Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).

1 files changed, 153 insertions, 65 deletions

diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index e15a8e9..07381e6 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -2,8 +2,9 @@
 #
 # Necessary preparations/configurations for the reproducible project.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021      Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022      Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # This script is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -112,7 +113,7 @@ absolute_dir ()
 # Check file permission handling (POSIX-compatibility)
 # ----------------------------------------------------
 #
-# Check if a `given' directory handles permissions as expected.
+# Check if a 'given' directory handles permissions as expected.
 #
 # This is to prevent a known bug in the NTFS filesystem that prevents
 # proper installation of Perl, and probably some other packages. This
@@ -120,15 +121,15 @@ absolute_dir ()
 # file, and examines whether the given directory handles the file
 # permissions as expected.
 #
-# Returns `0' if everything is fine, and `255' otherwise. Choosing `0' is
-# to mimic the `$ echo $?' behavior, while choosing `255' is to prevent
+# Returns '0' if everything is fine, and '255' otherwise. Choosing '0' is
+# to mimic the '$ echo $?' behavior, while choosing '255' is to prevent
 # misunderstanding 0 and 1 as true and false.
 #
 # ===== CAUTION! ===== #
 #
-# Since there is a `set -e' before running this function, the whole script
-# stops and exits IF the `check_permission' (or any other function) returns
-# anything OTHER than `0'! So, only use this function as a test. Here's a
+# Since there is a 'set -e' before running this function, the whole script
+# stops and exits IF the 'check_permission' (or any other function) returns
+# anything OTHER than '0'! So, only use this function as a test. Here's a
 # minimal example:
 #
 #     if $(check_permission $some_directory) ; then
@@ -136,7 +137,7 @@ absolute_dir ()
 #     fi ;
 check_permission ()
 {
-    # Make a `junk' file, activate its executable flag and record its
+    # Make a 'junk' file, activate its executable flag and record its
     # permissions generally.
     local junkfile="$1"/check_permission_tmp_file
     rm -f "$junkfile"
@@ -158,7 +159,7 @@ check_permission ()
         return 1
     else
         # Setting permission SUCCESSFUL
-	return 0
+        return 0
     fi
 }
 
@@ -309,7 +310,9 @@ fi
 # system.  Here, it is checked that this is the case, and if not, warn the user
 # about not having Xcode already installed.
 if [ x$on_mac_os = xyes ]; then
-  xcode=$(which xcodebuild)
+
+  # 'which' isn't in POSIX, so we are using 'command -v' instead.
+  xcode=$(command -v xcodebuild)
   if [ x$xcode != x ]; then
     xcode_version=$(xcodebuild -version | grep Xcode)
     echo "                                              "
@@ -475,8 +478,8 @@ fi
 # See if we need the dynamic-linker (-ldl)
 # ----------------------------------------
 #
-# Some programs (like Wget) need dynamic loading (using `libdl'). On
-# GNU/Linux systems, we'll need the `-ldl' flag to link such programs.  But
+# Some programs (like Wget) need dynamic loading (using 'libdl'). On
+# GNU/Linux systems, we'll need the '-ldl' flag to link such programs.  But
 # Mac OS doesn't need any explicit linking. So we'll check here to see if
 # it is present (thus necessary) or not.
 cat > $testsource <<EOF
@@ -508,7 +511,7 @@ fi
 # programs will go and find their necessary libraries on the host system.
 #
 # Another good advantage of shared libraries is that we can actually use
-# the shared library tool of the system (`ldd' with GNU C Library) and see
+# the shared library tool of the system ('ldd' with GNU C Library) and see
 # exactly where each linked library comes from. But in static building,
 # unless you follow the build closely, its not easy to see if the source of
 # the library came from the system or our build.
@@ -545,7 +548,7 @@ fi
 #
 # On some systems (in particular Debian-based OSs), the static C library
 # and necessary headers in a non-standard place, and we can't build GCC. So
-# we need to find them first. The `sys/cdefs.h' header is also in a
+# we need to find them first. The 'sys/cdefs.h' header is also in a
 # similarly different location.
 sys_cpath=""
 sys_library_path=""
@@ -576,7 +579,7 @@ fi
 # See if a link-able static C library exists
 # ------------------------------------------
 #
-# A static C library and the `sys/cdefs.h' header are necessary for
+# A static C library and the 'sys/cdefs.h' header are necessary for
 # building GCC.
 if [ x"$host_cc" = x0 ]; then
     echo; echo; echo "Checking if static C library is available...";
@@ -752,9 +755,9 @@ EOF
 # What to do with possibly existing configuration file
 # ----------------------------------------------------
 #
-# `LOCAL.conf' is the top-most local configuration for the project. If it
+# 'LOCAL.conf' is the top-most local configuration for the project. If it
 # already exists when this script is run, we'll make a copy of it as backup
-# (for example the user might have ran `./project configure' by mistake).
+# (for example the user might have ran './project configure' by mistake).
 printnotice=yes
 rewritepconfig=yes
 if [ -f $pconf ]; then
@@ -807,16 +810,18 @@ fi
 # need to check the host's available tool for downloading at this step.
 if [ $rewritepconfig = yes ]; then
     if type wget > /dev/null 2>/dev/null; then
-        name=$(which wget)
+
+        # 'which' isn't in POSIX, so we are using 'command -v' instead.
+        name=$(command -v wget)
 
         # By default Wget keeps the remote file's timestamp, so we'll have
         # to disable it manually.
         downloader="$name --no-use-server-timestamps -O";
     elif type curl > /dev/null 2>/dev/null; then
-        name=$(which curl)
+        name=$(command -v curl)
 
         # - cURL doesn't keep the remote file's timestamp by default.
-        # - With the `-L' option, we tell cURL to follow redirects.
+        # - With the '-L' option, we tell cURL to follow redirects.
         downloader="$name -L -o"
     else
         cat <<EOF
@@ -913,7 +918,7 @@ EOF
                 # If it was newly created, it will be empty, so delete it.
                 if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi
 
-                # Inform the user that this is not acceptable and reset `bdir'.
+                # Inform the user that this is not acceptable and reset 'bdir'.
                 bdir=
                 echo " ** The build-directory cannot be under the source-directory."
             fi
@@ -938,10 +943,10 @@ EOF
             fi
         fi
 
-	# If everything is still fine so far, see if we're able to
-	# manipulate file permissions in the directory's filesystem and if
-	# so, see if there is atleast 5GB free space.
-	if ! [ x"$bdir" = x ]; then
+        # If everything is still fine so far, see if we're able to
+        # manipulate file permissions in the directory's filesystem and if
+        # so, see if there is atleast 5GB free space.
+        if ! [ x"$bdir" = x ]; then
             if ! $(check_permission "$bdir"); then
                 # Unable to handle permissions well
                 bdir=
@@ -960,7 +965,7 @@ EOF
         fi
 
         # If the build directory was good, the loop will stop, if not,
-        # reset `build_dir' to blank, so it continues asking for another
+        # reset 'build_dir' to blank, so it continues asking for another
         # directory and let the user know that they must select a new
         # directory.
         if [ x"$bdir" = x ]; then
@@ -1118,7 +1123,7 @@ else
     if [ x"$downloader" = x ]; then novalue="$novalue"DOWNLOADER;  fi
     if [ x"$novalue"   != x ]; then verr=1; err=1;                 fi
 
-    # Make sure `bdir' is an absolute path and it exists.
+    # Make sure 'bdir' is an absolute path and it exists.
     berr=0
     ierr=0
     bdir="$(absolute_dir "$inbdir")"
@@ -1202,6 +1207,10 @@ if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi
 ipydir="$verdir"/python
 if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi
 
+# R module versions and citation.
+ircrandir="$verdir"/r-cran
+if ! [ -d "$ircrandir" ]; then mkdir "$ircrandir"; fi
+
 # Used software BibTeX entries.
 ictdir="$verdir"/cite
 if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
@@ -1210,21 +1219,14 @@ if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
 itidir="$verdir"/tex
 if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi
 
-# Temporary software un-packing/build directory: if the host has the
-# standard `/dev/shm' mounting-point, we'll do it in shared memory (on the
-# RAM), to avoid harming/over-using the HDDs/SSDs. The RAM of most systems
-# today (>8GB) is large enough for the parallel building of the software.
-#
-# For the name of the directory under `/dev/shm' (for this project), we'll
-# use the names of the two parent directories to the current/running
-# directory, separated by a `-' instead of `/'. We'll then appended that
-# with the user's name (in case multiple users may be working on similar
-# project names). Maybe later, we can use something like `mktemp' to add
-# random characters to this name and make it unique to every run (even for
-# a single user).
-tmpblddir="$sdir"/build-tmp
-rm -rf "$tmpblddir"/* "$tmpblddir"  # If its a link, we need to empty its
-                                    # contents first, then itself.
+# Some software install their libraries in '$(idir)/lib64'. But all other
+# libraries are in '$(idir)/lib'. Since Maneage's build is only for a
+# single architecture, we can set the '$(idir)/lib64' as a symbolic link to
+# '$(idir)/lib' so all the libraries are always available in the same
+# place.
+instlibdir="$instdir"/lib
+if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi
+ln -fs "$instlibdir" "$instdir"/lib64
 
 
 
@@ -1297,29 +1299,106 @@ rm -f .gnuastro
 
 
 
-# Set the top-level shared memory location.
+
+
+# Software building directory (possibly in RAM)
+# ---------------------------------------------
+#
+# Building the software for the project will need the creation of many
+# small temporary files that will ultimately be deleted. To avoid harming
+# HDDs/SSDs and improve speed, it is therefore better to build them in the
+# RAM when possible. The RAM of most systems today (>8GB) is large enough
+# for the parallel building of the software.
+
+# Set the top-level shared memory location. Currently there is only one
+# standard location (for GNU/Linux OSs), so doing this check here and the
+# main job below may seem redundant. However, it is written separately from
+# the main code below because later, we expect to add more possible
+# mounting locations (for other OSs).
 if [ -d /dev/shm ]; then     shmdir=/dev/shm
 else                         shmdir=""
 fi
 
-# If a shared memory mounted directory exists and there is enough space
-# there (in RAM), build a temporary directory for this project.
-needed_space=2000000
+# If a shared memory mounted directory exists and has the necessary
+# conditions, set that directory to build software.
 if [ x"$shmdir" != x ]; then
+
+    # Make sure it has enough space.
+    needed_space=2000000
     available_space=$(df "$shmdir" | awk 'NR==2{print $4}')
     if [ $available_space -gt $needed_space ]; then
+
+        # Set the Maneage-specific directory within the shared
+        # memory. We'll use the names of the two parent directories to the
+        # current/running directory, separated by a '-' instead of
+        # '/'. We'll then appended that with the user's name (in case
+        # multiple users may be working on similar project names).
+        #
+        # Maybe later, we can use something like 'mktemp' to add random
+        # characters to this name and make it unique to every run (even for
+        # a single user).
         dirname=$(pwd | sed -e's/\// /g' \
-                      | awk '{l=NF-1; printf("%s-%s",$l, $NF)}')
+                      | awk '{l=NF-1; printf("%s-%s", $l, $NF)}')
         tbshmdir="$shmdir"/"$dirname"-$(whoami)
-        if ! [ -d "$tbshmdir" ]; then mkdir "$tbshmdir"; fi
+
+        # Try to make the directory if it does not yet exist. A failed
+        # directory creation will be tested for a few lines later, when
+        # testing for the existence and executability of a test file.
+        if ! [ -d "$tbshmdir" ]; then (mkdir "$tbshmdir" || true); fi
+
+        # Some systems may protect '/dev/shm' against the right to execute
+        # programs by ordinary users. We thus need to check that the device
+        # allows execution within this directory by this user.
+        shmexecfile="$tbshmdir"/shm-execution-check.sh
+        rm -f $shmexecfile      # We also don't want any existing flags.
+
+        # Create the file to be executed, but do not fail fatally if it
+        # cannot be created. We will check a few lines later if the file
+        # really exists.
+        (cat > "$shmexecfile" <<EOF || true)
+#!/bin/sh
+echo "This file successfully executed."
+EOF
+
+        # If the file was successfully created, then make the file
+        # executable and see if it runs. If not, set 'tbshmdir' to an empty
+        # string so it is not used in later steps.  In any case, delete the
+        # temporary file afterwards.
+        #
+        # We aren't adding '&> /dev/null' after the execution command
+        # because it can produce false failures randomly on some systems.
+        if [ -e "$shmexecfile" ]; then
+
+            # Add the executable flag.
+            chmod +x "$shmexecfile"
+
+            # The following line tries to execute the file.
+            if "$shmexecfile"; then
+                # Successful execution. The colon is a "no-op" (no
+                # operation) shell command.
+                :
+            else
+                tbshmdir=""
+            fi
+            rm "$shmexecfile"
+        else
+            tbshmdir=""
+        fi
     fi
 else
     tbshmdir=""
 fi
 
-# If a shared memory directory was created set `build-tmp' to be a
-# symbolic link to it. Otherwise, just build the temporary build
-# directory under the project build directory.
+
+
+
+
+# If a shared memory directory was created, set the software building
+# directory to be a symbolic link to it. Otherwise, just build the
+# temporary build directory under the project's build directory.
+tmpblddir="$sdir"/build-tmp
+rm -rf "$tmpblddir"/* "$tmpblddir"  # If it is a link, we need to empty
+                                    # its contents first, then itself.
 if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir";
 else                          ln -s "$tbshmdir" "$tmpblddir";
 fi
@@ -1330,6 +1409,9 @@ fi
 
 # Inform the user that the build process is starting
 # -------------------------------------------------
+#
+# Everything is ready, let the user know that the building is going to
+# start.
 if [ $printnotice = yes ]; then
     tsec=10
     cat <<EOF
@@ -1338,12 +1420,13 @@ if [ $printnotice = yes ]; then
 Building dependencies ...
 -------------------------
 
-Necessary dependency programs and libraries will be built in
+Necessary dependency programs and libraries will be installed in
 
   $sdir/installed
 
-NOTE: the built software will NOT BE INSTALLED on your system (no root
-access is required). They are only for local usage by this project.
+NOTE: the built software will NOT BE INSTALLED in standard places of your
+OS (so no root access is required). They are only for local usage by this
+project.
 
 **TIP**: you can see which software are being installed at every moment
 with the following command. See "Inspecting status" section of
@@ -1392,7 +1475,7 @@ fi
 # See if the linker accepts -Wl,-rpath-link
 # -----------------------------------------
 #
-# `-rpath-link' is used to write the information of the linked shared
+# '-rpath-link' is used to write the information of the linked shared
 # library into the shared object (library or program). But some versions of
 # LLVM's linker don't accept it an can cause problems.
 #
@@ -1425,13 +1508,13 @@ rm -rf $compilertestdir
 
 
 
-# Paths needed by the host compiler (only for `basic.mk')
+# Paths needed by the host compiler (only for 'basic.mk')
 # -------------------------------------------------------
 #
 # At the end of the basic build, we need to build GCC. But GCC will build
 # in multiple phases, making its own simple compiler in order to build
 # itself completely. The intermediate/simple compiler doesn't recognize
-# some system specific locations like `/usr/lib/ARCHITECTURE' that some
+# some system specific locations like '/usr/lib/ARCHITECTURE' that some
 # operating systems use. We thus need to tell the intermediate compiler
 # where its necessary libraries and headers are.
 if [ x"$sys_library_path" != x ]; then
@@ -1468,7 +1551,7 @@ fi
 # which will download the DOI-resolved webpage, and extract the Zenodo-URL
 # of the most recent version from there (using the 'coreutils' tarball as
 # an example, the directory part of the URL for all the other software are
-# the same). This is not done if the option `--debug' is used.
+# the same). This is not done if the option '--debug' is used.
 zenodourl=""
 user_backup_urls=""
 zenodocheck=.build/software/zenodo-check.html
@@ -1501,6 +1584,7 @@ user_backup_urls="$user_backup_urls $zenodourl"
 # (compression program), GNU Make (that 'basic.mk' is written in), Dash
 # (minimal Bash-like shell) and Flock (to lock files and enable serial
 # download).
+export on_mac_os
 ./reproduce/software/shell/pre-make-build.sh \
     "$bdir" "$ddir" "$downloader" "$user_backup_urls"
 
@@ -1610,17 +1694,21 @@ 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.
 
-If you later have internet access and would like to add TeX live to your
-project, please delete the respective files, then re-run configure as shown
-below.
+If you later have internet access and would like to add TeX Live to your
+project, then please delete the following two files:
 
     rm .local/version-info/tex/texlive-ready-tlmgr
+    rm .build/software/tarballs/install-tl-unx.tar.gz
+
+and re-run configure:
+
     ./project configure -e
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 EOF
+  sleep 10 # increase the chance that an interactive user reads this message
 fi
 
 
@@ -1634,7 +1722,7 @@ fi
 # software.
 prepare_name_version ()
 {
-    # First see if the (possible) `*' in the input arguments corresponds to
+    # First see if the (possible) '*' in the input arguments corresponds to
     # anything. Note that some of the given directories may be empty (no
     # software installed).
     hasfiles=0
@@ -1735,9 +1823,9 @@ hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')"
 # ---------------------------------
 #
 # By the time the script reaches here the temporary software build
-# directory should be empty, so just delete it. Note `tmpblddir' may be a
+# directory should be empty, so just delete it. Note 'tmpblddir' may be a
 # symbolic link to shared memory. So, to work in any scenario, first delete
-# the contents of the directory (if it has any), then delete `tmpblddir'.
+# the contents of the directory (if it has any), then delete 'tmpblddir'.
 .local/bin/rm -rf $tmpblddir/* $tmpblddir