Configuration: Imported recent updates from Maneageaas-journals

Until this commit, the AAS journals branch was based on Maneage commit
8161194 (dated 2022-05-22). However, maneage has been updated recently so
it is necessary to also update this branch.

With this commit, the merge has been done (and tested).

9 files changed, 283 insertions, 157 deletions

diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md
index d2b6952..00afef4 100644
--- a/reproduce/software/make/README.md
+++ b/reproduce/software/make/README.md
@@ -1,7 +1,7 @@
 Software building instructions
 ------------------------------
 
-Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
+Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
 See the end of the file for license conditions.
 
 This directory contains Makefiles that are called by the high-level
diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk
index 5c8f14c..6e7d415 100644
--- a/reproduce/software/make/atlas-multiple.mk
+++ b/reproduce/software/make/atlas-multiple.mk
@@ -8,7 +8,7 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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
diff --git a/reproduce/software/make/atlas-single.mk b/reproduce/software/make/atlas-single.mk
index 4e2b04a..2b68677 100644
--- a/reproduce/software/make/atlas-single.mk
+++ b/reproduce/software/make/atlas-single.mk
@@ -8,7 +8,7 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 99e81d2..cf155f0 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -21,9 +21,9 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # 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
@@ -49,14 +49,15 @@ include reproduce/software/config/checksums.conf
 include reproduce/software/config/urls.conf
 
 # Basic directories
-lockdir = $(BDIR)/software/locks
-tdir    = $(BDIR)/software/tarballs
-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
+lockdir  = $(BDIR)/software/locks
+tdir     = $(BDIR)/software/tarballs
+ddir     = $(BDIR)/software/build-tmp
+idir     = $(BDIR)/software/installed
+ibdir    = $(BDIR)/software/installed/bin
+ildir    = $(BDIR)/software/installed/lib
+iidir    = $(BDIR)/software/installed/include
+shsrcdir = "$(shell pwd)"/reproduce/software/shell
+ibidir   = $(BDIR)/software/installed/version-info/proglib
 
 # Ultimate Makefile target. GNU Nano (a simple and very light-weight text
 # editor) is installed by default, it is recommended to have it in the
@@ -107,6 +108,15 @@ export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings)
 # 'LD_LIBRARY_PATH', then we'll add our own newly installed libraries.  We
 # will also make sure that there is no "current directory" in it (by
 # removing a starting or trailing ':' and any occurance of '::'.
+#
+# But first: in case LD_LIBRARY_PATH is empty, give it the default value of
+# $(sys_library_sh_path) (which was the location of the libraries needed by
+# the host's shell). This is because after we add the Maneage's library
+# path, on some systems, no other libraries will be checked except those
+# that are in 'LD_LIBRARY_PATH'.
+ifeq ($(strip $(LD_LIBRARY_PATH)),)
+export LD_LIBRARY_PATH=$(sys_library_sh_path)
+endif
 export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \
                                   | sed -e's/::/:/g' -e's/^://' -e's/:$$//')
 
@@ -127,7 +137,7 @@ export DYLD_LIBRARY_PATH :=
 # Afer putting everything together, we use the first server as the
 # reference for all software if their '-url' variable isn't defined (in
 # 'reproduce/software/config/urls.conf').
-downloadwrapper = ./reproduce/analysis/bash/download-multi-try
+downloadwrapper = ./reproduce/analysis/bash/download-multi-try.sh
 maneage_backup_urls := $(shell awk '!/^#/{printf "%s ", $$1}' \
                                reproduce/software/config/servers-backup.conf)
 backupservers_all = $(user_backup_urls) $(maneage_backup_urls)
@@ -263,46 +273,10 @@ $(ibidir)/gzip-$(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))
-
-#	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
+	$(call gbuild, xz-$(xz-version), static)
 	echo "XZ Utils $(xz-version)" > $@
 
 $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
@@ -336,6 +310,7 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
 	rm -rf $$tdir
 	tar -xf $(tdir)/$$tarball
 	cd $$tdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	sed -e 's@\(ln -s -f \)$$(PREFIX)/bin/@\1@' Makefile \
 	    > Makefile.sed
 	mv Makefile.sed Makefile
@@ -634,6 +609,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
 	rm -rf perl-$(perl-version)
 	tar -xf $(tdir)/$$tarball
 	cd perl-$(perl-version)
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	./Configure -des \
 	            -Dusethreads \
 	            -Duseshrplib \
@@ -691,21 +667,16 @@ $(ibidir)/coreutils-$(coreutils-version): \
                     $(ibidir)/perl-$(perl-version) \
                     $(ibidir)/openssl-$(openssl-version)
 
-#	Import, unpack and enter the source directory.
+#	Import the source tarball.
 	tarball=coreutils-$(coreutils-version).tar.lz
 	$(call import-source, $(coreutils-url), $(coreutils-checksum))
+
+#	Unpack and enter the source.
 	cd $(ddir)
 	rm -rf coreutils-$(coreutils-version)
 	tar -xf $(tdir)/$$tarball
 	cd coreutils-$(coreutils-version)
-
-#	Set the configure script to use our shell, note that we can't
-#	assume GNU SED here yet (it installs after Coreutils).
-	sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \
-	    -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \
-	    configure > configure-tmp
-	mv configure-tmp configure
-	chmod +x configure
+	$(shsrcdir)/prep-source.sh $(ibdir)
 
 #	Configure, build and install Coreutils.
 	./configure --prefix=$(idir) SHELL=$(ibdir)/bash  \
@@ -744,6 +715,7 @@ $(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version)
 	rm -rf podlators-$(podlators-version)
 	tar -xf $(tdir)/$$tarball
 	cd podlators-$(podlators-version)
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	perl Makefile.PL
 	make
 	make install
@@ -766,7 +738,7 @@ $(ibidir)/openssl-$(openssl-version): $(ibidir)/podlators-$(podlators-version) \
 #	First download the certificates and copy them into the
 #	installation directory.
 	tarball=cert.pem-$(certpem-version)
-	$(call import-source, $(cert-url), $(cert-checksum))
+	$(call import-source, $(certpem-url), $(certpem-checksum))
 	cp $(tdir)/cert.pem-$(certpem-version) $(idir)/etc/ssl/cert.pem
 
 #	Now download the OpenSSL tarball.
@@ -1030,7 +1002,7 @@ $(ibidir)/gmp-$(gmp-version): \
 	$(call import-source, $(gmp-url), $(gmp-checksum))
 	$(call gbuild, gmp-$(gmp-version), static, \
 	               --enable-cxx --enable-fat, \
-	               -j$(numthreads) ,make check)
+	               -j$(numthreads))
 	echo "GNU Multiple Precision Arithmetic Library $(gmp-version)" > $@
 
 # Less is useful with Git (to view the diffs within a minimal container)
@@ -1070,16 +1042,27 @@ $(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version)
 $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version)
 	tarball=grep-$(grep-version).tar.lz
 	$(call import-source, $(grep-url), $(grep-checksum))
-	$(call gbuild, grep-$(grep-version), static,,V=1)
+	$(call gbuild, grep-$(grep-version), static,, \
+	               -j$(numthreads) V=1)
 	echo "GNU Grep $(grep-version)" > $@
 
 # M4 doesn't depend on PatchELF, but just to be consistent with the
 # levels/phases introduced here (where the compressors are level 1,
 # PatchELF is level 2, and ...), we'll set it as a dependency.
+#
+# The '--with-syscmd-shell' is used as the default shell and if not given,
+# 'm4' will use '/bin/sh' (which is not under Maneage control and can cause
+# problems in 'high-level.mk' because it closes off the system's
+# LD_LIBRARY_PATH and if the system's '/bin/sh' needs a special system
+# library, the high-level programs will not be built). We are setting this
+# default shell to Dash because M4 is built before our own Bash. Recall
+# that Dash is built before we enter this Makefile.
 $(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version)
 	tarball=m4-$(m4-version).tar.lz
 	$(call import-source, $(m4-url), $(m4-checksum))
-	$(call gbuild, m4-$(m4-version), static,,V=1)
+	$(call gbuild, m4-$(m4-version), static, \
+	               --with-syscmd-shell=$(ibdir)/dash, \
+	               -j$(numthreads) V=1)
 	echo "GNU M4 $(m4-version)" > $@
 
 $(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version)
@@ -1169,7 +1152,7 @@ $(ibidir)/mpc-$(mpc-version): $(ibidir)/mpfr-$(mpfr-version)
 	  echo "" > $@
 	else
 	  $(call gbuild, mpc-$(mpc-version), static, , \
-	                 -j$(numthreads), make check)
+	                 -j$(numthreads))
 	  echo "GNU Multiple Precision Complex library" > $@
 	fi
 
@@ -1228,7 +1211,8 @@ $(ibidir)/binutils-$(binutils-version): \
 
 #	  Build binutils with the standard 'gbuild' function.
 	  $(call gbuild, binutils-$(binutils-version), static, \
-	                 --with-lib-path=$(sys_library_path), \
+	                 --with-lib-path=$(sys_library_path) \
+	                 --enable-gprofng=no, \
 	                 -j$(numthreads) V=1)
 
 #	  The 'ld' linker of Binutils needs several '*crt*.o' files from
@@ -1356,21 +1340,35 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 #	  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:
+#	  GCC's build directory will become several gigabytes and the build
+#	  also needs RAM. You can track the RAM usage of the system with a
+#	  1-second resolution (if no other RAM consuming program is running
+#	  while building GCC) with the command below (example outputs can
+#	  be seen in https://savannah.nongnu.org/task/index.php?16623).
 #
-#	  https://savannah.nongnu.org/task/?16244#comment12
+#	     c=1; while true; do POSIXLY_CORRECT=1 df -P /dev/shm/maneage-* | awk 'NR==2{print '$c', $3}'; c=$((c+1)); sleep 1; done > mem-usage.txt
+#	    asttable mem-usage.txt -c1,'arith $2 512 x 1024 / 1024 / 1024 /' -o mem.fits
 #
 #	  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.
+#	  POSIXLY_CORRECT=1, so the 'block size' is 512 bytes. In this way,
+#	  to get the actual GiB amount, multiply the value returned above
+#	  by 512 (B/block), then divide by 1024^3 (B/GiB).
+#
+#	  To get the final value to use here, get the maximum used value
+#	  after GCC is fully built and you have stopped the 'while true'
+#	  command above. You can do this with the command below (assumes
+#	  you have Gnuastro).
+#
+#	     aststatistics mem-usage.txt -c2 --maximum | asttable -c'arith $1 7000000 +' -Afixed -B0
+#
+#	  The extra space is because we will assume an extra 3 GiB = 3GiB *
+#	  1024^3 (B/GiB) / 512 (B/block) = 6291456 blocks are necessary for
+#	  the building (let's round it to 7000000!).
 #
-#	  So we need 8 GiB * 1024^3 (B/GiB) / 512 blocks/B = 16777216
-#	  blocks, in blocks of 512 bytes.
+#	  Therefore, we need to make sure that the running system more than
+#	  the necessary amount of space in the RAM. To do this, we use 'df'
+#	  below.
 #
 #	  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
@@ -1380,7 +1378,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 #	  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"}'); \
+	               | awk 'NR==2{print ($$4>26613216) ? "yes" : "no"}'); \
 	  if [ $$in_ram = "yes" ]; then odir=$(ddir)
 	  else
 	    odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space
@@ -1399,6 +1397,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	    ln -s $$odir/gcc-$(gcc-version) $(ddir)/gcc-$(gcc-version)
 	  fi
 	  cd gcc-$(gcc-version)
+	  $(shsrcdir)/prep-source.sh $(ibdir)
 
 #	  Unfortunately binutils installs headers like 'ansidecl.h' that
 #	  have been seen to conflict with GCC's internal versions of those
@@ -1506,7 +1505,18 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 
 
 
-# Software that need re-compilation (to use our own libraries)
+# Level 6: need re-compilation
+# ----------------------------
+#
+# The initial build of these was done with the host's settings, which will
+# cause problems later when we completely close-off the host environment.
+$(ibidir)/make-$(make-version): $(ibidir)/gcc-$(gcc-version)
+	tarball=make-$(make-version).tar.lz
+	$(call import-source, $(make-url), $(make-checksum))
+	$(call gbuild, make-$(make-version), static, \
+	               --disable-dependency-tracking --without-guile)
+	echo "GNU Make $(make-version)" > $@
+
 $(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version)
 	tarball=lzip-$(lzip-version).tar
 	unpackdir=lzip-$(lzip-version)
@@ -1514,6 +1524,7 @@ $(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version)
 	rm -rf $$unpackdir
 	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	./configure --build --check --installdir="$(ibdir)"
 	if [ -f $(ibdir)/patchelf ]; then
 	  $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/lzip;
@@ -1526,11 +1537,7 @@ $(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version)
 
 
 
-
-
-
-
-# Level 6: Basic text editor
+# Level 7: Basic text editor
 # --------------------------
 #
 # If the project is built in a minimal environment, there is no text
@@ -1547,7 +1554,8 @@ $(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-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): $(ibidir)/lzip-$(lzip-version)
+$(ibidir)/nano-$(nano-version): $(ibidir)/lzip-$(lzip-version) \
+                                $(ibidir)/make-$(make-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/build-rules.mk b/reproduce/software/make/build-rules.mk
index c160d33..62cb6d5 100644
--- a/reproduce/software/make/build-rules.mk
+++ b/reproduce/software/make/build-rules.mk
@@ -3,7 +3,7 @@
 # imported into 'basic.mk' and 'high-level.mk'. They should be activated
 # with Make's 'Call' function.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -207,17 +207,10 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
 	 else confscript="$(strip $(6))"; \
 	 fi; \
 	     \
-	 if   [ -f $(ibdir)/bash ]; then \
-	   if [ -f "$$confscript" ]; then \
-	     sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \
-	         -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \
-	         $$confscript > $$confscript-tmp; \
-	     mv $$confscript-tmp $$confscript; \
-	     chmod +x $$confscript; \
-	   fi; \
+	 $(shsrcdir)/prep-source.sh $(ibdir); \
+	 if [ -f $(ibdir)/bash ]; then \
 	   shellop="SHELL=$(ibdir)/bash"; \
-	 elif [ -f /bin/bash ]; then shellop="SHELL=/bin/bash"; \
-	 else shellop="SHELL=/bin/sh"; \
+	 else shellop="SHELL=$(ibdir)/dash"; \
 	 fi; \
 	     \
 	 if [ x$$gbuild_prefix = x ]; then prefixdir="$(idir)"; \
@@ -255,10 +248,7 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
 # CMake
 # -----
 #
-# According to the link below, in CMake '/bin/sh' is hardcoded, so there is
-# no way to change it unfortunately!
-#
-# https://stackoverflow.com/questions/21167014/how-to-set-shell-variable-in-makefiles-generated-by-cmake
+# Used by packages that are built with CMake.
 cbuild = if [ x$(static_build) = xyes ] && [ $(2)x = staticx ]; then \
 	   export LDFLAGS="$$LDFLAGS -static"; \
 	   opts="-DBUILD_SHARED_LIBS=OFF"; \
@@ -268,13 +258,18 @@ cbuild = if [ x$(static_build) = xyes ] && [ $(2)x = staticx ]; then \
 	 utarball=$(tdir)/$$tarball; \
 	 $(call uncompress); \
 	 cd $(1); \
-	 rm -rf project-build; \
-	 mkdir project-build; \
-	 cd project-build; \
+	 $(shsrcdir)/prep-source.sh $(ibdir); \
+	 if [ -f $(ibdir)/bash ]; then \
+	   shellop="SHELL=$(ibdir)/bash"; \
+	 else shellop="SHELL=$(ibdir)/dash"; \
+	 fi; \
+	 rm -rf maneage-build; \
+	 mkdir maneage-build; \
+	 cd maneage-build; \
 	 cmake .. -DCMAKE_LIBRARY_PATH=$(ildir) \
 	          -DCMAKE_INSTALL_PREFIX=$(idir) \
 	          -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON $$opts $(3); \
-	 make; \
-	 make install; \
+	 make $$shellop; \
+	 make $$shellop install; \
 	 cd ../..; \
 	 rm -rf $(1)
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 3f9c40c..928d0a2 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -12,8 +12,8 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # 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
@@ -64,6 +64,12 @@ ipydir   = $(BDIR)/software/installed/version-info/python
 ircrandir    = $(BDIR)/software/installed/version-info/r-cran
 ilibrcrandir = $(BDIR)/software/installed/lib/R/library
 
+# Special files.
+makewshell = $(ibdir)/make-with-shell
+
+
+
+
 
 # Targets to build.
 ifeq ($(strip $(all_highlevel)),1)
@@ -112,11 +118,16 @@ else
 
 endif
 
+# Disable the TeXLive target if `--offline`
+ifneq ($(strip $(offline)),1)
+  target-texlive := $(itidir)/texlive
+endif
+
 # Ultimate Makefile target.
 all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \
      $(foreach p, $(targets-python), $(ipydir)/$(p)) \
      $(foreach p, $(targets-r-cran),  $(ircrandir)/$(p)) \
-     $(itidir)/texlive
+     $(target-texlive)
 
 # Define the shell environment
 # ----------------------------
@@ -232,7 +243,7 @@ $(idircustom):; mkdir $@
 # Afer putting everything together, we use the first server as the
 # reference for all software if their '-url' variable isn't defined (in
 # 'reproduce/software/config/urls.conf').
-downloadwrapper = ./reproduce/analysis/bash/download-multi-try
+downloadwrapper = ./reproduce/analysis/bash/download-multi-try.sh
 maneage_backup_urls := $(shell awk '!/^#/{printf "%s ", $$1}' \
                                reproduce/software/config/servers-backup.conf)
 backupservers_all = $(user_backup_urls) $(maneage_backup_urls)
@@ -339,6 +350,7 @@ $(ibidir)/atlas-$(atlas-version):
 	cd $(ddir)
 	tar -xf $(tdir)/atlas-$(atlas-version).tar.lz
 	cd ATLAS
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	rm -rf build
 	mkdir build
 	cd build
@@ -395,6 +407,7 @@ $(ibidir)/boost-$(boost-version): \
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	./bootstrap.sh --prefix=$(idir) --with-libraries=all \
 	               --with-python=python3
 	echo "using mpi ;" > project-config.jam
@@ -417,9 +430,7 @@ $(ibidir)/cfitsio-$(cfitsio-version):
 	topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball
 	customtar=cfitsio-$(cfitsio-version)-custom.tar.gz
 	cd cfitsio-$(cfitsio-version)
-	sed configure -e's|@rpath|$(ildir)|g' > configure_tmp
-	mv configure_tmp configure
-	chmod +x configure
+	sed -i -e's|@rpath|$(ildir)|g' configure
 	cd ..
 	tar cf $$customtar cfitsio-$(cfitsio-version)
 	cd $$topdir
@@ -427,11 +438,14 @@ $(ibidir)/cfitsio-$(cfitsio-version):
 #	Continue the standard build on the customized tarball. Note that
 #	with the installation of CFITSIO, 'fpack' and 'funpack' are not
 #	installed by default. Because of that, they are added explicity.
+#
+#	Note that older versions of CFITSIO (before 4.4.0) require a
+#	specific 'shared' target for the building of the shared libraries.
 	export gbuild_tar=$(ddir)/$$customtar
 	$(call gbuild, cfitsio-$(cfitsio-version), , \
 	               --enable-sse2 --enable-reentrant \
 	               --with-bzip2=$(idir), , \
-	               make shared fpack funpack)
+	               make fpack funpack)
 	rm $$customtar
 	echo "CFITSIO $(cfitsio-version)" > $@
 
@@ -518,6 +532,12 @@ $(ibidir)/fftw-$(fftw-version):
 	echo "FFTW $(fftw-version) \citep{fftw}" > $@
 
 $(ibidir)/freetype-$(freetype-version): $(ibidir)/libpng-$(libpng-version)
+#	As of version 2.13.2, FreeType doesn't account for the 'SHELL'
+#	environment variable. The issue has been reported to the
+#	developers. But until future versions, the work-around was
+#	discoverd to be setting the 'GNUMAKE' environment variable so it
+#	includes 'SHELL'.
+	export GNUMAKE="$(makewshell)"
 	tarball=freetype-$(freetype-version).tar.lz
 	$(call import-source, $(freetype-url), $(freetype-checksum))
 	$(call gbuild, freetype-$(freetype-version), static)
@@ -578,7 +598,9 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
 	rm -rf $(ddir)/Healpix_$(healpix-version)
 	topdir=$(pwd); cd $(ddir);
 	tar -xf $(tdir)/$$tarball
-	cd Healpix_$(healpix-version)/src/C/autotools/
+	cd Healpix_$(healpix-version)
+	$(shsrcdir)/prep-source.sh $(ibdir)
+	cd src/C/autotools
 	autoreconf --install
 	./configure --prefix=$(idir)
 	make V=1 -j$(numthreads) SHELL=$(ibdir)/bash
@@ -670,6 +692,7 @@ $(ibidir)/libpaper-$(libpaper-version): \
 	tar -xf $(tdir)/$$tarball
 	unpackdir=libpaper-$(libpaper-version)
 	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	autoreconf -fi
 	./configure --prefix=$(idir) --sysconfdir=$(idir)/etc \
 	            --disable-static
@@ -799,6 +822,7 @@ $(ibidir)/openblas-$(openblas-version):
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
 	cd OpenBLAS-$(openblas-version)
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	make -j$(numthreads)
 	make PREFIX=$(idir) install
 	cd ..
@@ -905,8 +929,8 @@ $(ibidir)/libgit2-$(libgit2-version): $(ibidir)/cmake-$(cmake-version)
 	              -DUSE_SSH=OFF -DBUILD_CLAR=OFF \
 	              -DTHREADSAFE=ON -DUSE_ICONV=OFF )
 	if [ x$(on_mac_os) = xyes ]; then
-	  install_name_tool -id $(ildir)/libgit2.1.3.dylib \
-	                        $(ildir)/libgit2.1.3.dylib
+	  install_name_tool -id $(ildir)/libgit2.1.9.dylib \
+	                        $(ildir)/libgit2.1.9.dylib
 	fi
 	echo "Libgit2 $(libgit2-version)" > $@
 
@@ -1007,6 +1031,7 @@ $(ibidir)/astrometrynet-$(astrometrynet-version): \
 	rm -rf astrometry.net-$(astrometrynet-version)
 	tar -xf $(tdir)/$$tarball
 	cd astrometry.net-$(astrometrynet-version)
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	sed -e 's|cat /proc/cpuinfo|echo "Ignoring CPU info"|' \
 	    -e 's|-free|echo "Ignoring RAM info"|' Makefile > Makefile.tmp
 	mv Makefile.tmp Makefile
@@ -1045,6 +1070,7 @@ $(ibidir)/cdsclient-$(cdsclient-version):
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
 	cd cdsclient-$(cdsclient-version)
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	touch *
 	./configure --prefix=$(idir)
 	make
@@ -1061,25 +1087,39 @@ $(ibidir)/cmake-$(cmake-version):
 	tarball=cmake-$(cmake-version).tar.lz
 	$(call import-source, $(cmake-url), $(cmake-checksum))
 
-#	After searching in 'bootstrap', I couldn't find 'LIBS', only
-#	'LDFLAGS'. So the extra libraries are being added to 'LDFLAGS', not
-#	'LIBS'.
-#
 #	On Mac systems, the build complains about 'clang' specific
 #	features, so we can't use our own GCC build here.
 	if [ x$(on_mac_os) = xyes ]; then
 	  export CC=clang
 	  export CXX=clang++
 	fi
+
+#	CMake wants a single executable for 'MAKE', so we can't use 'make
+#	SHELL=$(SHELL) and we have defined this script.
+	export MAKE="$(makewshell)"
+
+#	Go into the unpacked directory and prepare CMake.
 	cd $(ddir)
 	rm -rf cmake-$(cmake-version)
 	tar -xf $(tdir)/$$tarball
 	cd cmake-$(cmake-version)
-	./bootstrap --prefix=$(idir) --system-curl --system-zlib \
-	            --system-bzip2 --system-liblzma --no-qt-gui \
+	$(shsrcdir)/prep-source.sh $(ibdir)
+
+#	Bootstrap, build and install CMake:
+#	- With the '--no-system-libs' option, CMake builds and statically
+#	  links all the libraries it needs. Even though some of those (like
+#	  liblzma, libcurl, zlib or bzip2) are within Maneage, we
+#	  discovered that CMake can get confused and use out-of-Maneage
+#	  libraries (https://savannah.nongnu.org/bugs/?63043).
+	./bootstrap --no-qt-gui \
+	            --prefix=$(idir) \
+	            --no-system-libs \
 	            --parallel=$(numthreads)
-	make -j$(numthreads) LIBS="$$LIBS -lssl -lcrypto -lz" VERBOSE=1
-	make install
+	$(makewshell) VERBOSE=1 LIBS="$$LIBS -lssl -lcrypto -lz" \
+	              -j$(numthreads)
+	$(makewshell) install
+
+#	Clean up.
 	cd ..
 	rm -rf cmake-$(cmake-version)
 	echo "CMake $(cmake-version)" > $@
@@ -1129,11 +1169,14 @@ $(ibidir)/ghostscript-$(ghostscript-version): \
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
 	cd ghostscript-$(ghostscript-version)
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	./configure --prefix=$(idir) \
 	            --disable-cups \
 	            --enable-dynamic \
 	            --disable-compile-inits \
-	            CFLAGS="-DPNG_ARM_NEON_OPT=0"
+		    --disable-hidden-visibility \
+		    CFLAGS="-DPNG_ARM_NEON_OPT=0" \
+		    LDFLAGS=-Wl,--copy-dt-needed-entries
 
 #	Build and install the program and the shared libraries.
 	make    V=1 -j$(numthreads)
@@ -1170,7 +1213,7 @@ $(ibidir)/gnuastro-$(gnuastro-version): \
 	$(call gbuild, gnuastro-$(gnuastro-version), static, , \
 	               -j$(numthreads))
 	cp $(dtexdir)/gnuastro.tex $(ictdir)/
-	echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro,akhlaghi19}" > $@
+	echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
 
 $(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version)
 
@@ -1188,7 +1231,9 @@ $(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version)
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
 	unpackdir=icu-$(icu-version)
-	cd $$unpackdir/icu4c/source
+	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
+	cd icu4c/source
 	./configure --enable-static --prefix=$(idir)
 	make -j$(numthreads) V=1
 	make install
@@ -1255,6 +1300,7 @@ $(ibidir)/imfit-$(imfit-version): \
 	rm -rf $$unpackdir
 	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	sed -i 's|/usr/local|$(idir)|g' SConstruct
 	sed -i 's|/usr/include|$(idir)/include|g' SConstruct
 	sed -i 's|.append(|.insert(0,|g' SConstruct
@@ -1302,6 +1348,7 @@ $(ibidir)/minizip-$(minizip-version): $(ibidir)/automake-$(automake-version)
 	mkdir $$unpackdir
 	tar -xf $(tdir)/$$tarball -C$$unpackdir --strip-components=1
 	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	./configure --prefix=$(idir)
 	make
 	cd contrib/minizip
@@ -1363,6 +1410,7 @@ $(ibidir)/netpbm-$(netpbm-version): \
 	rm -rf $$unpackdir
 	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 
 #	As of NetPBM 10.73.39 and Flex 2.6.4-410-74a89fd (commit 74a89fd in
 #	Flex's Git that is 410 commits after version 2.6.4), there is the
@@ -1482,6 +1530,7 @@ $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version)
 	rm -rf $$unpackdir
 	tar -xf $(tdir)/$$tarball
 	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 
 #	Unfortuantely SCons hard-codes its search PATH in its source (to
 #	use POSIX operating system defaults)! So the only way to modify it
@@ -1613,7 +1662,10 @@ $(ibidir)/swig-$(swig-version):
 # '$(ibdir)'. If any program does need 'util-linux' libraries, they can
 # simply add the proper directories to the environment variables, see
 # 'fontconfig' for example.
-$(ibidir)/util-linux-$(util-linux-version): | $(idircustom)
+$(ibidir)/util-linux-$(util-linux-version): \
+                     $(ibidir)/autoconf-$(autoconf-version) \
+                     $(ibidir)/automake-$(automake-version) \
+                     | $(idircustom)
 
 #	Import the source.
 	tarball=util-linux-$(util-linux-version).tar.lz
@@ -1625,26 +1677,29 @@ $(ibidir)/util-linux-$(util-linux-version): | $(idircustom)
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball
 	cd util-linux-$(util-linux-version)
+	$(shsrcdir)/prep-source.sh $(ibdir)
 
-#       If a patch exists for the current version, apply it.
+#       If a patch is necessary, 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.
+#	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'.
 	sed -e's|UL_BUILD_INIT(\[mkswap\], \[yes\])|UL_BUILD_INIT(\[mkswap\], \[no\])|' \
 	    -i configure.ac
 
+#	Having updated 'configure.ac', we need to re-generate the
+#	'./configure' script with 'autoreconf' (which is part of Autoconf
+#	and needs Automake; hence why they are dependencies.
+	autoreconf -f
 
 #	Configure Util-linux
 	export CONFIG_SHELL=$(ibdir)/bash
@@ -1652,6 +1707,7 @@ $(ibidir)/util-linux-$(util-linux-version): | $(idircustom)
 	            --disable-dependency-tracking \
 	            --enable-libmount-support-mtab \
 	            --disable-silent-rules \
+	            --disable-liblastlog2 \
 	            --disable-mountpoint \
 	            --disable-libmount \
 	            --disable-unshare \
@@ -1727,6 +1783,7 @@ $(ibidir)/vim-$(vim-version):
 	tar -xf $(tdir)/$$tarball
 	unpackdir=vim-$(vim-version)
 	cd $(ddir)/$$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	./configure --prefix=$(idir) \
 	            --disable-canberra \
 	            --enable-multibyte \
@@ -1795,10 +1852,16 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 	rm -rf install-tl-*
 	tar -xf $(tdir)/install-tl-unx.tar.gz
 	cd install-tl-*
+	$(shsrcdir)/prep-source.sh $(ibdir)
 	sed -e's|@installdir[@]|$(idir)|g' \
 	    "$$topdir"/reproduce/software/config/texlive.conf \
 	    > texlive.conf
 
+#	We do not build TeXLive from source and for its installation it
+#	downloads components from the web internally; and those components
+#	can use '/bin/sh' (which will need '$(sys_library_sh_path)').
+	export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH"
+
 #	TeX Live's installation may fail due to any reason. But TeX Live is
 #	optional (only necessary for building the final PDF). So we don't
 #	want the configure script to fail if it can't run.  Possible error
@@ -1867,13 +1930,16 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 	    tarballurl=$$url/install-tl-unx.tar.gz
 	    touch $(lockdir)/download
 	    downloader="wget --no-use-server-timestamps -O"
-	    if $(downloadwrapper) "$$downloader" $(lockdir)/download \
-	                          $$tarballurl "$(tdir)/install-tl-unx.tar.gz" \
-	                          "$(backupservers)"; then
+	    if $(downloadwrapper) "$$downloader" \
+	                          $(lockdir)/download \
+	                          $$tarballurl \
+	                          "$(tdir)/install-tl-unx.tar.gz" \
+                                 "$(backupservers)"; then
 	      cd $(ddir)
 	      rm -rf install-tl-*
 	      tar -xf $(tdir)/install-tl-unx.tar.gz
 	      cd install-tl-*
+	      $(shsrcdir)/prep-source.sh $(ibdir)
 	      sed -e's|@installdir[@]|$(idir)|g' \
 	          $$topdir/reproduce/software/config/texlive.conf \
 	          > texlive.conf
@@ -1904,10 +1970,19 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 # Live itself (only very basic TeX and LaTeX) and the installation of its
 # necessary packages into two packages.
 #
-# Note that Biber needs to link with libraries like libnsl. However, we
-# don't currently build biber from source. So we can't choose the library
-# version. But we have the source and build instructions for the 'nsl'
-# library. When we later build biber from source, we can easily use them.
+# Note that we do not build the TeXLive executables (like Biber) from
+# source. So in case they need special libraries, we can't choose the
+# library version here (for example see [1] and [2]). In such cases there
+# is no solution but to manually add the location necessary library to
+# LD_LIBRARY_PATH when calling the respective LaTeX command in
+# 'reproduce/analysis/make/paper.mk'. Fortunately as of Biber 2.20, it does
+# not depend on anything except the C library (all dependencies are now
+# statically linked), so problems [1] and [2] will not happen. But this can
+# generally happen for any other tool/OS, so it is important to build
+# TeXLive from source as soon as possible [3].
+#      [1] https://github.com/plk/biber/issues/445
+#      [2] https://savannah.nongnu.org/bugs/index.php?63175
+#      [3] https://savannah.nongnu.org/task/?15267
 $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
                    $(itidir)/texlive-ready-tlmgr
 
@@ -1917,6 +1992,11 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
 	  echo "" > $@
 	else
 
+#	  We do not build TeXLive from source and for its installation it
+#	  downloads components from the web internally; and those
+#	  components can use '/bin/sh' (which needs 'sys_library_sh_path').
+	  export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH"
+
 #	  To update itself, tlmgr needs a backup directory.
 	  backupdir=$(idir)/texlive/backups
 	  mkdir -p $$backupdir
@@ -1940,6 +2020,13 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
 #	  directory so we don't have to modify 'PATH'.
 	  ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/
 
+#	  Correct any reference to '/bin/sh' within the installed LaTeX
+#	  files (this is because we do no yet install LaTeX from source):
+	  cdir=$$(pwd)
+	  cd $(idir)/texlive
+	  $(shsrcdir)/prep-source.sh $(ibdir)
+	  cd $$cdir
+
 #	  Get all the necessary versions.
 	  texlive=$$(pdflatex --version \
 	                      | awk 'NR==1' \
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 936fab1..43e2e77 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -12,8 +12,8 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -93,13 +93,48 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
 	  export CC=clang
 	  export CXX=clang++
 	fi
-	$(call gbuild, python-$(python-version),, \
-	       --without-ensurepip \
-	       --with-system-ffi \
-	       --enable-shared, -j$(numthreads))
+
+#	Unpack the tarball (see below for the necessary modification).
+	cd $(ddir)
+	unpackdir=python-$(python-version)
+	tar -xf $(tdir)/$$unpackdir.tar.lz
+	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
+
+#	Python's 'setup.py' uses 'os.system' to run shell scripts. On the
+#	other hand 'os.system' only runs '/bin/sh' (which has its own
+#	libraries to link to and those are blocked at this level). So we
+#	need to add an extra line on top of the 'os.system' funciton and
+#	put '/usr/lib' in 'LD_LIBRARY_PATH' within Python's environment for
+#	system calls (with 'os.putenv'). As of Python 3.13.2 the tarball no
+#	longer has an 'setup.py'. But when it did, the change below was
+#	necessary.
+	if [ -f setup.py ]; then
+	   awk '{if(/os.system\(/) \
+	          { print "    os.putenv(\"LD_LIBRARY_PATH\", \"$$LD_LIBRARY_PATH:$(sys_library_sh_path)\");"; \
+	            print $$0;} \
+	         else print $$0}' \
+	       setup.py > setup-tmp.py
+	   mv setup-tmp.py setup.py
+	fi
+
+#	Do the basic installation and delete the temporary directory.
+	./configure SHELL=$(ibdir)/bash \
+	            --enable-optimizations \
+	            --without-ensurepip \
+	            --prefix="$(idir)" \
+	            --with-system-ffi \
+	            --enable-shared
+	$(makewshell) -j$(numthreads)
+	$(makewshell) install -j$(numthreads)
+	cd ..
+	rm -rf $$unpackdir
+
+#	Set the necessary environment variables and finish the build.
 	ln -sf $(ildir)/python$(python-major-version)  $(ildir)/python
 	ln -sf $(ibdir)/python$(python-major-version)  $(ibdir)/python
-	ln -sf $(iidir)/python$(python-major-version)m $(iidir)/python$(python-major-version)
+	ln -sf $(iidir)/python$(python-major-version)m \
+	       $(iidir)/python$(python-major-version)
 	rm -rf $(ipydir)
 	mkdir $(ipydir)
 	echo "Python $(python-version)" > $@
diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk
index 484fe74..7c86c23 100644
--- a/reproduce/software/make/r-cran.mk
+++ b/reproduce/software/make/r-cran.mk
@@ -12,8 +12,8 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2022-2023 Boud Roukema <boud@cosmo.torun.pl>
-# Copyright (C) 2022-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2022-2025 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2022-2025 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
@@ -204,6 +204,7 @@ $(ibidir)/r-cran-$(r-cran-version): \
 	tar -xf $(tdir)/$$tarball
 	unpackdir=R-$(r-cran-version)
 	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
 
 #	We need to manually remove the lines with '~autodetect~', they
 #	cause the configure script to crash in version 4.0.2. They are used
diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk
index 1cc87a5..864c32a 100644
--- a/reproduce/software/make/xorg.mk
+++ b/reproduce/software/make/xorg.mk
@@ -14,8 +14,8 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2021-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021-2023 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # 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
@@ -79,7 +79,7 @@ $(ibidir)/libxau-$(libxau-version): $(ibidir)/xorgproto-$(xorgproto-version)
 
 # Library implementing the X Display Manager Control Protocol.
 $(ibidir)/libxdmcp-$(libxdmcp-version): $(ibidir)/libxau-$(libxau-version)
-	tarball=libXdmcp-$(libxdmcp-version).tar.bz2
+	tarball=libXdmcp-$(libxdmcp-version).tar.lz
 	$(call import-source, $(libxdmcp-url), $(libxdmcp-checksum))
 	$(call gbuild, libXdmcp-$(libxdmcp-version),,$(XORG_CONFIG), V=1)
 	echo "libXdmcp (Xorg) $(libxdmcp-version)" > $@