IMPORTANT: Software update

SUMMARY: This is a software update to make Maneage more portable and up to
date. It does not involve any Maneage infrastructure changes. You should
just re-build your project to make sure the updated software haven't
removed/changed any of their features that you were using. In particular,
for Astrometry.net users, please see the respective note in P.S.2 below.

Until now, there have been many updates in the software that are built
within Maneage. The last software upadte was almost one year ago.

With this commit, the software in the P.S.1 have been updated. A
description of notable changes in the software environment is given in
P.S.2. This software environment has been tested on an Arch GNU/Linux,
Debian, CentOS-7 and macOS.

This commit is the merging of 24 individual commits by Raul Infante-Sainz
(who put a lot of energy on porting the software below for macOS, and
updating citations), Boudewijn Roukema (who helped with memory checking for
GCC, and testing on Debian and CentOS), Sepideh Eskandarlou (who tested the
environment) and myself.

Besides the updates in the core software, the followimg improvements have
also been implemented in this commit:

 - When you run './project shell':

   - A welcome message is printed that will remind the caller that they
     have entered a new environment, it will print the location of 'HOME'
     and the location of the shell startup file.

   - The 'reproduce/software/shell/bashrc.sh' is loaded as a startup
     file. This allows you to customize your interactive Maneage shell. A
     default step has already been placed there that will put the git
     branch name (in green) within the shell prompt (which was
     purple). This greatly helps when dealing with directories under Git
     version control. These settings won't bother with Maneage's default
     operations: through environment variables we make sure that these
     './project shell' features will not slow-down the calls to the shell
     within the non-interactive Make calls.

   - The host's 'COLORTERM' is passed to the Maneage environment. It is
     used by some programs that can have color outputs on the terminal.

 - Updates to citations:
   - Numpy and Scipy (as requested on their pages):
     https://numpy.org/citing-numpy and https://scipy.org/citing-scipy
   - Gnuastro: Added https://arxiv.org/abs/1909.11230 which describes major
     updates to Gnuastro after 10 releases.
   - When a software's paper is indexed in the SAO/NASA Astrophysics Data
     System (ADS), Maneage now use the BibTeX entries provided by ADS. This
     helps to give a unified format to most software, and more information
     (like ADS+arXiv hyperlinks in the BibLaTeX compilation of the default
     bibliography).

 - We were able to build this version of Maneage on a Debian system from
   2010 (+12 years ago!). Only three downgrades were necessary in the
   "basic" software (not affecting the high-level science software!). A
   description of the necessary downgrades for such old systems has been
   added in 'README.md'.

P.S.1 List of updated software:

 Basic software:
   cURL                                7.79.1    -->  7.84.0
   Dash                                0.5.11.5  -->  0.5.11-057cd65
   File                                5.41      -->  5.42
   GNU AWK                             5.1.0     -->  5.1.1
   GNU Bash                            5.1.8     -->  5.2-rc2
   GNU Binutils                        2.37      -->  2.39
   GNU Compiler Collection (GCC)       11.2.1    -->  12.1.0
   GNU Findutils                       4.8.0     -->  4.9.0
   GNU Gzip                            1.11      -->  1.12
   GNU Help2man                        1.48.5    -->  1.49.2
   GNU Integer Set Library (ISL)       0.18      -->  0.24
   GNU Libtool                         2.4.6     -->  2.4.7
   GNU Nano                            6.0       -->  6.4
   GNU Readline                        8.1.1     -->  8.2-rc2
   GNU libiconv                        0.16      -->  0.17
   Git                                 2.36.0    -->  2.37.1
   OpenSSL                             3.0.0     -->  3.0.5
   PatchELF                            0.13      -->  0.15.0
   Perl                                5.34.0    -->  5.36.0

 High-level software:
   Astrometry.net                      0.89      -->  0.91
   CFITSIO                             4.0.0     -->  4.1.0
   CMake                               3.21.4    -->  3.24.0
   GNU Astronomy Utilities (Gnuastro)  0.16.1    -->  0.18
   GPL Ghostscript                     9.55.0    -->  9.56.1
   HDF5                                1.10.5    -->  1.13.1
   Libjpeg                             9d        -->  9e
   Libtiff                             4.3.0     -->  4.4.0
   OpenBLAS                            0.3.18    -->  0.3.21
   PLplot                              n/a       -->  5.15.0
   Python                              3.10.0    -->  3.10.6
   SCAMP                               2.6.7     -->  2.10.0
   SWarp                               2.38.0    -->  2.41.5
   Util-Linux                          2.37.2    -->  2.38.1
   Vim                                 8.2       -->  9.0
   WCSLIB                              7.7       -->  7.11

 X.org packages (used by graphical software like Ghostscript and LaTeX):
   Fontconfig                          2.13.94   -->  2.14.0
   LibX11                              1.7.2     -->  1.8
   LibXCB                              1.14      -->  1.15
   XCB-proto                           1.14.1    -->  1.15
   Xorg-proto                          2021.5    -->  2022.1

 Python modules:
   Astropy                             5.0       -->  5.1
   GalSim                              2.3.3     -->  2.3.5

P.S.2: Notable points regarding the software environment:

 - Two new links from the host's low-level tools are now included in
   Maneage's build environment:
   - On GNU/Linux systems, the host's 'ldd' is linked inside the custom
     environment. This belongs to the GNU C Library (which is not yet
     installed in Maneage). But helps in checking the linking status of the
     binaries on GNU/Linux systems.
   - On macOS: the 'codesign' binary is included, which is used by GNU
     Emacs on macOS to sign the built executable.

 - GNU Bison has been moved in basic software (necessary for GNU Binutils).

 - The Zip and Unzip programs have been moved as high-level software that
   have to be manually requested when necessary. This is because they are
   not used by any of the basic software anymore. They were just installed
   as dependencies of GNU Tar to be close the other compression
   programs. Also, in the past we would use the original tarballs, and some
   (for example Numpy) were distributed in Zip format. However, by default,
   we now use a custom Lzip tarball and don't need Zip or Unzip. This was
   suggested by Zahra Sharbaf and Raul Infante-Sainz.

 - Some minor edits in 'reproduce/software/shell/tarball-prepare.sh'. In
   particular the 'awk' command was effectively just replacing a '_' with
   '-', so it just uses a simple SED expression instead.

 - Fixed bug 62700 (https://savannah.nongnu.org/bugs/index.php?62700) by
   compiling 'xz' with a patched version of the xz source file
   'src/liblzma/liblzma.map'.

 - Astrometry.net doesn't depend on NetPBM any more. NetPBM (and its
   dependencies) were causing many crashes on macOS and it also a very
   strange build system that is hard to maintain. Astrometry.net uses it to
   take images as input. However, it isn't necessary when you provide
   Astrometry.net with a catalog. Therefore, Raul added some instructions
   on how to run astrometry from your own custom X-Y catalog. These
   instruction can be seen on top of the build rule of Astrometry.net in
   'reproduce/software/make/high-level.mk'.

 - h5py has been removed as a dependency of Astropy. It is an optional
   dependency to write tables into HDF5 format. But since we couldn't get
   it to build on macOS it has been removed. None of the current Maneage
   users/developers also use this feature of Astropy!

 - PLplot is added a new software, but not a default pre-requisite of SCAMP
   (which can use it to generate figures), because there were many build
   problems on macOS. Instructions have been added on top of SCAMP on how
   to add PLplot as a dependency.

 - With the aim of being able to install Plplot on macOS, we have wrote
   several lines to fix header problems. However, we didn't succeed. In any
   case we are leaving these lines in case they are useful in the future.

 - The '-Wno-nullability-completeness' compiler flag (which is primarily
   necessary for macOS) is now only added for macOS systems. It was causing
   many warnings of un-recognized option in GNU/Linux systems.

 - The 'mkswap' program of Util-Linux has been disabled because it caused
   crashes on older kernels. Generally, its not necessary for a Maneage
   project because it needs root permissions to run!

 - LibXT (of the x.org software) has been added as a dependency of Cairo.

 - ImageMagick and Lzip were using the host's C++ standard library! But on
   GNU/Linux we build our own C++ Standard Library with GCC, so with this
   commit, they properly link with Maneage's C++ standard library.

 - ImageMagick on macOS couldn't properly link with Maneage's Ghostscript
   library! This has been fixed using macOS's install_name_tool.

 - Necessary RAM to build GCC on GNU/Linux systems changed to ~8GB, see
   https://savannah.nongnu.org/task/?16244#comment12

 - Pythran is no longer as prerequisite of Scipy. Until now, Pythran was a
   prerequisite of Scipy. But we noticed that it is optional and was
   causing problems on macOS.

 - The URLs of some of the software have been updated in
   'reproduce/software/config/urls.conf'. By default, these are all
   commented, but they can be useful when searching for new versions or
   when a project needs custom software that is not (yet) in Maneage.

3 files changed, 362 insertions, 98 deletions

diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index d90d945..14d63cf 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -55,6 +55,7 @@ ddir    = $(BDIR)/software/build-tmp
 idir    = $(BDIR)/software/installed
 ibdir   = $(BDIR)/software/installed/bin
 ildir   = $(BDIR)/software/installed/lib
+iidir   = $(BDIR)/software/installed/include
 ibidir  = $(BDIR)/software/installed/version-info/proglib
 
 # Ultimate Makefile target. GNU Nano (a simple and very light-weight text
@@ -87,13 +88,18 @@ export SHELL := $(ibdir)/dash
 export PATH := $(ibdir):$(PATH)
 export PKG_CONFIG_PATH := $(ildir)/pkgconfig
 export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
-export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) \
-                   -Wno-nullability-completeness
 export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
 
 # Disable built-in rules (which are not needed here!)
 .SUFFIXES:
 
+# See description of '-Wno-nullability-completeness' in
+# 'reproduce/software/shell/configure.sh'.
+ifeq ($(on_mac_os),yes)
+  noccwarnings=-Wno-nullability-completeness
+endif
+export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings)
+
 # This is the "basic" tools where we are relying on the host operating
 # system, but are slowly populating our basic software envirnoment. To run
 # (system or template) programs, 'LD_LIBRARY_PATH' is necessary, so here,
@@ -202,6 +208,7 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
 	$(call makelink,xcrun)
 	$(call makelink,sysctl)
 	$(call makelink,sw_vers)
+	$(call makelink,codesign)
 	$(call makelink,dsymutil)
 	$(call makelink,install_name_tool)
 
@@ -222,6 +229,10 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
 	  fi
 	done
 
+#	Useful tools: 'ldd' (list libraries linked by binary on GNU
+#	systems)
+	$(call makelink,ldd)
+
 #	We want this to be empty (so it doesn't interefere with the other
 #	files in 'ibidir'.
 	touch $@
@@ -252,10 +263,46 @@ $(ibidir)/gzip-$(gzip-version): | $(ibdir) $(ildir) $(lockdir)
 	$(call gbuild, gzip-$(gzip-version), static, , V=1)
 	echo "GNU Gzip $(gzip-version)" > $@
 
+# 2022-07-14 B Roukema
+#
+# xz-5.2.5 fails on (at least) CentOS 7 (Redhat) systems while trying
+# to compile 'cmake' in Maneage - this is Maneage bug 62700 [1].
+#
+# The fix appears to be just a few lines, although it's not clear
+# how robust or long-term it is. Since we don't yet have 'patch' in
+# 'basic.mk', this file has to be copied into place rather than patched.
+
+# xz-5.2.5_src_liblzma_liblzma.map is a patched
+# version of xz-5.2.5/src/liblzma/liblzma.map based on discussion at
+# [1] + [2] + the patch file [3].
+#
+# [1] https://savannah.nongnu.org/bugs/index.php?62700
+# [2] https://github.com/easybuilders/easybuild-easyconfigs/issues/14991
+# [3] https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/bcebb3320ffb63f9804ca8d4d64d1822ec7c9792/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch
 $(ibidir)/xz-$(xz-version): $(ibidir)/gzip-$(gzip-version)
+
+#	Prepare the tarball.
 	tarball=xz-$(xz-version).tar.lz
 	$(call import-source, $(xz-url), $(xz-checksum))
-	$(call gbuild, xz-$(xz-version), static)
+
+#	Until the bug mentioned above is fixed, we'll can't use the generic
+#	rule.
+#	$(call gbuild, xz-$(xz-version), static)
+
+#	Configure and build with patched file.
+	srcdir=$$(pwd)
+	unpackdir=xz-$(xz-version)
+	patchedfile=xz-5.2.5_src_liblzma_liblzma.map
+	cd $(ddir)
+	rm -rf $$unpackdir
+	tar -x -f $(tdir)/$$tarball
+	cd $$unpackdir
+	cp -pv $$srcdir/reproduce/software/patches/$$patchedfile \
+	       src/liblzma/liblzma.map # copy the fixed file into place
+	./configure --prefix=$(idir)
+	make install
+	cd ..
+	rm -rf $$unpackdir
 	echo "XZ Utils $(xz-version)" > $@
 
 $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
@@ -303,26 +350,6 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
 	ln -fs libbz2.so.$(bzip2-version) libbz2.so
 	echo "Bzip2 $(bzip2-version)" > $@
 
-$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
-	tarball=unzip-$(unzip-version).tar.lz
-	$(call import-source, $(unzip-url), $(unzip-checksum))
-	$(call gbuild, unzip-$(unzip-version), static,, \
-	               -f unix/Makefile generic \
-	               CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
-	               -f unix/Makefile generic \
-	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
-	echo "Unzip $(unzip-version)" > $@
-
-$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
-	tarball=zip-$(zip-version).tar.lz
-	$(call import-source, $(zip-url), $(zip-checksum))
-	$(call gbuild, zip-$(zip-version), static,, \
-	               -f unix/Makefile generic \
-	               CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
-	               -f unix/Makefile generic \
-	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
-	echo "Zip $(zip-version)" > $@
-
 # Some programs (like Wget and CMake) that use zlib need it to be dynamic
 # so they use our custom build. So we won't force a static-only build.
 #
@@ -341,11 +368,9 @@ $(ibidir)/zlib-$(zlib-version): $(ibidir)/gzip-$(gzip-version)
 # software to be built).
 $(ibidir)/tar-$(tar-version): \
               $(ibidir)/xz-$(xz-version) \
-              $(ibidir)/zip-$(zip-version) \
               $(ibidir)/gzip-$(gzip-version) \
               $(ibidir)/zlib-$(zlib-version) \
-              $(ibidir)/bzip2-$(bzip2-version) \
-              $(ibidir)/unzip-$(unzip-version)
+              $(ibidir)/bzip2-$(bzip2-version)
 
 #	Since all later programs depend on Tar, the configuration will hit
 #	a bottleneck here: only making Tar. So its more efficient to built
@@ -629,7 +654,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
 	            -Dcccdlflags='-fPIC' \
 	            $(perl-conflddlflags) \
 	            -Dldflags="$$LDFLAGS"
-	make -j$(numthreads)
+	make -j$(numthreads) V=1
 	make install
 	cd ..
 	rm -rf perl-$(perl-version)
@@ -807,6 +832,8 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
 	               --without-librtmp \
 	               --without-libidn2 \
 	               --without-wolfssl \
+	               --without-nghttp2 \
+	               --without-nghttp3 \
 	               --without-brotli \
 	               --without-gnutls \
 	               --without-cyassl \
@@ -814,6 +841,7 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
 	               --without-axtls \
 	               --disable-ldaps \
 	               --disable-ldap \
+	               --without-zstd \
 	               --without-nss, V=1)
 
 	if [ -f $(ibdir)/patchelf ]; then
@@ -875,6 +903,12 @@ $(ibidir)/wget-$(wget-version): \
 # process of the higher-level programs and libraries. Note that during the
 # building of those higher-level programs (after this Makefile finishes),
 # there is no access to the system's PATH.
+$(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version)
+	tarball=bison-$(bison-version).tar.lz
+	$(call import-source, $(bison-url), $(bison-checksum))
+	$(call gbuild, bison-$(bison-version), static, ,V=1 -j$(numthreads))
+	echo "GNU Bison $(bison-version)" > $@
+
 $(ibidir)/diffutils-$(diffutils-version): \
                     $(ibidir)/coreutils-$(coreutils-version)
 	tarball=diffutils-$(diffutils-version).tar.lz
@@ -928,6 +962,13 @@ $(ibidir)/gawk-$(gawk-version): \
 #	Build final target.
 	echo "GNU AWK $(gawk-version)" > $@
 
+$(ibidir)/help2man-$(help2man-version): \
+                   $(ibidir)/coreutils-$(coreutils-version)
+	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)" > $@
+
 $(ibidir)/libiconv-$(libiconv-version): \
                    $(ibidir)/pkg-config-$(pkgconfig-version)
 	tarball=libiconv-$(libiconv-version).tar.lz
@@ -1070,6 +1111,17 @@ $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version)
 $(ibidir)/texinfo-$(texinfo-version): \
                   $(ibidir)/perl-$(perl-version) \
                   $(ibidir)/gettext-$(gettext-version)
+
+#	Setting for the XS sub-package. "This is because in theory, the XS
+#	module could be built with a different compiler to the rest of the
+#	project, needing completely different flags" (part of [1])
+#
+#       [1] https://lists.gnu.org/archive/html/bug-texinfo/2022-08/msg00068.html
+	export PERL="$(ibdir)/perl"
+	export PERL_EXT_LDFLAGS="-L$(ildir)"
+	export PERL_EXT_CPPFLAGS="-I$(iidir)"
+
+#	Basic build commands.
 	tarball=texinfo-$(texinfo-version).tar.lz
 	$(call import-source, $(texinfo-url), $(texinfo-checksum))
 	$(call gbuild, texinfo-$(texinfo-version), static)
@@ -1136,6 +1188,7 @@ $(ibidir)/binutils-$(binutils-version): \
                    $(ibidir)/gawk-$(gawk-version) \
                    $(ibidir)/grep-$(grep-version) \
                    $(ibidir)/wget-$(wget-version) \
+                   $(ibidir)/bison-$(bison-version) \
                    $(ibidir)/which-$(which-version) \
                    $(ibidir)/libtool-$(libtool-version) \
                    $(ibidir)/texinfo-$(texinfo-version) \
@@ -1164,7 +1217,7 @@ $(ibidir)/binutils-$(binutils-version): \
 #	  Build binutils with the standard 'gbuild' function.
 	  $(call gbuild, binutils-$(binutils-version), static, \
 	                 --with-lib-path=$(sys_library_path), \
-	                 -j$(numthreads) )
+	                 -j$(numthreads) V=1)
 
 #	  The 'ld' linker of Binutils needs several '*crt*.o' files from
 #	  the host's GNU C Library to run. On some systems these object
@@ -1287,20 +1340,35 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	  current_dir=$$(pwd)
 
 #	  By default 'ddir' (where GCC is decompressed and built) is in the
-#	  RAM (on systems that support '/dev/shm'). This is done to avoid
-#	  building so many small/temporary files and possibly harming the
-#	  hard-drive or SSD. But if the RAM doesn't have enough space, we
-#	  should use the hard-drive or SSD. During its build GCC's build
-#	  directory will become about 7GB (multiple of 1024 bytes, for GCC
-#	  11.2.0). So at this step, we are making sure we have more than
-#	  7.5GiB (multiple of 1000 bytes, which corresponds to 7.32GB)
-#	  before GCC starts to build. Note that the 4th column of 'df' is
-#	  the "available" space at the time of running, not the full
-#	  space. So the background RAM that the OS will be using during
-#	  Maneage is accounted for. Also consider that GCC is built alone
-#	  (no other Maneage software is built at the same time as GCC).
-	  in_ram=$$(df $(ddir) \
-	               | awk 'NR==2{print ($$4>7500000) ? "yes" : "no"}'); \
+#	  RAM (on systems that support a '/dev/shm' RAM disk). This is done
+#	  to avoid building so many small/temporary files and possibly
+#	  harming the hard-drive or SSD. But if the RAM doesn't have enough
+#	  space, we should use the hard-drive or SSD. During its build,
+#	  GCC's build directory will become about 7GiB (in units of 1024^3
+#	  bytes, for GCC 12.1.0, which corresponds to 7.5GB, in units of
+#	  1000^3 bytes). So at this step, we make sure that we have more
+#	  than 12GiB before GCC starts to build. See the figure in the link
+#	  below for GCC's RAM consumption as a function of time:
+#
+#	  https://savannah.nongnu.org/task/?16244#comment12
+#
+#	  For POSIX portability and longevity (default sizes might change),
+#	  we use the '-P' option, and we use the environment variable
+#	  POSIXLY_CORRECT=1, so the 'block size' is 512 bytes. We'll also
+#	  allow for about ~0.5 GB at the start.
+#
+#	  So we need 8 GiB * 1024^3 (B/GiB) / 512 blocks/B = 16777216
+#	  blocks, in blocks of 512 bytes.
+#
+#	  The 4th column of 'df' is the "available" space at the time of
+#	  running, not the full space. So the 'RAM disk' that the OS
+#	  will be using as "pretend" disk space (e.g. using 'tmpfs'; this
+#	  is physically RAM, but appears as if it is disk space)
+#	  during this stage of Maneage is accounted for. GCC is built
+#	  alone - no other Maneage software is built at the same time as
+#	  GCC - so this amount of RAM should be enough.
+	  in_ram=$$(POSIXLY_CORRECT=1 df -P $(ddir) \
+	               | awk 'NR==2{print ($$4>16777216) ? "yes" : "no"}'); \
 	  if [ $$in_ram = "yes" ]; then odir=$(ddir)
 	  else
 	    odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space
@@ -1308,9 +1376,11 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	    mkdir $$odir
 	  fi
 
-#	  Go into the proper directory, unpack GCC and prepare the 'build'
-#	  directory inside it for all the built files.
+#	  Go into the directory to uncompress GCC.
 	  cd $$odir
+
+#	  Unpack GCC and prepare the 'build' directory inside it for all
+#	  the built files.
 	  rm -rf gcc-$(gcc-version)
 	  tar -xf $(tdir)/$$tarball
 	  if [ $$odir != $(ddir) ]; then
@@ -1318,6 +1388,34 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	  fi
 	  cd gcc-$(gcc-version)
 
+#	  Unfortunately binutils installs headers like 'ansidecl.h' that
+#	  have been seen to conflict with GCC's internal versions of those
+#	  headers. For example in the 'ansidecl.h' of Binutils 2.39, the
+#	  'PTR' macro isn't defined, while the same file in GCC 12.1.0 has
+#	  defined it. Therefore, without this change, GCC will include the
+#	  file installed from Binutils, not find what it needs and crash!
+#	  Therefore, with the 'CPPFLAGS' modification below, we tell GCC to
+#	  first look into its own 'include' directory before anything else.
+	  export CPPFLAGS="-I$$(pwd)/include $(CPPFLAGS)"
+
+#	  In the GNU C Library 2.36 (which is more recent than GCC 12.1.0),
+#	  the 'linux/mount.h' (loaded by 'linux/fs.h', which is loaded by
+#	  'libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp'
+#	  in GCC) conflicts with 'sys/mount.h' which is directly loaded by
+#	  the same file! This is a known conflict in glibc 2.36 (see
+#	  [1]). As described in [1], one solution is the final job done in
+#	  [2]. We therefore do this process here: 1) Not loading
+#	  'linux/fs.h', and adding the necessary macros directly.
+#
+#	  [1] https://sourceware.org/glibc/wiki/Release/2.36#Usage_of_.3Clinux.2Fmount.h.3E_and_.3Csys.2Fmount.h.3E
+#         [2] https://reviews.llvm.org/D129471
+	  sed -e's|\#include <linux/fs.h>||' \
+	      -e"s|FS_IOC_GETFLAGS;|_IOR('f', 1, long);|" \
+	      -e"s|FS_IOC_GETVERSION;|_IOR('v', 1, long);|" \
+	      -e"s|FS_IOC_SETFLAGS;|_IOW('f', 2, long);|" \
+	      -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \
+	      -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
+
 #	  Set the build directory for the processing.
 	  mkdir build
 	  cd build
@@ -1396,6 +1494,25 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 
 
 
+# Software that need re-compilation (to use our own libraries)
+$(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version)
+	tarball=lzip-$(lzip-version).tar
+	unpackdir=lzip-$(lzip-version)
+	cd $(ddir)
+	rm -rf $$unpackdir
+	tar -xf $(tdir)/$$tarball
+	cd $$unpackdir
+	./configure --build --check --installdir="$(ibdir)"
+	if [ -f $(ibdir)/patchelf ]; then
+	  $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/lzip;
+	fi
+	cd ..
+	rm -rf $$unpackdir
+	echo "Lzip $(lzip-version)" > $@
+
+
+
+
 
 
 
@@ -1418,7 +1535,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 # nano (and use their own optional high-level text editor). To do this, you
 # can just have to manually remove 'nano' from 'targets-proglib' above and
 # add their optional text editor in 'TARGETS.conf'.
-$(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version)
+$(ibidir)/nano-$(nano-version): $(ibidir)/lzip-$(lzip-version)
 	tarball=nano-$(nano-version).tar.lz
 	$(call import-source, $(nano-url), $(nano-checksum))
 	$(call gbuild, nano-$(nano-version), static)
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 20e758a..a2474af 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -49,6 +49,7 @@ ddir    = $(BDIR)/software/build-tmp
 idir    = $(BDIR)/software/installed
 ibdir   = $(BDIR)/software/installed/bin
 ildir   = $(BDIR)/software/installed/lib
+iidir   = $(BDIR)/software/installed/include
 ibidir  = $(BDIR)/software/installed/version-info/proglib
 
 # Basic directories (specific to this Makefile).
@@ -147,7 +148,6 @@ export SHELL := $(ibdir)/bash
 .SHELLFLAGS := --noprofile --norc -ec
 export LDFLAGS := $(rpath_command) -L$(ildir)
 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!)
@@ -160,6 +160,13 @@ export F77 := $(ibdir)/gfortran
 export LD_RUN_PATH := $(ildir):$(il64dir)
 export LD_LIBRARY_PATH := $(ildir):$(il64dir)
 
+# See description of '-Wno-nullability-completeness' in
+# 'reproduce/software/shell/configure.sh'.
+ifeq ($(on_mac_os),yes)
+  noccwarnings=-Wno-nullability-completeness
+endif
+export CPPFLAGS := -I$(idir)/include $(noccwarnings)
+
 # In macOS, if a directory exists in both 'C_INCLUDE_PATH' and 'CPPFLAGS'
 # it will be ignored in 'CPPFLAGS' (which has higher precedence). So, we
 # should not define 'C_INCLUDE_PATH' on macOS. This happened with clang
@@ -429,6 +436,7 @@ $(ibidir)/cfitsio-$(cfitsio-version):
 	echo "CFITSIO $(cfitsio-version)" > $@
 
 $(ibidir)/cairo-$(cairo-version): \
+                $(ibidir)/libxt-$(libxt-version) \
                 $(ibidir)/pixman-$(pixman-version) \
                 $(ibidir)/libpng-$(libpng-version) \
                 $(ibidir)/freetype-$(freetype-version)
@@ -448,7 +456,8 @@ $(ibidir)/eigen-$(eigen-version):
 	topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball
 	cd eigen-$(eigen-version)
 	if ! [ -d $(iidir)/eigen3 ]; then mkdir $(iidir)/eigen3; fi
-	cp -r Eigen/* $(iidir)/eigen3/
+	cp -r Eigen/* $(iidir)/eigen3/         # Some expect 'eigen3'.
+	ln -s $(iidir)/eigen3 $(iidir)/Eigen   # Others expect 'Eigen'.
 	cd $$topdir
 	rm -rf $(ddir)/eigen-$(eigen-version)
 	echo "Eigen $(eigen-version)" > $@
@@ -529,7 +538,7 @@ $(ibidir)/gsl-$(gsl-version):
 $(ibidir)/hdf5-$(hdf5-version): $(ibidir)/openmpi-$(openmpi-version)
 	export CC=mpicc
 	export FC=mpif90
-	tarball=hdf5-$(hdf5-version).tar.gz
+	tarball=hdf5-$(hdf5-version).tar.lz
 	$(call import-source, $(hdf5-url), $(hdf5-checksum))
 	$(call gbuild, hdf5-$(hdf5-version), static, \
 	               --enable-parallel \
@@ -919,8 +928,8 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
                        --with-cfitsioinc=$(idir)/include \
                        --without-pgplot $$fortranopt)
 	if [ x$(on_mac_os) = xyes ]; then
-	  install_name_tool -id $(ildir)/libwcs.7.7.dylib \
-	                        $(ildir)/libwcs.7.7.dylib
+	  install_name_tool -id $(ildir)/libwcs.7.11.dylib \
+	                        $(ildir)/libwcs.7.11.dylib
 	fi
 	echo "WCSLIB $(wcslib-version)" > $@
 
@@ -938,14 +947,42 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
 #
 # Astrometry-net contains a lot of programs. We need to specify the
 # installation directory and the Python executable (by default it will look
-# for /usr/bin/python)
+# for /usr/bin/python).
+#
+# An optional dependency is 'netpbm' but it has many dependencies and a
+# crazy build system. So, it is not in the default preprequisites. If you
+# need it you can add it as a prerequisite and pray that it will work.
+#
+# A consequence of not having 'netpbm' is that for obtaining the
+# astrometric solution of one image using 'solve-field', it is necessary to
+# build a catalog of sources with image coordinates and flux (x,y,flux) in
+# advance. The catalog has to be sorted by flux. Finally, when invoking
+# 'solve-field', the width and heigh of the original image have to be
+# provided.
+#
+# More explicitly, raw basic steps using Gnuastro:
+#
+# - Obtain a catalog with image coordinates and flux (x,y,brightness):
+#   $ astnoisechisel img.fits -o det.fits
+#   $ astsegment det.fits -o seg.fits
+#   $ astmkcatalog seg.fits --clumpscat --x --y --brightness -o cat-raw.fits
+#
+# - Sort by flux:
+#   $ asttable cat-raw.fits --hdu 2 --sort brightness --descending \
+#              --output cat.fits
+#
+# - Get the x-size and y-size from the header:
+#   $ xsize=$(astfits img.fits --keyvalue NAXIS1 --quiet)
+#   $ ysize=$(astfits img.fits --keyvalue NAXIS2 --quiet)
+#
+# - Run 'solve-field' to obtain the astrometric solution:
+#   $ solve-field cat.fits --width $xsize --height $ysize [--other-parameters]
 $(ibidir)/astrometrynet-$(astrometrynet-version): \
                         $(ibidir)/gsl-$(gsl-version) \
                         $(ibidir)/swig-$(swig-version) \
                         $(ipydir)/numpy-$(numpy-version) \
                         $(ibidir)/cairo-$(cairo-version) \
                         $(ibidir)/libpng-$(libpng-version) \
-                        $(ibidir)/netpbm-$(netpbm-version) \
                         $(ibidir)/wcslib-$(wcslib-version) \
                         $(ipydir)/astropy-$(astropy-version) \
                         $(ibidir)/cfitsio-$(cfitsio-version) \
@@ -987,12 +1024,6 @@ $(ibidir)/automake-$(automake-version): $(ibidir)/autoconf-$(autoconf-version)
 	$(call gbuild, automake-$(automake-version), static, ,V=1)
 	echo "GNU Automake $(automake-version)" > $@
 
-$(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version)
-	tarball=bison-$(bison-version).tar.lz
-	$(call import-source, $(bison-url), $(bison-checksum))
-	$(call gbuild, bison-$(bison-version), static, ,V=1 -j$(numthreads))
-	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
 # reference catalogues.
@@ -1049,7 +1080,11 @@ $(ibidir)/cmake-$(cmake-version):
 $(ibidir)/flex-$(flex-version): $(ibidir)/bison-$(bison-version)
 	tarball=flex-$(flex-version).tar.lz
 	$(call import-source, $(flex-url), $(flex-checksum))
-	$(call gbuild, flex-$(flex-version), static, ,V=1 -j$(numthreads))
+	$(call gbuild, flex-$(flex-version), static, \
+	       --with-libiconv-prefix=$(idir) \
+	       --with-libintl-prefix=$(idir) \
+	       --disable-dependency-tracking, \
+	       V=1 -j$(numthreads))
 	echo "Flex $(flex-version)" > $@
 
 $(ibidir)/gdb-$(gdb-version): $(ibidir)/python-$(python-version)
@@ -1128,13 +1163,7 @@ $(ibidir)/gnuastro-$(gnuastro-version): \
 	$(call gbuild, gnuastro-$(gnuastro-version), static, , \
 	               -j$(numthreads))
 	cp $(dtexdir)/gnuastro.tex $(ictdir)/
-	echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
-
-$(ibidir)/help2man-$(help2man-version):
-	tarball=help2man-$(help2man-version).tar.lz
-	$(call import-source, $(help2man-url), $(help2man-checksum))
-	$(call gbuild, help2man-$(help2man-version), static, ,V=1)
-	echo "Help2man $(Help2man-version)" > $@
+	echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro,akhlaghi19}" > $@
 
 $(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version)
 
@@ -1168,8 +1197,25 @@ $(ibidir)/imagemagick-$(imagemagick-version): \
 	tarball=ImageMagick-$(imagemagick-version).tar.lz
 	$(call import-source, $(imagemagick-url), $(imagemagick-checksum))
 	$(call gbuild, ImageMagick-$(imagemagick-version), static, \
-	               --with-gslib --without-x --disable-openmp, \
+	               --without-x \
+	               --with-gslib \
+	               --disable-openmp \
+	               --with-libstdc=$(ildir), \
 	               V=1 -j$(numthreads))
+
+#	On macOS, an executable and several libraries are not properly
+#	linked with the Ghostscript library (libgs), so we need to fix it
+#	manually.
+	if [ x$(on_mac_os) = xyes ]; then
+	  gsversion=$$(echo $(ghostscript-version) \
+	                    | awk -F'.' '{print $$1"."$$2}')
+	  libMagicks=$$(ls -l $(ildir)/libMagick*.dylib  \
+	                   | awk '/^-/{print $$NF}')
+	  libMagicks_all="$(ibdir)/magick $$libMagicks"
+	  for f in $$libMagicks_all; do \
+	      install_name_tool -change libgs.dylib.$$gsversion \
+	      $(ildir)/libgs.dylib.$$gsversion $$f; done
+	fi
 	echo "ImageMagick $(imagemagick-version)" > $@
 
 # 'imfit' doesn't use the traditional 'configure' and 'make' to install
@@ -1281,12 +1327,12 @@ $(ibidir)/missfits-$(missfits-version):
 	cp $(dtexdir)/missfits.tex $(ictdir)/
 	echo "MissFITS $(missfits-version) \citep{missfits}" > $@
 
-# 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
-# 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).
+# Netpbm is an optional 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 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) \
@@ -1352,15 +1398,43 @@ $(ibidir)/pcre-$(pcre-version):
 	               , V=1 -j$(numthreads))
 	echo "Perl Compatible Regular Expressions $(pcre-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'.
+# On macOS 12.3 Monterey with AppleClang 13.1.6.13160021, Plplot 5.15.0
+# needs the 'finite' function of 'math.h' which has been deprecated in
+# macOS. By manually adding "#define finite isfinite" in 'math.h' like
+# below, we fixed this problem but still it can't find 'exit' during the
+# configuration phase so we stopped trying to port it to macOS. It means
+# that on macOS Plplot is not available. For other OSs it should be fine.
+# On macOS, the file 'tmath.h' can be found with 'xcrun --show-sdk-path'.
+#
+#	cp /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h \
+#	   $(iidir)/math.h
+#	awk '{if($$0 ~ /#define isinf\(x\)/) {print "#define finite isfinite"; print $$0} else print $$0 }' \
+#            $(iidir)/math.h > $(iidir)/math-tmp.h
+#	mv $(iidir)/math-tmp.h $(iidir)/math.h
+$(ibidir)/plplot-$(plplot-version): \
+          $(ibidir)/cairo-$(cairo-version) \
+          $(ibidir)/freetype-$(freetype-version)
+	tarball=plplot-$(plplot-version).tar.lz
+	$(call import-source, $(plplot-url), $(plplot-checksum))
+	$(call cbuild, plplot-$(plplot-version), static, \
+                       -DDEFAULT_NO_BINDINGS:BOOL=ON \
+                       -DENABLE_cxx:BOOL=ON \
+	               -DENABLE_fortran:BOOL=ON \
+	               -DDEFAULT_NO_QT_DEVICES:BOOL=ON)
+	echo "PLplot $(pcre-version)" > $@
 
 # 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'.
+#
+# Plplot in SCAMP cannot be built for macOS. See comments on top of Plplot.
+# But if you are not using macOS and want to enable plots, follow the
+# steps below:
+#
+#  1. Add '$(ibidir)/plplot-$(plplot-version)' to the prerequisites
+#  2. Remove the option '--enable-plplot=no' from the call of 'gbuild'
 $(ibidir)/scamp-$(scamp-version): \
                 $(ibidir)/fftw-$(fftw-version) \
                 $(ibidir)/openblas-$(openblas-version) \
@@ -1430,32 +1504,56 @@ $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version)
 	echo "SCons $(scons-version)" > $@
 
 # Sextractor crashes complaining about not linking with some ATLAS
-# libraries. But we can override this issue since we have Openblas
+# libraries. But we can override this issue since we have OpenBLAS
 # installed, it is just necessary to explicity tell sextractor to use it in
 # the configuration step.
-#
-# The '-fcommon' is a necessary C compilation flag for GCC 10 and above. It
-# is necessary for astromatic libraries, otherwise their build will crash.
 $(ibidir)/sextractor-$(sextractor-version): \
                      $(ibidir)/fftw-$(fftw-version) \
                      $(ibidir)/openblas-$(openblas-version)
+#	Import the source.
 	tarball=sextractor-$(sextractor-version).tar.lz
 	$(call import-source, $(sextractor-url), $(sextractor-checksum))
 
+#	Unpack the tarball and enter the directory.
+	unpackdir=sextractor-$(sextractor-version)
+	cd $(ddir)
+	rm -rf $$unpackdir
+	tar -xf $(tdir)/$$tarball
+	cd $$unpackdir
+
 #	See comment above 'missfits' for '-fcommon'.
-	$(call gbuild, sextractor-$(sextractor-version), static, \
-	               CFLAGS="-fcommon" \
-	               --enable-threads \
-	               --enable-openblas \
-	               --with-openblas-libdir=$(ildir) \
-	               --with-openblas-incdir=$(idir)/include)
+	./configure --prefix="$(idir)" \
+	            CFLAGS="-fcommon" \
+	            --enable-threads \
+	            --enable-openblas \
+	            --libdir=$(ildir) \
+	            --includedir=$(iidir) \
+	            --with-openblas-libdir=$(ildir) \
+	            --with-openblas-incdir=$(iidir)
+
+#	On macOS we need to manually change 'finite' to 'isfinite' in the
+#	header file 'src/levmar/compiler.h'. Until this problem is
+#	hopefully fixed in next releases, we are doing it manually using
+#	'sed'.  Consequently we are not installing it using 'gbuild'. Once
+#	this is fixed upstream, we can use the standard 'gbuild'.
+	sed -i -e's|define LM_FINITE finite |define LM_FINITE isfinite |' \
+	    src/levmar/compiler.h
+
+#	Build, install and delete the temporary files.
+	make V=1
+	make install
+	cd ..
+	rm -rf $$unpackdir
+
+#	Make links for other possibly used names, copy citation and build
+#	the final target.
 	ln -fs $(ibdir)/sex $(ibdir)/sextractor
 	ln -fs $(ibdir)/sex $(ibdir)/source-extractor
 	cp $(dtexdir)/sextractor.tex $(ictdir)/
 	echo "SExtractor $(sextractor-version) \citep{sextractor}" > $@
 
 $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version)
-	tarball=swarp-$(swarp-version).tar.gz
+	tarball=swarp-$(swarp-version).tar.lz
 	$(call import-source, $(swarp-url), $(swarp-checksum))
 
 #	See comment above 'missfits' for '-fcommon'.
@@ -1520,6 +1618,29 @@ $(ibidir)/util-linux-$(util-linux-version): | $(idircustom)
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
 	cd util-linux-$(util-linux-version)
+
+#       If a patch exists for the current version, apply it.
+	if [ -f $(patchdir)/util-linux-$(util-linux-version)-macos.patch ]; then
+	  cp $(patchdir)/util-linux-$(util-linux-version)-macos.patch \
+	     util-linux-$(util-linux-version)-macos.patch
+	  git apply util-linux-$(util-linux-version)-macos.patch
+	fi
+
+#       The 'mkswap' feature needs low-level file system and kernel headers
+#       that are not always available (in particular on older Linux
+#       kernels). Also, creating SWAP space will need root permissions, so
+#       its not something a Maneager may need! Unfortunately there is no
+#       configuration option to disable this so we'll have to disable it
+#       manually by commenting the relevant files in the
+#       'configure.ac'. Having a more recent 'configure.ac' will trigger
+#       the './configure' script to be re-created after the first run, but
+#       it is pretty fast and not a problem.
+	sed -e's|UL_BUILD_INIT(\[mkswap\], \[yes\])|UL_BUILD_INIT(\[mkswap\], \[no\])|' \
+	    -i configure.ac
+
+
+#	Configure Util-linux
+	export CONFIG_SHELL=$(ibdir)/bash
 	./configure --prefix=$(idircustom)/util-linux \
 	            --disable-dependency-tracking \
 	            --enable-libmount-support-mtab \
@@ -1593,12 +1714,12 @@ $(ibidir)/xlsxio-$(xlsxio-version): \
 # useful in projects during its development, for more see the comment above
 # GNU Emacs.
 $(ibidir)/vim-$(vim-version):
-	tarball=vim-$(vim-version).tar.bz2
+	tarball=vim-$(vim-version).tar.lz
 	$(call import-source, $(vim-url), $(vim-checksum))
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
-	n=$$(echo $(vim-version) | sed -e's|\.||')
-	cd $(ddir)/vim$$n
+	unpackdir=vim-$(vim-version)
+	cd $(ddir)/$$unpackdir
 	./configure --prefix=$(idir) \
 	            --disable-canberra \
 	            --enable-multibyte \
@@ -1611,9 +1732,29 @@ $(ibidir)/vim-$(vim-version):
 	make -j$(numthreads)
 	make install
 	cd ..
-	rm -rf vim$$n
+	rm -rf $$unpackdir
 	echo "VIM $(vim-version)" > $@
 
+$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
+	tarball=unzip-$(unzip-version).tar.lz
+	$(call import-source, $(unzip-url), $(unzip-checksum))
+	$(call gbuild, unzip-$(unzip-version), static,, \
+	               -f unix/Makefile generic \
+	               CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
+	               -f unix/Makefile generic \
+	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
+	echo "Unzip $(unzip-version)" > $@
+
+$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
+	tarball=zip-$(zip-version).tar.lz
+	$(call import-source, $(zip-url), $(zip-checksum))
+	$(call gbuild, zip-$(zip-version), static,, \
+	               -f unix/Makefile generic \
+	               CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
+	               -f unix/Makefile generic \
+	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
+	echo "Zip $(zip-version)" > $@
+
 
 
 
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 6766744..546195b 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -172,8 +172,10 @@ $(ipydir)/astroquery-$(astroquery-version): \
 	$(call pybuild, tar -xf, astroquery-$(astroquery-version), , \
 	                Astroquery $(astroquery-version))
 
+# The optional dependency 'h5py' that is necessary for writting tables in
+# HDF5 format has been removed from Astropy because on macOS it cannot be
+# installed.
 $(ipydir)/astropy-$(astropy-version): \
-                  $(ipydir)/h5py-$(h5py-version) \
                   $(ibidir)/expat-$(expat-version) \
                   $(ipydir)/scipy-$(scipy-version) \
                   $(ipydir)/numpy-$(numpy-version) \
@@ -400,7 +402,9 @@ $(ipydir)/lmfit-$(lmfit-version): \
 	                LMFIT $(lmfit-version))
 
 $(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \
-                        $(ipydir)/cython-$(cython-version)
+                        $(ipydir)/cffi-$(cffi-version) \
+                        $(ipydir)/numpy-$(numpy-version) \
+                        $(ipydir)/future-$(future-version)
 	tarball=lsstdesccoord-$(lsstdesccoord-version).tar.gz
 	$(call import-source, $(lsstdesccoord-url), $(lsstdesccoord-checksum))
 	$(call pybuild, tar -xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \
@@ -455,7 +459,6 @@ $(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version)
 	                mpmath $(mpmath-version))
 
 $(ipydir)/numpy-$(numpy-version): \
-                $(ibidir)/unzip-$(unzip-version) \
                 $(ipydir)/cython-$(cython-version) \
                 $(ibidir)/openblas-$(openblas-version) \
                 $(ipydir)/setuptools-$(setuptools-version)
@@ -471,7 +474,7 @@ $(ipydir)/numpy-$(numpy-version): \
 	$(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \
 	                Numpy $(numpy-version))
 	cp $(dtexdir)/numpy.tex $(ictdir)/
-	echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
+	echo "Numpy $(numpy-version) \citep{numpy2020}" > $@
 
 $(ipydir)/packaging-$(packaging-version): \
                     $(ipydir)/pyparsing-$(pyparsing-version)
@@ -594,9 +597,12 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
 	$(call pybuild, tar -xf, requests-$(requests-version), , \
 	                Requests $(requests-version))
 
+# 'pythran' is disabled in the build of Scipy because of complications it
+# caused on some systems. It is explicitly disabled using the environmental
+# variable. If for some reason it is needed, set the environment variable
+# to 1, and add it as a prerequisite of 'scipy'.
 $(ipydir)/scipy-$(scipy-version): \
                   $(ipydir)/numpy-$(numpy-version) \
-                  $(ipydir)/pythran-$(pythran-version) \
                   $(ipydir)/pybind11-$(pybind11-version)
 	tarball=scipy-$(scipy-version).tar.lz
 	$(call import-source, $(scipy-url), $(scipy-checksum))
@@ -605,10 +611,11 @@ $(ipydir)/scipy-$(scipy-version): \
 	else
 	  export LDFLAGS="$(LDFLAGS) -shared"
 	fi
+	export SCIPY_USE_PYTHRAN=0
 	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
 	$(call pybuild, tar -xf, scipy-$(scipy-version),$$conf)
 	cp $(dtexdir)/scipy.tex $(ictdir)/
-	echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@
+	echo "Scipy $(scipy-version) \citep{scipy2020}" > $@
 
 $(ipydir)/secretstorage-$(secretstorage-version): \
                         $(ipydir)/jeepney-$(jeepney-version) \
@@ -619,7 +626,6 @@ $(ipydir)/secretstorage-$(secretstorage-version): \
 	                SecretStorage $(secretstorage-version))
 
 $(ipydir)/setuptools-$(setuptools-version): \
-                     $(ibidir)/unzip-$(unzip-version) \
                      $(ibidir)/python-$(python-version)
 	tarball=setuptools-$(setuptools-version).tar.lz
 	$(call import-source, $(setuptools-url), $(setuptools-checksum))