Better control of shared library linking

Until now we weren't explicity writing the full path of the dynamic
libraries necessary for linking a program. But now with
`-Wl,-rpath=$(ildir)' we ensure that the linker keeps the address of the
dynamic libraries necessary for linking at linking time, not running
time. Also, `pkg-config' is also built when preparing the basics. Several
other minor corrections were made thanks to the great help of Raúl Infante
Sainz.

6 files changed, 70 insertions, 47 deletions

diff --git a/paper.tex b/paper.tex
index 6aa30bd..3388ece 100644
--- a/paper.tex
+++ b/paper.tex
@@ -210,22 +210,22 @@ research (in alphabetical order): Bzip2 \bziptwoversion, CFITSIO
 GNU Libtool \libtoolversion, GNU Make \makeversion, GNU Sed \sedversion,
 GNU Scientific Library (GSL) \gslversion, GNU Tar \tarversion, GNU Which
 \whichversion, Lzip \lzipversion, GPL Ghostscript \ghostscriptversion,
-Libgit2 \libgitwoversion, Libtiff \libtiffversion, WCSLIB \wcslibversion,
-XZ Utils \xzversion, and ZLib \zlibversion. The final paper was produced
-with \TeX{} Live \texliveversion, using the following packages: \TeX{}
-\textexversion, EC \texecversion, NewTX \texnewtxversion, Fontaxes
-\texfontaxesversion, Keyval, \texxkeyvalversion, Etoolbox
-\texetoolboxversion, Xcolor \texxcolorversion, Setspace
-\texsetspaceversion, Caption \texcaptionversion, Footmisc
-\texfootmiscversion, Datetime \texdatetimeversion, Fmtcount
-\texfmtcountversion, Titlesec \textitlesecversion, Preprint
-\texpreprintversion, Ulem \texulemversion, Bib\LaTeX{} \texbiblatexversion,
-Biber \texbiberversion, Logreq \texlogreqversion, PGF/TiKZ \texpgfversion,
-PGFPlots \texpgfplotsversion, FP \texfpversion, Courier \texcourierversion,
-\TeX-gyre \textexgyreversion, TXFonts \textxfontsversion, Times
-\textimesversion. We are very grateful to all their creators for freely
-providing this necessary infrastructure. This research would not be
-possible without them.
+Libgit2 \libgitwoversion, Libtiff \libtiffversion, Pkg-config
+\pkgconfigversion, WCSLIB \wcslibversion, XZ Utils \xzversion, and ZLib
+\zlibversion. The final paper was produced with \TeX{} Live
+\texliveversion, using the following packages: \TeX{} \textexversion, EC
+\texecversion, NewTX \texnewtxversion, Fontaxes \texfontaxesversion,
+Keyval, \texxkeyvalversion, Etoolbox \texetoolboxversion, Xcolor
+\texxcolorversion, Setspace \texsetspaceversion, Caption
+\texcaptionversion, Footmisc \texfootmiscversion, Datetime
+\texdatetimeversion, Fmtcount \texfmtcountversion, Titlesec
+\textitlesecversion, Preprint \texpreprintversion, Ulem \texulemversion,
+Bib\LaTeX{} \texbiblatexversion, Biber \texbiberversion, Logreq
+\texlogreqversion, PGF/TiKZ \texpgfversion, PGFPlots \texpgfplotsversion,
+FP \texfpversion, Courier \texcourierversion, \TeX-gyre \textexgyreversion,
+TXFonts \textxfontsversion, Times \textimesversion. We are very grateful to
+all their creators for freely providing this necessary infrastructure. This
+research would not be possible without them.
 
 %% Tell BibLaTeX to put the bibliography list here.
 \printbibliography
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
index 9c6f18f..ca18f8b 100644
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -11,12 +11,13 @@ flock-version       = 0.2.3
 gawk-version        = 4.2.1
 ghostscript-version = 9.26
 git-version         = 2.19.1
-gnuastro-version    = 0.7.65-ff7a
+gnuastro-version    = 0.7.66-0ad3
 grep-version        = 3.1
 gzip-version        = 1.9.10-051e
 libtool-version     = 2.4.6
 lzip-version        = 1.20
 make-version        = 4.2.90
+pkgconfig-version   = 0.29.2
 sed-version         = 4.5
 tar-version         = 1.30
 which-version       = 2.21
diff --git a/reproduce/src/make/dependencies-basic.mk b/reproduce/src/make/dependencies-basic.mk
index a3d679e..196d457 100644
--- a/reproduce/src/make/dependencies-basic.mk
+++ b/reproduce/src/make/dependencies-basic.mk
@@ -55,12 +55,14 @@ syspath         := $(PATH)
 
 # As we build more programs, we want to use our own pipeline's built
 # programs and libraries, not the host's.
-PATH            := $(ibdir):$(PATH)
-LDFLAGS         := -L$(ildir) $(LDFLAGS)
-CPPFLAGS        := -I$(idir)/include $(CPPFLAGS)
-LD_LIBRARY_PATH := $(ildir):$(LD_LIBRARY_PATH)
-
-top-level-programs = bash which ls sed gawk grep diff find
+export PATH              := $(ibdir):$(PATH)
+export PKG_CONFIG_PATH   := $(ildir)/pkgconfig
+export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
+export LDFLAGS           := -L$(ildir) $(LDFLAGS)
+export CPPFLAGS          := -I$(idir)/include $(CPPFLAGS)
+export LD_LIBRARY_PATH   := $(ildir):$(LD_LIBRARY_PATH)
+
+top-level-programs = bash which ls sed gawk grep diff find pkg-config
 all: $(foreach p, $(top-level-programs), $(ibdir)/$(p))
 
 
@@ -99,6 +101,7 @@ tarballs = $(foreach t, bash-$(bash-version).tar.gz                         \
                         gzip-$(gzip-version).tar.gz                         \
                         lzip-$(lzip-version).tar.gz                         \
                         make-$(make-version).tar.lz                         \
+                        pkg-config-$(pkgconfig-version).tar.gz              \
                         sed-$(sed-version).tar.xz                           \
 	                tar-$(tar-version).tar.gz                           \
                         which-$(which-version).tar.gz                       \
@@ -123,6 +126,7 @@ $(tarballs): $(tdir)/%:
 	  elif [ $$n = gzip      ]; then w=http://akhlaghi.org/src;         \
 	  elif [ $$n = lzip      ]; then w=http://download.savannah.gnu.org/releases/lzip; \
 	  elif [ $$n = make      ]; then w=http://akhlaghi.org/src;         \
+	  elif [ $$n = pkg       ]; then w=https://pkg-config.freedesktop.org/releases; \
 	  elif [ $$n = sed       ]; then w=http://ftp.gnu.org/gnu/sed;      \
 	  elif [ $$n = tar       ]; then w=http://ftp.gnu.org/gnu/tar;      \
 	  elif [ $$n = which     ]; then w=http://ftp.gnu.org/gnu/which;    \
@@ -171,6 +175,13 @@ $(ibdir)/low-level: | $(ibdir)
         # The linker
 	$(call makelink,ar)
 	$(call makelink,ld)
+	$(call makelink,nm)
+	$(call makelink,ps)
+
+        # 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)
@@ -279,6 +290,11 @@ $(ibdir)/ls: $(tdir)/coreutils-$(coreutils-version).tar.xz \
              $(ibdir)/make
 	$(call gbuild, $<, coreutils-$(coreutils-version), static)
 
+$(ibdir)/pkg-config: $(tdir)/pkg-config-$(pkgconfig-version).tar.gz \
+                     $(ibdir)/make
+	$(call gbuild, $<, pkg-config-$(pkgconfig-version), static, \
+                       --with-internal-glib)
+
 $(ibdir)/sed: $(tdir)/sed-$(sed-version).tar.xz \
               $(ibdir)/make
 	$(call gbuild, $<, sed-$(sed-version), static)
diff --git a/reproduce/src/make/dependencies-build-rules.mk b/reproduce/src/make/dependencies-build-rules.mk
index 7b3a419..c0561a7 100644
--- a/reproduce/src/make/dependencies-build-rules.mk
+++ b/reproduce/src/make/dependencies-build-rules.mk
@@ -53,7 +53,6 @@ gbuild = if [ x$(static_build) = xyes ] && [ $(3)x = staticx ]; then          \
 	 fi;                                                                  \
 	 check="$(6)";                                                        \
 	 if [ x"$$check" = x ]; then check="echo Skipping-check"; fi;         \
-	 export SHELL=$(ibdir)/bash;                                          \
 	 cd $(ddir) && rm -rf $(2) && tar xf $(1) && cd $(2) &&               \
 	 ./configure $(4) --prefix=$(idir) &&                                 \
 	 make $(5) &&                                                         \
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index c795b34..6f4aa78 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -51,12 +51,14 @@ all: $(foreach p, $(top-level-programs), $(ibdir)/$(p))
 # compiler and linker. For the library binaries and headers, we are only
 # using our internally built libraries.
 .ONESHELL:
-.SHELLFLAGS     := -ec
-PATH            := $(ibdir)
-LD_LIBRARY_PATH := $(ildir)
-LDFLAGS         := -L$(ildir)
-SHELL           := $(ibdir)/bash
-CPPFLAGS        := -I$(idir)/include
+.SHELLFLAGS              := -ec
+export PATH              := $(ibdir)
+export LD_LIBRARY_PATH   := $(ildir)
+export SHELL             := $(ibdir)/bash
+export CPPFLAGS          := -I$(idir)/include
+export PKG_CONFIG_PATH   := $(ildir)/pkgconfig
+export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
+export LDFLAGS           := -Wl,-rpath=$(ildir) -L$(ildir)
 
 
 
@@ -183,15 +185,14 @@ $(ilidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz | $(ilidir)
 $(ilidir)/libjpeg: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz | $(ilidir)
 	$(call gbuild, $<, jpeg-9b, static) && echo "Libjpeg is built" > $@
 
-$(ilidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz | $(ilidir)
+$(ilidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \
+                   $(ilidir)/libjpeg | $(ilidir)
 	$(call gbuild, $<, tiff-$(libtiff-version), static)               \
 	&& echo "Libtiff is built" > $@
 
 $(ilidir)/wcslib: $(tdir)/wcslib-$(wcslib-version).tar.bz2                \
 	          $(ilidir)/cfitsio | $(ilidir)
-        # Unfortunately WCSLIB forces the building of shared libraries. So
-        # we'll allow it to finish, then remove the shared libraries
-        # afterwards.
+        # Unfortunately WCSLIB forces the building of shared libraries.
 	$(call gbuild, $<, wcslib-$(wcslib-version), ,                     \
 	              LIBS="-pthread -lcurl -lm" --without-pgplot          \
 	              --disable-fortran)                                   \
@@ -225,8 +226,11 @@ $(ibdir)/curl: $(tdir)/curl-$(curl-version).tar.gz                           \
                $(ilidir)/zlib
 	$(call gbuild, $<, curl-$(curl-version), static, --without-brotli)
 
-$(ibdir)/libtool: $(tdir)/libtool-$(libtool-version).tar.xz
-	$(call gbuild, $<, libtool-$(libtool-version), static)
+# On Mac OS, libtool does different things, so to avoid confusion, we'll
+# prefix GNU's libtool executables with `glibtool'.
+$(ibdir)/glibtool: $(tdir)/libtool-$(libtool-version).tar.xz
+	$(call gbuild, $<, libtool-$(libtool-version), static, \
+                       --program-prefix=g)
 
 $(ibdir)/gs: $(tdir)/ghostscript-$(ghostscript-version).tar.gz
 	$(call gbuild, $<, ghostscript-$(ghostscript-version))
@@ -243,7 +247,7 @@ $(ibdir)/astnoisechisel: $(tdir)/gnuastro-$(gnuastro-version).tar.lz \
                          $(ibdir)/gs                                 \
                          $(ilidir)/gsl                               \
                          $(ilidir)/wcslib                            \
-                         $(ibdir)/libtool                            \
+                         $(ibdir)/glibtool                           \
                          $(ilidir)/libjpeg                           \
                          $(ilidir)/libtiff                           \
                          $(ilidir)/libgit2
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index 3453d4e..9141b30 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -42,6 +42,7 @@ texbdir     = $(texdir)/build
 tikzdir     = $(texbdir)/tikz
 mtexdir     = $(texdir)/macros
 pconfdir    = reproduce/config/pipeline
+installdir  = $(BDIR)/dependencies/installed
 # --------- Delete for no Gnuastro ---------
 gconfdir    = reproduce/config/gnuastro
 # ------------------------------------------
@@ -72,12 +73,12 @@ curdir   := $(shell echo $$(pwd))
 # environment variables, we are setting it to prefer the software we have
 # build here.
 .ONESHELL:
-.SHELLFLAGS      = -ec
-SHELL           := .local/bin/bash
-PATH            := $(curdir)/.local/bin
-LD_LIBRARY_PATH := $(curdir)/.local/lib
-LDFLAGS         := -L$(curdir)/.local/lib
-CPPFLAGS        := -I$(curdir)/.local/include
+.SHELLFLAGS            = -ec
+export PATH            := $(installdir)/bin
+export LD_LIBRARY_PATH := $(installdir)/lib
+export LDFLAGS         := -L$(installdir)/lib
+export SHELL           := $(installdir)/bin/bash
+export CPPFLAGS        := -I$(installdir)/include
 
 
 
@@ -197,18 +198,20 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	$(call pvcheck, curl, $(curl-version), cURL, curlversion)
 	$(call pvcheck, diff, $(diffutils-version), GNU Diffutils,     \
 	                diffutilsversion)
-	$(call pvcheck, find, $(findutils-version), GNU Findutils,       \
+	$(call pvcheck, find, $(findutils-version), GNU Findutils,     \
 	                findutilsversion)
 	$(call pvcheck, gs, $(ghostscript-version), GPL Ghostscript,   \
-	                    ghostscriptversion)
+	                ghostscriptversion)
 	$(call pvcheck, git, $(git-version), Git, gitversion)
 	$(call pvcheck, grep, $(grep-version), GNU Grep, grepversion)
-	$(call pvcheck, libtool, $(libtool-version), GNU Libtool,      \
+	$(call pvcheck, glibtool, $(libtool-version), GNU Libtool,     \
 	                libtoolversion)
 	$(call pvcheck, ls, $(coreutils-version), GNU Coreutils,       \
 	                coreutilsversion)
 	$(call pvcheck, lzip, $(lzip-version), Lzip, lzipversion)
 	$(call pvcheck, make, $(make-version), GNU Make, makeversion)
+	$(call pvcheck, pkg-config, $(pkgconfig-version), pkg-config,  \
+	                pkgconfigversion)
 	$(call pvcheck, sed, $(sed-version), GNU SED, sedversion)
 	$(call pvcheck, tar, $(tar-version), GNU Tar, tarversion)
 	$(call pvcheck, which, $(which-version), GNU Which, whichversion)
@@ -216,7 +219,7 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 
         # --------- Delete for no Gnuastro ---------
 	$(call pvcheck, astnoisechisel, $(gnuastro-version), Gnuastro, \
-                         gnuastroversion)
+                        gnuastroversion)
         # ------------------------------------------
 
         # Bzip2 prints its version in standard error, not standard output!