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, 487 insertions, 0 deletions

diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk
new file mode 100644
index 0000000..617b8de
--- /dev/null
+++ b/reproduce/software/make/r-cran.mk
@@ -0,0 +1,487 @@
+# Build the project's R (here called R-CRAN) dependencies.
+#
+# ------------------------------------------------------------------------
+#                      !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be loaded into 'high-level.mk', which is called by the
+# './project configure' script. It is not included into the project
+# afterwards.
+#
+# This Makefile contains instructions to build all the R-CRAN-related
+# software within the project.
+#
+# ------------------------------------------------------------------------
+#
+# Copyright (C) 2022 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This Makefile is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this Makefile.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# BUGS/IMPROVEMENTS
+# -----------------
+#
+# As of 2021-06-20, the R system is still very new and has not yet
+# been tested on non-Debian-derived systems. Please provide bug
+# reports ( https://savannah.nongnu.org/task/?15772 ) or propose fixes
+# as git pull requests on a public git server (e.g.  on a fork of
+# https://codeberg.org/boud/maneage_dev ).
+
+
+
+
+
+# R-CRAN enviroment
+# -----------------
+#
+# It may be necessary to override host-level R-related environment
+# variables that interfere with the Maneage-installed R system.
+# systems which might interfere.
+
+# Ideas for which environment variables might create problems
+# and might need to be set to be empty here:
+#
+# https://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html
+
+# These first variables should be set automatically when R starts:
+#export R_HOME             := $(idir)/lib/R
+#export R_INCLUDE_DIR      := $(idir)/lib/R/include
+
+
+
+
+
+# R-CRAN-specific installation directories.
+r-cran-major-version = $(shell echo $(r-cran-version) \
+                                    | awk 'BEGIN{FS="."} \
+	                            {printf "%d.%d\n", $$1, $$2}')
+
+
+
+
+
+# R-CRAN-specific build rules for 'make'
+# ======================================
+
+# Double-check an already downloaded R source
+# -------------------------------------------
+#
+# Check that the tarball with the version in
+# 'reproduce/software/conf/versions.conf' has the sha512sum (checksum)
+# stated 'reproduce/software/conf/checksums.conf'. This does not do any
+# security checks; it only checks that the source file package is the one
+# that is expected the last time that someone updated these two files for
+# the R package of interest.
+#
+# Calculate the checksum and exit with a non-zero error code if there's a
+# mismatch, after informing the user.
+#
+# Arguments:
+#   1: The expected checksum of the tarball.
+#
+# Necessary shell variables
+#   'tarball': This is the name of the actual tarball file without a
+#   directory.
+double-check-R-source = final=$(tdir)/$$tarball; \
+	exp_checksum="$(strip $(1))"; \
+	if [ x"$$exp_checksum" = x"NO-CHECK-SUM" ]; then \
+	  result=0; \
+	else \
+	  if type sha512sum > /dev/null 2>/dev/null; then \
+	    checksum=$$(sha512sum "$$final" | awk '{print $$1}'); \
+	    if [ x"$$checksum" = x"$$exp_checksum" ]; then \
+	      result=0; \
+	    else \
+	      echo "ERROR: Non-matching checksum: $$final"; \
+	      echo "Checksum should be: $$exp_checksum"; \
+	      echo "Checksum is:        $$checksum"; \
+	      result=1; \
+	      exit 1; \
+	    fi; \
+	  else \
+	    echo "ERROR: sha512sum is unavailable."; \
+	    exit 1; \
+	  fi; \
+	fi
+
+# Default 'make' build rules for an CRAN package
+# -----------------------------------------------
+#
+# The default 'install.packages' function of R only recognizes 'tar.gz'
+# tarballs. But Maneage uses '.tar.lz' format for its archival. So to be
+# agnostic to the compression algorithm, we will be using 'tar' externally
+# (before entering R), then give the un-compressed directory to
+# 'install.packages'.
+#
+# Parameters:
+# 1. package name (without 'r-cran', without the version string)
+# 2. version string
+# 3. checksum of the package
+r_cran_build = \
+	pkg=$(strip $(1)); \
+	version=$(strip $(2)); \
+	checksum=$(strip $(3)); \
+	$(call import-source, \
+	       https://cran.r-project.org/src/contrib, \
+	       $$checksum, \
+	       $$tarball, \
+	       https://cran.r-project.org/src/contrib/00Archive/$$pkg); \
+	cd "$(ddir)"; \
+	tar -xf $(tdir)/$$tarball; \
+	unpackdir=$$pkg-$$version; \
+	(printf "install.packages(c(\"$(ddir)/$$unpackdir\"),"; \
+	 printf 'lib="$(ilibrcrandir)",'; \
+	 printf 'repos=NULL,'; \
+	 printf 'type="source")\n'; \
+	 printf 'quit()\n'; \
+	 printf 'n\n') | R --no-save; \
+	rm -rf $$unpackdir; \
+	if [ $$pkg = r-pkgconfig ]; then iname=pkgconfig; \
+	else                             iname=$$pkg; fi; \
+	if [ -e "$(ilibrcrandir)"/$$iname/Meta/nsInfo.rds ]; then \
+	   $(call double-check-R-source, $$checksum) \
+	          && echo "$$pkg $$version" > $@; \
+	else \
+	   printf "r-cran-$$pkg failed: Meta/nsInfo.rds missing.\n"; \
+	   exit 1; \
+	fi
+
+
+
+
+
+# Necessary programs and libraries
+# --------------------------------
+#
+# While this Makefile is for R programs, in some cases, we need certain
+# programs (like R itself), or libraries for the modules.  Comment on
+# building R without GUI support ('--without-tcltlk')
+#
+# Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support
+# in some software. But they are not yet natively built within Maneage,
+# primarily because we have higher-priority work right now (if anyone is
+# interested, they can ofcourse contribute!). GUI tools in general aren't
+# high on our priority list right now because they are generally good for
+# human interaction (which is contrary to the reproducible philosophy:
+# there will always be human-error and frustration, for example in GUI
+# tools the best level of reproducibility is statements like this: "move
+# your mouse to button XXX, then click on menu YYY and etc"). A robust
+# reproducible solution must be done automatically.
+#
+# If someone wants to use R's GUI functionalities while investigating for
+# their analysis, they can do the GUI part on their host OS
+# implementation. Later, they can bring the finalized source into Maneage
+# to be automatically run in Maneage. This will also be the recommended way
+# to deal with GUI tools later when we do install them within Maneage.
+$(ibidir)/r-cran-$(r-cran-version): \
+            $(itidir)/texlive \
+            $(ibidir)/icu-$(icu-version) \
+            $(ibidir)/pcre-$(pcre-version) \
+            $(ibidir)/cairo-$(cairo-version) \
+            $(ibidir)/libpng-$(libpng-version) \
+            $(ibidir)/libjpeg-$(libjpeg-version) \
+            $(ibidir)/libtiff-$(libtiff-version) \
+            $(ibidir)/libpaper-$(libpaper-version)
+
+#	Prepare the tarball, unpack it and enter the directory.
+	tarball=R-$(r-cran-version).tar.lz
+	$(call import-source, $(r-cran-url), $(r-cran-checksum))
+	cd $(ddir)
+	tar -xf $(tdir)/$$tarball
+	unpackdir=R-$(r-cran-version)
+	cd $$unpackdir
+
+#	We need to manually remove the lines with '~autodetect~', they
+#	cause the configure script to crash in version 4.0.2. They are used
+#	in relation to Java, and we don't use Java anyway.
+	sed -i -e '/\~autodetect\~/ s/^/#/g' configure
+	export R_SHELL=$(SHELL)
+	./configure --prefix=$(idir) \
+	            --without-x \
+	            --with-pcre1 \
+	            --disable-java \
+	            --with-readline \
+	            --without-tcltk \
+	            --disable-openmp
+	make -j$(numthreads)
+	make install
+	cd ..
+	rm -rf R-$(r-cran-version)
+	cp -p $(dtexdir)/r-cran.tex $(ictdir)/
+	echo "R $(r-cran-version) \citep{RIhakaGentleman1996}" > $@
+
+
+
+
+
+# Non-Maneage'd tarballs
+# ----------------------
+#
+# CRAN tarballs differ in two aspects from Maneage'd tarballs:
+#    - CRAN uses '.tar.gz', while Maneage uses 'tar.lz'.
+#    - CRAN uses 'name_version', while Maneage uses 'name-version'.
+#
+# So if you add a new R package, or update the version of an existing one
+# (that is not yet in Maneage's archive), you need to use the CRAN naming
+# format for the 'tarball' variable.
+
+
+
+
+
+# R-CRAN modules
+# ---------------
+#
+# The rules for downloading, compiling and installing any R-CRAN modules
+# that are needed should be provided here. Each target (before the colon)
+# is first shown with its dependence on prerequisites (which are listed
+# after the colon. The default macro 'r_cran_build' will install the
+# package without checking on dependencies.
+
+$(ircrandir)/r-cran-cli-$(r-cran-cli-version): \
+                        $(ibidir)/r-cran-$(r-cran-version) \
+                        $(ircrandir)/r-cran-glue-$(r-cran-glue-version)
+	tarball=cli-$(r-cran-cli-version).tar.lz
+	$(call r_cran_build, cli, $(r-cran-cli-version), \
+	                     $(r-cran-cli-checksum))
+
+$(ircrandir)/r-cran-colorspace-$(r-cran-colorspace-version): \
+                               $(ibidir)/r-cran-$(r-cran-version)
+	tarball=colorspace-$(r-cran-colorspace-version).tar.lz
+	$(call r_cran_build, colorspace, $(r-cran-colorspace-version), \
+	                     $(r-cran-colorspace-checksum))
+
+$(ircrandir)/r-cran-cowplot-$(r-cran-cowplot-version): \
+                 $(ibidir)/r-cran-$(r-cran-version) \
+                 $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+                 $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) \
+                 $(ircrandir)/r-cran-scales-$(r-cran-scales-version) \
+                 $(ircrandir)/r-cran-ggplot2-$(r-cran-ggplot2-version)
+	tarball=cowplot-$(r-cran-cowplot-version).tar.lz
+	$(call r_cran_build, cowplot, $(r-cran-cowplot-version), \
+	                     $(r-cran-cowplot-checksum))
+
+$(ircrandir)/r-cran-crayon-$(r-cran-crayon-version): \
+                           $(ibidir)/r-cran-$(r-cran-version)
+	tarball=crayon-$(r-cran-crayon-version).tar.lz
+	$(call r_cran_build, crayon, $(r-cran-crayon-version), \
+	                     $(r-cran-crayon-checksum))
+
+$(ircrandir)/r-cran-digest-$(r-cran-digest-version): \
+                           $(ibidir)/r-cran-$(r-cran-version)
+	tarball=digest-$(r-cran-digest-version).tar.lz
+	$(call r_cran_build, digest, $(r-cran-digest-version), \
+	                     $(r-cran-digest-checksum))
+
+$(ircrandir)/r-cran-farver-$(r-cran-farver-version): \
+                           $(ibidir)/r-cran-$(r-cran-version)
+	tarball=farver-$(r-cran-farver-version).tar.lz
+	$(call r_cran_build, farver, $(r-cran-farver-version), \
+	                     $(r-cran-farver-checksum))
+
+$(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version): \
+                    $(ibidir)/r-cran-$(r-cran-version) \
+                    $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version)
+	tarball=ellipsis-$(r-cran-ellipsis-version).tar.lz
+	$(call r_cran_build, ellipsis, $(r-cran-ellipsis-version), \
+	                     $(r-cran-ellipsis-checksum))
+
+$(ircrandir)/r-cran-fansi-$(r-cran-fansi-version): \
+                          $(ibidir)/r-cran-$(r-cran-version)
+	tarball=fansi-$(r-cran-fansi-version).tar.lz
+	$(call r_cran_build, fansi, $(r-cran-fansi-version), \
+	                     $(r-cran-fansi-checksum))
+
+$(ircrandir)/r-cran-ggplot2-$(r-cran-ggplot2-version): \
+                $(ibidir)/r-cran-$(r-cran-version) \
+                $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+                $(ircrandir)/r-cran-mgcv-$(r-cran-mgcv-version) \
+                $(ircrandir)/r-cran-MASS-$(r-cran-MASS-version) \
+                $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+                $(ircrandir)/r-cran-withr-$(r-cran-withr-version) \
+                $(ircrandir)/r-cran-digest-$(r-cran-digest-version) \
+                $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) \
+                $(ircrandir)/r-cran-scales-$(r-cran-scales-version) \
+                $(ircrandir)/r-cran-tibble-$(r-cran-tibble-version) \
+                $(ircrandir)/r-cran-isoband-$(r-cran-isoband-version)
+	tarball=ggplot2-$(r-cran-ggplot2-version).tar.lz
+	$(call r_cran_build, ggplot2, $(r-cran-ggplot2-version), \
+	                     $(r-cran-ggplot2-checksum))
+
+$(ircrandir)/r-cran-glue-$(r-cran-glue-version): \
+                         $(ibidir)/r-cran-$(r-cran-version)
+	tarball=glue-$(r-cran-glue-version).tar.lz
+	$(call r_cran_build, glue, $(r-cran-glue-version), \
+	                     $(r-cran-glue-checksum))
+
+$(ircrandir)/r-cran-gridExtra-$(r-cran-gridExtra-version): \
+                  $(ibidir)/r-cran-$(r-cran-version) \
+                  $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version)
+	tarball=gridExtra-$(r-cran-gridExtra-version).tar.lz
+	$(call r_cran_build, gridExtra, $(r-cran-gridExtra-version), \
+	                     $(r-cran-gridExtra-checksum))
+
+$(ircrandir)/r-cran-gtable-$(r-cran-gtable-version): \
+                           $(ibidir)/r-cran-$(r-cran-version)
+	tarball=gtable-$(r-cran-gtable-version).tar.lz
+	$(call r_cran_build, gtable, $(r-cran-gtable-version), \
+	                     $(r-cran-gtable-checksum))
+
+$(ircrandir)/r-cran-isoband-$(r-cran-isoband-version): \
+                            $(ibidir)/r-cran-$(r-cran-version)
+	tarball=isoband-$(r-cran-isoband-version).tar.lz
+	$(call r_cran_build, isoband, $(r-cran-isoband-version), \
+	                     $(r-cran-isoband-checksum))
+
+$(ircrandir)/r-cran-labeling-$(r-cran-labeling-version): \
+                             $(ibidir)/r-cran-$(r-cran-version)
+	tarball=labeling-$(r-cran-labeling-version).tar.lz
+	$(call r_cran_build, labeling, $(r-cran-labeling-version), \
+                             $(r-cran-labeling-checksum))
+
+$(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version): \
+                    $(ibidir)/r-cran-$(r-cran-version) \
+                    $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+                    $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version)
+	tarball=lifecycle-$(r-cran-lifecycle-version).tar.lz
+	$(call r_cran_build, lifecycle, $(r-cran-lifecycle-version), \
+	                     $(r-cran-lifecycle-checksum))
+
+$(ircrandir)/r-cran-magrittr-$(r-cran-magrittr-version): \
+                             $(ibidir)/r-cran-$(r-cran-version)
+	tarball=magrittr-$(r-cran-magrittr-version).tar.lz
+	$(call r_cran_build, magrittr, $(r-cran-magrittr-version), \
+	                     $(r-cran-magrittr-checksum))
+
+$(ircrandir)/r-cran-MASS-$(r-cran-MASS-version): \
+                         $(ibidir)/r-cran-$(r-cran-version)
+	tarball=MASS-$(r-cran-MASS-version).tar.lz
+	$(call r_cran_build, MASS, $(r-cran-MASS-version), \
+	                     $(r-cran-MASS-checksum))
+
+# The base R-2.0.4 install includes nlme and Matrix.
+# https://cran.r-project.org/web/packages/mgcv/index.html
+$(ircrandir)/r-cran-mgcv-$(r-cran-mgcv-version): \
+                         $(ibidir)/r-cran-$(r-cran-version)
+	tarball=mgcv-$(r-cran-mgcv-version).tar.lz
+	$(call r_cran_build, mgcv, $(r-cran-mgcv-version), \
+	                     $(r-cran-mgcv-checksum))
+
+$(ircrandir)/r-cran-munsell-$(r-cran-munsell-version): \
+                 $(ibidir)/r-cran-$(r-cran-version) \
+                 $(ircrandir)/r-cran-colorspace-$(r-cran-colorspace-version)
+	tarball=munsell-$(r-cran-munsell-version).tar.lz
+	$(call r_cran_build, munsell, $(r-cran-munsell-version), \
+	                     $(r-cran-munsell-checksum))
+
+#TODO: https://cran.r-project.org/web/packages/pillar/index.html
+$(ircrandir)/r-cran-pillar-$(r-cran-pillar-version): \
+              $(ibidir)/r-cran-$(r-cran-version) \
+              $(ircrandir)/r-cran-cli-$(r-cran-cli-version) \
+              $(ircrandir)/r-cran-utf8-$(r-cran-utf8-version) \
+              $(ircrandir)/r-cran-fansi-$(r-cran-fansi-version) \
+              $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+              $(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version) \
+              $(ircrandir)/r-cran-crayon-$(r-cran-crayon-version) \
+              $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) \
+              $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version)
+	tarball=pillar-$(r-cran-pillar-version).tar.lz
+	$(call r_cran_build, pillar, $(r-cran-pillar-version), \
+	                     $(r-cran-pillar-checksum))
+
+# Since we have other software packages with the name 'pkgconfig', to avoid
+# confusion with those tarballs, we have put a 'r-' prefix in the tarball
+# name. If you want to use the CRAN tarball, please correct the name
+# accordingly (as described in the comment above this group of rules).
+$(ircrandir)/r-cran-pkgconfig-$(r-cran-pkgconfig-version): \
+                              $(ibidir)/r-cran-$(r-cran-version)
+	tarball=r-pkgconfig-$(r-cran-pkgconfig-version).tar.lz
+	$(call r_cran_build, r-pkgconfig, $(r-cran-pkgconfig-version), \
+	                     $(r-cran-pkgconfig-checksum))
+
+$(ircrandir)/r-cran-RColorBrewer-$(r-cran-RColorBrewer-version): \
+                                 $(ibidir)/r-cran-$(r-cran-version)
+	tarball=RColorBrewer-$(r-cran-RColorBrewer-version).tar.lz
+	$(call r_cran_build, RColorBrewer, $(r-cran-RColorBrewer-version), \
+	                     $(r-cran-RColorBrewer-checksum))
+
+$(ircrandir)/r-cran-R6-$(r-cran-R6-version): \
+                       $(ibidir)/r-cran-$(r-cran-version)
+	tarball=R6-$(r-cran-R6-version).tar.lz
+	$(call r_cran_build, R6, $(r-cran-R6-version), $(r-cran-R6-checksum))
+
+$(ircrandir)/r-cran-rlang-$(r-cran-rlang-version): \
+                          $(ibidir)/r-cran-$(r-cran-version)
+	tarball=rlang-$(r-cran-rlang-version).tar.lz
+	$(call r_cran_build, rlang, $(r-cran-rlang-version), \
+	                     $(r-cran-rlang-checksum))
+
+# https://cran.r-project.org/web/packages/scales/index.html
+$(ircrandir)/r-cran-scales-$(r-cran-scales-version): \
+           $(ibidir)/r-cran-$(r-cran-version) \
+           $(ircrandir)/r-cran-R6-$(r-cran-R6-version) \
+           $(ircrandir)/r-cran-farver-$(r-cran-farver-version) \
+           $(ircrandir)/r-cran-munsell-$(r-cran-munsell-version) \
+           $(ircrandir)/r-cran-labeling-$(r-cran-labeling-version) \
+           $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) \
+           $(ircrandir)/r-cran-viridisLite-$(r-cran-viridisLite-version) \
+           $(ircrandir)/r-cran-RColorBrewer-$(r-cran-RColorBrewer-version)
+	tarball=scales-$(r-cran-scales-version).tar.lz
+	$(call r_cran_build, scales, $(r-cran-scales-version), \
+	                     $(r-cran-scales-checksum))
+
+#https://cran.r-project.org/web/packages/tibble/index.html
+$(ircrandir)/r-cran-tibble-$(r-cran-tibble-version): \
+              $(ibidir)/r-cran-$(r-cran-version) \
+              $(ircrandir)/r-cran-fansi-$(r-cran-fansi-version) \
+              $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+              $(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version) \
+              $(ircrandir)/r-cran-pillar-$(r-cran-pillar-version) \
+              $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) \
+              $(ircrandir)/r-cran-magrittr-$(r-cran-magrittr-version) \
+              $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) \
+              $(ircrandir)/r-cran-pkgconfig-$(r-cran-pkgconfig-version)
+	tarball=tibble-$(r-cran-tibble-version).tar.lz
+	$(call r_cran_build, tibble, $(r-cran-tibble-version), \
+	                     $(r-cran-tibble-checksum))
+
+$(ircrandir)/r-cran-utf8-$(r-cran-utf8-version): \
+                         $(ibidir)/r-cran-$(r-cran-version)
+	tarball=utf8-$(r-cran-utf8-version).tar.lz
+	$(call r_cran_build, utf8, $(r-cran-utf8-version), \
+	                     $(r-cran-utf8-checksum))
+
+$(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version): \
+              $(ibidir)/r-cran-$(r-cran-version) \
+              $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+              $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+              $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version)
+	tarball=vctrs-$(r-cran-vctrs-version).tar.lz
+	$(call r_cran_build, vctrs, $(r-cran-vctrs-version), \
+	                     $(r-cran-vctrs-checksum))
+
+$(ircrandir)/r-cran-viridisLite-$(r-cran-viridisLite-version): \
+                                $(ibidir)/r-cran-$(r-cran-version)
+	tarball=viridisLite-$(r-cran-viridisLite-version).tar.lz
+	$(call r_cran_build, viridisLite, $(r-cran-viridisLite-version), \
+	                     $(r-cran-viridisLite-checksum))
+
+$(ircrandir)/r-cran-withr-$(r-cran-withr-version): \
+                          $(ibidir)/r-cran-$(r-cran-version)
+	tarball=withr-$(r-cran-withr-version).tar.lz
+	$(call r_cran_build, withr, $(r-cran-withr-version), \
+	                     $(r-cran-withr-checksum))