Configuration: new server for tarballs and portability fixed

SUMMARY: no change is necessary for your pipeline after upgrading to this
commit.

Until this commit, the following noteworthy portability problems existed
that have been fixed as described in each item.

  - In commit 8908587 (titled "IMPORTANT: 73 software upgrades and added
    offline mode"; committed on 2025-02-11); the versions of all (except
    those that were not updated upstream) basic software as well as the
    high-level software necessary for Gnuastro were updated. This included
    Python. However, the update of Python could cause crashes in the
    Python-related software that are also in Maneage but not tested for
    that commit.
    -- With this commit, Python has been revered back to 3.10.6 (from
       3.13.2) and it has been taken to a dedicated part of 'versions.conf'
       (reminding the reader that the version of Python should only be
       updated by the Python maintainer: to ensure it doesn't conflict with
       Python-based builds).

  - Following the update of XZ Utils in 8908587, the custom build recipe
    that was necessary is no longer necessary. This was reported by Boud
    Roukema (see https://savannah.nongnu.org/bugs/index.php?62700).
    -- With this commit, XZ Utils uses our basic high-level build scripts.

  - CMake could use out-of-Maneage libraries for those that we already had
    in Maneage on some systems. This was reported by Boud Roukema (see
    https://savannah.nongnu.org/bugs/?63043)
    -- With this commit, CMake is built with '--no-system-libs'; so it
       builds and statically links to all its necessary libraries
       internally (not confusing between Maneage and the host).

  - Building Binutils 2.39 was likely to fail on older GCC versions due to
    special features (such as the 'gprofng' feature when building with GCC
    6.2.0). This was reported by Boud Roukema in
    https://savannah.nongnu.org/bugs/index.php?63242.
    -- With this commit, the 'gprofng' feature of Binutils has been
       disabled by default to allow reproducibility on older systems. If
       you need it, remove the '--enable-gprofng=no' option in the build
       recipe of Binutils.

  - The Maneage tarball repository is now also kept in 'gitlab.cefca.es'.
    -- With this commit, a new server URL has been added for this.

  - The list of TeXLive packages included some packages that get installed
    in the basic scheme that we do for the initial setup of TeXLive.
    -- With this commit, the extra packages have been removed.

7 files changed, 78 insertions, 70 deletions

diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index 01ef8c8..130c116 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -128,7 +128,7 @@ patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187d
 pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb
 pixman-checksum = 333732b99994f7ea636d647e0b6123075351b27601b5b6370c9bc821a1ab3921386ddb92b51e015f3fc35104ba09be1e0d7bef47f0b4f73036b01d1d70396dd9
 plplot-checksum = 2c5a36d84ebd948402c924d304427b5702bc75bdd22753c9b3b910b382dfdcc26910382aae452f02d86b25c1c813bbe1f40c9305de1d2809d575975f610fdf10
-python-checksum = de940d7eceee69b8a04f12c613753f61db53ddac1c5cde5388dd342e88a09bae8da1f56b71b96f20997f6203d169e92e9e2558c43b38dbc323221d7bb362abfc
+python-checksum = b3d6b4187b31167b382e195037d7ca01d5e9c112fceb0f12a30c101dbcc91079601c01aa449f9d33d2fc53c795c33305e80c891e986a0e24cbecc14beaf90199
 r-cran-checksum = 54cc07956a70c09b5a533188eb063d2a9dc67a8aa5648ec7f9c107f626220c9f6e17ab7175e65dd54a8d608a1ca4106c8ad2856709eb995ab66439b5f033e725
 rpcsvc-proto-checksum = c3011d7d7ef97a4a751f6921df1a23e1dd8ac50fb0690c759d37010ed7be27968a2130e3b8872cb48d5914216f9d539096a424f1ec38a75f7ed899748151c6f4
 scamp-checksum = c7a192f357c6808acd16d1c5d2657c5c8c2f61e4fecb8a4b18d39b07f4c444f85d5029c21571d41ec3ba9c8d075de8bd660b0e029bf5dd63e3819e963430a938
diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf
index d4aa25e..f0e040e 100644
--- a/reproduce/software/config/servers-backup.conf
+++ b/reproduce/software/config/servers-backup.conf
@@ -9,6 +9,6 @@
 # permitted in any medium without royalty provided the copyright notice and
 # this notice are preserved.  This file is offered as-is, without any
 # warranty.
+http://gitlab.cefca.es/maneage/tarballs-software/-/raw/master/
 http://gitlab.com/maneage/tarballs-software/-/raw/master
 http://git.maneage.org/tarballs-software.git/plain
-http://akhlaghi.org/maneage-software
diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf
index bb38d5a..e68a771 100644
--- a/reproduce/software/config/texlive-packages.conf
+++ b/reproduce/software/config/texlive-packages.conf
@@ -5,14 +5,20 @@
 # name).
 #
 # Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2022-2025 Boud Roukema <boud@astro.uni.torun.pl>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
 # this notice are preserved.  This file is offered as-is, without any
 # warranty.
 
-# Notes
-# -----
+# Hints:
+#
+# - For debugging: after a partial or successful build, look through
+#   '.build/software/installed/texlive/maneage/tlpkg/texlive.tlpdb.main.*'
+#   to see what packages and files were looked at during the install.
+
+# Notes:
 #
 # - tex and fancyhdr: These two packages are installed along with the basic
 #   installation scheme that we used to install tlmgr, they will be ignored
@@ -22,31 +28,23 @@
 # - fancyvrb: needed by R.
 texlive-packages = biber \
                    biblatex \
-                   bitset \
                    caption \
                    courier \
                    csquotes \
                    datetime \
-                   ec \
-                   etoolbox \
-                   fancyhdr \
                    fancyvrb \
                    fmtcount \
                    fontaxes \
                    footmisc \
                    fp \
                    kastrup \
-                   letltxmacro \
                    logreq \
                    mweights \
                    newtx \
-                   pdfescape \
-                   pdftexcmds \
                    pgf \
                    pgfplots \
                    preprint \
                    setspace \
-                   tex \
                    tex-gyre \
                    times \
                    titlesec \
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 07bdb9e..861b5c5 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -149,7 +149,6 @@ patch-version = 2.7.6
 pcre-version = 8.44
 pixman-version = 0.40.0
 plplot-version = 5.15.0
-python-version = 3.13.2
 r-cran-version = 4.1.2
 rpcsvc-proto-version = 1.4
 scamp-version = 2.10.0
@@ -186,6 +185,10 @@ xtrans-version = 1.5.2
 lapack-version = 3.8.0
 libgit2-version = 1.9.0
 
+# Python should only be updated by the maintainer for Python packages; see
+# https://savannah.nongnu.org/task/?16622.
+python-version = 3.10.6
+
 # Netpbm's questions in the configure steps maybe change with different or
 # new versions.
 netpbm-version = 10.73.39
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 628a0e2..cf155f0 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -273,46 +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)
@@ -1247,7 +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
@@ -1375,21 +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
@@ -1399,7 +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
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index fdab193..928d0a2 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -1098,18 +1098,28 @@ $(ibidir)/cmake-$(cmake-version):
 #	SHELL=$(SHELL) and we have defined this script.
 	export MAKE="$(makewshell)"
 
-#	Go into the unpacked directory and build CMake.
+#	Go into the unpacked directory and prepare CMake.
 	cd $(ddir)
 	rm -rf cmake-$(cmake-version)
 	tar -xf $(tdir)/$$tarball
 	cd cmake-$(cmake-version)
 	$(shsrcdir)/prep-source.sh $(ibdir)
-	./bootstrap --prefix=$(idir) --system-curl --system-zlib \
-	            --system-bzip2 --system-liblzma --no-qt-gui \
+
+#	Bootstrap, build and install CMake:
+#	- With the '--no-system-libs' option, CMake builds and statically
+#	  links all the libraries it needs. Even though some of those (like
+#	  liblzma, libcurl, zlib or bzip2) are within Maneage, we
+#	  discovered that CMake can get confused and use out-of-Maneage
+#	  libraries (https://savannah.nongnu.org/bugs/?63043).
+	./bootstrap --no-qt-gui \
+	            --prefix=$(idir) \
+	            --no-system-libs \
 	            --parallel=$(numthreads)
 	$(makewshell) VERBOSE=1 LIBS="$$LIBS -lssl -lcrypto -lz" \
 	              -j$(numthreads)
 	$(makewshell) install
+
+#	Clean up.
 	cd ..
 	rm -rf cmake-$(cmake-version)
 	echo "CMake $(cmake-version)" > $@
@@ -1960,10 +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
 
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index f226ced..d58a829 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -1439,6 +1439,15 @@ fi
 
 
 
+# Make sure the temporary build directory is empty (un-finished
+# source/build files from previous builds can remain there during debugging
+# or software updates).
+rm -rf $tmpblddir/*
+
+
+
+
+
 # Inform the user that the build process is starting
 # -------------------------------------------------
 #
@@ -1575,7 +1584,7 @@ fi
 # cause a crash! To avoid such cases, we need to find the locations of the
 # libraries that the shell needs and temporarily add them to the library
 # search path.
-if [ x"$$on_mac_os" != xyes ]; then
+if [ x"$on_mac_os" != xyes ]; then
     sys_library_sh_path=$(otool -L /bin/sh \
                               | awk '/\/lib/{print $1}' \
                               | sed 's#/[^/]*$##' \