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

6 files changed, 132 insertions, 62 deletions

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