New architecture to separate software-building and analysis steps

Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.

Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.

Also, some of the software versions were also updated after some checks
with their webpages.

This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).

1 files changed, 903 insertions, 0 deletions

diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
new file mode 100644
index 0000000..cfa05d2
--- /dev/null
+++ b/reproduce/software/make/basic.mk
@@ -0,0 +1,903 @@
+# Build the VERY BASIC project software before higher-level ones. Assuming
+# minimal/generic Make and Shell.
+#
+# ------------------------------------------------------------------------
+#                      !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be run by the initial `./configure' script. It is not
+# included into the project after that.
+#
+# This Makefile builds very low-level and basic tools like GNU Tar, GNU
+# Bash, GNU Make, GCC and etc. Therefore this is the only Makefile in the
+# project where you CANNOT assume that GNU Bash or GNU Make are used. After
+# this Makefile (where GNU Bash and GNU Make are built), other Makefiles
+# can safely assume the fixed version of all these software.
+#
+# ------------------------------------------------------------------------
+#
+# Copyright (C) 2018-2019 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.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+# Top level environment
+include reproduce/software/make/build-rules.mk
+include reproduce/software/config/installation/LOCAL.mk
+include reproduce/software/config/installation/versions.mk
+
+lockdir = $(BDIR)/locks
+tdir    = $(BDIR)/software/tarballs
+ddir    = $(BDIR)/software/build-tmp
+idir    = $(BDIR)/software/installed
+ibdir   = $(BDIR)/software/installed/bin
+ildir   = $(BDIR)/software/installed/lib
+ibidir  = $(BDIR)/software/installed/version-info/bin
+ilidir  = $(BDIR)/software/installed/version-info/lib
+
+# We'll need the system's PATH for making links to low-level programs we
+# won't be building ourselves.
+syspath         := $(PATH)
+
+# As we build more programs, we want to use this project's built programs
+# and libraries, not the host's.
+export CCACHE_DISABLE    := 1
+export PATH              := $(ibdir):$(PATH)
+export PKG_CONFIG_PATH   := $(ildir)/pkgconfig
+export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
+export LD_LIBRARY_PATH   := $(ildir):$(LD_LIBRARY_PATH)
+export CPPFLAGS          := -I$(idir)/include $(CPPFLAGS)
+export LDFLAGS           := $(rpath_command) -L$(ildir) $(LDFLAGS)
+
+# Define the top-level programs (that don't depend on any other).
+top-level-programs = low-level-links wget gcc
+all: $(foreach p, $(top-level-programs), $(ibidir)/$(p))
+
+
+
+
+
+# Tarballs
+# --------
+#
+# Prepare tarballs. Difference with that in `high-level.mk': `.ONESHELL' is
+# not recognized by some versions of Make (even older GNU Makes). So we'll
+# have to make sure the recipe doesn't break into multiple shell calls (so
+# we can preserve the variables).
+#
+# Software hosted at akhlaghi.org/src: As of our latest check (November
+# 2018) their major release tarballs either crash or don't build on some
+# systems (for example Make or Gzip), or they don't exist (for example
+# Bzip2).
+#
+# In the first case, we used their Git repo and bootstrapped them (just
+# like Gnuastro) and built the most recent tarball off of that. In the case
+# of Bzip2: its webpage has expired and doesn't host the data any more. It
+# is available on the link below (archive.org):
+#
+# https://web.archive.org/web/20180624184806/http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
+#
+# However, downloading from this link is slow (because its just a link). So
+# its easier to just keep a with the others.
+$(lockdir): | $(BDIR); mkdir $@
+downloadwrapper = ./reproduce/analysis/bash/download-multi-try
+tarballs = $(foreach t, bash-$(bash-version).tar.gz                         \
+                        binutils-$(binutils-version).tar.lz                 \
+                        bzip2-$(bzip2-version).tar.gz                       \
+                        cert.pem                                            \
+                        coreutils-$(coreutils-version).tar.xz               \
+                        diffutils-$(diffutils-version).tar.xz               \
+                        file-$(file-version).tar.gz                         \
+                        findutils-$(findutils-version).tar.lz               \
+                        gawk-$(gawk-version).tar.lz                         \
+                        gcc-$(gcc-version).tar.xz                           \
+                        gmp-$(gmp-version).tar.lz                           \
+                        grep-$(grep-version).tar.xz                         \
+                        gzip-$(gzip-version).tar.gz                         \
+                        isl-$(isl-version).tar.bz2                          \
+                        libtool-$(libtool-version).tar.xz                   \
+                        lzip-$(lzip-version).tar.gz                         \
+                        m4-$(m4-version).tar.gz                             \
+                        make-$(make-version).tar.lz                         \
+                        mpfr-$(mpfr-version).tar.xz                         \
+                        mpc-$(mpc-version).tar.gz                           \
+                        ncurses-$(ncurses-version).tar.gz                   \
+                        openssl-$(openssl-version).tar.gz                   \
+                        patchelf-$(patchelf-version).tar.gz                 \
+                        pkg-config-$(pkgconfig-version).tar.gz              \
+                        readline-$(readline-version).tar.gz                 \
+                        sed-$(sed-version).tar.xz                           \
+                        tar-$(tar-version).tar.gz                           \
+                        unzip-$(unzip-version).tar.gz                       \
+                        wget-$(wget-version).tar.lz                         \
+                        which-$(which-version).tar.gz                       \
+                        xz-$(xz-version).tar.gz                             \
+                        zip-$(zip-version).tar.gz                           \
+                        zlib-$(zlib-version).tar.gz                         \
+                      , $(tdir)/$(t) )
+$(tarballs): $(tdir)/%: | $(lockdir)
+	if [ -f $(DEPENDENCIES-DIR)/$* ]; then                              \
+	  cp $(DEPENDENCIES-DIR)/$* $@;                                     \
+	else                                                                \
+	  n=$$(echo $* | sed -e's/[0-9\-]/ /g'                              \
+	                     -e's/\./ /g'                                   \
+	               | awk '{print $$1}' );                               \
+	                                                                    \
+	  mergenames=1;                                                     \
+	  if   [ $$n = bash      ]; then w=http://ftp.gnu.org/gnu/bash;     \
+	  elif [ $$n = binutils  ]; then w=http://ftp.gnu.org/gnu/binutils; \
+	  elif [ $$n = bzip      ]; then w=http://akhlaghi.org/src;         \
+	  elif [ $$n = cert      ]; then w=http://akhlaghi.org/src;         \
+	  elif [ $$n = coreutils ]; then w=http://ftp.gnu.org/gnu/coreutils;\
+	  elif [ $$n = diffutils ]; then w=http://ftp.gnu.org/gnu/diffutils;\
+	  elif [ $$n = file      ]; then w=ftp://ftp.astron.com/pub/file;   \
+	  elif [ $$n = findutils ]; then w=http://akhlaghi.org/src;         \
+	  elif [ $$n = gawk      ]; then w=http://ftp.gnu.org/gnu/gawk;     \
+	  elif [ $$n = gcc       ]; then w=http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version); \
+	  elif [ $$n = gmp       ]; then w=https://gmplib.org/download/gmp; \
+	  elif [ $$n = grep      ]; then w=http://ftp.gnu.org/gnu/grep;     \
+	  elif [ $$n = gzip      ]; then w=http://ftp.gnu.org/gnu/gzip;     \
+	  elif [ $$n = isl       ]; then w=ftp://gcc.gnu.org/pub/gcc/infrastructure; \
+	  elif [ $$n = libtool   ]; then w=http://ftp.gnu.org/gnu/libtool;  \
+	  elif [ $$n = lzip      ]; then w=http://download.savannah.gnu.org/releases/lzip; \
+	  elif [ $$n = m         ]; then                                    \
+	    mergenames=0;                                                   \
+	    w=http://akhlaghi.org/src/m4-1.4.18-patched.tar.gz;             \
+	  elif [ $$n = make      ]; then w=http://akhlaghi.org/src;         \
+	  elif [ $$n = mpfr      ]; then w=http://www.mpfr.org/mpfr-current;\
+	  elif [ $$n = mpc       ]; then w=http://ftp.gnu.org/gnu/mpc;      \
+	  elif [ $$n = ncurses   ]; then w=http://ftp.gnu.org/gnu/ncurses;  \
+	  elif [ $$n = openssl   ]; then w=http://www.openssl.org/source;   \
+	  elif [ $$n = patchelf  ]; then w=http://nixos.org/releases/patchelf/patchelf-$(patchelf-version); \
+	  elif [ $$n = pkg       ]; then w=http://pkg-config.freedesktop.org/releases; \
+	  elif [ $$n = readline  ]; then w=http://ftp.gnu.org/gnu/readline; \
+	  elif [ $$n = sed       ]; then w=http://ftp.gnu.org/gnu/sed;      \
+	  elif [ $$n = tar       ]; then w=http://ftp.gnu.org/gnu/tar;      \
+	  elif [ $$n = unzip     ]; then                                    \
+	    mergenames=0; v=$$(echo $(unzip-version) | sed -e's/\.//');     \
+	    w=ftp://ftp.info-zip.org/pub/infozip/src/unzip$$v.tgz;          \
+	  elif [ $$n = wget      ]; then w=http://ftp.gnu.org/gnu/wget;     \
+	  elif [ $$n = which     ]; then w=http://ftp.gnu.org/gnu/which;    \
+	  elif [ $$n = xz        ]; then w=http://tukaani.org/xz;           \
+	  elif [ $$n = zip       ]; then                                    \
+	    mergenames=0; v=$$(echo $(zip-version) | sed -e's/\.//');       \
+	    w=ftp://ftp.info-zip.org/pub/infozip/src/zip$$v.tgz;            \
+	  elif [ $$n = zlib      ]; then w=http://www.zlib.net;             \
+	  else                                                              \
+	    echo; echo; echo;                                               \
+	    echo "'$$n' not a basic dependency name (for downloading)."     \
+	    echo; echo; echo;                                               \
+	    exit 1;                                                         \
+	  fi;                                                               \
+	                                                                    \
+	  if [ $$mergenames = 1 ]; then  tarballurl=$$w/"$*";               \
+	  else                           tarballurl=$$w;                    \
+	  fi;                                                               \
+	                                                                    \
+	  echo "Downloading $$tarballurl";                                  \
+	  if [ -f $(ibdir)/wget ]; then                                     \
+	    downloader="wget --no-use-server-timestamps -O";                \
+	  else                                                              \
+	    downloader="$(DOWNLOADER)";                                     \
+	  fi;                                                               \
+	                                                                    \
+	  touch $(lockdir)/download;                                        \
+	  $(downloadwrapper) "$$downloader" $(lockdir)/download             \
+	                     $$tarballurl $@;                               \
+	fi
+
+
+
+
+
+# Low-level (not built) programs
+# ------------------------------
+#
+# For the time being, we aren't building a local C compiler, but we'll use
+# any C compiler that the system already has and just make a symbolic link
+# to it.
+#
+# ccache: ccache acts like a wrapper over the C compiler and is made to
+# avoid/speed-up compiling of identical files in a system (it is commonly
+# used on large servers). It actually makes `gcc' or `g++' a symbolic link
+# to itself so it can control them internally. So, for our purpose here, it
+# is very annoying and can cause many complications. We thus remove any
+# part of PATH of that has `ccache' in it before making symbolic links to
+# the programs we are not building ourselves.
+makelink = origpath="$$PATH";                                      \
+	   export PATH=$$(echo $(syspath) | tr : '\n' | grep -v ccache \
+	                       | tr '\n' :);                           \
+	   a=$$(which $(1) 2> /dev/null);                              \
+	   if [ -e $(ibdir)/$(1) ]; then rm $(ibdir)/$(1); fi;         \
+	   if [ x$$a = x ]; then                                       \
+	     if [ "x$(strip $(2))" = xmandatory ]; then                \
+	       echo "'$(1)' is necessary for higher-level tools.";     \
+	       echo "Please install it for the configuration to continue."; \
+	       exit 1;                                                 \
+	     fi;                                                       \
+	   else                                                        \
+	     ln -s $$a $(ibdir)/$(1);                                  \
+	   fi;                                                         \
+	   export PATH="$$origpath"
+$(ibdir) $(ildir):; mkdir $@
+$(ibidir)/low-level-links: | $(ibdir) $(ildir)
+
+        # The Assembler
+	$(call makelink,as)
+
+        # Compiler (Cmake needs the clang compiler which we aren't building
+        # yet in the project).
+	$(call makelink,clang)
+	$(call makelink,clang++)
+
+        # The linker
+	$(call makelink,ar)
+	$(call makelink,ld)
+	$(call makelink,nm)
+	$(call makelink,ps)
+	$(call makelink,ranlib)
+
+        # Mac OS specific
+	$(call makelink,sysctl)
+	$(call makelink,sw_vers)
+	$(call makelink,dsymutil)
+	$(call makelink,install_name_tool)
+
+        # On Mac OS, libtool is different compared to GNU Libtool. The
+        # libtool we'll build in the high-level dependencies has the
+        # executable name `glibtool'.
+	$(call makelink,libtool)
+
+        # GNU Gettext (translate messages)
+	$(call makelink,msgfmt)
+
+        # Needed by TeXLive specifically.
+	$(call makelink,perl)
+
+        # Necessary libraries:
+        #   Libdl (for dynamic loading libraries at runtime)
+        #   POSIX Threads library for multi-threaded programs.
+	for l in dl pthread; do                    \
+          rm -f $(ildir)/lib$$l*;                  \
+	  if [ -f /usr/lib/lib$$l.a ]; then        \
+	    ln -s /usr/lib/lib$$l.* $(ildir)/;     \
+	  fi;                                      \
+	done
+
+        # We want this to be empty (so it doesn't interefere with the other
+        # files in `ibidir'.
+	touch $@
+
+
+
+
+
+
+
+
+
+
+# Level 1 (MOST BASIC): Compression programs
+# ------------------------------------------
+#
+# The first set of programs to be built are those that we need to unpack
+# the source code tarballs of each program. First, we'll build the
+# necessary programs, then we'll build GNU Tar.
+$(ibidir)/gzip: $(tdir)/gzip-$(gzip-version).tar.gz
+	$(call gbuild, $<, gzip-$(gzip-version), static, , V=1) \
+	&& echo "GNU Gzip $(gzip-version)" > $@
+
+# GNU Lzip: For a static build, the `-static' flag should be given to
+# LDFLAGS on the command-line (not from the environment).
+ifeq ($(static_build),yes)
+lzipconf="LDFLAGS=-static"
+else
+lzipconf=
+endif
+$(ibidir)/lzip: $(tdir)/lzip-$(lzip-version).tar.gz
+	$(call gbuild, $<, lzip-$(lzip-version), , $(lzipconf)) \
+	&& echo "Lzip $(lzip-version)" > $@
+
+$(ibidir)/xz: $(tdir)/xz-$(xz-version).tar.gz
+	$(call gbuild, $<, xz-$(xz-version), static) \
+	&& echo "XZ Utils $(xz-version)" > $@
+
+$(ibidir)/bzip2: $(tdir)/bzip2-$(bzip2-version).tar.gz
+        # Bzip2 doesn't have a `./configure' script, and its Makefile
+        # doesn't build a shared library. So we can't use the `gbuild'
+        # function here and we need to take some extra steps (inspired
+        # from the "Linux from Scratch" guide for Bzip2):
+        #   1) The `sed' call is for relative installed symbolic links.
+        #   2) The special Makefile-libbz2_so builds shared libraries.
+        #
+        # NOTE: the major version number appears in the final symbolic
+        # link.
+	tdir=bzip2-$(bzip2-version);                                  \
+	if [ $(static_build) = yes ]; then                            \
+	  makecommand="make LDFLAGS=-static";                         \
+	  makeshared="echo no-shared";                                \
+	else                                                          \
+	  makecommand="make";                                         \
+	  if [ x$(on_mac_os) = xyes ]; then                           \
+	    makeshared="echo no-shared";                              \
+	  else                                                        \
+	    makeshared="make -f Makefile-libbz2_so";                  \
+	  fi;                                                         \
+	fi;                                                           \
+	cd $(ddir) && rm -rf $$tdir && tar xf $< && cd $$tdir         \
+	&& sed -e 's@\(ln -s -f \)$$(PREFIX)/bin/@\1@' Makefile       \
+	       > Makefile.sed                                         \
+	&& mv Makefile.sed Makefile                                   \
+	&& $$makeshared                                               \
+	&& cp -a libbz2* $(ildir)/                                    \
+	&& make clean                                                 \
+	&& $$makecommand                                              \
+	&& make install PREFIX=$(idir)                                \
+	&& cd ..                                                      \
+	&& rm -rf $$tdir                                              \
+	&& cd $(ildir)                                                \
+	&& ln -fs libbz2.so.1.0 libbz2.so                             \
+	&& echo "Bzip2 $(bzip2-version)" > $@
+
+$(ibidir)/unzip: $(tdir)/unzip-$(unzip-version).tar.gz
+	v=$$(echo $(unzip-version) | sed -e's/\.//');            \
+	$(call gbuild, $<, unzip$$v, static,,                    \
+	               -f unix/Makefile generic_gcc              \
+	               CFLAGS="-DBIG_MEM -DMMAP",,pwd,           \
+	               -f unix/Makefile                          \
+	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) \
+	&& echo "Unzip $(unzip-version)" > $@
+
+$(ibidir)/zip: $(tdir)/zip-$(zip-version).tar.gz
+	v=$$(echo $(zip-version) | sed -e's/\.//');              \
+	$(call gbuild, $<, zip$$v, static,,                      \
+	               -f unix/Makefile generic_gcc              \
+	               CFLAGS="-DBIG_MEM -DMMAP",,pwd,           \
+	               -f unix/Makefile                          \
+	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 ) \
+	&& echo "Zip $(zip-version)" > $@
+
+# Some programs (like Wget and CMake) that use zlib need it to be dynamic
+# so they use our custom build. So we won't force a static-only build.
+#
+# Note for a static-only build: Zlib's `./configure' doesn't use Autoconf's
+# configure script, it just accepts a direct `--static' option.
+$(ilidir)/zlib: $(tdir)/zlib-$(zlib-version).tar.gz
+	$(call gbuild, $<, zlib-$(zlib-version)) \
+	&& echo "Zlib $(zlib-version)" > $@
+
+# GNU Tar: When built statically, tar gives a segmentation fault on
+# unpacking Bash. So we'll build it dynamically. Note that technically, zip
+# and unzip aren't dependencies of Tar, but for a clean build, we'll set
+# Tar to be the last compression-related software (the first-set of
+# software to be built).
+$(ibidir)/tar: $(tdir)/tar-$(tar-version).tar.gz \
+	       $(ibidir)/bzip2                   \
+	       $(ibidir)/unzip                   \
+	       $(ibidir)/gzip                    \
+	       $(ibidir)/lzip                    \
+               $(ilidir)/zlib                    \
+	       $(ibidir)/zip                     \
+	       $(ibidir)/xz
+        # Since all later programs depend on Tar, the configuration will be
+        # stuck here, only making Tar. So its more efficient to built it on
+        # multiple threads (when the user's Make doesn't pass down the
+        # number of threads).
+	$(call gbuild, $<, tar-$(tar-version), , , -j$(numthreads) V=1) \
+	&& echo "GNU Tar $(tar-version)" > $@
+
+
+
+
+
+
+
+
+
+
+# Level 2 (SECOND MOST BASIC): Bash and Make
+# ------------------------------------------
+#
+# GNU Make and GNU Bash are the second layer that we'll need to build the
+# basic dependencies.
+#
+# Unfortunately Make needs dynamic linking in two instances: when loading
+# objects (dynamically linked libraries), or when using the `getpwnam'
+# function (for tilde expansion). The first can be disabled with
+# `--disable-load', but unfortunately I don't know any way to fix the
+# second. So, we'll have to build it dynamically for now.
+$(ibidir)/make: $(tdir)/make-$(make-version).tar.lz \
+                $(ibidir)/tar
+        # See Tar's comments for the `-j' option.
+	$(call gbuild, $<, make-$(make-version), , , -j$(numthreads)) \
+	&& echo "GNU Make $(make-version)" > $@
+
+$(ilidir)/ncurses: $(tdir)/ncurses-$(ncurses-version).tar.gz       \
+                   $(ibidir)/make
+
+        # Delete the library that will be installed (so we can make sure
+        # the build process completed afterwards and reset the links).
+	rm -f $(ildir)/libncursesw*
+
+        # Delete the (possibly existing) low-level programs that depend on
+        # `readline', and thus `ncurses'. Since these programs are actually
+        # used during the building of `ncurses', we need to delete them so
+        # the build process doesn't use the project's Bash and AWK, but the
+        # host's.
+	rm -f $(ibdir)/bash* $(ibdir)/awk* $(ibdir)/gawk*
+
+        # Standard build process.
+	$(call gbuild, $<, ncurses-$(ncurses-version), static,            \
+	               --with-shared --enable-rpath --without-normal      \
+	               --without-debug --with-cxx-binding                 \
+	               --with-cxx-shared --enable-widec --enable-pc-files \
+	               --with-pkg-config=$(ildir)/pkgconfig )
+
+        # Unfortunately there are many problems with `ncurses' using
+        # "normal" (or 8-bit) characters. The standard way that will work
+        # is to build it with wide character mode as you see above in the
+        # configuration (or the `w' prefix you see below). Also, most
+        # programs (and in particular Bash and AWK), first look for other
+        # (mostly obsolete) libraries like tinfo, which define the same
+        # symbols. The links below address both situations: we need to fool
+        # higher-level packages to find this library even if they aren't
+        # explicitly mentioning its name correctly (as a value to `-l' at
+        # link time in their configure scripts).
+        #
+        # This part is taken from the Arch Linux build script[1], then
+        # extended to Mac thanks to Homebrew's script [2].
+        #
+        # [1] https://git.archlinux.org/svntogit/packages.git/tree/trunk/PKGBUILD?h=packages/ncurses
+        # [2] https://github.com/Homebrew/homebrew-core/blob/master/Formula/ncurses.rb
+        #
+        # Since we can't have comments, in the connected script, here is a
+        # summary:
+        #
+        #   1. We find the actual suffix of the library, from the file that
+        #      is not a symbolic link (starting with `-' in the output of
+        #      `ls -l').
+        #
+        #   2. We make symbolic links to all the "ncurses", "ncurses++",
+        #      "form", "panel" and "menu" libraries to point to their
+        #      "wide" (character) library.
+        #
+        #   3. We make symbolic links to the "tic" and "tinfo" libraries to
+        #      point to the same `libncursesw' library.
+        #
+        #   4. Some programs link with "curses" (not "ncurses", notice the
+        #      starting "n"), so we'll also make links for these to point
+        #      to the `libncursesw' library.
+        #
+        #   5. A link is made to also be able to include files from the
+        #      `ncurses' headers.
+	if [ x$(on_mac_os) = xyes ]; then so="dylib"; else so="so"; fi;    \
+	if [ -f $(ildir)/libncursesw.$$so ]; then                          \
+	                                                                   \
+	  sov=$$(ls -l $(ildir)/libncursesw*                               \
+	               | awk '/^-/{print $$NF}'                            \
+	               | sed -e's|'$(ildir)/libncursesw.'||');             \
+	                                                                   \
+	  cd "$(ildir)";                                                   \
+	  for lib in ncurses ncurses++ form panel menu; do                 \
+	    ln -fs lib$$lib"w".$$sov     lib$$lib.$$so;                    \
+	    ln -fs $(ildir)/pkgconfig/"$$lib"w.pc pkgconfig/$$lib.pc;      \
+	  done;                                                            \
+	  for lib in tic tinfo; do                                         \
+	    ln -fs libncursesw.$$sov     lib$$lib.$$so;                    \
+	    ln -fs libncursesw.$$sov     lib$$lib.$$sov;                   \
+	    ln -fs $(ildir)/pkgconfig/ncursesw.pc pkgconfig/$$lib.pc;      \
+	  done;                                                            \
+	  ln -fs libncursesw.$$sov libcurses.$$so;                         \
+	  ln -fs libncursesw.$$sov libcursesw.$$sov;                       \
+	  ln -fs $(ildir)/pkgconfig/ncursesw.pc pkgconfig/curses.pc;       \
+	  ln -fs $(ildir)/pkgconfig/ncursesw.pc pkgconfig/cursesw.pc;      \
+	                                                                   \
+	  ln -fs $(idir)/include/ncursesw $(idir)/include/ncurses;         \
+	  echo "GNU NCURSES $(ncurses-version)" > $@;                      \
+	else                                                               \
+	  exit 1;                                                          \
+	fi
+
+$(ilidir)/readline: $(tdir)/readline-$(readline-version).tar.gz      \
+                    $(ilidir)/ncurses
+	$(call gbuild, $<, readline-$(readline-version), static,     \
+	                --with-curses --disable-install-examples,    \
+	                SHLIB_LIBS="-lncursesw" )                    \
+	&& echo "GNU Readline $(readline-version)" > $@
+
+$(ibidir)/patchelf: $(tdir)/patchelf-$(patchelf-version).tar.gz \
+                    $(ibidir)/make
+	$(call gbuild, $<, patchelf-$(patchelf-version), static) \
+	&& echo "PatchELF $(patchelf-version)" > $@
+
+
+# IMPORTANT: Even though we have enabled `rpath', Bash doesn't write the
+# absolute adddress of the libraries it depends on! Therefore, if we
+# configure Bash with `--with-installed-readline' (so the installed version
+# of Readline, that we build below as a prerequisite or AWK, is used) and
+# you run `ldd $(ibdir)/bash' on the resulting binary, it will say that it
+# is linking with the system's `readline'. But if you run that same command
+# within a rule in this project, you'll see that it is indeed linking with
+# our own built readline.
+ifeq ($(on_mac_os),yes)
+needpatchelf =
+else
+needpatchelf = $(ibidir)/patchelf
+endif
+$(ibidir)/bash: $(tdir)/bash-$(bash-version).tar.gz \
+                $(ilidir)/readline                  \
+                $(needpatchelf)
+
+        # Delete the (possibly) existing Bash executable.
+	rm -f $(ibdir)/bash
+
+        # Build Bash. Note that we aren't building Bash with
+        # `--with-installed-readline'. This is because (as described above)
+        # Bash needs the `LD_LIBRARY_PATH' set properly before it is
+        # run. Within a recipe, things are fine (we do set
+        # `LD_LIBRARY_PATH'). However, Make will also call the shell
+        # outside of the recipe (for example in the `foreach' Make
+        # function!). In such cases, our new `LD_LIBRARY_PATH' is not set.
+        # This will cause a crash in the shell and thus the Makefile,
+        # complaining that it can't find `libreadline'. Therefore, even
+        # though we build readline below, we won't link Bash with an
+        # external readline.
+        #
+        # Bash has many `--enable' features which are already enabled by
+        # default. As described in the manual, they are mainly useful when
+        # you disable them all with `--enable-minimal-config' and enable a
+        # subset using the `--enable' options.
+	if [ "x$(static_build)" = xyes ]; then stopt="--enable-static-link";\
+	else                                   stopt="";                    \
+	fi;                                             \
+	$(call gbuild, $<, bash-$(bash-version),,       \
+	                   --with-installed-readline=$(ildir) $$stopt )
+
+        # Atleast on GNU/Linux systems, Bash doesn't include RPATH by
+        # default. So, we have to manually include it, currently we are
+        # only doing this on GNU/Linux systems (using the `patchelf'
+        # program).
+	if [ "x$(needpatchelf)" != x ]; then                         \
+	  if [ -f $(ibdir)/bash ]; then                              \
+	    $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/bash; fi \
+	fi
+
+        # To be generic, some systems use the `sh' command to call the
+        # shell. By convention, `sh' is just a symbolic link to the
+        # preferred shell executable. So we'll define `$(ibdir)/sh' as a
+        # symbolic link to the Bash that we just built and installed.
+        #
+        # Just to be sure that the installation step above went well,
+        # before making the link, we'll see if the file actually exists
+        # there.
+	if [ -f $(ibdir)/bash ]; then            \
+	  ln -fs $(ibdir)/bash $(ibdir)/sh;      \
+	  echo "GNU Bash $(bash-version)" > $@;  \
+	else                                     \
+	  echo "GNU Bash not built!"; exit 1; fi
+
+
+
+
+
+# Downloader
+# ----------
+#
+# OpenSSL: Some programs/libraries later need dynamic linking. So we'll
+# build libssl (and libcrypto) dynamically also.
+#
+# Until we find a nice and generic way to create an updated CA file in the
+# project, the certificates will be available in a file for this project
+# along with the other tarballs.
+#
+# In case you do want a static OpenSSL and libcrypto, then uncomment the
+# following conditional and put $(openssl-static) in the configure options.
+#
+#ifeq ($(static_build),yes)
+#openssl-static = no-dso no-dynamic-engine no-shared
+#endif
+$(idir)/etc:; mkdir $@
+$(ilidir)/openssl: $(tdir)/openssl-$(openssl-version).tar.gz         \
+                   $(tdir)/cert.pem                                  \
+                   $(ibidir)/bash | $(idir)/etc
+        # According to OpenSSL's Wiki (link bellow), it can't automatically
+        # detect Mac OS's structure. It will need some help. So we'll use
+        # the `on_mac_os' Make variable that we defined in the configure
+        # script and help it with some extra configuration options and an
+        # environment variable.
+        #
+        # https://wiki.openssl.org/index.php/Compilation_and_Installation
+	if [ x$(on_mac_os) = xyes ]; then                            \
+	  export KERNEL_BITS=64;                                     \
+	  copt="shared no-ssl2 no-ssl3 enable-ec_nistp_64_gcc_128";  \
+	fi;                                                          \
+	$(call gbuild, $<, openssl-$(openssl-version), ,             \
+                   zlib                                          \
+	               $$copt                                        \
+                   $(rpath_command)                              \
+                   --openssldir=$(idir)/etc/ssl                  \
+	               --with-zlib-lib=$(ildir)                      \
+                   --with-zlib-include=$(idir)/include, , ,      \
+	               ./config ) &&                                 \
+	cp $(tdir)/cert.pem $(idir)/etc/ssl/cert.pem;                \
+	if [ $$? = 0 ]; then                                         \
+	  if [ x$(on_mac_os) = xyes ]; then                          \
+	    echo "No need to fix rpath in libssl";                   \
+	  else                                                       \
+	    patchelf --set-rpath $(ildir) $(ildir)/libssl.so;        \
+	  fi;                                                        \
+	  echo "OpenSSL $(openssl-version)" > $@;                    \
+	fi
+
+# GNU Wget
+#
+# Note that on some systems (for example GNU/Linux) Wget needs to explicity
+# link with `libdl', but on others (for example Mac OS) it doesn't. We
+# check this at configure time and define the `needs_ldl' variable.
+#
+# Also note that since Wget needs to load outside libraries dynamically, it
+# gives a segmentation fault when built statically.
+#
+# There are many network related libraries that we are currently not
+# building as part of this project. So to avoid too much dependency on the
+# host system (especially a crash when these libraries are updated on the
+# host), they are disabled here.
+$(ibidir)/wget: $(tdir)/wget-$(wget-version).tar.lz \
+                $(ibidir)/pkg-config                \
+                $(ilidir)/openssl
+	libs="-pthread";                                          \
+	if [ x$(needs_ldl) = xyes ]; then libs="$$libs -ldl"; fi; \
+	$(call gbuild, $<, wget-$(wget-version), ,                \
+	               LIBS="$$LIBS $$libs"                       \
+	               --with-libssl-prefix=$(idir)               \
+	               --with-ssl=openssl                         \
+	               --with-openssl=yes                         \
+	               --without-metalink                         \
+	               --without-libuuid                          \
+	               --without-libpsl                           \
+	               --without-libidn                           \
+	               --disable-pcre2                            \
+	               --disable-pcre                             \
+	               --disable-iri )                            \
+	&& echo "GNU Wget $(wget-version)" > $@
+
+
+
+
+
+# Basic command-line tools and their dependencies
+# -----------------------------------------------
+#
+# These are basic programs which are commonly necessary in the build
+# process of the higher-level programs and libraries. Note that during the
+# building of those higher-level programs (after this Makefile finishes),
+# there is no access to the system's PATH.
+$(ibidir)/coreutils: $(tdir)/coreutils-$(coreutils-version).tar.xz \
+                     $(ilidir)/openssl
+        # Coreutils will use the hashing features of OpenSSL's `libcrypto'.
+        # See Tar's comments for the `-j' option.
+	$(call gbuild, $<, coreutils-$(coreutils-version), static,           \
+	               LDFLAGS="$(LDFLAGS)" CPPFLAGS="$(CPPFLAGS)"           \
+	               --enable-rpath --disable-silent-rules --with-openssl, \
+	               -j$(numthreads))                                      \
+	&& echo "GNU Coreutils $(coreutils-version)" > $@
+
+$(ibidir)/diffutils: $(tdir)/diffutils-$(diffutils-version).tar.xz \
+                     $(ibidir)/bash
+	$(call gbuild, $<, diffutils-$(diffutils-version), static, , V=1) \
+	&& echo "GNU Diffutils $(diffutils-version)" > $@
+
+$(ibidir)/findutils: $(tdir)/findutils-$(findutils-version).tar.lz \
+                     $(ibidir)/bash
+	$(call gbuild, $<, findutils-$(findutils-version), static, , V=1) \
+	&& echo "GNU Findutils $(findutils-version)" > $@
+
+$(ibidir)/gawk: $(tdir)/gawk-$(gawk-version).tar.lz \
+                $(ibidir)/bash                      \
+                $(ilidir)/mpfr                      \
+                $(ilidir)/gmp
+        # AWK doesn't include RPATH by default, so we'll have to manually
+        # include it using the `patchelf' program (which was a dependency
+        # of Bash). Just note that AWK produces two executables (for
+        # example `gawk-4.2.1' and `gawk') and a symbolic link `awk' to one
+        # of those executables.
+	$(call gbuild, $<, gawk-$(gawk-version), static,              \
+	               --with-readline=$(idir))                       \
+	&& if [ "x$(needpatchelf)" != x ]; then                       \
+	     if [ -f $(ibdir)/gawk ]; then                            \
+	       $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/gawk;  \
+	     fi;                                                      \
+	     if [ -f $(ibdir)/gawk-$(gawk-version) ]; then            \
+	       $(ibdir)/patchelf --set-rpath $(ildir)                 \
+	                         $(ibdir)/gawk-$(gawk-version);       \
+	    fi;                                                       \
+	   fi                                                         \
+	&& echo "GNU AWK $(gawk-version)" > $@
+
+$(ilidir)/gmp: $(tdir)/gmp-$(gmp-version).tar.lz \
+               $(ibidir)/bash
+	$(call gbuild, $<, gmp-$(gmp-version), static, , , make check)  \
+	&& echo "GNU Multiple Precision Arithmetic Library $(gmp-version)" > $@
+
+# On Mac OS, libtool does different things, so to avoid confusion, we'll
+# prefix GNU's libtool executables with `glibtool'.
+$(ibidir)/glibtool: $(tdir)/libtool-$(libtool-version).tar.xz \
+                    $(ibidir)/m4
+	$(call gbuild, $<, libtool-$(libtool-version), static, \
+                       --program-prefix=g)                     \
+	&& echo "GNU Libtool $(libtool-version)" > $@
+
+$(ibidir)/grep: $(tdir)/grep-$(grep-version).tar.xz \
+                $(ibidir)/bash
+	$(call gbuild, $<, grep-$(grep-version), static) \
+	&& echo "GNU Grep $(grep-version)" > $@
+
+$(ibidir)/m4: $(tdir)/m4-$(m4-version).tar.gz \
+              $(ibidir)/bash
+	$(call gbuild, $<, m4-$(m4-version), static) \
+	&& echo "GNU M4 $(m4-version)" > $@
+
+$(ilidir)/mpfr: $(tdir)/mpfr-$(mpfr-version).tar.xz \
+                $(ilidir)/gmp
+	$(call gbuild, $<, mpfr-$(mpfr-version), static, , , make check)  \
+	&& echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@
+
+$(ibidir)/pkg-config: $(tdir)/pkg-config-$(pkgconfig-version).tar.gz \
+                      $(ibidir)/bash
+        # Some Mac OS systems may have a version of the GNU C Compiler
+        # (GCC) installed that doesn't support some necessary features of
+        # building Glib (as part of pkg-config). So to be safe, for Mac
+        # systems, we'll make sure it will use LLVM's Clang.
+	if [ x$(on_mac_os) = xyes ]; then export compiler="CC=clang"; \
+	else                              export compiler="";         \
+	fi;                                                           \
+	$(call gbuild, $<, pkg-config-$(pkgconfig-version), static,   \
+	               $$compiler --with-internal-glib                \
+	               --with-pc-path=$(ildir)/pkgconfig)             \
+	&& echo "pkg-config $(pkgconfig-version)" > $@
+
+$(ibidir)/sed: $(tdir)/sed-$(sed-version).tar.xz \
+               $(ibidir)/bash
+	$(call gbuild, $<, sed-$(sed-version), static) \
+	&& echo "GNU Sed $(sed-version)" > $@
+
+$(ibidir)/which: $(tdir)/which-$(which-version).tar.gz \
+                 $(ibidir)/bash
+	$(call gbuild, $<, which-$(which-version), static) \
+	&& echo "GNU Which $(which-version)" > $@
+
+
+
+
+
+
+
+
+
+
+# GCC and its prerequisites
+# -------------------------
+#
+# Binutils' linker `ld' is apparently only good for GNU/Linux systems and
+# other OSs have their own. So for now we aren't actually building
+# Binutils (`ld' isn't a prerequisite of GCC).
+$(ibidir)/binutils: $(tdir)/binutils-$(binutils-version).tar.lz \
+                    $(ibidir)/bash
+	$(call gbuild, $<, binutils-$(binutils-version), static) \
+	&& echo "GNU Binutils $(binutils-version)" > $@
+
+# `file' is not a prerequisite of GCC. However, since it is low level, it is
+# set as a prerequisite of GCC to have it installed.
+$(ibidir)/file: $(tdir)/file-$(file-version).tar.gz \
+                $(ibidir)/bash
+	$(call gbuild, $<, file-$(file-version), static) \
+	&& echo "File $(file-version)" > $@
+
+$(ilidir)/isl: $(tdir)/isl-$(isl-version).tar.bz2 \
+               $(ilidir)/gmp
+	$(call gbuild, $<, isl-$(isl-version), static)  \
+	&& echo "GNU Integer Set Library $(isl-version)" > $@
+
+$(ilidir)/mpc: $(tdir)/mpc-$(mpc-version).tar.gz \
+               $(ilidir)/mpfr
+	$(call gbuild, $<, mpc-$(mpc-version), static, , , make check)  \
+	&& echo "GNU Multiple Precision Complex library" > $@
+
+# We are having issues with `libiberty' (part of GCC) on Mac. So for now,
+# GCC won't be built there. Since almost no natural science paper's
+# processing depends so strongly on the compiler used, for now, this isn't
+# a bad assumption, but we are indeed searching for a solution.
+#
+# Based on the GCC manual, the GCC build can benefit from a GNU
+# environment. So, we'll build GCC after building all the basic tools that
+# are often used in a configure and build scripts of GCC components.
+#
+# Objective C and Objective C++ is necessary for installing `matplotlib'.
+#
+# We are currently having problems installing GCC on macOS, so for the time
+# being, if the project is being run on a macOS, we'll just set a link.
+ifeq ($(host_cc),1)
+gcc-prerequisites =
+else
+gcc-prerequisites = $(tdir)/gcc-$(gcc-version).tar.xz \
+                    $(ilidir)/isl                     \
+                    $(ilidir)/mpc
+endif
+$(ibidir)/gcc: $(gcc-prerequisites)   \
+               $(ibidir)/sed          \
+               $(ibidir)/bash         \
+               $(ibidir)/file         \
+               $(ibidir)/gawk         \
+               $(ibidir)/grep         \
+               $(ibidir)/which        \
+               $(ibidir)/glibtool     \
+               $(ibidir)/coreutils    \
+               $(ibidir)/diffutils    \
+               $(ibidir)/findutils
+
+        # GCC builds is own libraries in '$(idir)/lib64'. But all other
+        # libraries are in '$(idir)/lib'. Since this project is only for a
+        # single architecture, we can trick GCC into building its libraries
+        # in '$(idir)/lib' by defining the '$(idir)/lib64' as a symbolic
+        # link to '$(idir)/lib'.
+	if [ $(host_cc) = 1 ]; then                                        \
+	  $(call makelink,gcc);                                            \
+	  $(call makelink,g++,mandatory);                                  \
+	  $(call makelink,gfortran,mandatory);                             \
+	  ccinfo=$$(gcc --version | awk 'NR==1');                          \
+	  echo "C compiler (""$$ccinfo"")" > $@;                           \
+	else                                                               \
+	  rm -f $(ibdir)/gcc* $(ibdir)/g++ $(ibdir)/gfortran $(ibdir)/gcov*;\
+	  rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc*;            \
+	  rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*;\
+	                                                                   \
+	  ln -fs $(ildir) $(idir)/lib64;                                   \
+	                                                                   \
+	  cd $(ddir);                                                      \
+	  rm -rf gcc-build gcc-$(gcc-version);                             \
+	  tar xf $<                                                        \
+	  && mkdir $(ddir)/gcc-build                                       \
+	  && cd $(ddir)/gcc-build                                          \
+	  && ../gcc-$(gcc-version)/configure SHELL=$(ibdir)/bash           \
+	                    --prefix=$(idir)                               \
+	                    --with-mpc=$(idir)                             \
+	                    --with-mpfr=$(idir)                            \
+	                    --with-gmp=$(idir)                             \
+	                    --with-isl=$(idir)                             \
+	                    --with-build-time-tools=$(idir)                \
+	                    --enable-shared                                \
+	                    --disable-multilib                             \
+	                    --disable-multiarch                            \
+	                    --enable-threads=posix                         \
+	                    --with-local-prefix=$(idir)                    \
+	                    --enable-languages=c,c++,fortran,objc,obj-c++  \
+	                    --disable-libada                               \
+	                    --disable-nls                                  \
+	                    --enable-default-pie                           \
+	                    --enable-default-ssp                           \
+	                    --enable-cet=auto                              \
+	                    --enable-decimal-float                         \
+	  && make SHELL=$(ibdir)/bash -j$$(nproc)                          \
+	  && make SHELL=$(ibdir)/bash install                              \
+	  && cd ..                                                         \
+	  && rm -rf gcc-build gcc-$(gcc-version)                           \
+	                                                                   \
+	  && if [ "x$(on_mac_os)" != xyes ]; then                          \
+	       for f in $$(find $(idir)/libexec/gcc); do                   \
+	         if ldd $$f &> /dev/null; then                             \
+	           patchelf --set-rpath $(ildir) $$f;                      \
+	         fi;                                                       \
+	       done;                                                       \
+	     fi                                                            \
+	  && echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@;     \
+	fi