IMPORTANT: version updates and improved portability

Summary: this commit involves a major version update of many basic software
and Gnuastro's major dependencies. So it may affect your configuration and
analysis.

Until now, the most recent software updates weren't properly tested on
MacOS, causing the software configuration step to fail. In particular, the
'prep-source.sh' (that corrects any hard-coded '/bin/sh' within the
unpacked tarballs of all software) as well as some issues in the 'tar',
'util-linux' and 'ghostscript' programs. These portability issues were
found and fixed by Raul Infante-Sainz and Giacomo Lorenzetti.

With this commit, those portability issues have been addressed while
updating the following software. Also see notes below the list.

   High-level software:
     CFITSIO             4.5.0       -->     4.6.3
     Ghostscript         10.04.0     -->     10.06.0
     Gnuastro            0.23        -->     0.24
     Util-linux          2.40.4      -->     2.41.3
     WCSLIB              8.4         -->     8.5

   Basic software:
     cURL                8.11.1      -->     8.17.0
     GNU Bash            5.2.37      -->     5.3.9
     GNU Binutils        2.43.1      -->     2.45.1
     GNU Coreutils       9.6         -->     9.9
     GNU Diffutils       3.10        -->     3.12
     GNU AWK             5.3.1       -->     5.3.2
     GNU GCC             14.2.0      -->     15.2.0
     GNU Gettext         0.23.1      -->     0.26
     GNU Grep            3.11        -->     3.12
     GNU Gzip            1.13        -->     1.14
     GNU Libunistring    1.3         -->     1.4.1
     GNU M4              1.4.19      -->     1.4.20
     GNU MPFR            4.2.1       -->     4.2.2
     GNU Nano            8.3         -->     8.7
     GNU Readline        8.2.13      -->     8.3.3
     Git                 2.48.1      -->     2.52.0
     Less                668         -->     685
     Libxml2             2.13.1      -->     2.15.1
     OpenSSL             3.4.0       -->     3.6.0
     Perl                5.40.1      -->     5.42.0

The latest versions of Bash and M4 were prepared for the new default C
standard of GCC 15.*, so the '-std=gnu17' was removed for them. Also, while
a new version of Dash was available, it would cause an issue when building
in Apptainer, so it has been described in 'versions.conf' to be aware in
the future updates.

Libgit2 has been removed as a dependency of Gnuastro. The reason is fully
described in the comment on top of Gnuastro's build rule in
'high-level.mk'.

5 files changed, 31 insertions, 10 deletions

diff --git a/reproduce/software/shell/apptainer-README.md b/reproduce/software/shell/apptainer-README.md
index a7826ec..49ce82f 100644
--- a/reproduce/software/shell/apptainer-README.md
+++ b/reproduce/software/shell/apptainer-README.md
@@ -47,7 +47,7 @@ software environment) to easily move it from one computer to another.
       project. This file is necessary for future runs of your project
       within the container.
 
- 3. To execute your project remote the `--build-only` and use `./run.sh` to
+ 3. To execute your project remove the `--build-only` and use `./run.sh` to
     execute it. If you want to enter your Maneage'd project shell, add the
     `--project-shell` option to the call inside `./run.sh`.
 
diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh
index c581ade..51b36db 100755
--- a/reproduce/software/shell/apptainer.sh
+++ b/reproduce/software/shell/apptainer.sh
@@ -291,10 +291,11 @@ else
     # necessary tools.
     if [ -f $base_name ]; then
         if [ $quiet = 0 ]; then
-            printf "$scriptname: info: base OS docker image ('$base_name') "
-            printf "already exists and will be used. If you want to build a "
-            printf "new base OS image, give a new name to '--base-name'. "
-            printf "To remove this message run with '--quiet'\n"
+            printf "$scriptname: info: base OS apptainer image "
+            printf "('$base_name') already exists and will be used. "
+            printf "If you want to build a new base OS image, give "
+            printf "a new name to '--base-name'. To remove this "
+            printf "message run with '--quiet'\n"
         fi
     else
 
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index a409920..29b0ea6 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -1891,9 +1891,10 @@ ______________________________________________________
 !!!!!!!!!!!!!!!        Warning        !!!!!!!!!!!!!!!!
 
 TeX Live couldn't be installed during the configuration (probably because
-there were downloading problems). TeX Live is only necessary in making the
-final PDF (which is only done after all the analysis has been complete). It
-is not used at all during the analysis.
+there were downloading problems, or you used the '--offline' option). TeX
+Live is only necessary in making the final PDF (which is only done after
+all the analysis has been complete). It is not used at all during the
+analysis.
 
 Therefore, if you don't need the final PDF, and just want to do the
 analysis, you can safely ignore this warning and continue.
diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh
index dcdc472..2545460 100755
--- a/reproduce/software/shell/prep-source.sh
+++ b/reproduce/software/shell/prep-source.sh
@@ -77,6 +77,20 @@ fi
 if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash
 else                           shpath="$bindir"/dash
 fi
+
+# On MacOS the syntax for 'stat' is a bit different, so if we are using the
+# system one on mac we need a specific syntax. The one installed by maneage
+# instead uses the ordinary Linux syntax.
+if [ -f "$bindir/stat" ] || [ x"$on_mac_os" = xno ]; then
+  format="--format %a"
+else
+  format="-f %OLp"
+fi
+
+# On MacOS 'touch' wants the time expressed according to ISO8601 with a
+# precision up to the seconds. We then use 'sed' to remove the information
+# regarding the timezone, as the format is not accepted by 'touch'.
+# LCTYPE and LANG are also required on macos systems by sed.
 grep -I -r -e'/bin/sh' $(pwd)/* \
     | sed -e's|:|\t|' \
     | awk 'BEGIN{FS="\t"}{print $1}' \
@@ -84,8 +98,10 @@ grep -I -r -e'/bin/sh' $(pwd)/* \
     | uniq \
     | while read filename; do \
          tmp="$filename".tmp; \
-         origtime="$(date -R -r "$filename")"; \
-         origperm=$(stat -c '%a' "$filename"); \
+         origtimex="$(date -Iseconds -r "$filename")"; \
+         origtime=$(echo $origtimex | sed 's/.\{6\}$//'); \
+         origperm=$(stat $format "$filename"); \
+         LC_CTYPE=C; LANG=C; \
          sed -e's|/bin/sh|'"$shpath"'|g' "$filename" > "$tmp"; \
          mv "$tmp" "$filename"; \
          chmod $origperm "$filename"; \
diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh
index 8e30931..4d6d1e2 100755
--- a/reproduce/software/shell/tarball-prepare.sh
+++ b/reproduce/software/shell/tarball-prepare.sh
@@ -51,6 +51,9 @@ basedir=$PWD
 scriptname=$0
 
 
+
+
+
 # The --help output
 print_help() {
     cat <<EOF