD. But if the RAM doesn't have enough space, we
+#	  should use the hard-drive or SSD. During its build GCC's build
+#	  directory will become about 7GB (multiple of 1024 bytes, for GCC
+#	  11.2.0). So at this step, we are making sure we have more than
+#	  7.5GiB (multiple of 1000 bytes, which corresponds to 7.32GB)
+#	  before GCC starts to build. Note that the 4th column of 'df' is
+#	  the "available" space at the time of running, not the full
+#	  space. So the background RAM that the OS will be using during
+#	  Maneage is accounted for. Also consider that GCC is built alone
+#	  (no other Maneage software is built at the same time as GCC).
 	  in_ram=$$(df $(ddir) \
-	               | awk 'NR==2{print ($$4>10000000) ? "yes" : "no"}'); \
+	               | awk 'NR==2{print ($$4>7500000) ? "yes" : "no"}'); \
 	  if [ $$in_ram = "yes" ]; then odir=$(ddir)
 	  else
-	    odir=$(BDIR)/software/build-tmp-gcc
+	    odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space
 	    if [ -d $$odir ]; then rm -rf $$odir; fi
 	    mkdir $$odir
 	  fi
 
-          # Go into the proper directory, unpack GCC and prepare the
-          # 'build' directory inside it for all the built files.
+#	  Go into the proper directory, unpack GCC and prepare the 'build'
+#	  directory inside it for all the built files.
 	  cd $$odir
 	  rm -rf gcc-$(gcc-version)
-	  tar xf $(tdir)/$$tarball
+	  tar -xf $(tdir)/$$tarball
 	  if [ $$odir != $(ddir) ]; then
 	    ln -s $$odir/gcc-$(gcc-version) $(ddir)/gcc-$(gcc-version)
 	  fi
 	  cd gcc-$(gcc-version)
 
-          # Handle bug https://savannah.nongnu.org/bugs/index.php?61240 in
-          # which gcc preferentially uses a system-level 'unwind' library
-          # rather than using its own one.
-	  ln -sf ../../libgcc/unwind-generic.h libstdc++-v3/libsupc++/unwind.h
-	  ln -sf ../libgcc/unwind-generic.h libitm/unwind.h
-
+#	  Set the build directory for the processing.
 	  mkdir build
 	  cd build
 
-          # Configure, build and install GCC, if any of three steps fails,
-          # the error message will be printed.
+#	  Configure, build and install GCC, if any of three steps fails,
+#	  the error message will be printed.
 	  if ! ../configure SHELL=$(ibdir)/bash \
 	                    --prefix=$(idir) \
 	                    --with-mpc=$(idir) \
@@ -1447,26 +1341,25 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	                    --enable-languages=c,c++,fortran,objc,obj-c++ \
 	                    --disable-nls \
 	                    --disable-libada \
-	                    --disable-multilib \
-	                    --disable-multiarch; then error_message; fi
+	                    --disable-multilib; then error_message; fi
 	  if ! make SHELL=$(ibdir)/bash -j$(numthreads); then error_message; fi
 	  if ! make SHELL=$(ibdir)/bash install; then error_message; fi
 
-          # We need to manually fix the RPATH inside GCC's libraries, the
-          # programs built by GCC already have RPATH.
+#	  We need to manually fix the RPATH inside GCC's libraries, the
+#	  programs built by GCC already have RPATH.
 	  tempname=$$odir/gcc-$(gcc-version)/build/rpath-temp-copy
 	  if [ -f $(ibdir)/patchelf ]; then
 
-            # Go over all the installed GCC libraries (its executables are
-            # fine!).
+#	    Go over all the installed GCC libraries (its executables are
+#	    fine!).
 	    for f in $$(find $(idir)/libexec/gcc -type f) $(ildir)/libstdc++*; do
 
-              # Make sure this is a static library, copy it to a temporary
-              # name (to avoid any possible usage of the file while it is
-              # being corrected), and add RPATH inside of it and put the
-              # corrected file back in its place. In the case of the
-              # standard C++ library, we also need to manually insert a
-              # linking to libiconv.
+#	      Make sure this is a static library, copy it to a temporary
+#	      name (to avoid any possible usage of the file while it is
+#	      being corrected), and add RPATH inside of it and put the
+#	      corrected file back in its place. In the case of the standard
+#	      C++ library, we also need to manually insert a linking to
+#	      libiconv.
 	      if file $$f | grep -q "dynamically linked"; then
 	        cp $$f $$tempname
 	        patchelf --set-rpath $(ildir) $$tempname
@@ -1480,8 +1373,8 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	    done
 	  fi
 
-          # Come back up to the un-packing directory and delete the GCC
-          # source directory.
+#	  Come back up to the un-packing directory and delete the GCC
+#	  source directory.
 	  cd ../..
 	  rm -rf gcc-$(gcc-version)
 	  cd $$current_dir
@@ -1490,11 +1383,11 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	    rm $(ddir)/gcc-$(gcc-version);
 	  fi
 
-          # Set 'cc' to point to 'gcc'.
+#	  Set 'cc' to point to 'gcc'.
 	  ln -sf $(ibdir)/gcc $(ibdir)/cc
 	  ln -sf $(ibdir)/g++ $(ibdir)/c++
 
-          # Write the final target.
+#	  Write the final target.
 	  echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@
 	fi
 
@@ -1513,18 +1406,19 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 # If the project is built in a minimal environment, there is no text
 # editor, making it hard to work on the project. By default a minimal
 # (relatively user-friendly: GNU Nano) text editor will thus also be built
-# at the end of the "basic" tools. More advanced editors are available as
-# optional high-level programs. GNU Nano is a very light-weight and small
-# command-line text editor (around 3.5 Mb after installation!).
+# at the end of the "basic" tools. More advanced editors (for example Emacs
+# and Vim) are available as optional high-level programs. GNU Nano is a
+# very light-weight and small command-line text editor (around 3.5 Mb after
+# installation!).
 #
 # The editor is a top-level target in the basic tools (given to
 # 'targets-proglib' above). Hence nothing depends on it, and it just
 # depends on GCC. This is done because some projects may choose to not have
-# nano (and use their own optional high-level text editor). To do this,
-# they just have to manually remove 'nano' from 'targets-proglib' above and
+# nano (and use their own optional high-level text editor). To do this, you
+# can just have to manually remove 'nano' from 'targets-proglib' above and
 # add their optional text editor in 'TARGETS.conf'.
 $(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version)
-	tarball=nano-$(nano-version).tar.xz
+	tarball=nano-$(nano-version).tar.lz
 	$(call import-source, $(nano-url), $(nano-checksum))
 	$(call gbuild, nano-$(nano-version), static)
 	echo "GNU Nano $(nano-version)" > $@
diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
index 66c77bc..c25dfb1 100644
--- a/reproduce/software/make/build-rules.mk
+++ b/reproduce/software/make/build-rules.mk
@@ -3,7 +3,7 @@
 # imported into 'basic.mk' and 'high-level.mk'. They should be activated
 # with Make's 'Call' function.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -29,8 +29,13 @@
 # its checksum and if it is correct, remove the extra suffix.
 #
 # Arguments:
-#   1: The optional URL to use for this tarball.
-#   2: The expeced checksum of the tarball.
+#   1: The optional base URL (directory) to use for this tarball.
+#   2: The expected checksum of the tarball.
+#   3: The upstream name of the tarball file, if not automatically derived
+#        from the version number.
+#   4: [Optional]: Alternative upstream base URL (directory) for the
+#        tarball, to be used in preference to user or Maneage backup
+#        servers.
 #
 # Necessary shell variables
 #   'tarball': This is the name of the actual tarball file without a
@@ -56,7 +61,14 @@ import-source = final=$(tdir)/$$tarball; \
 	      tarballurl=$(topbackupserver)/$$tarball; \
 	    else \
 	      bservers="$(backupservers_all)"; \
-	      tarballurl=$$url/$$tarball; \
+	      if [ "x$(strip $(3))" = "x" ]; then \
+	          tarballurl=$$url/$$tarball; \
+	      else \
+	          tarballurl=$$url/$(strip $(3)); \
+	      fi; \
+	    fi; \
+	    if [ x"$(4)" != x ]; then \
+	      bservers="$(strip $(4)) $$bservers"; \
 	    fi; \
 	    if [ -f $(ibdir)/wget ]; then \
 	      downloader="wget --no-use-server-timestamps -O"; \
@@ -89,6 +101,48 @@ import-source = final=$(tdir)/$$tarball; \
 
 
 
+# Double-check an already downloaded R source
+# -------------------------------------------
+#
+# It is probably too late to protect the system if you have already
+# installed an insecure or wrong R package. However, it's still useful
+# to check that the source package is the one that you think it is.
+#
+# Calculate the checksum and exit with a non-zero error code if
+# there's a mismatch, after informing the user.
+#
+# Arguments:
+#   1: The expected checksum of the tarball.
+#
+# Necessary shell variables
+#   'tarball': This is the name of the actual tarball file without a
+#   directory.
+double-check-R-source = final=$(tdir)/R-project/$$tarball; \
+	exp_checksum="$(strip $(1))"; \
+	if [ x"$$exp_checksum" = x"NO-CHECK-SUM" ]; then \
+	  result=0; \
+	else \
+	  if type sha512sum > /dev/null 2>/dev/null; then \
+	    checksum=$$(sha512sum "$$final" | awk '{print $$1}'); \
+	    if [ x"$$checksum" = x"$$exp_checksum" ]; then \
+	      result=0; \
+	    else \
+	      echo "ERROR: Non-matching checksum: $$final"; \
+	      echo "Checksum should be: $$exp_checksum"; \
+	      echo "Checksum is:        $$checksum"; \
+	      result=1; \
+	      exit 1; \
+	    fi; \
+	  else \
+	    echo "ERROR: sha512sum is unavailable."; \
+	    exit 1; \
+	  fi; \
+	fi
+
+
+
+
+
 # Unpack a tarball
 # ----------------
 #
@@ -106,7 +160,7 @@ uncompress = csuffix=$$(echo $$utarball \
 	  intarrm=0; \
 	  intar=$$utarball; \
 	fi; \
-	if tar xf $$intar; then \
+	if tar -xf $$intar; then \
 	  if [ x$$intarrm = x1 ]; then rm $$intar; fi; \
 	else \
 	  echo; echo "Tar error"; exit 1; \
@@ -166,10 +220,13 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
 	 else shellop="SHELL=/bin/sh"; \
 	 fi; \
 	     \
+	 if [ x$$gbuild_prefix = x ]; then prefixdir="$(idir)"; \
+	 else prefixdir="$$gbuild_prefix"; fi; \
+	                                       \
 	 if [ -f "$$confscript" ]; then \
 	   if [ x"$(strip $(1))" = x"zlib-$(zlib-version)" ]; then \
-	     configop="--prefix=$(idir)"; \
-	   else configop="$$shellop --prefix=$(idir)"; \
+	     configop="--prefix=$$prefixdir"; \
+	   else configop="$$shellop --prefix=$$prefixdir"; \
 	   fi; \
 	 fi; \
 	     \
@@ -190,7 +247,7 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
 	   make "$$shellop" install $(7); \
 	   cd ..; \
 	 fi; \
-	 rm -rf $(1)
+	 rm -rf $(1);
 
 
 
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 6ea782c..34c829b 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -3,7 +3,7 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run by the initial `./project configure' script. It
+# This Makefile will be run by the initial './project configure' script. It
 # is not included into the project afterwards.
 #
 # This Makefile builds the high-level (optional) software in Maneage that
@@ -12,8 +12,8 @@
 #
 # ------------------------------------------------------------------------
 #
-# 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>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -60,6 +60,9 @@ patchdir = "$(shell pwd)"/reproduce/software/patches
 itidir   = $(BDIR)/software/installed/version-info/tex
 ictdir   = $(BDIR)/software/installed/version-info/cite
 ipydir   = $(BDIR)/software/installed/version-info/python
+ircrandir    = $(BDIR)/software/installed/version-info/r-cran
+ilibrcrandir = $(BDIR)/software/installed/lib/R/library
+
 
 # Targets to build.
 ifeq ($(strip $(all_highlevel)),1)
@@ -75,7 +78,7 @@ ifeq ($(strip $(all_highlevel)),1)
   # included here because there is no explicit target for them: they will
   # be built as part of the other package.
   targets-proglib := $(filter-out minizip-% lapack-% ghostscript-fonts-%, \
-      $(shell awk '/^# CLASS:PYTHON/{good=0} \
+      $(shell awk '/^# CLASS:(PYTHON|R-CRAN)/{good=0} \
                    good==1 && !/^#/ && $$1 ~ /-version$$/ { \
                        printf("%s %s ", $$1, $$3)} \
                    /^# CLASS:HIGHLEVEL/{good=1}' \
@@ -85,14 +88,25 @@ ifeq ($(strip $(all_highlevel)),1)
 
   # List all existing Python packages.
   targets-python := $(shell \
-    awk '/^# CLASS:PYTHON/{good=1} \
-         good==1 && !/^#/ && $$1 ~ /-version$$/ {printf("%s %s ",$$1,$$3)}' \
-        reproduce/software/config/versions.conf | sed 's/version //g')
+    awk '/^# CLASS:PYTHON-START/{good=1} good; \
+         /^# CLASS:PYTHON-END/{good=0}' \
+         reproduce/software/config/versions.conf \
+        | awk '!/^#/' \
+        | sed 's/-version = /-/g')
+
+  # List all existing R-CRAN packages.
+  targets-r-cran := $(shell \
+    awk '/^# CLASS:R-CRAN-START/{good=1} good; \
+         /^# CLASS:R-CRAN-END/{good=0}' \
+         reproduce/software/config/versions.conf \
+        | awk '!/^#/' \
+        | sed 's/-version = /-/g')
 else
 
-  # Append the version of each software to its name. We are using a Make
+  # Append the version of each software package to its name. We are using a Make
   # feature where a variable name is defined with another variable.
   targets-python := $(foreach p,$(top-level-python),$(p)-$($(p)-version))
+  targets-r-cran := $(foreach p,$(top-level-r-cran),$(p)-$($(p)-version))
   targets-proglib := $(foreach p,$(top-level-programs),$(p)-$($(p)-version))
 
 endif
@@ -100,6 +114,7 @@ endif
 # Ultimate Makefile target.
 all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \
      $(foreach p, $(targets-python), $(ipydir)/$(p)) \
+     $(foreach p, $(targets-r-cran),  $(ircrandir)/$(p)) \
      $(itidir)/texlive
 
 # Define the shell environment
@@ -112,14 +127,18 @@ all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \
 #
 # To investigate:
 #
-#    1) Set SHELL to `$(ibdir)/env - NAME=VALUE $(ibdir)/bash' and set all
-#       the parameters defined bellow as `NAME=VALUE' statements before
+#    1) Set SHELL to '$(ibdir)/env - NAME=VALUE $(ibdir)/bash' and set all
+#       the parameters defined bellow as 'NAME=VALUE' statements before
 #       calling Bash. This will enable us to completely ignore the user's
 #       native environment.
 #
-#    2) Add `--noprofile --norc' to `.SHELLFLAGS' so doesn't load the
+#    2) Add '--noprofile --norc' to '.SHELLFLAGS' so doesn't load the
 #       user's environment.
 #
+#    3) Add the '-u' flag so that an error occurs if an environment
+#       variable is empty; this reduces the chance of catastrophic
+#       file removal with 'rm -fr ../../$${FORGOT_TO_DEFINE_THIS}'.
+#
 # Shell settings similar to 'basic.mk':
 .ONESHELL:
 export PATH := $(ibdir)
@@ -131,6 +150,9 @@ export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
 export CPPFLAGS := -I$(idir)/include -Wno-nullability-completeness
 export PKG_CONFIG_PATH := $(ildir)/pkgconfig:$(idir)/share/pkgconfig
 
+# Disable built-in rules (which are not needed here!)
+.SUFFIXES:
+
 # Settings specific to this Makefile.
 export CC := $(ibdir)/gcc
 export CXX := $(ibdir)/g++
@@ -147,16 +169,16 @@ export C_INCLUDE_PATH     := $(iidir)
 export CPLUS_INCLUDE_PATH := $(iidir)
 endif
 
-# Recipe startup script, see `reproduce/software/shell/bashrc.sh'.
+# Recipe startup script, see 'reproduce/software/shell/bashrc.sh'.
 export PROJECT_STATUS := configure_highlevel
 export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
 
 # Until we build our own C library, without this, our GCC won't be able to
 # compile anything! Note that on most systems (in particular
-# non-Debian-based), `sys_cpath' will be empty.
+# non-Debian-based), 'sys_cpath' will be empty.
 export CPATH := $(sys_cpath)
 
-# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
+# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
 # ultimately redundant. But on some systems, even having a single value
 # causes crashs (see bug #56682). So we'll just give it no value at all.
 export DYLD_LIBRARY_PATH :=
@@ -164,8 +186,8 @@ export DYLD_LIBRARY_PATH :=
 # On Debian-based OSs, the basic C libraries are in a target-specific
 # location, not in standard places. Until we merge the building of the C
 # library, it is thus necessary to include this location here. On systems
-# that don't need it, `sys_library_path' is just empty. This is necessary
-# for `ld'.
+# that don't need it, 'sys_library_path' is just empty. This is necessary
+# for 'ld'.
 #
 # If this variable is not defined, it will be interpretted as the current
 # directory. In this case, when the program source has a 'specs' directory,
@@ -179,12 +201,18 @@ endif
 # Building flags:
 #
 # C++ flags: when we build GCC, the C++ standard library needs to link with
-# libiconv. So it is necessary to generically include `-liconv' for all C++
+# libiconv. So it is necessary to generically include '-liconv' for all C++
 # builds.
 ifeq ($(host_cc),0)
 export CXXFLAGS          := -liconv
 endif
 
+# Custom installation prefix for software that can cause conflicts with
+# others, to avoid crowding the to Maneage installed software directory,
+# we'll put them all in a 'custom' directory.
+idircustom = $(idir)/custom
+$(idircustom):; mkdir $@
+
 # Servers to use as backup. Maneage already has some fixed servers that can
 # be used to download software tarballs. They are in a configuation
 # file. But we give precedence to the "user" backup servers.
@@ -211,6 +239,8 @@ backupservers = $(filter-out $(topbackupserver),$(backupservers_all))
 # Import rules to build specialized software
 include reproduce/software/make/xorg.mk
 include reproduce/software/make/python.mk
+include reproduce/software/make/r-cran.mk
+
 
 
 
@@ -226,61 +256,27 @@ include reproduce/software/make/python.mk
 #
 # We would prefer to build static libraries, but some compilers like LLVM
 # don't have static capabilities, so they'll only build dynamic/shared
-# libraries. Therefore, we can't use the easy `.a' suffix for static
+# libraries. Therefore, we can't use the easy '.a' suffix for static
 # libraries as targets and there are different conventions for shared
 # library names.
-
-# Until version 0.11.0 is released, we are using the version corresponding
-# to commit 014954db (603 commits after version 0.10.0, most recent when
-# first importing log4cxx into this project).
-#
-# Note that after cloning the project, the following changes are necessary
-# in `configure.ac'.
-#  - Update the final name of the tarball and its version (from `git
-#  - describe') by modifying the `AC_INIT' line:
-#        AC_INIT([apachelog4cxx], [0.10.0-603-014954db])
-#  - Because of the long file names in the project, some files will not be
-#    packaged by default, so pass the `tar-ustar' option to Automake (the
-#    `AM_INIT_AUTOMAKE' line of `configure.ac':
-#        AM_INIT_AUTOMAKE([foreign subdir-objects -Wall tar-ustar])
-#
-# You can then simply bootstrap the project and make the distribution
-# tarball like this:
-#        ./autogen.sh && ./configure && make -j8 && make dist-lzip
-#
-# Unfortunately we have to re-run the `autogen.sh' script on the tarball to
-# build it because it will complain about the version of libtool, so until
-# the version 0.11.0 of log4cxx, we'll have to run `autogen.sh' on the
-# unpacked source also.
 $(ibidir)/apachelog4cxx-$(apachelog4cxx-version): \
+                        $(ibidir)/cmake-$(cmake-version) \
                         $(ibidir)/expat-$(expat-version) \
                         $(ibidir)/apr-util-$(apr-util-version) \
                         $(ibidir)/automake-$(automake-version)
-	tarball=apachelog4cxx-$(apachelog4cxx-version).tar.lz
+	tarball=apache-log4cxx-$(apachelog4cxx-version).tar.lz
 	$(call import-source, $(apachelog4cxx-url), $(apachelog4cxx-checksum))
-	pdir=apachelog4cxx-$(apachelog4cxx-version)
-	rm -rf $(ddir)/$$pdir
-	topdir=$(pwd)
-	cd $(ddir)
-	tar xf $(tdir)/$$tarball
-	cd $$pdir
-	./autogen.sh
-	./configure SHELL=$(ibdir)/bash --prefix=$(idir)
-	make -j$(numthreads) SHELL=$(ibdir)/bash
-	make install
-	cd ..
-	rm -rf $$pdir
-	cd $$topdir
+	$(call cbuild, apache-log4cxx-$(apachelog4cxx-version), static)
 	echo "Apache log4cxx $(apachelog4cxx-version)" > $@
 
 $(ibidir)/apr-$(apr-version):
-	tarball=apr-$(apr-version).tar.gz
+	tarball=apr-$(apr-version).tar.lz
 	$(call import-source, $(apr-url), $(apr-checksum))
 	$(call gbuild, apr-$(apr-version), ,--disable-static)
 	echo "Apache Portable Runtime $(apr-version)" > $@
 
 $(ibidir)/apr-util-$(apr-util-version): $(ibidir)/apr-$(apr-version)
-	tarball=apr-util-$(apr-util-version).tar.gz
+	tarball=apr-util-$(apr-util-version).tar.lz
 	$(call import-source, $(apr-util-url), $(apr-util-checksum))
 	$(call gbuild, apr-util-$(apr-util-version), , \
 	               --disable-static \
@@ -291,20 +287,19 @@ $(ibidir)/apr-util-$(apr-util-version): $(ibidir)/apr-$(apr-version)
 
 $(ibidir)/atlas-$(atlas-version):
 
-	tarball=lapack-$(lapack-version).tar.gz
+	tarball=lapack-$(lapack-version).tar.lz
 	$(call import-source, $(lapack-url), $(lapack-checksum))
 
-	tarball=atlas-$(atlas-version).tar.bz2
+	tarball=atlas-$(atlas-version).tar.lz
 	$(call import-source, $(atlas-url), $(atlas-checksum))
 
-        # Get the operating system specific features (how to get
-        # CPU frequency and the library suffixes). To make the steps
-        # more readable, the different library version suffixes are
-        # named with a single character: `s' for no version in the
-        # name, `m' for the major version suffix, and `f' for the
-        # full version suffix.
-        # GCC in Mac OS doesn't work. To work around this issue, on Mac
-        # systems we force ATLAS to use `clang' instead of `gcc'.
+#	Get the operating system specific features (how to get CPU
+#	frequency and the library suffixes). To make the steps more
+#	readable, the different library version suffixes are named with a
+#	single character: 's' for no version in the name, 'm' for the major
+#	version suffix, and 'f' for the full version suffix.  GCC in Mac OS
+#	doesn't work. To work around this issue, on Mac systems we force
+#	ATLAS to use 'clang' instead of 'gcc'.
 	if [ x$(on_mac_os) = xyes ]; then
 	  s=dylib
 	  m=3.dylib
@@ -321,8 +316,8 @@ $(ibidir)/atlas-$(atlas-version):
 	              | sed "s/.*: \([0-9.]*\).*/\1/")
 	fi
 
-        # See if the shared libraries should be build for a single CPU
-        # thread or multiple threads.
+#	See if the shared libraries should be build for a single CPU thread
+#	or multiple threads.
 	N=$$(nproc)
 	srcdir=$$(pwd)/reproduce/software/make
 	if [ $$N = 1 ]; then
@@ -331,25 +326,25 @@ $(ibidir)/atlas-$(atlas-version):
 	  sharedmk=$$srcdir/atlas-multiple.mk
 	fi
 
-        # The linking step here doesn't recognize the `-Wl' in the
-        # `rpath_command'.
+#	The linking step here doesn't recognize the '-Wl' in the
+#	'rpath_command'.
 	export LDFLAGS=-L$(ildir)
 	cd $(ddir)
-	tar xf $(tdir)/atlas-$(atlas-version).tar.bz2
+	tar -xf $(tdir)/atlas-$(atlas-version).tar.lz
 	cd ATLAS
 	rm -rf build
 	mkdir build
 	cd build
 	../configure -b 64 -D c -DPentiumCPS=$$core \
-	             --with-netlib-lapack-tarfile=$(tdir)/lapack-$(lapack-version).tar.gz \
+	             --with-netlib-lapack-tarfile=$(tdir)/lapack-$(lapack-version).tar.lz \
 	             --cripple-atlas-performance \
 	             -Fa alg -fPIC --shared $$clangflag \
 	             --prefix=$(idir)
 
-        # Static build.
+#	Static build.
 	make
 
-        # Currently the shared libraries have problems on macOS.
+#	Currently the shared libraries have problems on macOS.
 	if [ "x$(on_mac_os)" != xyes ]; then
 	     cd lib
 	     make -f $$sharedmk
@@ -362,21 +357,21 @@ $(ibidir)/atlas-$(atlas-version):
 	     ln -fs $(ildir)/liblapack.$$f  $(ildir)/liblapack.$$m
 	   fi
 
-        # Install the libraries.
+#	Install the libraries.
 	make install
 
-        # We need to check the existance of `libptlapack.a', but we can't
-        # do this in the `&&' steps above (it will conflict). So we'll do
-        # the check after seeing if `libtatlas.so' is installed, then we'll
-        # finalize the build (delete the untarred directory).
+#	We need to check the existance of 'libptlapack.a', but we can't do
+#	this in the '&&' steps above (it will conflict). So we'll do the
+#	check after seeing if 'libtatlas.so' is installed, then we'll
+#	finalize the build (delete the untarred directory).
 	if [ "x$(on_mac_os)" != xyes ]; then \
 	  [ -e lib/libptlapack.a ] && cp lib/libptlapack.a $(ildir); \
 	  cd $(ddir); \
 	  rm -rf ATLAS; \
 	fi
 
-        # We'll check the full installation with the static library (not
-        # currently building shared library on Mac.
+#	We'll check the full installation with the static library (not
+#	currently building shared library on Mac.
 	if [ -f $(ildir)/libatlas.a ]; then \
 	  echo "ATLAS $(atlas-version)" > $@; \
 	fi
@@ -391,7 +386,7 @@ $(ibidir)/boost-$(boost-version): \
 	rm -rf $(ddir)/$$unpackdir
 	topdir=$(pwd)
 	cd $(ddir)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
 	./bootstrap.sh --prefix=$(idir) --with-libraries=all \
 	               --with-python=python3
@@ -404,15 +399,15 @@ $(ibidir)/boost-$(boost-version): \
 
 $(ibidir)/cfitsio-$(cfitsio-version):
 
-        # Download the tarball
-	tarball=cfitsio-$(cfitsio-version).tar.gz
+#	Download the tarball
+	tarball=cfitsio-$(cfitsio-version).tar.lz
 	$(call import-source, $(cfitsio-url), $(cfitsio-checksum))
 
-        # CFITSIO hard-codes '@rpath' inside the shared library on
-        # Mac systems. So we need to change it to our library
-        # installation path. It doesn't affect GNU/Linux, so we'll
-        # just do it in any case to keep things clean.
-	topdir=$(pwd); cd $(ddir); tar xf $(tdir)/$$tarball
+#	CFITSIO hard-codes '@rpath' inside the shared library on Mac
+#	systems. So we need to change it to our library installation
+#	path. It doesn't affect GNU/Linux, so we'll just do it in any case
+#	to keep things clean.
+	topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball
 	customtar=cfitsio-$(cfitsio-version)-custom.tar.gz
 	cd cfitsio-$(cfitsio-version)
 	sed configure -e's|@rpath|$(ildir)|g' > configure_tmp
@@ -422,9 +417,9 @@ $(ibidir)/cfitsio-$(cfitsio-version):
 	tar cf $$customtar cfitsio-$(cfitsio-version)
 	cd $$topdir
 
-        # Continue the standard build on the customized tarball. Note that
-        # with the installation of CFITSIO, `fpack' and `funpack' are not
-        # installed by default. Because of that, they are added explicity.
+#	Continue the standard build on the customized tarball. Note that
+#	with the installation of CFITSIO, 'fpack' and 'funpack' are not
+#	installed by default. Because of that, they are added explicity.
 	export gbuild_tar=$(ddir)/$$customtar
 	$(call gbuild, cfitsio-$(cfitsio-version), , \
 	               --enable-sse2 --enable-reentrant \
@@ -437,24 +432,25 @@ $(ibidir)/cairo-$(cairo-version): \
                 $(ibidir)/pixman-$(pixman-version) \
                 $(ibidir)/libpng-$(libpng-version) \
                 $(ibidir)/freetype-$(freetype-version)
-	tarball=cairo-$(cairo-version).tar.xz
+	tarball=cairo-$(cairo-version).tar.lz
 	$(call import-source, $(cairo-url), $(cairo-checksum))
 	$(call gbuild, cairo-$(cairo-version), static, \
 	               --with-x=yes, -j$(numthreads) V=1)
 	echo "Cairo $(cairo-version)" > $@
 
 # Eigen is just headers! So it doesn't need to be compiled. Once unpacked
-# it has a checksum after `eigen-eigen', so we'll just use a `*' to choose
+# it has a checksum after 'eigen-eigen', so we'll just use a '*' to choose
 # the unpacked directory.
 $(ibidir)/eigen-$(eigen-version):
-	tarball=eigen-$(eigen-version).tar.gz
+	tarball=eigen-$(eigen-version).tar.lz
 	$(call import-source, $(eigen-url), $(eigen-checksum))
 	rm -rf $(ddir)/eigen-eigen-*
-	topdir=$(pwd); cd $(ddir); tar xf $(tdir)/$$tarball
-	cd eigen-eigen-*
-	cp -r Eigen $(iidir)/eigen3
+	topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball
+	cd eigen-$(eigen-version)
+	if ! [ -d $(iidir)/eigen3 ]; then mkdir $(iidir)/eigen3; fi
+	cp -r Eigen/* $(iidir)/eigen3/
 	cd $$topdir
-	rm -rf $(ddir)/eigen-eigen-*
+	rm -rf $(ddir)/eigen-$(eigen-version)
 	echo "Eigen $(eigen-version)" > $@
 
 # GNU Emacs is an advanced text editor (among many other things!), so it
@@ -468,7 +464,7 @@ $(ibidir)/eigen-$(eigen-version):
 # except the core Emacs functionality (using '--without-all') and we are
 # also disabling all graphic user interface features (using '--without-x').
 $(ibidir)/emacs-$(emacs-version):
-	tarball=emacs-$(emacs-version).tar.xz
+	tarball=emacs-$(emacs-version).tar.lz
 	$(call import-source, $(emacs-url), $(emacs-checksum))
 	$(call gbuild, emacs-$(emacs-version), static, \
 	               --without-all --without-x \
@@ -483,15 +479,28 @@ $(ibidir)/expat-$(expat-version):
 	echo "Expat $(expat-version)" > $@
 
 $(ibidir)/fftw-$(fftw-version):
-        # Prepare the source tarball.
-	tarball=fftw-$(fftw-version).tar.gz
+
+#	Prepare the source tarball.
+	tarball=fftw-$(fftw-version).tar.lz
 	$(call import-source, $(fftw-url), $(fftw-checksum))
 
-        # FFTW's single and double precission libraries must be built
-        # independently: for the the single-precision library, we need to
-        # add the `--enable-float' option. We will build this first, then
-        # the default double-precision library.
-	confop="--enable-shared --enable-threads --enable-avx --enable-sse2"
+#	FFTW's single and double precision libraries must be built
+#	independently: for the the single-precision library, we need to add
+#	the '--enable-float' option. We will build this first, then the
+#	default double-precision library.
+#
+#	There are Intel-specific optimizations that can be enabled by
+#	adding the following two options to 'confop'
+#
+#           --enable-avx --enable-sse2
+#
+#	However, they cause crashs on non-Intel processors (has been
+#	confirmed in ARM's aarch64). So in the generic scenario they are
+#	removed. Checking how these optimizations affect the numeric
+#	accuracy of the result (and thus optionally adding them for
+#	Intel-based processors) should be studied before they are
+#	optionally added for Intel-based CPUs (and ignored for others).
+	confop="--enable-shared --enable-threads"
 	$(call gbuild, fftw-$(fftw-version), static, \
 	               $$confop --enable-float)
 	$(call gbuild, fftw-$(fftw-version), static, \
@@ -500,19 +509,19 @@ $(ibidir)/fftw-$(fftw-version):
 	echo "FFTW $(fftw-version) \citep{fftw}" > $@
 
 $(ibidir)/freetype-$(freetype-version): $(ibidir)/libpng-$(libpng-version)
-	tarball=freetype-$(freetype-version).tar.gz
+	tarball=freetype-$(freetype-version).tar.lz
 	$(call import-source, $(freetype-url), $(freetype-checksum))
 	$(call gbuild, freetype-$(freetype-version), static)
 	echo "FreeType $(freetype-version)" > $@
 
 $(ibidir)/gperf-$(gperf-version):
-	tarball=gperf-$(gperf-version).tar.gz
+	tarball=gperf-$(gperf-version).tar.lz
 	$(call import-source, $(gperf-url), $(gperf-checksum))
 	$(call gbuild, gperf-$(gperf-version), static)
 	echo "GNU gperf $(gperf-version)" > $@
 
 $(ibidir)/gsl-$(gsl-version):
-	tarball=gsl-$(gsl-version).tar.gz
+	tarball=gsl-$(gsl-version).tar.lz
 	$(call import-source, $(gsl-url), $(gsl-checksum))
 	$(call gbuild, gsl-$(gsl-version), static)
 	echo "GNU Scientific Library $(gsl-version)" > $@
@@ -531,14 +540,14 @@ $(ibidir)/hdf5-$(hdf5-version): $(ibidir)/openmpi-$(openmpi-version)
 # HEALPix includes the source of its C, C++, Python (and several other
 # languages) libraries within one tarball. We will include the Python
 # installation only when any other Python module is requested (in
-# `TARGETS.conf').
+# 'TARGETS.conf').
 #
-# Note that the default `./configure' script is an interactive script which
-# is hard to automate. So we need to go into the `autotools' directory of
-# the `C' and `cxx' directories and configure the GNU Build System (with
-# `autoreconf', which uses `autoconf' and `automake') to easily build the
+# Note that the default './configure' script is an interactive script which
+# is hard to automate. So we need to go into the 'autotools' directory of
+# the 'C' and 'cxx' directories and configure the GNU Build System (with
+# 'autoreconf', which uses 'autoconf' and 'automake') to easily build the
 # HEALPix C/C++ libraries in batch mode.
-ifeq ($(strip $(top-level-python)),)
+ifeq ($(strip $(targets-python)),)
 healpix-python-dep =
 else
 healpix-python-dep = $(ipydir)/matplotlib-$(matplotlib-version) \
@@ -548,7 +557,7 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
                   $(ibidir)/cfitsio-$(cfitsio-version) \
                   $(ibidir)/autoconf-$(autoconf-version) \
                   $(ibidir)/automake-$(automake-version)
-	tarball=healpix-$(healpix-version).tar.gz
+	tarball=healpix-$(healpix-version).tar.lz
 	$(call import-source, $(healpix-url), $(healpix-checksum))
 	if [ x"$(healpix-python-dep)" = x ]; then
 	   pycommand1="echo no-healpy-because-no-other-python"
@@ -559,7 +568,7 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
 	fi
 	rm -rf $(ddir)/Healpix_$(healpix-version)
 	topdir=$(pwd); cd $(ddir);
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd Healpix_$(healpix-version)/src/C/autotools/
 	autoreconf --install
 	./configure --prefix=$(idir)
@@ -568,6 +577,13 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
 	cd ../../cxx/autotools/
 	autoreconf --install
 	./configure --prefix=$(idir)
+
+#	With CFITSIO 4.0, the 'CFITSIO_VERSION' macro has three
+#	components. But this version of Healpix doesn't yet account for
+#	this.
+	sed -i -e's/CFITSIO_VERSION/fitsversion/' cxxsupport/fitshandle.cc
+
+#	Continue with the building.
 	make V=1 -j$(numthreads) SHELL=$(ibdir)/bash
 	make install
 	cd ../../healpy
@@ -578,19 +594,52 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
 	cp $(dtexdir)/healpix.tex $(ictdir)/
 	echo "HEALPix $(healpix-version) \citep{healpix}" > $@
 
+$(ibidir)/libbsd-$(libbsd-version): $(ibidir)/libmd-$(libmd-version)
+	tarball=libbsd-$(libbsd-version).tar.lz
+	$(call import-source, $(libbsd-url), $(libbsd-checksum))
+	if [ x$(on_mac_os) = xyes ]; then
+	  echo "" > $@
+	else
+	  export LDFLAGS="-L$(idirlibmd)/lib $$LDFLAGS"
+	  export CPPFLAGS="-I$(idirlibmd)/include $$CPPFLAGS"
+	  $(call gbuild, libbsd-$(libbsd-version), static,,V=1)
+	  echo "Libbsd $(libbsd-version)" > $@
+	fi
+
 $(ibidir)/libidn-$(libidn-version):
-	tarball=libidn-$(libidn-version).tar.gz
+	tarball=libidn-$(libidn-version).tar.lz
 	$(call import-source, $(libidn-url), $(libidn-checksum))
 	$(call gbuild, libidn-$(libidn-version), static, \
 	               --disable-doc, -j$(numthreads) V=1)
 	echo "Libidn $(libidn-version)" > $@
 
 $(ibidir)/libjpeg-$(libjpeg-version):
-	tarball=jpegsrc.$(libjpeg-version).tar.gz
+	tarball=libjpeg-$(libjpeg-version).tar.lz
 	$(call import-source, $(libjpeg-url), $(libjpeg-checksum))
-	$(call gbuild, jpeg-9b, static,,V=1)
+	$(call gbuild, libjpeg-$(libjpeg-version), static,,V=1)
 	echo "Libjpeg $(libjpeg-version)" > $@
 
+# libmd is a set of "message digest" functions that are available in in the
+# C library of BSD-based systems, but not others (like GNU-based
+# systems). It includes hash functions like MD5 and SHAs.
+#
+# Libmd is being installed in a non-standard location because its headers
+# (like 'md5.h') will conflict with similarly named headers by the system
+# during the building of Binutils later! So any program that needs libmd's
+# headers or libraries (like 'libbsd'), should add this special location to
+# its CPPFLAGS and LDFLAGS.
+idirlibmd=$(idircustom)/libmd
+$(ibidir)/libmd-$(libmd-version): | $(idircustom)
+	tarball=libmd-$(libmd-version).tar.lz
+	$(call import-source, $(libmd-url), $(libmd-checksum))
+	if [ x$(on_mac_os) = xyes ]; then
+	  echo "" > $@
+	else
+	  export gbuild_prefix=$(idirlibmd)
+	  $(call gbuild, libmd-$(libmd-version), static,,V=1)
+	  echo "Libmd $(libmd-version)" > $@
+	fi
+
 $(ibidir)/libnsl-$(libnsl-version): \
                  $(ibidir)/libtirpc-$(libtirpc-version) \
                  $(ibidir)/rpcsvc-proto-$(rpcsvc-proto-version)
@@ -603,11 +652,11 @@ $(ibidir)/libnsl-$(libnsl-version): \
 $(ibidir)/libpaper-$(libpaper-version): \
                    $(ibidir)/automake-$(automake-version)
 
-        # Download the tarball.
-	tarball=libpaper-$(libpaper-version).tar.gz
+#	Download the tarball.
+	tarball=libpaper-$(libpaper-version).tar.lz
 	$(call import-source, $(libpaper-url), $(libpaper-checksum))
 
-        # Unpack, build the configure system, build and install.
+#	Unpack, build the configure system, build and install.
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
 	unpackdir=libpaper-$(libpaper-version)
@@ -620,10 +669,10 @@ $(ibidir)/libpaper-$(libpaper-version): \
 	cd ..
 	rm -rf $$unpackdir
 
-        # Post-processing: according to Linux From Scratch, libpaper
-        # expects that packages will install files into this directory and
-        # 'paperconfig' is a script which will invoke 'run-parts' if
-        # '/etc/libpaper.d' exists
+#	Post-processing: according to Linux From Scratch, libpaper expects
+#	that packages will install files into this directory and
+#	'paperconfig' is a script which will invoke 'run-parts' if
+#	'/etc/libpaper.d' exists
 	mkdir -vp $(idir)/etc/libpaper.d
 	sed -e's|MANEAGESHELL|$(SHELL)|' $(shsrcdir)/run-parts.in \
 	    > $(ibdir)/run-parts
@@ -631,15 +680,19 @@ $(ibidir)/libpaper-$(libpaper-version): \
 	echo "Libpaper $(libpaper-version)" > $@
 
 $(ibidir)/libpng-$(libpng-version):
-	tarball=libpng-$(libpng-version).tar.xz
+
+#	The option '-DPNG_ARM_NEON_OPT=0' prevents an arm64 'neon' library
+#	from being required at compile time.
+	tarball=libpng-$(libpng-version).tar.lz
 	$(call import-source, $(libpng-url), $(libpng-checksum))
-	$(call gbuild, libpng-$(libpng-version), static)
+	$(call gbuild, libpng-$(libpng-version), static, \
+	               CFLAGS="-DPNG_ARM_NEON_OPT=0")
 	echo "Libpng $(libpng-version)" > $@
 
 $(ibidir)/libtiff-$(libtiff-version): $(ibidir)/libjpeg-$(libjpeg-version)
-	tarball=tiff-$(libtiff-version).tar.gz
+	tarball=libtiff-$(libtiff-version).tar.lz
 	$(call import-source, $(libtiff-url), $(libtiff-checksum))
-	$(call gbuild, tiff-$(libtiff-version), static, \
+	$(call gbuild, libtiff-$(libtiff-version), static, \
 	               --disable-jbig \
 	               --disable-webp \
 	               --disable-zstd)
@@ -652,12 +705,90 @@ $(ibidir)/libtirpc-$(libtirpc-version):
 	               --disable-gssapi, V=1)
 	echo "libtirpc $(libtirpc-version)" > $@
 
+# Metastore is used (through a Git hook) to restore the source modification
+# dates of files after a Git checkout. Another Git hook saves all file
+# metadata just before a commit (to allow restoration after a
+# checkout). Since this project is managed in Makefiles, file modification
+# dates are critical to not having to redo the whole analysis after
+# checking out between branches.
+#
+# Note that we aren't using the standard version of Metastore, but a fork
+# of it that is maintained in this repository:
+#    https://gitlab.com/makhlaghi/metastore-fork
+#
+# Libbsd is not necessary on macOS systems, because macOS is already a
+# BSD-based distribution. But on GNU/Linux systems, it is necessary.
+$(ibidir)/metastore-$(metastore-version): \
+                    $(ibidir)/libbsd-$(libbsd-version)
+
+#	Download the tarball.
+	tarball=metastore-$(metastore-version).tar.lz
+	$(call import-source, $(metastore-url), $(metastore-checksum))
+
+#	Metastore doesn't have any './configure' script. So we'll just call
+#	'pwd' as a place-holder for the './configure' command.
+#
+#	File attributes are also not available on some systems, since the
+#	main purpose here is modification dates (and not attributes), we'll
+#	also set the 'NO_XATTR' flag.
+#
+#	After installing Metastore, write the relevant hooks into this
+#	system's Git hooks, while setting the system-specific
+#	directories/files.
+#
+#	Note that the metastore -O and -G options used in this template are
+#	currently only available in a fork of 'metastore' hosted at:
+#	https://github.com/mohammad-akhlaghi/metastore
+#
+#	Checking for presence of '.git'. When the project source is
+#	downloaded from a non-Git source (for example from arXiv), there is
+#	no '.git' directory to work with. So until we find a better
+#	solution, avoid the step to to add the Git hooks.
+	current_dir=$$(pwd); \
+	$(call gbuild, metastore-$(metastore-version), static,, \
+	               NO_XATTR=1 V=1,,pwd,PREFIX=$(idir))
+
+#	Correct RPATH when necessary.
+	if [ -f $(ibdir)/patchelf ]; then
+	  $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/metastore
+	fi
+
+#	If this project is being built in a directory version controlled
+#	by Git, copy the hooks into the Git configuation.
+	if [ -f $(ibdir)/metastore ]; then
+	  if [ -d .git ]; then
+	    user=$$(whoami)
+	    group=$$(groups | awk '{print $$1}')
+	    cd $$current_dir
+	    for f in pre-commit post-checkout; do
+	       sed -e's|@USER[@]|'$$user'|g' \
+	           -e's|@GROUP[@]|'$$group'|g' \
+	           -e's|@BINDIR[@]|$(ibdir)|g' \
+	           -e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \
+	           reproduce/software/shell/git-$$f > .git/hooks/$$f
+	       chmod +x .git/hooks/$$f
+	    done
+	  fi
+	  echo "Metastore (forked) $(metastore-version)" > $@
+	else
+	  echo; echo; echo
+	  echo "*****************"
+	  echo "metastore couldn't be installed!"
+	  echo
+	  echo "Its used for preserving timestamps on Git commits."
+	  echo "Its useful for development, not simple running of "
+	  echo "the project. So we won't stop the configuration "
+	  echo "because it wasn't built."
+	  echo "*****************"
+	  echo "" > $@
+	fi
+
 $(ibidir)/openblas-$(openblas-version):
-	tarball=OpenBLAS-$(openblas-version).tar.gz
+	tarball=OpenBLAS-$(openblas-version).tar.lz
 	$(call import-source, $(openblas-url), $(openblas-checksum))
 	if [ x$(on_mac_os) = xyes ]; then export CC=clang; fi
 	cd $(ddir)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd OpenBLAS-$(openblas-version)
 	make -j$(numthreads)
 	make PREFIX=$(idir) install
@@ -666,7 +797,7 @@ $(ibidir)/openblas-$(openblas-version):
 	echo "OpenBLAS $(openblas-version)" > $@
 
 $(ibidir)/openmpi-$(openmpi-version):
-	tarball=openmpi-$(openmpi-version).tar.gz
+	tarball=openmpi-$(openmpi-version).tar.lz
 	$(call import-source, $(openmpi-url), $(openmpi-checksum))
 	$(call gbuild, openmpi-$(openmpi-version), static, \
 	               --with-pmix=internal \
@@ -692,22 +823,22 @@ $(ibidir)/openssh-$(openssh-version):
 	echo "OpenSSH $(openssh-version)" > $@
 
 $(ibidir)/pixman-$(pixman-version):
-	tarball=pixman-$(pixman-version).tar.gz
+	tarball=pixman-$(pixman-version).tar.lz
 	$(call import-source, $(pixman-url), $(pixman-checksum))
 	$(call gbuild, pixman-$(pixman-version), static, , \
 	               -j$(numthreads) V=1)
 	echo "Pixman $(pixman-version)" > $@
 
 $(ibidir)/rpcsvc-proto-$(rpcsvc-proto-version):
-        # 'libintl' is installed as part of GNU Gettext in
-        # 'basic.mk'. rpcsvc-proto needs to link with it on macOS.
+#	'libintl' is installed as part of GNU Gettext in
+#	'basic.mk'. rpcsvc-proto needs to link with it on macOS.
 	if [ x$(on_mac_os) = xyes ]; then
 	  export CC=clang
 	  export CXX=clang++
 	  export LDFLAGS="-lintl $$LDFLAGS"
 	fi
 
-        # Download the tarball and build rpcsvc-proto.
+#	Download the tarball and build rpcsvc-proto.
 	tarball=rpcsvc-proto-$(rpcsvc-proto-version).tar.xz
 	$(call import-source, $(rpcsvc-proto-url), $(rpcsvc-proto-checksum))
 	$(call gbuild, rpcsvc-proto-$(rpcsvc-proto-version), static)
@@ -721,35 +852,10 @@ $(ibidir)/tides-$(tides-version):
 	cp $(dtexdir)/tides.tex $(ictdir)/
 	echo "TIDES $(tides-version) \citep{tides}" > $@
 
-$(ibidir)/valgrind-$(valgrind-version): \
-                   $(ibidir)/patch-$(patch-version) \
-                   $(ibidir)/autoconf-$(autoconf-version) \
-                   $(ibidir)/automake-$(automake-version)
-        # Import the tarball
-	tarball=valgrind-$(valgrind-version).tar.bz2
+$(ibidir)/valgrind-$(valgrind-version):
+	tarball=valgrind-$(valgrind-version).tar.lz
 	$(call import-source, $(valgrind-url), $(valgrind-checksum))
-
-        # For valgrind-3.15.0, see
-        # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329 for a
-        # report on an MPI-related compile bug and the two patches
-        # below. These two patches and `automake` should allow valgrind to
-        # compile with gcc-9.2.0.
-	cd $(ddir)
-	tar -xf $(tdir)/$$tarball
-	valgrinddir=valgrind-$(valgrind-version)
-	cd $${valgrinddir}
-	printf "valgrindir=$${valgrinddir} ; pwd = %s .\n" $$($(ibdir)/pwd)
-	if [ "x$(valgrind-version)" = "x3.15.0" ]; then
-	  patch --verbose -p1 < $(patchdir)/valgrind-3.15.0-mpi-fix1.patch
-	  patch --verbose -p1 < $(patchdir)/valgrind-3.15.0-mpi-fix2.patch
-	fi
-	autoreconf
-	./configure --prefix=$(idir)
-	make -j$(numthreads)
-	if ! make check -j$(numthreads); then
-	  echo; echo "Valgrind's 'make check' failed!"; echo
-	fi
-	make install
+	$(call gbuild, valgrind-$(valgrind-version), static)
 	echo "Valgrind $(valgrind-version)" > $@
 
 $(ibidir)/yaml-$(yaml-version):
@@ -773,47 +879,48 @@ $(ibidir)/yaml-$(yaml-version):
 # manually.
 #
 # For example, Libgit2 page recommends doing a static build, especially for
-# Mac systems (with `-DBUILD_SHARED_LIBS=OFF'): "It’s highly recommended
+# Mac systems (with '-DBUILD_SHARED_LIBS=OFF'): "It’s highly recommended
 # that you build libgit2 as a static library for Xcode projects. This
 # simplifies distribution significantly, as the resolution of dynamic
 # libraries at runtime can be extremely problematic.". This is a major
 # problem we have been having so far with Mac systems:
 # https://libgit2.org/docs/guides/build-and-link
-# On macOS system, `libgit2' complains about not finding `_iconv*'
-# functions! But apparently `libgit2' has its own implementation of libiconv
+# On macOS system, 'libgit2' complains about not finding '_iconv*'
+# functions! But apparently 'libgit2' has its own implementation of libiconv
 # that it uses if it can't find libiconv on macOS. So, to fix this problem
-# it is necessary to use the option `-DUSE_ICONV=OFF` in the configure step.
+# it is necessary to use the option '-DUSE_ICONV=OFF' in the configure step.
 $(ibidir)/libgit2-$(libgit2-version): $(ibidir)/cmake-$(cmake-version)
-	tarball=libgit2-$(libgit2-version).tar.gz
+	tarball=libgit2-$(libgit2-version).tar.lz
 	$(call import-source, $(libgit2-url), $(libgit2-checksum))
 	$(call cbuild, libgit2-$(libgit2-version), static, \
 	              -DUSE_SSH=OFF -DBUILD_CLAR=OFF \
 	              -DTHREADSAFE=ON -DUSE_ICONV=OFF )
 	if [ x$(on_mac_os) = xyes ]; then
-	  install_name_tool -id $(ildir)/libgit2.1.0.dylib \
-	                        $(ildir)/libgit2.1.0.dylib
+	  install_name_tool -id $(ildir)/libgit2.1.3.dylib \
+	                        $(ildir)/libgit2.1.3.dylib
 	fi
 	echo "Libgit2 $(libgit2-version)" > $@
 
 $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
-        # Import the tarball.
-	tarball=wcslib-$(wcslib-version).tar.bz2
+
+#	Import the tarball.
+	tarball=wcslib-$(wcslib-version).tar.lz
 	$(call import-source, $(wcslib-url), $(wcslib-checksum))
 
-        # If Fortran isn't present, don't build WCSLIB with it.
+#	If Fortran isn't present, don't build WCSLIB with it.
 	if type gfortran &> /dev/null; then fortranopt="";
 	else fortranopt="--disable-fortran"
 	fi
 
-        # Build WCSLIB.
+#	Build WCSLIB.
 	$(call gbuild, wcslib-$(wcslib-version), , \
 	               LIBS="-pthread -lcurl -lm" \
                        --with-cfitsiolib=$(ildir) \
                        --with-cfitsioinc=$(idir)/include \
                        --without-pgplot $$fortranopt)
 	if [ x$(on_mac_os) = xyes ]; then
-	  install_name_tool -id $(ildir)/libwcs.7.3.dylib \
-	                        $(ildir)/libwcs.7.3.dylib
+	  install_name_tool -id $(ildir)/libwcs.7.7.dylib \
+	                        $(ildir)/libwcs.7.7.dylib
 	fi
 	echo "WCSLIB $(wcslib-version)" > $@
 
@@ -843,17 +950,17 @@ $(ibidir)/astrometrynet-$(astrometrynet-version): \
                         $(ibidir)/cfitsio-$(cfitsio-version) \
                         $(ibidir)/libjpeg-$(libjpeg-version)
 
-        # Import the tarball
-	tarball=astrometry.net-$(astrometrynet-version).tar.gz
+#	Import the tarball
+	tarball=astrometry.net-$(astrometrynet-version).tar.lz
 	$(call import-source, $(astrometrynet-url), $(astrometrynet-checksum))
 
-        # We are modifying the Makefile in two steps because on Mac OS
-        # system we do not have `/proc/cpuinfo' nor `free'. Since this is
-        # only for the `report.txt', this changes do not causes problems in
-        # running `astrometrynet'
+#	We are modifying the Makefile in two steps because on Mac OS system
+#	we do not have '/proc/cpuinfo' nor 'free'. Since this is only for
+#	the 'report.txt', this changes do not causes problems in running
+#	'astrometrynet'
 	cd $(ddir)
 	rm -rf astrometry.net-$(astrometrynet-version)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd astrometry.net-$(astrometrynet-version)
 	sed -e 's|cat /proc/cpuinfo|echo "Ignoring CPU info"|' \
 	    -e 's|-free|echo "Ignoring RAM info"|' Makefile > Makefile.tmp
@@ -874,7 +981,7 @@ $(ibidir)/autoconf-$(autoconf-version):
 	echo "GNU Autoconf $(autoconf-version)" > $@
 
 $(ibidir)/automake-$(automake-version): $(ibidir)/autoconf-$(autoconf-version)
-	tarball=automake-$(automake-version).tar.gz
+	tarball=automake-$(automake-version).tar.lz
 	$(call import-source, $(automake-url), $(automake-checksum))
 	$(call gbuild, automake-$(automake-version), static, ,V=1)
 	echo "GNU Automake $(automake-version)" > $@
@@ -886,17 +993,18 @@ $(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version)
 	echo "GNU Bison $(bison-version)" > $@
 
 # cdsclient is a set of software written in c to interact with astronomical
-# database servers. It is a dependency of `scamp' to be able to download
+# database servers. It is a dependency of 'scamp' to be able to download
 # reference catalogues.
-# NOTE: we do not use a convencional `gbuild' installation because the
+#
+# NOTE: we do not use a convencional 'gbuild' installation because the
 # programs are scripts and we need to touch them before installing.
 # Otherwise this software will be re-built each time the configure step is
 # invoked.
 $(ibidir)/cdsclient-$(cdsclient-version):
-	tarball=cdsclient-$(cdsclient-version).tar.gz
+	tarball=cdsclient-$(cdsclient-version).tar.lz
 	$(call import-source, $(cdsclient-url), $(cdsclient-checksum))
 	cd $(ddir)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd cdsclient-$(cdsclient-version)
 	touch *
 	./configure --prefix=$(idir)
@@ -906,25 +1014,27 @@ $(ibidir)/cdsclient-$(cdsclient-version):
 	rm -rf cdsclient-$(cdsclient-version)
 	echo "cdsclient $(cdsclient-version)" > $@
 
-# CMake can be built with its custom `./bootstrap' script.
-$(ibidir)/cmake-$(cmake-version): $(ibidir)/curl-$(curl-version)
-        # Import the tarball
-	tarball=cmake-$(cmake-version).tar.gz
+# CMake can be built with its custom './bootstrap' script and has no
+# dependencies beyond the basic Maneage software.
+$(ibidir)/cmake-$(cmake-version):
+
+#	Import the tarball
+	tarball=cmake-$(cmake-version).tar.lz
 	$(call import-source, $(cmake-url), $(cmake-checksum))
 
-        # After searching in `bootstrap', I couldn't find `LIBS', only
-        # `LDFLAGS'. So the extra libraries are being added to `LDFLAGS',
-        # not `LIBS'.
-        #
-        # On Mac systems, the build complains about `clang' specific
-        # features, so we can't use our own GCC build here.
+#	After searching in 'bootstrap', I couldn't find 'LIBS', only
+#	'LDFLAGS'. So the extra libraries are being added to 'LDFLAGS', not
+#	'LIBS'.
+#
+#	On Mac systems, the build complains about 'clang' specific
+#	features, so we can't use our own GCC build here.
 	if [ x$(on_mac_os) = xyes ]; then
 	  export CC=clang
 	  export CXX=clang++
 	fi
 	cd $(ddir)
 	rm -rf cmake-$(cmake-version)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd cmake-$(cmake-version)
 	./bootstrap --prefix=$(idir) --system-curl --system-zlib \
 	            --system-bzip2 --system-liblzma --no-qt-gui \
@@ -942,7 +1052,7 @@ $(ibidir)/flex-$(flex-version): $(ibidir)/bison-$(bison-version)
 	echo "Flex $(flex-version)" > $@
 
 $(ibidir)/gdb-$(gdb-version): $(ibidir)/python-$(python-version)
-	tarball=gdb-$(gdb-version).tar.gz
+	tarball=gdb-$(gdb-version).tar.lz
 	export configure_in_different_directory=1;
 	$(call import-source, $(gdb-url), $(gdb-checksum))
 	$(call gbuild, gdb-$(gdb-version),,,V=1 -j$(numthreads))
@@ -956,49 +1066,51 @@ $(ibidir)/ghostscript-$(ghostscript-version): \
                       $(ibidir)/libtiff-$(libtiff-version) \
                       $(ibidir)/libpaper-$(libpaper-version)
 
-        # Download the standard collection of Ghostscript fonts.
-	tarball=ghostscript-fonts-std-$(ghostscript-fonts-std-version).tar.gz
+#	Download the standard collection of Ghostscript fonts.
+	tarball=ghostscript-fonts-std-$(ghostscript-fonts-std-version).tar.lz
 	$(call import-source, $(ghostscript-fonts-std-url), \
 	                      $(ghostscript-fonts-std-checksum))
 
-        # Download the extra GNU fonts for Ghostscript.
-	tarball=ghostscript-fonts-gnu-$(ghostscript-fonts-gnu-version).tar.gz
+#	Download the extra GNU fonts for Ghostscript.
+	tarball=ghostscript-fonts-gnu-$(ghostscript-fonts-gnu-version).tar.lz
 	$(call import-source, $(ghostscript-fonts-gnu-url), \
 	                      $(ghostscript-fonts-gnu-checksum))
 
-        # Download the tarball
-	tarball=ghostscript-$(ghostscript-version).tar.gz
+#	Download the tarball
+	tarball=ghostscript-$(ghostscript-version).tar.lz
 	$(call import-source, $(ghostscript-url), $(ghostscript-checksum))
 
-        # Unpack it and configure Ghostscript.
+#	Unpack it and configure Ghostscript. The option
+#	'-DPNG_ARM_NEON_OPT=0' prevents an arm64 'neon' library from being
+#	required at compile time.
 	cd $(ddir)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd ghostscript-$(ghostscript-version)
 	./configure --prefix=$(idir) \
 	            --disable-cups \
 	            --enable-dynamic \
-	            --with-system-libtiff \
-	            --disable-compile-inits
+	            --disable-compile-inits \
+	            CFLAGS="-DPNG_ARM_NEON_OPT=0"
 
-        # Build and install the program and the shared libraries.
+#	Build and install the program and the shared libraries.
 	make    V=1 -j$(numthreads)
 	make so V=1 -j$(numthreads)
 	make install
 	make soinstall
 
-        # Install headers and set PostScript (PS) headers to point there.
+#	Install headers and set PostScript (PS) headers to point there.
 	install -v -m644 base/*.h $(iidir)/ghostscript
 	ln -sfvn $(iidir)/ghostscript $(iidir)/ps
 
-        # Install the fonts.
-	tar -xvf $(tdir)/ghostscript-fonts-std-$(ghostscript-fonts-std-version).tar.gz \
+#	Install the fonts.
+	tar -xvf $(tdir)/ghostscript-fonts-std-$(ghostscript-fonts-std-version).tar.lz \
 	    -C $(idir)/share/ghostscript
-	tar -xvf $(tdir)/ghostscript-fonts-gnu-$(ghostscript-fonts-gnu-version).tar.gz \
+	tar -xvf $(tdir)/ghostscript-fonts-gnu-$(ghostscript-fonts-gnu-version).tar.lz \
 	    -C $(idir)/share/ghostscript
 	fc-cache -v $(idir)/share/ghostscript/fonts/
 	echo; echo "Ghostscript fonts added to Fontconfig."; echo;
 
-        # Clean up and write the output target.
+#	Clean up and write the output target.
 	cd ..
 	rm -rf ghostscript-$(ghostscript-version)
 	echo "GPL Ghostscript $(ghostscript-version)" > $@
@@ -1018,48 +1130,74 @@ $(ibidir)/gnuastro-$(gnuastro-version): \
 	echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
 
 $(ibidir)/help2man-$(help2man-version):
-	tarball=help2man-$(help2man-version).tar.xz
+	tarball=help2man-$(help2man-version).tar.lz
 	$(call import-source, $(help2man-url), $(help2man-checksum))
 	$(call gbuild, help2man-$(help2man-version), static, ,V=1)
 	echo "Help2man $(Help2man-version)" > $@
 
+$(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version)
+
+#	First, we need to remove any possibly existing ICU installation
+#	because it can cause conflicts during a new configuration
+#	(especially if a new version is to replace the old one).
+	for i in data i18n io test tu uc; do
+	  rm -fv $(ildir)/libicu$$i.*;
+	done
+
+#	Prepare the tarball, unpack, build and install ICU (some
+#	customizations are necessary, so we're not using 'gbuild').
+	tarball=icu-$(icu-version).tar.lz
+	$(call import-source, $(icu-url), $(icu-checksum))
+	cd $(ddir)
+	tar -xf $(tdir)/$$tarball
+	unpackdir=icu-$(icu-version)
+	cd $$unpackdir/icu4c/source
+	./configure --enable-static --prefix=$(idir)
+	make -j$(numthreads) V=1
+	make install
+	cd $(ddir)
+	rm -rf $$unpackdir
+	echo "ICU $(icu-version)" > $@
+
 $(ibidir)/imagemagick-$(imagemagick-version): \
                       $(ibidir)/zlib-$(zlib-version) \
                       $(ibidir)/libjpeg-$(libjpeg-version) \
                       $(ibidir)/libtiff-$(libtiff-version)
-	tarball=imagemagick-$(imagemagick-version).tar.xz
+	tarball=ImageMagick-$(imagemagick-version).tar.lz
 	$(call import-source, $(imagemagick-url), $(imagemagick-checksum))
 	$(call gbuild, ImageMagick-$(imagemagick-version), static, \
 		       --without-x --disable-openmp, V=1 -j$(numthreads))
 	echo "ImageMagick $(imagemagick-version)" > $@
 
-# `imfit' doesn't use the traditional `configure' and `make' to install
-# itself.  Instead of that, it uses `scons'. As a consequence, the
+# 'imfit' doesn't use the traditional 'configure' and 'make' to install
+# itself.  Instead of that, it uses 'scons'. As a consequence, the
 # installation is manually done by decompressing the tarball, and running
-# `scons' with the necessary flags. Despite of that, it is necessary to
+# 'scons' with the necessary flags. Despite of that, it is necessary to
 # replace the default searching paths in this script by our installation
-# paths. This is done with `sed', replacing each ocurrence of `/usr/local'
-# by `$(idir)'. After that, each compiled program (`imfit', `imfit-mcmc'
-# and `makeimage') is copied into the installation directory and an `rpath'
+# paths. This is done with 'sed', replacing each ocurrence of '/usr/local'
+# by '$(idir)'. After that, each compiled program ('imfit', 'imfit-mcmc'
+# and 'makeimage') is copied into the installation directory and an 'rpath'
 # is added.
 $(ibidir)/imfit-$(imfit-version): \
                 $(ibidir)/gsl-$(gsl-version) \
                 $(ibidir)/fftw-$(fftw-version) \
                 $(ibidir)/scons-$(scons-version) \
                 $(ibidir)/cfitsio-$(cfitsio-version)
+
+#	Prepare the source.
 	tarball=imfit-$(imfit-version).tar.gz
 	$(call import-source, $(imfit-url), $(imfit-checksum))
 
-        # If the C library is in a non-standard location.
+#	If the C library is in a non-standard location.
 	if ! [ x$(SYS_CPATH) = x ]; then
 	  headerpath="--header-path=$(SYS_CPATH)"
 	fi
 
-        # Unpack and build imfit and its accompanying programs.
+#	Unpack and build imfit and its accompanying programs.
 	cd $(ddir)
 	unpackdir=imfit-$(imfit-version)
 	rm -rf $$unpackdir
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
 	sed -i 's|/usr/local|$(idir)|g' SConstruct
 	sed -i 's|/usr/include|$(idir)/include|g' SConstruct
@@ -1086,6 +1224,8 @@ $(ibidir)/imfit-$(imfit-version): \
 	  done
 	fi
 	cp $(dtexdir)/imfit.tex $(ictdir)/
+	cd ..
+	rm -rf $$unpackdir
 	echo "Imfit $(imfit-version) \citep{imfit2015}" > $@
 
 # Minizip 1.x is actually distributed within zlib. It doesn't have its own
@@ -1098,13 +1238,13 @@ $(ibidir)/imfit-$(imfit-version): \
 # About deleting the final crypt.h file after installation, see
 # https://bugzilla.redhat.com/show_bug.cgi?id=1424609
 $(ibidir)/minizip-$(minizip-version): $(ibidir)/automake-$(automake-version)
-	tarball=zlib-$(zlib-version).tar.gz
-	$(call import-source, $(minizip-url), $(minizip-checksum))
+	tarball=zlib-$(zlib-version).tar.lz
+	$(call import-source, $(zlib-url), $(zlib-checksum))
 	cd $(ddir)
 	unpackdir=minizip-$(minizip-version)
 	rm -rf $$unpackdir
 	mkdir $$unpackdir
-	tar xf $(tdir)/$$tarball -C$$unpackdir --strip-components=1
+	tar -xf $(tdir)/$$tarball -C$$unpackdir --strip-components=1
 	cd $$unpackdir
 	./configure --prefix=$(idir)
 	make
@@ -1140,16 +1280,18 @@ $(ibidir)/missfits-$(missfits-version):
 
 # Netpbm is a prerequisite of Astrometry-net, it contains a lot of programs.
 # This program has a crazy dialogue installation which is override using the
-# printf statment. Each `\n' is a new question that the installation process
+# printf statment. Each '\n' is a new question that the installation process
 # ask to the user. We give all answers with a pipe to the scripts (configure
 # and install). The questions are different depending on the system (tested
 # on GNU/Linux and Mac OS).
 $(ibidir)/netpbm-$(netpbm-version): \
+                 $(ibidir)/flex-$(flex-version) \
                  $(ibidir)/libpng-$(libpng-version) \
+                 $(ibidir)/libx11-$(libx11-version) \
                  $(ibidir)/libjpeg-$(libjpeg-version) \
                  $(ibidir)/libtiff-$(libtiff-version) \
                  $(ibidir)/libxml2-$(libxml2-version)
-	tarball=netpbm-$(netpbm-version).tar.gz
+	tarball=netpbm-$(netpbm-version).tar.lz
 	$(call import-source, $(netpbm-url), $(netpbm-checksum))
 	if [ x$(on_mac_os) = xyes ]; then
 	  answers='\n\n$(ildir)\n\n\n\n\n\n$(ildir)/include\n\n$(ildir)/include\n\n$(ildir)/include\nnone\n\n'
@@ -1159,7 +1301,7 @@ $(ibidir)/netpbm-$(netpbm-version): \
 	cd $(ddir)
 	unpackdir=netpbm-$(netpbm-version)
 	rm -rf $$unpackdir
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
 	printf "$$answers" | ./configure
 	make
@@ -1189,60 +1331,15 @@ $(ibidir)/pcre-$(pcre-version):
 	               , V=1 -j$(numthreads))
 	echo "Perl Compatible Regular Expressions $(pcre-version)" > $@
 
-# Comment on building R without GUI support ('--without-tcltlk')
-#
-# Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support
-# in some software. But they are not yet natively built within Maneage,
-# primarily because we have higher-priority work right now (if anyone is
-# interested, they can ofcourse contribute!). GUI tools in general aren't
-# high on our priority list right now because they are generally good for
-# human interaction (which is contrary to the reproducible philosophy:
-# there will always be human-error and frustration, for example in GUI
-# tools the best level of reproducibility is statements like this: "move
-# your mouse to button XXX, then click on menu YYY and etc"). A robust
-# reproducible solution must be done automatically.
-#
-# If someone wants to use R's GUI functionalities while investigating for
-# their analysis, they can do the GUI part on their host OS
-# implementation. Later, they can bring the finalized source into Maneage
-# to be automatically run in Maneage. This will also be the recommended way
-# to deal with GUI tools later when we do install them within Maneage.
-$(ibidir)/R-$(R-version): \
-            $(ibidir)/pcre-$(pcre-version) \
-            $(ibidir)/cairo-$(cairo-version) \
-            $(ibidir)/libpng-$(libpng-version) \
-            $(ibidir)/libjpeg-$(libjpeg-version) \
-            $(ibidir)/libtiff-$(libtiff-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)
-	./configure --prefix=$(idir) \
-	            --without-x \
-	            --with-pcre1 \
-	            --disable-java \
-	            --with-readline \
-	            --without-tcltk \
-	            --disable-openmp
-	make -j$(numthreads)
-	make install
-	cd ..
-	rm -rf R-$(R-version)
-	echo "R $(R-version)" > $@
+# 2022-01-01 The rules for building R - identified as r-cran to avoid the
+# difficulties in searching text for a one-letter string - were shifted to
+# 'r-cran.mk'.
 
 # SCAMP documentation says ATLAS is a mandatory prerequisite for using
 # SCAMP. We have ATLAS into the project but there are some problems with the
 # libraries that are not yet solved. However, we tried to install it with
 # the option --enable-openblas and it worked (same issue happened with
-# `sextractor'.
+# 'sextractor'.
 $(ibidir)/scamp-$(scamp-version): \
                 $(ibidir)/fftw-$(fftw-version) \
                 $(ibidir)/openblas-$(openblas-version) \
@@ -1250,7 +1347,7 @@ $(ibidir)/scamp-$(scamp-version): \
 	tarball=scamp-$(scamp-version).tar.lz
 	$(call import-source, $(scamp-url), $(scamp-checksum))
 
-        # See comment above 'missfits' for '-fcommon'.
+#	See comment above 'missfits' for '-fcommon'.
 	$(call gbuild, scamp-$(scamp-version), static, \
 	           CFLAGS="-fcommon" \
                    --enable-threads \
@@ -1263,17 +1360,19 @@ $(ibidir)/scamp-$(scamp-version): \
 	cp $(dtexdir)/scamp.tex $(ictdir)/
 	echo "SCAMP $(scamp-version) \citep{scamp}" > $@
 
-# Since `scons' doesn't use the traditional GNU installation with
-# `configure' and `make' it is installed manually using `python'.
+# Since 'scons' doesn't use the traditional GNU installation with
+# 'configure' and 'make' it is installed manually using 'python'.
 $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version)
 	tarball=scons-$(scons-version).tar.gz
 	$(call import-source, $(scons-url), $(scons-checksum))
 	cd $(ddir)
 	unpackdir=scons-$(scons-version)
 	rm -rf $$unpackdir
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
 	python setup.py install
+	cd ..
+	rm -rf $$unpackdir
 	echo "SCons $(scons-version)" > $@
 
 # Sextractor crashes complaining about not linking with some ATLAS
@@ -1289,7 +1388,7 @@ $(ibidir)/sextractor-$(sextractor-version): \
 	tarball=sextractor-$(sextractor-version).tar.lz
 	$(call import-source, $(sextractor-url), $(sextractor-checksum))
 
-        # See comment above 'missfits' for '-fcommon'.
+#	See comment above 'missfits' for '-fcommon'.
 	$(call gbuild, sextractor-$(sextractor-version), static, \
 	               CFLAGS="-fcommon" \
 	               --enable-threads \
@@ -1304,7 +1403,7 @@ $(ibidir)/swarp-$(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'.
+#	See comment above 'missfits' for '-fcommon'.
 	$(call gbuild, swarp-$(swarp-version), static, \
 	               CFLAGS="-fcommon" \
                        --enable-threads)
@@ -1312,10 +1411,11 @@ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version)
 	echo "SWarp $(swarp-version) \citep{swarp}" > $@
 
 $(ibidir)/swig-$(swig-version):
-        # Option --without-pcre was a suggestion once the configure step
-        # was tried and it failed. It was not recommended but it works!
-        # pcr is a dependency of swig
-	tarball=swig-$(swig-version).tar.gz
+
+#	Option --without-pcre was a suggestion once the configure step was
+#	tried and it failed. It was not recommended but it works!  pcr is a
+#	dependency of swig
+	tarball=swig-$(swig-version).tar.lz
 	$(call import-source, $(swig-url), $(swig-checksum))
 	$(call gbuild, swig-$(swig-version), static, \
 	               --without-pcre --without-tcl)
@@ -1345,19 +1445,19 @@ $(ibidir)/swig-$(swig-version):
 # '$(ibdir)'. If any program does need 'util-linux' libraries, they can
 # simply add the proper directories to the environment variables, see
 # 'fontconfig' for example.
-$(ibidir)/util-linux-$(util-linux-version):
+$(ibidir)/util-linux-$(util-linux-version): | $(idircustom)
 
-        # Import the source.
-	tarball=util-linux-$(util-linux-version).tar.xz
+#	Import the source.
+	tarball=util-linux-$(util-linux-version).tar.lz
 	$(call import-source, $(util-linux-url), $(util-linux-checksum))
 
-        # Unpack the source and set it to install in a special directory
-        # (as explained above). As shown below, later, we'll put a symbolic
-        # link of all the necessary binaries in the main '$(idir)/bin'.
+#	Unpack the source and set it to install in a special directory (as
+#	explained above). As shown below, later, we'll put a symbolic link
+#	of all the necessary binaries in the main '$(idir)/bin'.
 	cd $(ddir)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	cd util-linux-$(util-linux-version)
-	./configure --prefix=$(idir)/util-linux \
+	./configure --prefix=$(idircustom)/util-linux \
 	            --disable-dependency-tracking \
 	            --disable-silent-rules \
 	            --without-systemd \
@@ -1368,21 +1468,21 @@ $(ibidir)/util-linux-$(util-linux-version):
 	            --disable-wall \
 	            --disable-su
 
-        # Build and install it.
+#	Build and install it.
 	make V=1 -j$(numthreads)
 	make install
 
-        # Put a symbolic link to installed programs in main installation
-        # directory. If 'sbin' exists in the main installation directory,
-        # put util-linux's 'sbin/' directory there too.
-	ln -sf $(idir)/util-linux/bin/* $(ibdir)/
+#	Put a symbolic link to installed programs in main installation
+#	directory. If 'sbin' exists in the main installation directory, put
+#	util-linux's 'sbin/' directory there too.
+	ln -sf $(idircustom)/util-linux/bin/* $(ibdir)/
 	if [ -d $(idir)/sbin ]; then
-	  ln -sf $(idir)/util-linux/sbin/* $(idir)/sbin
+	  ln -sf $(idircustom)/util-linux/sbin/* $(idir)/sbin
 	else
-	  ln -sf $(idir)/util-linux/sbin/* $(idir)/bin
+	  ln -sf $(idircustom)/util-linux/sbin/* $(idir)/bin
 	fi
 
-        # Clean up and write the main target.
+#	Clean up and write the main target.
 	cd ../
 	rm -rf util-linux-$(util-linux-version)
 	echo "util-Linux $(util-linux-version)" > $@
@@ -1428,7 +1528,7 @@ $(ibidir)/vim-$(vim-version):
 	tarball=vim-$(vim-version).tar.bz2
 	$(call import-source, $(vim-url), $(vim-checksum))
 	cd $(ddir)
-	tar xf $(tdir)/$$tarball
+	tar -xf $(tdir)/$$tarball
 	n=$$(echo $(vim-version) | sed -e's|\.||')
 	cd $(ddir)/vim$$n
 	./configure --prefix=$(idir) \
@@ -1455,7 +1555,7 @@ $(ibidir)/vim-$(vim-version):
 # hard to track for Make (as a target). Also, TeX in general is optional
 # for the project (the processing is the main target, not the generation of
 # the final PDF). So we'll make a simple ASCII file called
-# `texlive-ready-tlmgr' and use its contents to mark if we can use it or
+# 'texlive-ready-tlmgr' and use its contents to mark if we can use it or
 # not.
 #
 # TeX Live mirror
@@ -1463,8 +1563,8 @@ $(ibidir)/vim-$(vim-version):
 #
 # The automatic mirror finding fails sometimes. So we'll manually set it to
 # use a fixed mirror. I first tried the LaTeX root webpage
-# (`ftp.dante.de'), however, it is far too slow (when I tested it). The
-# `rit.edu' server seems to be a good alternative (given the importance of
+# ('ftp.dante.de'), however, it is far too slow (when I tested it). The
+# 'rit.edu' server seems to be a good alternative (given the importance of
 # NY on the internet infrastructure).
 texlive-url=http://mirrors.rit.edu/CTAN/systems/texlive/tlnet
 $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
@@ -1472,81 +1572,81 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 	tarball=install-tl-unx.tar.gz
 	$(call import-source, $(texlive-url), NO-CHECK-SUM)
 
-        # Unpack, enter the directory, and install based on the given
-        # configuration (prerequisite of this rule).
+#	Unpack, enter the directory, and install based on the given
+#	configuration (prerequisite of this rule).
 	@topdir=$$(pwd)
 	cd $(ddir)
 	rm -rf install-tl-*
-	tar xf $(tdir)/install-tl-unx.tar.gz
+	tar -xf $(tdir)/install-tl-unx.tar.gz
 	cd install-tl-*
 	sed -e's|@installdir[@]|$(idir)|g' \
 	    "$$topdir"/reproduce/software/config/texlive.conf \
 	    > texlive.conf
 
-        # TeX Live's installation may fail due to any reason. But TeX Live
-        # is optional (only necessary for building the final PDF). So we
-        # don't want the configure script to fail if it can't run.
-        # Possible error messages will be saved into `log.txt' and if it
-        # fails, 'log.txt' will be checked to see if the error is due to
-        # the different version of the current tarball and the TeXLive
-        # server or something else.
-        #
-        # The problem with versions is this: each installer tarball (that
-        # is downloaded and a user may backup) is for a specific version of
-        # TeXLive (specified by year, usually around April). So if a user
-        # has an old tarball, but the CTAN server has been updated, the
-        # script will fail with a message like this:
-        #
-        #     =============================================================
-        #     ./install-tl: The TeX Live versions of the local installation
-        #     and the repository being accessed are not compatible:
-        #           local: 2019
-        #      repository: 2020
-        #     Perhaps you need to use a different CTAN mirror?
-        #     (For more, see the output of install-tl --help, especially the
-        #     -repository option.  Online via https://tug.org/texlive/doc.)
-        #     =============================================================
-        #
-        # To address this problem, when this happens, we simply download a
-        # the most recent tarball, and if it succeeds, we will build
-        # TeXLive using that. The old tarball will be preserved, but will
-        # have an '-OLD' suffix after it.
+#	TeX Live's installation may fail due to any reason. But TeX Live is
+#	optional (only necessary for building the final PDF). So we don't
+#	want the configure script to fail if it can't run.  Possible error
+#	messages will be saved into 'log.txt' and if it fails, 'log.txt'
+#	will be checked to see if the error is due to the different version
+#	of the current tarball and the TeXLive server or something else.
+#
+#	The problem with versions is this: each installer tarball (that is
+#	downloaded and a user may backup) is for a specific version of
+#	TeXLive (specified by year, usually around April). So if a user has
+#	an old tarball, but the CTAN server has been updated, the script
+#	will fail with a message like this:
+#
+#	      =============================================================
+#	      ./install-tl: The TeX Live versions of the local installation
+#	      and the repository being accessed are not compatible:
+#	              local: 2019
+#	         repository: 2020
+#	      Perhaps you need to use a different CTAN mirror?
+#	      (For more, see the output of install-tl --help, especially the
+#	      -repository option.  Online via https://tug.org/texlive/doc.)
+#	      =============================================================
+#
+#	To address this problem, when this happens, we simply download a
+#	the most recent tarball, and if it succeeds, we will build TeXLive
+#	using that. The old tarball will be preserved, but will have an
+#	'-OLD' suffix after it.
 	if ./install-tl --profile=texlive.conf -repository \
 	                $(texlive-url) 2> log.txt; then
 
-          # Put a symbolic link of the TeX Live executables in `ibdir' to
-          # avoid all the complexities of its sub-directories and additions
-          # to PATH.
+#	  Put a symbolic link of the TeX Live executables in 'ibdir' to
+#	  avoid all the complexities of its sub-directories and additions
+#	  to PATH.
 	  ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/
 
-          # Register that the build was successful.
+#	  Register that the build was successful.
 	  echo "TeX Live is ready." > $@
 
-        # The build failed!
+#	The build failed!
 	else
-	  # Print on the command line the error messages during the
-	  # installation.
+#	  Print on the command line the error messages during the
+#	  installation.
 	  cat log.txt
 
-	  # Look for words `repository:' and `local:' in `log.txt' and make
-	  # sure that two lines are returned. Note that we need to check
-	  # for two lines because one of them may exist, but another may
-	  # not (in this case, its not a version conflict scenario).
+#	  Look for words 'repository:' and 'local:' in 'log.txt' and make
+#	  sure that two lines are returned. Note that we need to check for
+#	  two lines because one of them may exist, but another may not (in
+#	  this case, its not a version conflict scenario).
 	  version_check=$$(grep -w 'repository:\|local:' log.txt | wc -l)
 
-	  # If these words exists and two lines are found, there is a
-	  # conflict with the main TeXLive version in the tarball and on
-	  # the server. So it is necessary to move the old tarball and
-	  # download the new one to install it.
+#	  If these words exists and two lines are found, there is a
+#	  conflict with the main TeXLive version in the tarball and on the
+#	  server. So it is necessary to move the old tarball and download
+#	  the new one to install it.
 	  if [ x"$$version_check" = x2 ]; then
-            # Go back to the top project directory, don't remove the
-            # tarball, just rename it.
+
+#	    Go back to the top project directory, don't remove the tarball,
+#	    just rename it.
 	    cd $$topdir
 	    mv $(tdir)/install-tl-unx.tar.gz $(tdir)/install-tl-unx-OLD.tar.gz
 
-            # Download using the script specially defined for this job. If
-            # the download of new tarball success, install it (same lines
-            # than above). If not, record the fail into the target.
+#	    Download using the script specially defined for this job. If
+#	    the download of new tarball success, install it (same lines
+#	    than above). If not, record the fail into the target.
 	    url=http://mirror.ctan.org/systems/texlive/tlnet
 	    tarballurl=$$url/install-tl-unx.tar.gz
 	    touch $(lockdir)/download
@@ -1556,7 +1656,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 	                          "$(backupservers)"; then
 	      cd $(ddir)
 	      rm -rf install-tl-*
-	      tar xf $(tdir)/install-tl-unx.tar.gz
+	      tar -xf $(tdir)/install-tl-unx.tar.gz
 	      cd install-tl-*
 	      sed -e's|@installdir[@]|$(idir)|g' \
 	          $$topdir/reproduce/software/config/texlive.conf \
@@ -1576,7 +1676,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 	  fi
 	fi
 
-        # Clean up
+#	Clean up
 	cd ..
 	rm -rf install-tl-*
 
@@ -1590,49 +1690,50 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 #
 # Note that Biber needs to link with libraries like libnsl. However, we
 # don't currently build biber from source. So we can't choose the library
-# version. But we have the source and build instructions for the `nsl'
+# version. But we have the source and build instructions for the 'nsl'
 # library. When we later build biber from source, we can easily use them.
 $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
                    $(itidir)/texlive-ready-tlmgr
 
-        # To work with TeX live installation, we'll need the internet.
+#	To work with TeX live installation, we'll need the internet.
 	@res=$$(cat $(itidir)/texlive-ready-tlmgr)
 	if [ x"$$res" = x"NOT!" ]; then
 	  echo "" > $@
 	else
-          # To update itself, tlmgr needs a backup directory.
+
+#	  To update itself, tlmgr needs a backup directory.
 	  backupdir=$(idir)/texlive/backups
 	  mkdir -p $$backupdir
 
-          # Before checking LaTeX packages, update tlmgr itself.
+#	  Before checking LaTeX packages, update tlmgr itself.
 	  tlmgr option backupdir $$backupdir
 	  tlmgr -repository $(texlive-url) update --self
 
-          # Install all the extra necessary packages. If LaTeX complains
-          # about not finding a command/file/what-ever/XXXXXX, simply run
-          # the following command to find which package its in, then add it
-          # to the `texlive-packages' variable of the first prerequisite.
-          #
-          #     ./.local/bin/tlmgr info XXXXXX
-          #
-          # We are putting a notice, because if there is no internet,
-          # `tlmgr' just hangs waiting.
+#	  Install all the extra necessary packages. If LaTeX complains
+#	  about not finding a command/file/what-ever/XXXXXX, simply run the
+#	  following command to find which package its in, then add it to
+#	  the 'texlive-packages' variable of the first prerequisite.
+#
+#	      ./.local/bin/tlmgr info XXXXXX
+#
+#	  We are putting a notice, because if there is no internet, 'tlmgr'
+#	  just hangs waiting.
 	  tlmgr install $(texlive-packages)
 
-          # Make a symbolic link of all the TeX Live executables in the bin
-          # directory so we don't have to modify `PATH'.
+#	  Make a symbolic link of all the TeX Live executables in the bin
+#	  directory so we don't have to modify 'PATH'.
 	  ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/
 
-          # Get all the necessary versions.
+#	  Get all the necessary versions.
 	  texlive=$$(pdflatex --version \
 	                      | awk 'NR==1' \
 	                      | sed 's/.*(\(.*\))/\1/' \
 	                      | awk '{print $$NF}');
 
-          # Package names and versions. Note that all TeXLive packages
-          # don't have a version unfortunately! So we need to also read the
-          # `revision' and `cat-date' elements and print them incase
-          # version isn't available.
+#	  Package names and versions. Note that all TeXLive packages
+#	  don't have a version unfortunately! So we need to also read the
+#	  'revision' and 'cat-date' elements and print them incase
+#	  version isn't available.
 	  tlmgr info $(texlive-packages) --only-installed | awk \
 	       '$$1=="package:" { \
 	           if(name!=0) \
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 18c68de..6766744 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -4,7 +4,7 @@
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
 # This Makefile will be loaded into 'high-level.mk', which is called by the
-# `./project configure' script. It is not included into the project
+# './project configure' script. It is not included into the project
 # afterwards.
 #
 # This Makefile contains instructions to build all the Python-related
@@ -12,8 +12,8 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -35,7 +35,7 @@
 # Python enviroment
 # -----------------
 #
-# The main Python environment variable is `PYTHONPATH'. However, so far we
+# The main Python environment variable is 'PYTHONPATH'. However, so far we
 # have found several other Python-related environment variables on some
 # systems which might interfere. To be safe, we are removing all their
 # values.
@@ -62,19 +62,20 @@ python-major-version = $(shell echo $(python-version) | awk 'BEGIN{FS="."} \
 # While this Makefile is for Python programs, in some cases, we need
 # certain programs (like Python itself), or libraries for the modules.
 $(ibidir)/libffi-$(libffi-version):
-        # Prepare the source.
-	tarball=libffi-$(libffi-version).tar.gz
+
+#	Prepare the source.
+	tarball=libffi-$(libffi-version).tar.lz
 	$(call import-source, $(libffi-url), $(libffi-checksum))
 
-        # Build libffi.
+#	Build libffi.
 	$(call gbuild, libffi-$(libffi-version), , \
                        CFLAGS="-DNO_JAVA_RAW_API=1")
 
-        # On some Fedora systems, libffi installs in `lib64', not
-        # `lib'. This will cause problems when building setuptools
-        # later. To fix this problem, we'll first check if this has indeed
-        # happened (it exists under `lib64', but not under `lib'). If so,
-        # we'll put a copy of the installed libffi libraries in `lib'.
+#	On some Fedora systems, libffi installs in 'lib64', not 'lib'. This
+#	will cause problems when building setuptools later. To fix this
+#	problem, we'll first check if this has indeed happened (it exists
+#	under 'lib64', but not under 'lib'). If so, we'll put a copy of the
+#	installed libffi libraries in 'lib'.
 	if [ -f $(idir)/lib64/libffi.a ] && ! [ -f $(idir)/lib/libffi.a ]; then
 	  cp $(idir)/lib64/libffi* $(ildir)/
 	fi
@@ -82,17 +83,17 @@ $(ibidir)/libffi-$(libffi-version):
 
 $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
 
-        # Download the source.
-	tarball=python-$(python-version).tar.gz
+#	Download the source.
+	tarball=python-$(python-version).tar.lz
 	$(call import-source, $(python-url), $(python-checksum))
 
-        # On Mac systems, the build complains about `clang' specific
-        # features, so we can't use our own GCC build here.
+#	On Mac systems, the build complains about 'clang' specific
+#	features, so we can't use our own GCC build here.
 	if [ x$(on_mac_os) = xyes ]; then
 	  export CC=clang
 	  export CXX=clang++
 	fi
-	$(call gbuild, Python-$(python-version),, \
+	$(call gbuild, python-$(python-version),, \
 	       --without-ensurepip \
 	       --with-system-ffi \
 	       --enable-shared, -j$(numthreads))
@@ -110,10 +111,10 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
 # Non-PiP Python module installation
 # ----------------------------------
 #
-# To build Python packages with direct access to a `setup.py' (if no direct
-# access to `setup.py' is needed, pip can be used). Note that the
+# To build Python packages with direct access to a 'setup.py' (if no direct
+# access to 'setup.py' is needed, pip can be used). Note that the
 # software's packaged source code is the first prerequisite that is in the
-# `tdir' directory.
+# 'tdir' directory.
 #
 # Arguments of this function are the numbers
 #   1) Unpack command
@@ -122,8 +123,8 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
 #   4) Official software name (for paper).
 #
 # Hooks:
-#   pyhook_before: optional steps before running `python setup.py build'
-#   pyhook_after: optional steps after running `python setup.py install'
+#   pyhook_before: optional steps before running 'python setup.py build'
+#   pyhook_after: optional steps after running 'python setup.py install'
 pybuild = cd $(ddir); rm -rf $(2); \
 	if ! $(1) $(tdir)/$$tarball; then \
 	  echo; echo "Tar error"; exit 1; \
@@ -153,13 +154,13 @@ pybuild = cd $(ddir); rm -rf $(2); \
 $(ipydir)/asn1crypto-$(asn1crypto-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=asn1crypto-$(asn1crypto-version).tar.gz
 	$(call import-source, $(asn1crypto-url), $(asn1crypto-checksum))
-	$(call pybuild, tar xf, asn1crypto-$(asn1crypto-version), , \
+	$(call pybuild, tar -xf, asn1crypto-$(asn1crypto-version), , \
 	                Asn1crypto $(asn1crypto-version))
 
 $(ipydir)/asteval-$(asteval-version): $(ipydir)/numpy-$(numpy-version)
 	tarball=asteval-$(asteval-version).tar.gz
 	$(call import-source, $(asteval-url), $(asteval-checksum))
-	$(call pybuild, tar xf, asteval-$(asteval-version), , \
+	$(call pybuild, tar -xf, asteval-$(asteval-version), , \
 	                ASTEVAL $(asteval-version))
 
 $(ipydir)/astroquery-$(astroquery-version): \
@@ -168,7 +169,7 @@ $(ipydir)/astroquery-$(astroquery-version): \
                      $(ipydir)/requests-$(requests-version)
 	tarball=astroquery-$(astroquery-version).tar.gz
 	$(call import-source, $(astroquery-url), $(astroquery-checksum))
-	$(call pybuild, tar xf, astroquery-$(astroquery-version), , \
+	$(call pybuild, tar -xf, astroquery-$(astroquery-version), , \
 	                Astroquery $(astroquery-version))
 
 $(ipydir)/astropy-$(astropy-version): \
@@ -177,87 +178,84 @@ $(ipydir)/astropy-$(astropy-version): \
                   $(ipydir)/scipy-$(scipy-version) \
                   $(ipydir)/numpy-$(numpy-version) \
                   $(ipydir)/pyyaml-$(pyyaml-version) \
+                  $(ipydir)/jinja2-$(jinja2-version) \
+                  $(ipydir)/pyerfa-$(pyerfa-version) \
                   $(ipydir)/html5lib-$(html5lib-version) \
-                  $(ipydir)/beautifulsoup4-$(beautifulsoup4-version)
-
-        # Download the source.
-	tarball=astropy-$(astropy-version).tar.gz
+                  $(ipydir)/beautifulsoup4-$(beautifulsoup4-version) \
+                  $(ipydir)/extension-helpers-$(extension-helpers-version)
+	tarball=astropy-$(astropy-version).tar.lz
 	$(call import-source, $(astropy-url), $(astropy-checksum))
-
-        # Currently, when the Expat library is already built in a project
-        # (for example as a dependency of another program), Astropy's
-        # internal building of Expat will conflict with the project's. So
-        # we have added Expat as a dependency of Astropy (so it is always
-        # built before it, and we tell Astropy to use the project's
-        # libexpat.
-	pyhook_before () {
-	  echo ""                   >> setup.cfg
-	  echo "[build]"            >> setup.cfg
-	  echo "use_system_expat=1" >> setup.cfg
-	}
-	$(call pybuild, tar xf, astropy-$(astropy-version))
+	$(call pybuild, tar -xf, astropy-$(astropy-version))
 	cp $(dtexdir)/astropy.tex $(ictdir)/
 	echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@
 
 $(ipydir)/beautifulsoup4-$(beautifulsoup4-version): \
                          $(ipydir)/soupsieve-$(soupsieve-version)
-	tarball=beautifulsoup4-$(beautifulsoup4-version).tar.gz
+	tarball=beautifulsoup4-$(beautifulsoup4-version).tar.lz
 	$(call import-source, $(beautifulsoup4-url), $(beautifulsoup4-checksum))
-	$(call pybuild, tar xf, beautifulsoup4-$(beautifulsoup4-version), , \
+	$(call pybuild, tar -xf, beautifulsoup4-$(beautifulsoup4-version), , \
 	                BeautifulSoup $(beautifulsoup4-version))
 
+$(ipydir)/beniget-$(beniget-version): $(ipydir)/setuptools-$(setuptools-version)
+	tarball=beniget-$(beniget-version).tar.lz
+	$(call import-source, $(beniget-url), $(beniget-checksum))
+	$(call pybuild, tar -xf, beniget-$(beniget-version), , \
+	                Beniget $(beniget-version))
+
 $(ipydir)/certifi-$(certifi-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=certifi-$(certifi-version).tar.gz
 	$(call import-source, $(certifi-url), $(certifi-checksum))
-	$(call pybuild, tar xf, certifi-$(certifi-version), , \
+	$(call pybuild, tar -xf, certifi-$(certifi-version), , \
 	                Certifi $(certifi-version))
 
 $(ipydir)/cffi-$(cffi-version): \
                $(ibidir)/libffi-$(libffi-version) \
                $(ipydir)/pycparser-$(pycparser-version)
-	tarball=cffi-$(cffi-version).tar.gz
+	tarball=cffi-$(cffi-version).tar.lz
 	$(call import-source, $(cffi-url), $(cffi-checksum))
-	$(call pybuild, tar xf, cffi-$(cffi-version), ,cffi $(cffi-version))
+	$(call pybuild, tar -xf, cffi-$(cffi-version), ,cffi $(cffi-version))
 
 $(ipydir)/chardet-$(chardet-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=chardet-$(chardet-version).tar.gz
 	$(call import-source, $(chardet-url), $(chardet-checksum))
-	$(call pybuild, tar xf, chardet-$(chardet-version), , \
+	$(call pybuild, tar -xf, chardet-$(chardet-version), , \
 	                Chardet $(chardet-version))
 
 $(ipydir)/corner-$(corner-version): $(ipydir)/matplotlib-$(matplotlib-version)
 	tarball=corner-$(corner-version).tar.gz
 	$(call import-source, $(corner-url), $(corner-checksum))
-	$(call pybuild, tar xf, corner-$(corner-version), , \
+	$(call pybuild, tar -xf, corner-$(corner-version), , \
 	                Corner $(corner-version))
 	cp $(dtexdir)/corner.tex $(ictdir)/
 	echo "Corner $(corner-version) \citep{corner}" > $@
 
 $(ipydir)/cryptography-$(cryptography-version): \
                        $(ipydir)/cffi-$(cffi-version) \
-                       $(ipydir)/asn1crypto-$(asn1crypto-version)
-	tarball=cryptography-$(cryptography-version).tar.gz
+                       $(ipydir)/asn1crypto-$(asn1crypto-version) \
+                       $(ipydir)/setuptools-rust-$(setuptools-rust-version)
+	tarball=cryptography-$(cryptography-version).tar.lz
 	$(call import-source, $(cryptography-url), $(cryptography-checksum))
-	$(call pybuild, tar xf, cryptography-$(cryptography-version), , \
+	$(call pybuild, tar -xf, cryptography-$(cryptography-version), , \
 	                Cryptography $(cryptography-version))
 
 $(ipydir)/cycler-$(cycler-version): $(ipydir)/six-$(six-version)
-	tarball=cycler-$(cycler-version).tar.gz
+	tarball=cycler-$(cycler-version).tar.lz
 	$(call import-source, $(cycler-url), $(cycler-checksum))
-	$(call pybuild, tar xf, cycler-$(cycler-version), , \
+	$(call pybuild, tar -xf, cycler-$(cycler-version), , \
 	                Cycler $(cycler-version))
 
 $(ipydir)/cython-$(cython-version): $(ipydir)/setuptools-$(setuptools-version)
-	tarball=cython-$(cython-version).tar.gz
+	tarball=Cython-$(cython-version).tar.lz
 	$(call import-source, $(cython-url), $(cython-checksum))
-	$(call pybuild, tar xf, Cython-$(cython-version))
+	$(call pybuild, tar -xf, Cython-$(cython-version))
 	cp $(dtexdir)/cython.tex $(ictdir)/
 	echo "Cython $(cython-version) \citep{cython2011}" > $@
 
 $(ipydir)/esutil-$(esutil-version): $(ipydir)/numpy-$(numpy-version)
-	tarball=esutil-$(esutil-version).tar.gz
+	export CFLAGS="-std=c++14 $$CFLAGS"
+	tarball=esutil-$(esutil-version).tar.lz
 	$(call import-source, $(esutil-url), $(esutil-checksum))
-	$(call pybuild, tar xf, esutil-$(esutil-version), , \
+	$(call pybuild, tar -xf, esutil-$(esutil-version), , \
 	                esutil $(esutil-version))
 
 $(ipydir)/eigency-$(eigency-version): \
@@ -266,7 +264,7 @@ $(ipydir)/eigency-$(eigency-version): \
                   $(ipydir)/cython-$(cython-version)
 	tarball=eigency-$(eigency-version).tar.gz
 	$(call import-source, $(eigency-url), $(eigency-checksum))
-	$(call pybuild, tar xf, eigency-$(eigency-version), , \
+	$(call pybuild, tar -xf, eigency-$(eigency-version), , \
 	                eigency $(eigency-version))
 
 $(ipydir)/emcee-$(emcee-version): \
@@ -274,28 +272,35 @@ $(ipydir)/emcee-$(emcee-version): \
                 $(ipydir)/setuptools_scm-$(setuptools_scm-version)
 	tarball=emcee-$(emcee-version).tar.gz
 	$(call import-source, $(emcee-url), $(emcee-checksum))
-	$(call pybuild, tar xf, emcee-$(emcee-version), , \
+	$(call pybuild, tar -xf, emcee-$(emcee-version), , \
 	                emcee $(emcee-version))
 
 $(ipydir)/entrypoints-$(entrypoints-version): \
                       $(ipydir)/setuptools-$(setuptools-version)
 	tarball=entrypoints-$(entrypoints-version).tar.gz
 	$(call import-source, $(entrypoints-url), $(entrypoints-checksum))
-	$(call pybuild, tar xf, entrypoints-$(entrypoints-version), , \
+	$(call pybuild, tar -xf, entrypoints-$(entrypoints-version), , \
 	                EntryPoints $(entrypoints-version))
 
+$(ipydir)/extension-helpers-$(extension-helpers-version): \
+                    $(ipydir)/setuptools-$(setuptools-version)
+	tarball=extension-helpers-$(extension-helpers-version).tar.lz
+	$(call import-source, $(extension-helpers-url), $(extension-helpers-checksum))
+	$(call pybuild, tar -xf, extension-helpers-$(extension-helpers-version), , \
+	                Extension-Helpers $(extension-helpers-version))
+
 $(ipydir)/flake8-$(flake8-version): \
                  $(ipydir)/pyflakes-$(pyflakes-version) \
                  $(ipydir)/pycodestyle-$(pycodestyle-version)
 	tarball=flake8-$(flake8-version).tar.gz
 	$(call import-source, $(flake8-url), $(flake8-checksum))
-	$(call pybuild, tar xf, flake8-$(flake8-version), , \
+	$(call pybuild, tar -xf, flake8-$(flake8-version), , \
 	                Flake8 $(flake8-version))
 
 $(ipydir)/future-$(future-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=future-$(future-version).tar.gz
 	$(call import-source, $(future-url), $(future-checksum))
-	$(call pybuild, tar xf, future-$(future-version), , \
+	$(call pybuild, tar -xf, future-$(future-version), , \
 	                Future $(future-version))
 
 $(ipydir)/galsim-$(galsim-version): \
@@ -304,12 +309,18 @@ $(ipydir)/galsim-$(galsim-version): \
                  $(ipydir)/eigency-$(eigency-version) \
                  $(ipydir)/pybind11-$(pybind11-version) \
                  $(ipydir)/lsstdesccoord-$(lsstdesccoord-version)
-	tarball=galsim-$(galsim-version).tar.gz
+	tarball=galsim-$(galsim-version).tar.lz
 	$(call import-source, $(galsim-url), $(galsim-checksum))
-	$(call pybuild, tar xf, GalSim-$(galsim-version))
+	$(call pybuild, tar -xf, galsim-$(galsim-version))
 	cp $(dtexdir)/galsim.tex $(ictdir)/
 	echo "Galsim $(galsim-version) \citep{galsim}" > $@
 
+$(ipydir)/gast-$(gast-version): $(ipydir)/setuptools-$(setuptools-version)
+	tarball=gast-$(gast-version).tar.lz
+	$(call import-source, $(gast-url), $(gast-checksum))
+	$(call pybuild, tar -xf, gast-$(gast-version), , \
+	                Gast $(gast-version))
+
 $(ipydir)/h5py-$(h5py-version): \
                $(ipydir)/six-$(six-version) \
                $(ibidir)/hdf5-$(hdf5-version) \
@@ -321,15 +332,15 @@ $(ipydir)/h5py-$(h5py-version): \
 	export HDF5_DIR=$(ildir)
 	tarball=h5py-$(h5py-version).tar.gz
 	$(call import-source, $(h5py-url), $(h5py-checksum))
-	$(call pybuild, tar xf, h5py-$(h5py-version), , \
+	$(call pybuild, tar -xf, h5py-$(h5py-version), , \
 	                h5py $(h5py-version))
 
-# `healpy' is actually installed as part of the HEALPix package. It will be
+# 'healpy' is actually installed as part of the HEALPix package. It will be
 # installed with its C/C++ libraries if any other Python library is
-# requested with HEALPix. So actually calling for `healpix' (when `healpix'
+# requested with HEALPix. So actually calling for 'healpix' (when 'healpix'
 # is requested) is not necessary. But some users might not know about this
-# and just ask for `healpy'. To avoid confusion in such cases, we'll just
-# set `healpy' to be dependent on `healpix' and not download any tarball
+# and just ask for 'healpy'. To avoid confusion in such cases, we'll just
+# set 'healpy' to be dependent on 'healpix' and not download any tarball
 # for it, or write anything in the final target.
 $(ipydir)/healpy-$(healpy-version): $(ibidir)/healpix-$(healpix-version)
 	touch $@
@@ -339,34 +350,40 @@ $(ipydir)/html5lib-$(html5lib-version): \
                    $(ipydir)/webencodings-$(webencodings-version)
 	tarball=html5lib-$(html5lib-version).tar.gz
 	$(call import-source, $(html5lib-url), $(html5lib-checksum))
-	$(call pybuild, tar xf, html5lib-$(html5lib-version), , \
+	$(call pybuild, tar -xf, html5lib-$(html5lib-version), , \
 	                HTML5lib $(html5lib-version))
 
 $(ipydir)/idna-$(idna-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=idna-$(idna-version).tar.gz
 	$(call import-source, $(idna-url), $(idna-checksum))
-	$(call pybuild, tar xf, idna-$(idna-version), , \
+	$(call pybuild, tar -xf, idna-$(idna-version), , \
 	       idna $(idna-version))
 
 $(ipydir)/jeepney-$(jeepney-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=jeepney-$(jeepney-version).tar.gz
 	$(call import-source, $(jeepney-url), $(jeepney-checksum))
-	$(call pybuild, tar xf, jeepney-$(jeepney-version), , \
+	$(call pybuild, tar -xf, jeepney-$(jeepney-version), , \
 	                Jeepney $(jeepney-version))
 
+$(ipydir)/jinja2-$(jinja2-version): $(ipydir)/markupsafe-$(markupsafe-version)
+	tarball=jinja2-$(jinja2-version).tar.lz
+	$(call import-source, $(jinja2-url), $(jinja2-checksum))
+	$(call pybuild, tar -xf, jinja2-$(jinja2-version), , \
+	                Jinja2 $(jinja2-version))
+
 $(ipydir)/keyring-$(keyring-version): \
                   $(ipydir)/entrypoints-$(entrypoints-version) \
                   $(ipydir)/secretstorage-$(secretstorage-version) \
                   $(ipydir)/setuptools_scm-$(setuptools_scm-version)
 	tarball=keyring-$(keyring-version).tar.gz
 	$(call import-source, $(keyring-url), $(keyring-checksum))
-	$(call pybuild, tar xf, keyring-$(keyring-version), , \
+	$(call pybuild, tar -xf, keyring-$(keyring-version), , \
 	                Keyring $(keyring-version))
 
 $(ipydir)/kiwisolver-$(kiwisolver-version): $(ipydir)/setuptools-$(setuptools-version)
-	tarball=kiwisolver-$(kiwisolver-version).tar.gz
+	tarball=kiwisolver-$(kiwisolver-version).tar.lz
 	$(call import-source, $(kiwisolver-url), $(kiwisolver-checksum))
-	$(call pybuild, tar xf, kiwisolver-$(kiwisolver-version), , \
+	$(call pybuild, tar -xf, kiwisolver-$(kiwisolver-version), , \
 	                Kiwisolver $(kiwisolver-version))
 
 $(ipydir)/lmfit-$(lmfit-version): \
@@ -379,20 +396,28 @@ $(ipydir)/lmfit-$(lmfit-version): \
                 $(ipydir)/uncertainties-$(uncertainties-version)
 	tarball=lmfit-$(lmfit-version).tar.gz
 	$(call import-source, $(lmfit-url), $(lmfit-checksum))
-	$(call pybuild, tar xf, lmfit-$(lmfit-version), , \
+	$(call pybuild, tar -xf, lmfit-$(lmfit-version), , \
 	                LMFIT $(lmfit-version))
 
 $(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \
-                        $(ipydir)/setuptools-$(setuptools-version)
+                        $(ipydir)/cython-$(cython-version)
 	tarball=lsstdesccoord-$(lsstdesccoord-version).tar.gz
 	$(call import-source, $(lsstdesccoord-url), $(lsstdesccoord-checksum))
-	$(call pybuild, tar xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \
+	$(call pybuild, tar -xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \
 	                LSSTDESC.Coord $(lsstdesccoord-version))
 
+$(ipydir)/markupsafe-$(markupsafe-version): \
+                     $(ipydir)/setuptools-$(setuptools-version)
+	tarball=markupsafe-$(markupsafe-version).tar.lz
+	$(call import-source, $(markupsafe-url), $(markupsafe-checksum))
+	$(call pybuild, tar -xf, markupsafe-$(markupsafe-version), , \
+	                MarkupSafe $(markupsafe-version))
+
 $(ipydir)/matplotlib-$(matplotlib-version): \
                      $(itidir)/texlive \
                      $(ipydir)/numpy-$(numpy-version) \
                      $(ipydir)/cycler-$(cycler-version) \
+                     $(ipydir)/pillow-$(pillow-version) \
                      $(ibidir)/freetype-$(freetype-version) \
                      $(ipydir)/pyparsing-$(pyparsing-version) \
                      $(ipydir)/kiwisolver-$(kiwisolver-version) \
@@ -400,33 +425,33 @@ $(ipydir)/matplotlib-$(matplotlib-version): \
                      $(ibidir)/imagemagick-$(imagemagick-version) \
                      $(ipydir)/python-dateutil-$(python-dateutil-version)
 
-        # Download the source.
-	tarball=matplotlib-$(matplotlib-version).tar.gz
+#	Prepare the source.
+	tarball=matplotlib-$(matplotlib-version).tar.lz
 	$(call import-source, $(matplotlib-url), $(matplotlib-checksum))
 
-        # On Mac systems, the build complains about `clang' specific
-        # features, so we can't use our own GCC build here.
+#	On Mac systems, the build complains about 'clang' specific
+#	features, so we can't use our own GCC build here.
 	if [ x$(on_mac_os) = xyes ]; then
 	  export CC=clang
 	  export CXX=clang++
 	fi
-	$(call pybuild, tar xf, matplotlib-$(matplotlib-version))
+	$(call pybuild, tar -xf, matplotlib-$(matplotlib-version))
 	cp $(dtexdir)/matplotlib.tex $(ictdir)/
 	echo "Matplotlib $(matplotlib-version) \citep{matplotlib2007}" > $@
 
 $(ipydir)/mpi4py-$(mpi4py-version): \
                  $(ibidir)/openmpi-$(openmpi-version) \
                  $(ipydir)/setuptools-$(setuptools-version)
-	tarball=mpi4py-$(mpi4py-version).tar.gz
+	tarball=mpi4py-$(mpi4py-version).tar.lz
 	$(call import-source, $(mpi4py-url), $(mpi4py-checksum))
-	$(call pybuild, tar xf, mpi4py-$(mpi4py-version))
+	$(call pybuild, tar -xf, mpi4py-$(mpi4py-version))
 	cp $(dtexdir)/mpi4py.tex $(ictdir)/
 	echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
 
 $(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=mpmath-$(mpmath-version).tar.gz
 	$(call import-source, $(mpmath-url), $(mpmath-checksum))
-	$(call pybuild, tar xf, mpmath-$(mpmath-version), , \
+	$(call pybuild, tar -xf, mpmath-$(mpmath-version), , \
 	                mpmath $(mpmath-version))
 
 $(ipydir)/numpy-$(numpy-version): \
@@ -434,7 +459,7 @@ $(ipydir)/numpy-$(numpy-version): \
                 $(ipydir)/cython-$(cython-version) \
                 $(ibidir)/openblas-$(openblas-version) \
                 $(ipydir)/setuptools-$(setuptools-version)
-	tarball=numpy-$(numpy-version).zip
+	tarball=numpy-$(numpy-version).tar.lz
 	$(call import-source, $(numpy-url), $(numpy-checksum))
 	if [ x$(on_mac_os) = xyes ]; then
 	  export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"
@@ -443,28 +468,48 @@ $(ipydir)/numpy-$(numpy-version): \
 	fi
 	export CFLAGS="--std=c99 $$CFLAGS"
 	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
-	$(call pybuild, unzip, numpy-$(numpy-version),$$conf, \
+	$(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \
 	                Numpy $(numpy-version))
 	cp $(dtexdir)/numpy.tex $(ictdir)/
 	echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
 
+$(ipydir)/packaging-$(packaging-version): \
+                    $(ipydir)/pyparsing-$(pyparsing-version)
+	tarball=packaging-$(packaging-version).tar.lz
+	$(call import-source, $(packaging-url), $(packaging-checksum))
+	$(call pybuild, tar -xf, packaging-$(packaging-version), , \
+	                Packaging $(packaging-version))
+
 $(ipydir)/pexpect-$(pexpect-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pexpect-$(pexpect-version).tar.gz
 	$(call import-source, $(pexpect-url), $(pexpect-checksum))
-	$(call pybuild, tar xf, pexpect-$(pexpect-version), , \
+	$(call pybuild, tar -xf, pexpect-$(pexpect-version), , \
 	                Pexpect $(pexpect-version))
 
+$(ipydir)/pillow-$(pillow-version): $(ibidir)/libjpeg-$(libjpeg-version) \
+                 $(ipydir)/setuptools-$(setuptools-version)
+	tarball=Pillow-$(pillow-version).tar.lz
+	$(call import-source, $(pillow-url), $(pillow-checksum))
+	$(call pybuild, tar -xf, Pillow-$(pillow-version), , \
+	                Pillow $(pillow-version))
+
 $(ipydir)/pip-$(pip-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pip-$(pip-version).tar.gz
 	$(call import-source, $(pip-url), $(pip-checksum))
-	$(call pybuild, tar xf, pip-$(pip-version), , \
+	$(call pybuild, tar -xf, pip-$(pip-version), , \
 	                PiP $(pip-version))
 
+$(ipydir)/ply-$(ply-version): $(ipydir)/setuptools-$(setuptools-version)
+	tarball=ply-$(ply-version).tar.lz
+	$(call import-source, $(ply-url), $(ply-checksum))
+	$(call pybuild, tar -xf, ply-$(ply-version), , \
+	                ply $(ply-version))
+
 $(ipydir)/pycodestyle-$(pycodestyle-version): \
                       $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pycodestyle-$(pycodestyle-version).tar.gz
 	$(call import-source, $(pycodestyle-url), $(pycodestyle-checksum))
-	$(call pybuild, tar xf, pycodestyle-$(pycodestyle-version), , \
+	$(call pybuild, tar -xf, pycodestyle-$(pycodestyle-version), , \
 	                pycodestyle $(pycodestyle-version))
 
 $(ipydir)/pybind11-$(pybind11-version): \
@@ -476,31 +521,40 @@ $(ipydir)/pybind11-$(pybind11-version): \
 	pyhook_after() {
 	  cp -r include/pybind11 $(iidir)/python$(python-major-version)m/
 	}
-	$(call pybuild, tar xf, pybind11-$(pybind11-version), , \
+	$(call pybuild, tar -xf, pybind11-$(pybind11-version), , \
 	                pybind11 $(pybind11-version))
 
 $(ipydir)/pycparser-$(pycparser-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pycparser-$(pycparser-version).tar.gz
 	$(call import-source, $(pycparser-url), $(pycparser-checksum))
-	$(call pybuild, tar xf, pycparser-$(pycparser-version), , \
+	$(call pybuild, tar -xf, pycparser-$(pycparser-version), , \
 	                pycparser $(pycparser-version))
 
+$(ipydir)/pyerfa-$(pyerfa-version): \
+                 $(ipydir)/numpy-$(numpy-version) \
+                 $(ipydir)/packaging-$(packaging-version)
+	tarball=pyerfa-$(pyerfa-version).tar.lz
+	$(call import-source, $(pyerfa-url), $(pyerfa-checksum))
+	$(call pybuild, tar -xf, pyerfa-$(pyerfa-version), , \
+	                PyERFA $(pyerfa-version))
+
 $(ipydir)/pyflakes-$(pyflakes-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pyflakes-$(pyflakes-version).tar.gz
 	$(call import-source, $(pyflakes-url), $(pyflakes-checksum))
-	$(call pybuild, tar xf, pyflakes-$(pyflakes-version), , \
+	$(call pybuild, tar -xf, pyflakes-$(pyflakes-version), , \
 	                pyflakes $(pyflakes-version))
 
-$(ipydir)/pyparsing-$(pyparsing-version): $(ipydir)/setuptools-$(setuptools-version)
-	tarball=pyparsing-$(pyparsing-version).tar.gz
+$(ipydir)/pyparsing-$(pyparsing-version): \
+                    $(ipydir)/setuptools-$(setuptools-version)
+	tarball=pyparsing-$(pyparsing-version).tar.lz
 	$(call import-source, $(pyparsing-url), $(pyparsing-checksum))
-	$(call pybuild, tar xf, pyparsing-$(pyparsing-version), , \
+	$(call pybuild, tar -xf, pyparsing-$(pyparsing-version), , \
 	                PyParsing $(pyparsing-version))
 
 $(ipydir)/pypkgconfig-$(pypkgconfig-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pkgconfig-$(pypkgconfig-version).tar.gz
 	$(call import-source, $(pypkgconfig-url), $(pypkgconfig-checksum))
-	$(call pybuild, tar xf, pkgconfig-$(pypkgconfig-version), ,
+	$(call pybuild, tar -xf, pkgconfig-$(pypkgconfig-version), ,
 	                pkgconfig $(pypkgconfig-version))
 
 $(ipydir)/python-dateutil-$(python-dateutil-version): \
@@ -508,15 +562,26 @@ $(ipydir)/python-dateutil-$(python-dateutil-version): \
                           $(ipydir)/setuptools_scm-$(setuptools_scm-version)
 	tarball=python-dateutil-$(python-dateutil-version).tar.gz
 	$(call import-source, $(python-dateutil-url), $(python-dateutil-checksum))
-	$(call pybuild, tar xf, python-dateutil-$(python-dateutil-version), , \
+	$(call pybuild, tar -xf, python-dateutil-$(python-dateutil-version), , \
 	                python-dateutil $(python-dateutil-version))
 
+$(ipydir)/pythran-$(pythran-version): \
+                  $(ipydir)/ply-$(ply-version) \
+                  $(ipydir)/gast-$(gast-version) \
+                  $(ibidir)/boost-$(boost-version) \
+                  $(ipydir)/beniget-$(beniget-version) \
+                  $(ipydir)/setuptools_scm-$(setuptools_scm-version)
+	tarball=pythran-$(pythran-version).tar.lz
+	$(call import-source, $(pythran-url), $(pythran-checksum))
+	$(call pybuild, tar -xf, pythran-$(pythran-version), , \
+	                pythran $(pythran-version))
+
 $(ipydir)/pyyaml-$(pyyaml-version): \
                  $(ibidir)/yaml-$(yaml-version) \
                  $(ipydir)/cython-$(cython-version)
 	tarball=pyyaml-$(pyyaml-version).tar.gz
 	$(call import-source, $(pyyaml-url), $(pyyaml-checksum))
-	$(call pybuild, tar xf, PyYAML-$(pyyaml-version), , \
+	$(call pybuild, tar -xf, PyYAML-$(pyyaml-version), , \
 	                PyYAML $(pyyaml-version))
 
 $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
@@ -526,13 +591,14 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
                     $(ipydir)/urllib3-$(urllib3-version)
 	tarball=requests-$(requests-version).tar.gz
 	$(call import-source, $(requests-url), $(requests-checksum))
-	$(call pybuild, tar xf, requests-$(requests-version), , \
+	$(call pybuild, tar -xf, requests-$(requests-version), , \
 	                Requests $(requests-version))
 
 $(ipydir)/scipy-$(scipy-version): \
                   $(ipydir)/numpy-$(numpy-version) \
+                  $(ipydir)/pythran-$(pythran-version) \
                   $(ipydir)/pybind11-$(pybind11-version)
-	tarball=scipy-$(scipy-version).tar.gz
+	tarball=scipy-$(scipy-version).tar.lz
 	$(call import-source, $(scipy-url), $(scipy-checksum))
 	if [ x$(on_mac_os) = xyes ]; then
 	  export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"
@@ -540,7 +606,7 @@ $(ipydir)/scipy-$(scipy-version): \
 	  export LDFLAGS="$(LDFLAGS) -shared"
 	fi
 	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
-	$(call pybuild, tar xf, scipy-$(scipy-version),$$conf)
+	$(call pybuild, tar -xf, scipy-$(scipy-version),$$conf)
 	cp $(dtexdir)/scipy.tex $(ictdir)/
 	echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@
 
@@ -549,68 +615,81 @@ $(ipydir)/secretstorage-$(secretstorage-version): \
                         $(ipydir)/cryptography-$(cryptography-version)
 	tarball=secretstorage-$(secretstorage-version).tar.gz
 	$(call import-source, $(secretstorage-url), $(secretstorage-checksum))
-	$(call pybuild, tar xf, SecretStorage-$(secretstorage-version), , \
+	$(call pybuild, tar -xf, SecretStorage-$(secretstorage-version), , \
 	                SecretStorage $(secretstorage-version))
 
 $(ipydir)/setuptools-$(setuptools-version): \
                      $(ibidir)/unzip-$(unzip-version) \
                      $(ibidir)/python-$(python-version)
-	tarball=setuptools-$(setuptools-version).zip
+	tarball=setuptools-$(setuptools-version).tar.lz
 	$(call import-source, $(setuptools-url), $(setuptools-checksum))
-	$(call pybuild, unzip, setuptools-$(setuptools-version), , \
+	$(call pybuild, tar -xf, setuptools-$(setuptools-version), , \
 	                Setuptools $(setuptools-version))
 
 $(ipydir)/setuptools_scm-$(setuptools_scm-version): \
                          $(ipydir)/setuptools-$(setuptools-version)
 	tarball=setuptools_scm-$(setuptools_scm-version).tar.gz
 	$(call import-source, $(setuptools_scm-url), $(setuptools_scm-checksum))
-	$(call pybuild, tar xf, setuptools_scm-$(setuptools_scm-version), , \
+	$(call pybuild, tar -xf, setuptools_scm-$(setuptools_scm-version), , \
 	                Setuptools-scm $(setuptools_scm-version))
 
+$(ipydir)/setuptools-rust-$(setuptools-rust-version): \
+                          $(ipydir)/setuptools-$(setuptools-version)
+	tarball=setuptools-rust-$(setuptools-rust-version).tar.lz
+	$(call import-source, $(setuptools-rust-url), $(setuptools-rust-checksum))
+	$(call pybuild, tar -xf, setuptools-rust-$(setuptools-rust-version), , \
+	                Setuptools-scm $(setuptools-rust-version))
+
 $(ipydir)/sip_tpv-$(sip_tpv-version): \
                   $(ipydir)/sympy-$(sympy-version) \
                   $(ipydir)/astropy-$(astropy-version)
 	tarball=sip_tpv-$(sip_tpv-version).tar.gz
 	$(call import-source, $(sip_tpv-url), $(sip_tpv-checksum))
-	$(call pybuild, tar xf, sip_tpv-$(sip_tpv-version), ,)
+	$(call pybuild, tar -xf, sip_tpv-$(sip_tpv-version), ,)
 	cp $(dtexdir)/sip_tpv.tex $(ictdir)/
 	echo "sip_tpv $(sip_tpv-version) \citep{sip-tpv}" > $@
 
 
 $(ipydir)/six-$(six-version): $(ipydir)/setuptools-$(setuptools-version)
-	tarball=six-$(six-version).tar.gz
+	tarball=six-$(six-version).tar.lz
 	$(call import-source, $(six-url), $(six-checksum))
-	$(call pybuild, tar xf, six-$(six-version), , \
+	$(call pybuild, tar -xf, six-$(six-version), , \
 	                Six $(six-version))
 
 $(ipydir)/soupsieve-$(soupsieve-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=soupsieve-$(soupsieve-version).tar.gz
 	$(call import-source, $(soupsieve-url), $(soupsieve-checksum))
-	$(call pybuild, tar xf, soupsieve-$(soupsieve-version), , \
+	$(call pybuild, tar -xf, soupsieve-$(soupsieve-version), , \
 	                SoupSieve $(soupsieve-version))
 
 $(ipydir)/sympy-$(sympy-version): $(ipydir)/mpmath-$(mpmath-version)
 	tarball=sympy-$(sympy-version).tar.gz
 	$(call import-source, $(sympy-url), $(sympy-checksum))
-	$(call pybuild, tar xf, sympy-$(sympy-version), ,)
+	$(call pybuild, tar -xf, sympy-$(sympy-version), ,)
 	cp $(dtexdir)/sympy.tex $(ictdir)/
 	echo "SymPy $(sympy-version) \citep{sympy}" > $@
 
 $(ipydir)/uncertainties-$(uncertainties-version): $(ipydir)/numpy-$(numpy-version)
-	tarball=uncertainties-$(uncertainties-version).tar.gz
+	tarball=uncertainties-$(uncertainties-version).tar.lz
 	$(call import-source, $(uncertainties-url), $(uncertainties-checksum))
-	$(call pybuild, tar xf, uncertainties-$(uncertainties-version), , \
+	$(call pybuild, tar -xf, uncertainties-$(uncertainties-version), , \
 	                uncertainties $(uncertainties-version))
 
 $(ipydir)/urllib3-$(urllib3-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=urllib3-$(urllib3-version).tar.gz
 	$(call import-source, $(urllib3-url), $(urllib3-checksum))
-	$(call pybuild, tar xf, urllib3-$(urllib3-version), , \
+	$(call pybuild, tar -xf, urllib3-$(urllib3-version), , \
 	                Urllib3 $(urllib3-version))
 
 $(ipydir)/webencodings-$(webencodings-version): \
                        $(ipydir)/setuptools-$(setuptools-version)
 	tarball=webencodings-$(webencodings-version).tar.gz
 	$(call import-source, $(webencodings-url), $(webencodings-checksum))
-	$(call pybuild, tar xf, webencodings-$(webencodings-version), , \
+	$(call pybuild, tar -xf, webencodings-$(webencodings-version), , \
 	                Webencodings $(webencodings-version))
+
+$(ipydir)/wheel-$(wheel-version): $(ipydir)/setuptools-$(setuptools-version)
+	tarball=wheel-$(wheel-version).tar.lz
+	$(call import-source, $(wheel-url), $(wheel-checksum))
+	$(call pybuild, tar -xf, wheel-$(wheel-version), , \
+	                Wheel $(wheel-version))
diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk
new file mode 100644
index 0000000..617b8de
--- /dev/null
+++ b/reproduce/software/make/r-cran.mk
@@ -0,0 +1,487 @@
+# Build the project's R (here called R-CRAN) dependencies.
+#
+# ------------------------------------------------------------------------
+#                      !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be loaded into 'high-level.mk', which is called by the
+# './project configure' script. It is not included into the project
+# afterwards.
+#
+# This Makefile contains instructions to build all the R-CRAN-related
+# software within the project.
+#
+# ------------------------------------------------------------------------
+#
+# Copyright (C) 2022 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This Makefile is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this Makefile.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# BUGS/IMPROVEMENTS
+# -----------------
+#
+# As of 2021-06-20, the R system is still very new and has not yet
+# been tested on non-Debian-derived systems. Please provide bug
+# reports ( https://savannah.nongnu.org/task/?15772 ) or propose fixes
+# as git pull requests on a public git server (e.g.  on a fork of
+# https://codeberg.org/boud/maneage_dev ).
+
+
+
+
+
+# R-CRAN enviroment
+# -----------------
+#
+# It may be necessary to override host-level R-related environment
+# variables that interfere with the Maneage-installed R system.
+# systems which might interfere.
+
+# Ideas for which environment variables might create problems
+# and might need to be set to be empty here:
+#
+# https://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html
+
+# These first variables should be set automatically when R starts:
+#export R_HOME             := $(idir)/lib/R
+#export R_INCLUDE_DIR      := $(idir)/lib/R/include
+
+
+
+
+
+# R-CRAN-specific installation directories.
+r-cran-major-version = $(shell echo $(r-cran-version) \
+                                    | awk 'BEGIN{FS="."} \
+	                            {printf "%d.%d\n", $$1, $$2}')
+
+
+
+
+
+# R-CRAN-specific build rules for 'make'
+# ======================================
+
+# Double-check an already downloaded R source
+# -------------------------------------------
+#
+# Check that the tarball with the version in
+# 'reproduce/software/conf/versions.conf' has the sha512sum (checksum)
+# stated 'reproduce/software/conf/checksums.conf'. This does not do any
+# security checks; it only checks that the source file package is the one
+# that is expected the last time that someone updated these two files for
+# the R package of interest.
+#
+# Calculate the checksum and exit with a non-zero error code if there's a
+# mismatch, after informing the user.
+#
+# Arguments:
+#   1: The expected checksum of the tarball.
+#
+# Necessary shell variables
+#   'tarball': This is the name of the actual tarball file without a
+#   directory.
+double-check-R-source = final=$(tdir)/$$tarball; \
+	exp_checksum="$(strip $(1))"; \
+	if [ x"$$exp_checksum" = x"NO-CHECK-SUM" ]; then \
+	  result=0; \
+	else \
+	  if type sha512sum > /dev/null 2>/dev/null; then \
+	    checksum=$$(sha512sum "$$final" | awk '{print $$1}'); \
+	    if [ x"$$checksum" = x"$$exp_checksum" ]; then \
+	      result=0; \
+	    else \
+	      echo "ERROR: Non-matching checksum: $$final"; \
+	      echo "Checksum should be: $$exp_checksum"; \
+	      echo "Checksum is:        $$checksum"; \
+	      result=1; \
+	      exit 1; \
+	    fi; \
+	  else \
+	    echo "ERROR: sha512sum is unavailable."; \
+	    exit 1; \
+	  fi; \
+	fi
+
+# Default 'make' build rules for an CRAN package
+# -----------------------------------------------
+#
+# The default 'install.packages' function of R only recognizes 'tar.gz'
+# tarballs. But Maneage uses '.tar.lz' format for its archival. So to be
+# agnostic to the compression algorithm, we will be using 'tar' externally
+# (before entering R), then give the un-compressed directory to
+# 'install.packages'.
+#
+# Parameters:
+# 1. package name (without 'r-cran', without the version string)
+# 2. version string
+# 3. checksum of the package
+r_cran_build = \
+	pkg=$(strip $(1)); \
+	version=$(strip $(2)); \
+	checksum=$(strip $(3)); \
+	$(call import-source, \
+	       https://cran.r-project.org/src/contrib, \
+	       $$checksum, \
+	       $$tarball, \
+	       https://cran.r-project.org/src/contrib/00Archive/$$pkg); \
+	cd "$(ddir)"; \
+	tar -xf $(tdir)/$$tarball; \
+	unpackdir=$$pkg-$$version; \
+	(printf "install.packages(c(\"$(ddir)/$$unpackdir\"),"; \
+	 printf 'lib="$(ilibrcrandir)",'; \
+	 printf 'repos=NULL,'; \
+	 printf 'type="source")\n'; \
+	 printf 'quit()\n'; \
+	 printf 'n\n') | R --no-save; \
+	rm -rf $$unpackdir; \
+	if [ $$pkg = r-pkgconfig ]; then iname=pkgconfig; \
+	else                             iname=$$pkg; fi; \
+	if [ -e "$(ilibrcrandir)"/$$iname/Meta/nsInfo.rds ]; then \
+	   $(call double-check-R-source, $$checksum) \
+	          && echo "$$pkg $$version" > $@; \
+	else \
+	   printf "r-cran-$$pkg failed: Meta/nsInfo.rds missing.\n"; \
+	   exit 1; \
+	fi
+
+
+
+
+
+# Necessary programs and libraries
+# --------------------------------
+#
+# While this Makefile is for R programs, in some cases, we need certain
+# programs (like R itself), or libraries for the modules.  Comment on
+# building R without GUI support ('--without-tcltlk')
+#
+# Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support
+# in some software. But they are not yet natively built within Maneage,
+# primarily because we have higher-priority work right now (if anyone is
+# interested, they can ofcourse contribute!). GUI tools in general aren't
+# high on our priority list right now because they are generally good for
+# human interaction (which is contrary to the reproducible philosophy:
+# there will always be human-error and frustration, for example in GUI
+# tools the best level of reproducibility is statements like this: "move
+# your mouse to button XXX, then click on menu YYY and etc"). A robust
+# reproducible solution must be done automatically.
+#
+# If someone wants to use R's GUI functionalities while investigating for
+# their analysis, they can do the GUI part on their host OS
+# implementation. Later, they can bring the finalized source into Maneage
+# to be automatically run in Maneage. This will also be the recommended way
+# to deal with GUI tools later when we do install them within Maneage.
+$(ibidir)/r-cran-$(r-cran-version): \
+            $(itidir)/texlive \
+            $(ibidir)/icu-$(icu-version) \
+            $(ibidir)/pcre-$(pcre-version) \
+            $(ibidir)/cairo-$(cairo-version) \
+            $(ibidir)/libpng-$(libpng-version) \
+            $(ibidir)/libjpeg-$(libjpeg-version) \
+            $(ibidir)/libtiff-$(libtiff-version) \
+            $(ibidir)/libpaper-$(libpaper-version)
+
+#	Prepare the tarball, unpack it and enter the directory.
+	tarball=R-$(r-cran-version).tar.lz
+	$(call import-source, $(r-cran-url), $(r-cran-checksum))
+	cd $(ddir)
+	tar -xf $(tdir)/$$tarball
+	unpackdir=R-$(r-cran-version)
+	cd $$unpackdir
+
+#	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=$(SHELL)
+	./configure --prefix=$(idir) \
+	            --without-x \
+	            --with-pcre1 \
+	            --disable-java \
+	            --with-readline \
+	            --without-tcltk \
+	            --disable-openmp
+	make -j$(numthreads)
+	make install
+	cd ..
+	rm -rf R-$(r-cran-version)
+	cp -p $(dtexdir)/r-cran.tex $(ictdir)/
+	echo "R $(r-cran-version) \citep{RIhakaGentleman1996}" > $@
+
+
+
+
+
+# Non-Maneage'd tarballs
+# ----------------------
+#
+# CRAN tarballs differ in two aspects from Maneage'd tarballs:
+#    - CRAN uses '.tar.gz', while Maneage uses 'tar.lz'.
+#    - CRAN uses 'name_version', while Maneage uses 'name-version'.
+#
+# So if you add a new R package, or update the version of an existing one
+# (that is not yet in Maneage's archive), you need to use the CRAN naming
+# format for the 'tarball' variable.
+
+
+
+
+
+# R-CRAN modules
+# ---------------
+#
+# The rules for downloading, compiling and installing any R-CRAN modules
+# that are needed should be provided here. Each target (before the colon)
+# is first shown with its dependence on prerequisites (which are listed
+# after the colon. The default macro 'r_cran_build' will install the
+# package without checking on dependencies.
+
+$(ircrandir)/r-cran-cli-$(r-cran-cli-version): \
+                        $(ibidir)/r-cran-$(r-cran-version) \
+                        $(ircrandir)/r-cran-glue-$(r-cran-glue-version)
+	tarball=cli-$(r-cran-cli-version).tar.lz
+	$(call r_cran_build, cli, $(r-cran-cli-version), \
+	                     $(r-cran-cli-checksum))
+
+$(ircrandir)/r-cran-colorspace-$(r-cran-colorspace-version): \
+                               $(ibidir)/r-cran-$(r-cran-version)
+	tarball=colorspace-$(r-cran-colorspace-version).tar.lz
+	$(call r_cran_build, colorspace, $(r-cran-colorspace-version), \
+	                     $(r-cran-colorspace-checksum))
+
+$(ircrandir)/r-cran-cowplot-$(r-cran-cowplot-version): \
+                 $(ibidir)/r-cran-$(r-cran-version) \
+                 $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+                 $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) \
+                 $(ircrandir)/r-cran-scales-$(r-cran-scales-version) \
+                 $(ircrandir)/r-cran-ggplot2-$(r-cran-ggplot2-version)
+	tarball=cowplot-$(r-cran-cowplot-version).tar.lz
+	$(call r_cran_build, cowplot, $(r-cran-cowplot-version), \
+	                     $(r-cran-cowplot-checksum))
+
+$(ircrandir)/r-cran-crayon-$(r-cran-crayon-version): \
+                           $(ibidir)/r-cran-$(r-cran-version)
+	tarball=crayon-$(r-cran-crayon-version).tar.lz
+	$(call r_cran_build, crayon, $(r-cran-crayon-version), \
+	                     $(r-cran-crayon-checksum))
+
+$(ircrandir)/r-cran-digest-$(r-cran-digest-version): \
+                           $(ibidir)/r-cran-$(r-cran-version)
+	tarball=digest-$(r-cran-digest-version).tar.lz
+	$(call r_cran_build, digest, $(r-cran-digest-version), \
+	                     $(r-cran-digest-checksum))
+
+$(ircrandir)/r-cran-farver-$(r-cran-farver-version): \
+                           $(ibidir)/r-cran-$(r-cran-version)
+	tarball=farver-$(r-cran-farver-version).tar.lz
+	$(call r_cran_build, farver, $(r-cran-farver-version), \
+	                     $(r-cran-farver-checksum))
+
+$(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version): \
+                    $(ibidir)/r-cran-$(r-cran-version) \
+                    $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version)
+	tarball=ellipsis-$(r-cran-ellipsis-version).tar.lz
+	$(call r_cran_build, ellipsis, $(r-cran-ellipsis-version), \
+	                     $(r-cran-ellipsis-checksum))
+
+$(ircrandir)/r-cran-fansi-$(r-cran-fansi-version): \
+                          $(ibidir)/r-cran-$(r-cran-version)
+	tarball=fansi-$(r-cran-fansi-version).tar.lz
+	$(call r_cran_build, fansi, $(r-cran-fansi-version), \
+	                     $(r-cran-fansi-checksum))
+
+$(ircrandir)/r-cran-ggplot2-$(r-cran-ggplot2-version): \
+                $(ibidir)/r-cran-$(r-cran-version) \
+                $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+                $(ircrandir)/r-cran-mgcv-$(r-cran-mgcv-version) \
+                $(ircrandir)/r-cran-MASS-$(r-cran-MASS-version) \
+                $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+                $(ircrandir)/r-cran-withr-$(r-cran-withr-version) \
+                $(ircrandir)/r-cran-digest-$(r-cran-digest-version) \
+                $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) \
+                $(ircrandir)/r-cran-scales-$(r-cran-scales-version) \
+                $(ircrandir)/r-cran-tibble-$(r-cran-tibble-version) \
+                $(ircrandir)/r-cran-isoband-$(r-cran-isoband-version)
+	tarball=ggplot2-$(r-cran-ggplot2-version).tar.lz
+	$(call r_cran_build, ggplot2, $(r-cran-ggplot2-version), \
+	                     $(r-cran-ggplot2-checksum))
+
+$(ircrandir)/r-cran-glue-$(r-cran-glue-version): \
+                         $(ibidir)/r-cran-$(r-cran-version)
+	tarball=glue-$(r-cran-glue-version).tar.lz
+	$(call r_cran_build, glue, $(r-cran-glue-version), \
+	                     $(r-cran-glue-checksum))
+
+$(ircrandir)/r-cran-gridExtra-$(r-cran-gridExtra-version): \
+                  $(ibidir)/r-cran-$(r-cran-version) \
+                  $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version)
+	tarball=gridExtra-$(r-cran-gridExtra-version).tar.lz
+	$(call r_cran_build, gridExtra, $(r-cran-gridExtra-version), \
+	                     $(r-cran-gridExtra-checksum))
+
+$(ircrandir)/r-cran-gtable-$(r-cran-gtable-version): \
+                           $(ibidir)/r-cran-$(r-cran-version)
+	tarball=gtable-$(r-cran-gtable-version).tar.lz
+	$(call r_cran_build, gtable, $(r-cran-gtable-version), \
+	                     $(r-cran-gtable-checksum))
+
+$(ircrandir)/r-cran-isoband-$(r-cran-isoband-version): \
+                            $(ibidir)/r-cran-$(r-cran-version)
+	tarball=isoband-$(r-cran-isoband-version).tar.lz
+	$(call r_cran_build, isoband, $(r-cran-isoband-version), \
+	                     $(r-cran-isoband-checksum))
+
+$(ircrandir)/r-cran-labeling-$(r-cran-labeling-version): \
+                             $(ibidir)/r-cran-$(r-cran-version)
+	tarball=labeling-$(r-cran-labeling-version).tar.lz
+	$(call r_cran_build, labeling, $(r-cran-labeling-version), \
+                             $(r-cran-labeling-checksum))
+
+$(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version): \
+                    $(ibidir)/r-cran-$(r-cran-version) \
+                    $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+                    $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version)
+	tarball=lifecycle-$(r-cran-lifecycle-version).tar.lz
+	$(call r_cran_build, lifecycle, $(r-cran-lifecycle-version), \
+	                     $(r-cran-lifecycle-checksum))
+
+$(ircrandir)/r-cran-magrittr-$(r-cran-magrittr-version): \
+                             $(ibidir)/r-cran-$(r-cran-version)
+	tarball=magrittr-$(r-cran-magrittr-version).tar.lz
+	$(call r_cran_build, magrittr, $(r-cran-magrittr-version), \
+	                     $(r-cran-magrittr-checksum))
+
+$(ircrandir)/r-cran-MASS-$(r-cran-MASS-version): \
+                         $(ibidir)/r-cran-$(r-cran-version)
+	tarball=MASS-$(r-cran-MASS-version).tar.lz
+	$(call r_cran_build, MASS, $(r-cran-MASS-version), \
+	                     $(r-cran-MASS-checksum))
+
+# The base R-2.0.4 install includes nlme and Matrix.
+# https://cran.r-project.org/web/packages/mgcv/index.html
+$(ircrandir)/r-cran-mgcv-$(r-cran-mgcv-version): \
+                         $(ibidir)/r-cran-$(r-cran-version)
+	tarball=mgcv-$(r-cran-mgcv-version).tar.lz
+	$(call r_cran_build, mgcv, $(r-cran-mgcv-version), \
+	                     $(r-cran-mgcv-checksum))
+
+$(ircrandir)/r-cran-munsell-$(r-cran-munsell-version): \
+                 $(ibidir)/r-cran-$(r-cran-version) \
+                 $(ircrandir)/r-cran-colorspace-$(r-cran-colorspace-version)
+	tarball=munsell-$(r-cran-munsell-version).tar.lz
+	$(call r_cran_build, munsell, $(r-cran-munsell-version), \
+	                     $(r-cran-munsell-checksum))
+
+#TODO: https://cran.r-project.org/web/packages/pillar/index.html
+$(ircrandir)/r-cran-pillar-$(r-cran-pillar-version): \
+              $(ibidir)/r-cran-$(r-cran-version) \
+              $(ircrandir)/r-cran-cli-$(r-cran-cli-version) \
+              $(ircrandir)/r-cran-utf8-$(r-cran-utf8-version) \
+              $(ircrandir)/r-cran-fansi-$(r-cran-fansi-version) \
+              $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+              $(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version) \
+              $(ircrandir)/r-cran-crayon-$(r-cran-crayon-version) \
+              $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) \
+              $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version)
+	tarball=pillar-$(r-cran-pillar-version).tar.lz
+	$(call r_cran_build, pillar, $(r-cran-pillar-version), \
+	                     $(r-cran-pillar-checksum))
+
+# Since we have other software packages with the name 'pkgconfig', to avoid
+# confusion with those tarballs, we have put a 'r-' prefix in the tarball
+# name. If you want to use the CRAN tarball, please correct the name
+# accordingly (as described in the comment above this group of rules).
+$(ircrandir)/r-cran-pkgconfig-$(r-cran-pkgconfig-version): \
+                              $(ibidir)/r-cran-$(r-cran-version)
+	tarball=r-pkgconfig-$(r-cran-pkgconfig-version).tar.lz
+	$(call r_cran_build, r-pkgconfig, $(r-cran-pkgconfig-version), \
+	                     $(r-cran-pkgconfig-checksum))
+
+$(ircrandir)/r-cran-RColorBrewer-$(r-cran-RColorBrewer-version): \
+                                 $(ibidir)/r-cran-$(r-cran-version)
+	tarball=RColorBrewer-$(r-cran-RColorBrewer-version).tar.lz
+	$(call r_cran_build, RColorBrewer, $(r-cran-RColorBrewer-version), \
+	                     $(r-cran-RColorBrewer-checksum))
+
+$(ircrandir)/r-cran-R6-$(r-cran-R6-version): \
+                       $(ibidir)/r-cran-$(r-cran-version)
+	tarball=R6-$(r-cran-R6-version).tar.lz
+	$(call r_cran_build, R6, $(r-cran-R6-version), $(r-cran-R6-checksum))
+
+$(ircrandir)/r-cran-rlang-$(r-cran-rlang-version): \
+                          $(ibidir)/r-cran-$(r-cran-version)
+	tarball=rlang-$(r-cran-rlang-version).tar.lz
+	$(call r_cran_build, rlang, $(r-cran-rlang-version), \
+	                     $(r-cran-rlang-checksum))
+
+# https://cran.r-project.org/web/packages/scales/index.html
+$(ircrandir)/r-cran-scales-$(r-cran-scales-version): \
+           $(ibidir)/r-cran-$(r-cran-version) \
+           $(ircrandir)/r-cran-R6-$(r-cran-R6-version) \
+           $(ircrandir)/r-cran-farver-$(r-cran-farver-version) \
+           $(ircrandir)/r-cran-munsell-$(r-cran-munsell-version) \
+           $(ircrandir)/r-cran-labeling-$(r-cran-labeling-version) \
+           $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) \
+           $(ircrandir)/r-cran-viridisLite-$(r-cran-viridisLite-version) \
+           $(ircrandir)/r-cran-RColorBrewer-$(r-cran-RColorBrewer-version)
+	tarball=scales-$(r-cran-scales-version).tar.lz
+	$(call r_cran_build, scales, $(r-cran-scales-version), \
+	                     $(r-cran-scales-checksum))
+
+#https://cran.r-project.org/web/packages/tibble/index.html
+$(ircrandir)/r-cran-tibble-$(r-cran-tibble-version): \
+              $(ibidir)/r-cran-$(r-cran-version) \
+              $(ircrandir)/r-cran-fansi-$(r-cran-fansi-version) \
+              $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+              $(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version) \
+              $(ircrandir)/r-cran-pillar-$(r-cran-pillar-version) \
+              $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) \
+              $(ircrandir)/r-cran-magrittr-$(r-cran-magrittr-version) \
+              $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) \
+              $(ircrandir)/r-cran-pkgconfig-$(r-cran-pkgconfig-version)
+	tarball=tibble-$(r-cran-tibble-version).tar.lz
+	$(call r_cran_build, tibble, $(r-cran-tibble-version), \
+	                     $(r-cran-tibble-checksum))
+
+$(ircrandir)/r-cran-utf8-$(r-cran-utf8-version): \
+                         $(ibidir)/r-cran-$(r-cran-version)
+	tarball=utf8-$(r-cran-utf8-version).tar.lz
+	$(call r_cran_build, utf8, $(r-cran-utf8-version), \
+	                     $(r-cran-utf8-checksum))
+
+$(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version): \
+              $(ibidir)/r-cran-$(r-cran-version) \
+              $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+              $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+              $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version)
+	tarball=vctrs-$(r-cran-vctrs-version).tar.lz
+	$(call r_cran_build, vctrs, $(r-cran-vctrs-version), \
+	                     $(r-cran-vctrs-checksum))
+
+$(ircrandir)/r-cran-viridisLite-$(r-cran-viridisLite-version): \
+                                $(ibidir)/r-cran-$(r-cran-version)
+	tarball=viridisLite-$(r-cran-viridisLite-version).tar.lz
+	$(call r_cran_build, viridisLite, $(r-cran-viridisLite-version), \
+	                     $(r-cran-viridisLite-checksum))
+
+$(ircrandir)/r-cran-withr-$(r-cran-withr-version): \
+                          $(ibidir)/r-cran-$(r-cran-version)
+	tarball=withr-$(r-cran-withr-version).tar.lz
+	$(call r_cran_build, withr, $(r-cran-withr-version), \
+	                     $(r-cran-withr-checksum))
diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk
index 3178cb4..6e62595 100644
--- a/reproduce/software/make/xorg.mk
+++ b/reproduce/software/make/xorg.mk
@@ -4,7 +4,7 @@
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
 # This Makefile will be loaded into 'high-level.mk', which is called by the
-# `./project configure' script. It is not included into the project
+# './project configure' script. It is not included into the project
 # afterwards.
 #
 # This Makefile contains instructions to build all the Xorg-related
@@ -14,8 +14,8 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2021-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -57,7 +57,7 @@ $(idir)/etc/profile.d/xorg.sh: | $(idir)/etc/profile.d
 $(ibidir)/util-macros-$(util-macros-version): \
                       $(idir)/etc/profile.d/xorg.sh \
                       $(ibidir)/automake-$(automake-version)
-	tarball=util-macros-$(util-macros-version).tar.bz2
+	tarball=util-macros-$(util-macros-version).tar.lz
 	$(call import-source, $(util-macros-url), $(util-macros-checksum))
 	$(call gbuild, util-macros-$(util-macros-version),,$(XORG_CONFIG),V=1)
 	echo "util-macros (Xorg) $(util-macros-version)" > $@
@@ -65,14 +65,14 @@ $(ibidir)/util-macros-$(util-macros-version): \
 # Necessaary headers to define the Xorg protocols.
 $(ibidir)/xorgproto-$(xorgproto-version): \
                     $(ibidir)/util-macros-$(util-macros-version)
-	tarball=xorgproto-$(xorgproto-version).tar.bz2
+	tarball=xorgproto-$(xorgproto-version).tar.lz
 	$(call import-source, $(xorg-proto-url), $(xorgproto-checksum))
 	$(call gbuild, xorgproto-$(xorgproto-version),,$(XORG_CONFIG),V=1)
 	echo "xorgproto $(xorgproto-version)" > $@
 
 # Necessaary headers to define the Xorg protocols.
 $(ibidir)/libxau-$(libxau-version): $(ibidir)/xorgproto-$(xorgproto-version)
-	tarball=libXau-$(libxau-version).tar.bz2
+	tarball=libXau-$(libxau-version).tar.lz
 	$(call import-source, $(libaxu-url), $(libxau-checksum))
 	$(call gbuild, libXau-$(libxau-version),,$(XORG_CONFIG), V=1)
 	echo "libXau (Xorg) $(libxau-version)" > $@
@@ -88,7 +88,7 @@ $(ibidir)/libxdmcp-$(libxdmcp-version): $(ibidir)/libxau-$(libxau-version)
 $(ibidir)/xcb-proto-$(xcb-proto-version): \
                     $(ibidir)/python-$(python-version) \
                     $(ibidir)/libxml2-$(libxml2-version)
-	tarball=xcb-proto-$(xcb-proto-version).tar.xz
+	tarball=xcb-proto-$(xcb-proto-version).tar.lz
 	$(call import-source, $(xcb-proto-url), $(xcb-proto-checksum))
 	$(call gbuild, xcb-proto-$(xcb-proto-version),,$(XORG_CONFIG), V=1)
 	echo "XCB-proto (Xorg) $(xcb-proto-version)" > $@
@@ -98,7 +98,7 @@ $(ibidir)/libxcb-$(libxcb-version): \
                  $(ibidir)/libxdmcp-$(libxdmcp-version) \
                  $(ibidir)/xcb-proto-$(xcb-proto-version) \
                  $(ibidir)/libpthread-stubs-$(libpthread-stubs-version)
-	tarball=libxcb-$(libxcb-version).tar.xz
+	tarball=libxcb-$(libxcb-version).tar.lz
 	$(call import-source, $(libxcb-url), $(libxcb-checksum))
 	$(call gbuild, libxcb-$(libxcb-version),, \
 	               $(XORG_CONFIG) --without-doxygen, \
@@ -107,7 +107,7 @@ $(ibidir)/libxcb-$(libxcb-version): \
 
 $(ibidir)/libpthread-stubs-$(libpthread-stubs-version): \
                       $(ibidir)/automake-$(automake-version)
-	tarball=libpthread-stubs-$(libpthread-stubs-version).tar.gz
+	tarball=libpthread-stubs-$(libpthread-stubs-version).tar.lz
 	$(call import-source, $(libpthread-stubs-url), $(libpthread-stubs-checksum))
 	$(call gbuild, libpthread-stubs-$(libpthread-stubs-version),, V=1)
 	echo "libpthread-stubs (Xorg) $(libpthread-stubs-version)" > $@
@@ -116,11 +116,12 @@ $(ibidir)/libpthread-stubs-$(libpthread-stubs-version): \
 $(ibidir)/fontconfig-$(fontconfig-version): \
                      $(ibidir)/gperf-$(gperf-version) \
                      $(ibidir)/expat-$(expat-version) \
+                     $(ibidir)/python-$(python-version) \
                      $(ibidir)/libxml2-$(libxml2-version) \
                      $(ibidir)/freetype-$(freetype-version) \
                      $(ibidir)/util-linux-$(util-linux-version)
         # Import the source.
-	tarball=fontconfig-$(fontconfig-version).tar.bz2
+	tarball=fontconfig-$(fontconfig-version).tar.lz
 	$(call import-source, $(fontconfig-url), $(fontconfig-checksum))
 
         # Add the extra environment variables for using 'libuuid' of
@@ -139,27 +140,27 @@ $(ibidir)/fontconfig-$(fontconfig-version): \
 $(ibidir)/xtrans-$(xtrans-version): \
                  $(ibidir)/libxcb-$(libxcb-version) \
                  $(ibidir)/fontconfig-$(fontconfig-version)
-	tarball=xtrans-$(xtrans-version).tar.bz2
+	tarball=xtrans-$(xtrans-version).tar.lz
 	$(call import-source, $(xtrans-url), $(xtrans-checksum))
 	$(call gbuild, xtrans-$(xtrans-version),,$(XORG_CONFIG), V=1)
 	echo "xtrans (Xorg) $(xtrans-version)" > $@
 
 $(ibidir)/libx11-$(libx11-version): $(ibidir)/xtrans-$(xtrans-version)
-	tarball=libX11-$(libx11-version).tar.bz2
+	tarball=libX11-$(libx11-version).tar.lz
 	$(call import-source, $(libx11-url), $(libx11-checksum))
 	$(call gbuild, libX11-$(libx11-version),,$(XORG_CONFIG), \
 	               -j$(numthreads) V=1)
 	echo "X11 library $(libx11-version)" > $@
 
 $(ibidir)/libxext-$(libxext-version): $(ibidir)/libx11-$(libx11-version)
-	tarball=libXext-$(libxext-version).tar.bz2
+	tarball=libXext-$(libxext-version).tar.lz
 	$(call import-source, $(libxext-url), $(libxext-checksum))
 	$(call gbuild, libXext-$(libxext-version),,$(XORG_CONFIG), \
 	               -j$(numthreads) V=1)
 	echo "libXext $(libxext-version)" > $@
 
 $(ibidir)/libice-$(libice-version): $(ibidir)/libxext-$(libxext-version)
-	tarball=libICE-$(libice-version).tar.bz2
+	tarball=libICE-$(libice-version).tar.lz
 	$(call import-source, $(libice-url), $(libice-checksum))
 	$(call gbuild, libICE-$(libice-version),, \
 	               $(XORG_CONFIG) ICE_LIBS=-lpthread, \
@@ -167,14 +168,14 @@ $(ibidir)/libice-$(libice-version): $(ibidir)/libxext-$(libxext-version)
 	echo "libICE $(libice-version)" > $@
 
 $(ibidir)/libsm-$(libsm-version): $(ibidir)/libice-$(libice-version)
-	tarball=libSM-$(libsm-version).tar.bz2
+	tarball=libSM-$(libsm-version).tar.lz
 	$(call import-source, $(libsm-url), $(libsm-checksum))
 	$(call gbuild, libSM-$(libsm-version),, \
 	               $(XORG_CONFIG), -j$(numthreads) V=1)
 	echo "libSM $(libsm-version)" > $@
 
 $(ibidir)/libxt-$(libxt-version): $(ibidir)/libsm-$(libsm-version)
-	tarball=libXt-$(libxt-version).tar.bz2
+	tarball=libXt-$(libxt-version).tar.lz
 	$(call import-source, $(libxt-url), $(libxt-checksum))
 	$(call gbuild, libXt-$(libxt-version),, \
 	               $(XORG_CONFIG), -j$(numthreads) V=1)
diff --git a/reproduce/software/patches/README.md b/reproduce/software/patches/README.md
new file mode 100644
index 0000000..804d7ec
--- /dev/null
+++ b/reproduce/software/patches/README.md
@@ -0,0 +1,6 @@
+Patches to apply to software source
+===================================
+
+This directory is for keeping patches that may be necessary for some
+versions of some software. So it may be empty in some instances (when no
+software in that commit needs a patch).
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
deleted file mode 100644
index 94dcab5..0000000
--- a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
+++ /dev/null
@@ -1,37 +0,0 @@
----
- mpi/libmpiwrap.c |   12 +++++++++++-
- 1 file changed, 11 insertions(+), 1 deletion(-)
- Patch by Samuel Thibault:
- https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=10
- and hacked further by Boud Roukema 2020-05-10.
---- a/mpi/libmpiwrap.c
-+++ b/mpi/libmpiwrap.c
-@@ -278,8 +278,12 @@ static void showTy ( FILE* f, MPI_Dataty
-    else if (ty == MPI_LONG_INT)       fprintf(f,"LONG_INT");
-    else if (ty == MPI_SHORT_INT)      fprintf(f,"SHORT_INT");
-    else if (ty == MPI_2INT)           fprintf(f,"2INT");
-+#  if defined(MPI_UB_ENABLED_IN_MPI1)
-    else if (ty == MPI_UB)             fprintf(f,"UB");
-+#  endif
-+#  if defined(MPI_LB_ENABLED_IN_MPI1)
-    else if (ty == MPI_LB)             fprintf(f,"LB");
-+#  endif
- #  if defined(MPI_WCHAR)
-    else if (ty == MPI_WCHAR)          fprintf(f,"WCHAR");
- #  endif
-@@ -733,8 +737,14 @@ void walk_type ( void(*f)(void*,long), c
-          f(base + offsetof(Ty,loc), sizeof(int));
-          return;
-       }
--      if (ty == MPI_LB || ty == MPI_UB)
-+#if defined(MPI_LB_ENABLED_IN_MPI1)
-+      if (ty == MPI_LB)
-+         return; /* have zero size, so nothing needs to be done */
-+#endif
-+#if defined(MPI_UB_ENABLED_IN_MPI1)
-+      if (ty == MPI_UB)
-          return; /* have zero size, so nothing needs to be done */
-+#endif
-       goto unhandled;
-       /*NOTREACHED*/
-    }
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
deleted file mode 100644
index 12b50a2..0000000
--- a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Index: valgrind-3.15.0/mpi/Makefile.am
-===================================================================
- Patch by Samuel Thibault:
- https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=22
---- valgrind-3.15.0.orig/mpi/Makefile.am
-+++ valgrind-3.15.0/mpi/Makefile.am
-@@ -42,14 +42,14 @@ libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@
- libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
- libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CFLAGS   = \
- 	$(CFLAGS_MPI) $(MPI_FLAG_M3264_PRI) -Wno-deprecated-declarations
--libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDFLAGS  = $(LDFLAGS_MPI)
-+libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDADD  = $(LDFLAGS_MPI)
- endif
- if BUILD_MPIWRAP_SEC
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_SOURCES  = libmpiwrap.c
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CFLAGS   = \
- 	$(CFLAGS_MPI) $(MPI_FLAG_M3264_SEC) -Wno-deprecated-declarations
--libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDFLAGS  = $(LDFLAGS_MPI)
-+libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDADD  = $(LDFLAGS_MPI)
- endif
- 
- #----------------------------------------------------------------------------
diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh
index 23845d6..6bb871b 100755
--- a/reproduce/software/shell/bashrc.sh
+++ b/reproduce/software/shell/bashrc.sh
@@ -3,10 +3,10 @@
 # To have better control over the environment of each analysis step (Make
 # recipe), besides having environment variables (directly included from
 # Make), it may also be useful to have a Bash startup file (this file). All
-# of the Makefiles set this file as the `BASH_ENV' environment variable, so
+# of the Makefiles set this file as the 'BASH_ENV' environment variable, so
 # it is loaded into all the Make recipes within the project.
 #
-# The special `PROJECT_STATUS' environment variable is defined in every
+# The special 'PROJECT_STATUS' environment variable is defined in every
 # top-level Makefile of the project. It defines the the state of the Make
 # that is calling this script. It can have three values:
 #
@@ -29,7 +29,7 @@
 #       versions.
 #
 #
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 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
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 0f7278f..07381e6 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -2,8 +2,9 @@
 #
 # Necessary preparations/configurations for the reproducible project.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021      Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022      Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # 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
@@ -112,7 +113,7 @@ absolute_dir ()
 # Check file permission handling (POSIX-compatibility)
 # ----------------------------------------------------
 #
-# Check if a `given' directory handles permissions as expected.
+# Check if a 'given' directory handles permissions as expected.
 #
 # This is to prevent a known bug in the NTFS filesystem that prevents
 # proper installation of Perl, and probably some other packages. This
@@ -120,15 +121,15 @@ absolute_dir ()
 # file, and examines whether the given directory handles the file
 # permissions as expected.
 #
-# Returns `0' if everything is fine, and `255' otherwise. Choosing `0' is
-# to mimic the `$ echo $?' behavior, while choosing `255' is to prevent
+# Returns '0' if everything is fine, and '255' otherwise. Choosing '0' is
+# to mimic the '$ echo $?' behavior, while choosing '255' is to prevent
 # misunderstanding 0 and 1 as true and false.
 #
 # ===== CAUTION! ===== #
 #
-# Since there is a `set -e' before running this function, the whole script
-# stops and exits IF the `check_permission' (or any other function) returns
-# anything OTHER than `0'! So, only use this function as a test. Here's a
+# Since there is a 'set -e' before running this function, the whole script
+# stops and exits IF the 'check_permission' (or any other function) returns
+# anything OTHER than '0'! So, only use this function as a test. Here's a
 # minimal example:
 #
 #     if $(check_permission $some_directory) ; then
@@ -136,7 +137,7 @@ absolute_dir ()
 #     fi ;
 check_permission ()
 {
-    # Make a `junk' file, activate its executable flag and record its
+    # Make a 'junk' file, activate its executable flag and record its
     # permissions generally.
     local junkfile="$1"/check_permission_tmp_file
     rm -f "$junkfile"
@@ -309,7 +310,9 @@ fi
 # system.  Here, it is checked that this is the case, and if not, warn the user
 # about not having Xcode already installed.
 if [ x$on_mac_os = xyes ]; then
-  xcode=$(which xcodebuild)
+
+  # 'which' isn't in POSIX, so we are using 'command -v' instead.
+  xcode=$(command -v xcodebuild)
   if [ x$xcode != x ]; then
     xcode_version=$(xcodebuild -version | grep Xcode)
     echo "                                              "
@@ -475,8 +478,8 @@ fi
 # See if we need the dynamic-linker (-ldl)
 # ----------------------------------------
 #
-# Some programs (like Wget) need dynamic loading (using `libdl'). On
-# GNU/Linux systems, we'll need the `-ldl' flag to link such programs.  But
+# Some programs (like Wget) need dynamic loading (using 'libdl'). On
+# GNU/Linux systems, we'll need the '-ldl' flag to link such programs.  But
 # Mac OS doesn't need any explicit linking. So we'll check here to see if
 # it is present (thus necessary) or not.
 cat > $testsource <<EOF
@@ -508,7 +511,7 @@ fi
 # programs will go and find their necessary libraries on the host system.
 #
 # Another good advantage of shared libraries is that we can actually use
-# the shared library tool of the system (`ldd' with GNU C Library) and see
+# the shared library tool of the system ('ldd' with GNU C Library) and see
 # exactly where each linked library comes from. But in static building,
 # unless you follow the build closely, its not easy to see if the source of
 # the library came from the system or our build.
@@ -545,7 +548,7 @@ fi
 #
 # On some systems (in particular Debian-based OSs), the static C library
 # and necessary headers in a non-standard place, and we can't build GCC. So
-# we need to find them first. The `sys/cdefs.h' header is also in a
+# we need to find them first. The 'sys/cdefs.h' header is also in a
 # similarly different location.
 sys_cpath=""
 sys_library_path=""
@@ -576,7 +579,7 @@ fi
 # See if a link-able static C library exists
 # ------------------------------------------
 #
-# A static C library and the `sys/cdefs.h' header are necessary for
+# A static C library and the 'sys/cdefs.h' header are necessary for
 # building GCC.
 if [ x"$host_cc" = x0 ]; then
     echo; echo; echo "Checking if static C library is available...";
@@ -752,9 +755,9 @@ EOF
 # What to do with possibly existing configuration file
 # ----------------------------------------------------
 #
-# `LOCAL.conf' is the top-most local configuration for the project. If it
+# 'LOCAL.conf' is the top-most local configuration for the project. If it
 # already exists when this script is run, we'll make a copy of it as backup
-# (for example the user might have ran `./project configure' by mistake).
+# (for example the user might have ran './project configure' by mistake).
 printnotice=yes
 rewritepconfig=yes
 if [ -f $pconf ]; then
@@ -807,16 +810,18 @@ fi
 # need to check the host's available tool for downloading at this step.
 if [ $rewritepconfig = yes ]; then
     if type wget > /dev/null 2>/dev/null; then
-        name=$(which wget)
+
+        # 'which' isn't in POSIX, so we are using 'command -v' instead.
+        name=$(command -v wget)
 
         # By default Wget keeps the remote file's timestamp, so we'll have
         # to disable it manually.
         downloader="$name --no-use-server-timestamps -O";
     elif type curl > /dev/null 2>/dev/null; then
-        name=$(which curl)
+        name=$(command -v curl)
 
         # - cURL doesn't keep the remote file's timestamp by default.
-        # - With the `-L' option, we tell cURL to follow redirects.
+        # - With the '-L' option, we tell cURL to follow redirects.
         downloader="$name -L -o"
     else
         cat <<EOF
@@ -913,7 +918,7 @@ EOF
                 # If it was newly created, it will be empty, so delete it.
                 if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi
 
-                # Inform the user that this is not acceptable and reset `bdir'.
+                # Inform the user that this is not acceptable and reset 'bdir'.
                 bdir=
                 echo " ** The build-directory cannot be under the source-directory."
             fi
@@ -960,7 +965,7 @@ EOF
         fi
 
         # If the build directory was good, the loop will stop, if not,
-        # reset `build_dir' to blank, so it continues asking for another
+        # reset 'build_dir' to blank, so it continues asking for another
         # directory and let the user know that they must select a new
         # directory.
         if [ x"$bdir" = x ]; then
@@ -1118,7 +1123,7 @@ else
     if [ x"$downloader" = x ]; then novalue="$novalue"DOWNLOADER;  fi
     if [ x"$novalue"   != x ]; then verr=1; err=1;                 fi
 
-    # Make sure `bdir' is an absolute path and it exists.
+    # Make sure 'bdir' is an absolute path and it exists.
     berr=0
     ierr=0
     bdir="$(absolute_dir "$inbdir")"
@@ -1202,6 +1207,10 @@ if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi
 ipydir="$verdir"/python
 if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi
 
+# R module versions and citation.
+ircrandir="$verdir"/r-cran
+if ! [ -d "$ircrandir" ]; then mkdir "$ircrandir"; fi
+
 # Used software BibTeX entries.
 ictdir="$verdir"/cite
 if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
@@ -1210,6 +1219,15 @@ if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
 itidir="$verdir"/tex
 if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi
 
+# Some software install their libraries in '$(idir)/lib64'. But all other
+# libraries are in '$(idir)/lib'. Since Maneage's build is only for a
+# single architecture, we can set the '$(idir)/lib64' as a symbolic link to
+# '$(idir)/lib' so all the libraries are always available in the same
+# place.
+instlibdir="$instdir"/lib
+if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi
+ln -fs "$instlibdir" "$instdir"/lib64
+
 
 
 
@@ -1312,38 +1330,69 @@ if [ x"$shmdir" != x ]; then
 
         # Set the Maneage-specific directory within the shared
         # memory. We'll use the names of the two parent directories to the
-        # current/running directory, separated by a `-' instead of
-        # `/'. We'll then appended that with the user's name (in case
+        # current/running directory, separated by a '-' instead of
+        # '/'. We'll then appended that with the user's name (in case
         # multiple users may be working on similar project names).
         #
-        # Maybe later, we can use something like `mktemp' to add random
+        # Maybe later, we can use something like 'mktemp' to add random
         # characters to this name and make it unique to every run (even for
         # a single user).
         dirname=$(pwd | sed -e's/\// /g' \
                       | awk '{l=NF-1; printf("%s-%s", $l, $NF)}')
         tbshmdir="$shmdir"/"$dirname"-$(whoami)
-        if ! [ -d "$tbshmdir" ]; then mkdir "$tbshmdir"; fi
+
+        # Try to make the directory if it does not yet exist. A failed
+        # directory creation will be tested for a few lines later, when
+        # testing for the existence and executability of a test file.
+        if ! [ -d "$tbshmdir" ]; then (mkdir "$tbshmdir" || true); fi
 
         # Some systems may protect '/dev/shm' against the right to execute
         # programs by ordinary users. We thus need to check that the device
         # allows execution within this directory by this user.
         shmexecfile="$tbshmdir"/shm-execution-check.sh
         rm -f $shmexecfile      # We also don't want any existing flags.
-        cat > "$shmexecfile" <<EOF
+
+        # Create the file to be executed, but do not fail fatally if it
+        # cannot be created. We will check a few lines later if the file
+        # really exists.
+        (cat > "$shmexecfile" <<EOF || true)
 #!/bin/sh
-printf "This file successfully executed.\n"
+echo "This file successfully executed."
 EOF
-        # Make the file executable and see if it runs. If not, set
-        # 'tbshmdir' to an empty string so it is not used in later steps.
-        # In any case, delete the temporary file afterwards.
-        chmod u+x "$shmexecfile"
-        if ! "$shmexecfile" &> /dev/null; then tbshmdir=""; fi
-        rm "$shmexecfile"
+
+        # If the file was successfully created, then make the file
+        # executable and see if it runs. If not, set 'tbshmdir' to an empty
+        # string so it is not used in later steps.  In any case, delete the
+        # temporary file afterwards.
+        #
+        # We aren't adding '&> /dev/null' after the execution command
+        # because it can produce false failures randomly on some systems.
+        if [ -e "$shmexecfile" ]; then
+
+            # Add the executable flag.
+            chmod +x "$shmexecfile"
+
+            # The following line tries to execute the file.
+            if "$shmexecfile"; then
+                # Successful execution. The colon is a "no-op" (no
+                # operation) shell command.
+                :
+            else
+                tbshmdir=""
+            fi
+            rm "$shmexecfile"
+        else
+            tbshmdir=""
+        fi
     fi
 else
     tbshmdir=""
 fi
 
+
+
+
+
 # If a shared memory directory was created, set the software building
 # directory to be a symbolic link to it. Otherwise, just build the
 # temporary build directory under the project's build directory.
@@ -1426,7 +1475,7 @@ fi
 # See if the linker accepts -Wl,-rpath-link
 # -----------------------------------------
 #
-# `-rpath-link' is used to write the information of the linked shared
+# '-rpath-link' is used to write the information of the linked shared
 # library into the shared object (library or program). But some versions of
 # LLVM's linker don't accept it an can cause problems.
 #
@@ -1459,13 +1508,13 @@ rm -rf $compilertestdir
 
 
 
-# Paths needed by the host compiler (only for `basic.mk')
+# Paths needed by the host compiler (only for 'basic.mk')
 # -------------------------------------------------------
 #
 # At the end of the basic build, we need to build GCC. But GCC will build
 # in multiple phases, making its own simple compiler in order to build
 # itself completely. The intermediate/simple compiler doesn't recognize
-# some system specific locations like `/usr/lib/ARCHITECTURE' that some
+# some system specific locations like '/usr/lib/ARCHITECTURE' that some
 # operating systems use. We thus need to tell the intermediate compiler
 # where its necessary libraries and headers are.
 if [ x"$sys_library_path" != x ]; then
@@ -1502,7 +1551,7 @@ fi
 # which will download the DOI-resolved webpage, and extract the Zenodo-URL
 # of the most recent version from there (using the 'coreutils' tarball as
 # an example, the directory part of the URL for all the other software are
-# the same). This is not done if the option `--debug' is used.
+# the same). This is not done if the option '--debug' is used.
 zenodourl=""
 user_backup_urls=""
 zenodocheck=.build/software/zenodo-check.html
@@ -1535,6 +1584,7 @@ user_backup_urls="$user_backup_urls $zenodourl"
 # (compression program), GNU Make (that 'basic.mk' is written in), Dash
 # (minimal Bash-like shell) and Flock (to lock files and enable serial
 # download).
+export on_mac_os
 ./reproduce/software/shell/pre-make-build.sh \
     "$bdir" "$ddir" "$downloader" "$user_backup_urls"
 
@@ -1672,7 +1722,7 @@ fi
 # software.
 prepare_name_version ()
 {
-    # First see if the (possible) `*' in the input arguments corresponds to
+    # First see if the (possible) '*' in the input arguments corresponds to
     # anything. Note that some of the given directories may be empty (no
     # software installed).
     hasfiles=0
@@ -1773,9 +1823,9 @@ hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')"
 # ---------------------------------
 #
 # By the time the script reaches here the temporary software build
-# directory should be empty, so just delete it. Note `tmpblddir' may be a
+# directory should be empty, so just delete it. Note 'tmpblddir' may be a
 # symbolic link to shared memory. So, to work in any scenario, first delete
-# the contents of the directory (if it has any), then delete `tmpblddir'.
+# the contents of the directory (if it has any), then delete 'tmpblddir'.
 .local/bin/rm -rf $tmpblddir/* $tmpblddir
 
 
diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout
index 7a90108..d49504d 100755
--- a/reproduce/software/shell/git-post-checkout
+++ b/reproduce/software/shell/git-post-checkout
@@ -1,14 +1,14 @@
 #!@BINDIR@/bash
 #
 # The example hook script to store the metadata information of version
-# controlled files (with each commit) using the `metastore' program.
+# controlled files (with each commit) using the 'metastore' program.
 #
 # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
-# This script is taken from the `examples/hooks/pre-commit' file of the
-# `metastore' package (installed within the project, with an MIT license
-# for copyright). We have just changed the name of the `MSFILE' and also
+# This script is taken from the 'examples/hooks/pre-commit' file of the
+# 'metastore' package (installed within the project, with an MIT license
+# for copyright). We have just changed the name of the 'MSFILE' and also
 # set special characters for the installation location of meta-store so our
 # own installation is found by Git.
 #
diff --git a/reproduce/software/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit
index 85d3474..10ad710 100755
--- a/reproduce/software/shell/git-pre-commit
+++ b/reproduce/software/shell/git-pre-commit
@@ -1,10 +1,10 @@
 #!@BINDIR@/bash
 #
 # The example hook script to store the metadata information of version
-# controlled files (with each commit) using the `metastore' program.
+# controlled files (with each commit) using the 'metastore' program.
 #
 # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # WARNING:
 #
@@ -17,9 +17,9 @@
 #     git reset HEAD -- .metadata
 #     git checkout HEAD -- .metadata
 #
-# This script is taken from the `examples/hooks/pre-commit' file of the
-# `metastore' package (installed within the project, with an MIT license
-# for copyright). Here, the name of the `MSFILE' and also set special
+# This script is taken from the 'examples/hooks/pre-commit' file of the
+# 'metastore' package (installed within the project, with an MIT license
+# for copyright). Here, the name of the 'MSFILE' and also set special
 # characters for the installation location of meta-store so our own
 # installation is found by Git.
 #
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index a033963..e7de93d 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -2,7 +2,7 @@
 #
 # Very basic tools necessary to start Maneage's default building.
 #
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# 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
@@ -185,6 +185,19 @@ build_program() {
         # All others accept the configure script.
         ./configure --prefix="$instdir" $configoptions
 
+        # In Flock 0.4.0 there is a crash that can be fixed by simply
+        # replacing '%1u' with '%ld' on GNU/Linux and '%d' on macOS. This
+        # has been reported to flock maintainers:
+        # https://github.com/discoteq/flock/issues/33
+        if [ x$progname = xflock ]; then
+            case $on_mac_os in
+                yes) sed -e's/\%1u/\%d/'  src/flock.c > src/flock-new.c;;
+                no)  sed -e's/\%1u/\%ld/' src/flock.c > src/flock-new.c;;
+                *)   echo "pre-make-build.sh: '$on_mac_os' unrecognized value for on_mac_os";;
+            esac
+            mv src/flock-new.c src/flock.c
+        fi
+
         # To build GNU Make, we don't want to assume the existance of a
         # Make program, so we use its 'build.sh' script and its own built
         # 'make' program to install itself.
@@ -192,7 +205,7 @@ build_program() {
             /bin/sh build.sh
             ./make install
         else
-            make
+            make V=1
             make install
         fi
     fi
@@ -235,13 +248,20 @@ build_program
 # '--disable-dependency-tracking' configure-time option is necessary so
 # Make doesn't check for an existing 'make' implementation (recall that we
 # aren't assuming any 'make' on the host).
+#
+# If GNU Guile is already present on the host system, Make will try to link
+# with it, and this will cause dependency problems later. So we have
+# distabled Guile. If a project needs the Guile extensions of Make, we need
+# to add a build rule for Guile in Maneage, with a special Guile-enabled
+# Make that has a different executable name (using the '--program-prefix='
+# configure option) from the "default" make (which is this one!).
 progname="make"
 progname_tex="GNU Make"
 url=$(awk '/^'$progname'-url/{print $3}' $urlfile)
 version=$(awk '/^'$progname'-version/{print $3}' $versionsfile)
 tarball=$progname-$version.tar.lz
 download_tarball
-build_program --disable-dependency-tracking
+build_program "--disable-dependency-tracking --without-guile"
 
 
 
@@ -274,11 +294,11 @@ fi
 # -----
 #
 # Flock (or file-lock) is necessary to serialize operations when
-# necessary. GNU/Linux machines have it as part of their `util-linux'
+# necessary. GNU/Linux machines have it as part of their 'util-linux'
 # programs. But to be consistent in non-GNU/Linux systems, we will be using
 # our own build.
 #
-# The reason that `flock' is built here is that generally the building of
+# The reason that 'flock' is built here is that generally the building of
 # software is done in parallel, but we need it to serialize the download
 # process of the software tarballs to avoid network complications when too
 # many simultaneous download commands are called.
diff --git a/reproduce/software/shell/run-parts.in b/reproduce/software/shell/run-parts.in
index 7e649b1..a6db9e0 100755
--- a/reproduce/software/shell/run-parts.in
+++ b/reproduce/software/shell/run-parts.in
@@ -10,8 +10,8 @@
 # However, it didn't have a copyright statement. So one is being added
 # here.
 #
-# Copyright (C) 2021 Authors mentioned above.
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2022 Authors mentioned above.
+# 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
author	Mohammad Akhlaghi <mohammad@akhlaghi.org>	2021-10-04 02:51:45 +0200
committer	Mohammad Akhlaghi <mohammad@akhlaghi.org>	2022-01-21 01:15:24 +0100
commit	8463df97c6f26ec4d22cd5828bb0574fd5e450d2 (patch)
tree	dbaa2e7c2fc44856eb98555b79c6814f210a6c17 /reproduce/software
parent	775fc036e0091f05ff56e41b855bc416b9ed36c8 (diff)