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

1 files changed, 491 insertions, 390 deletions

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) \