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, 65 insertions, 8 deletions

diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
index 66c77bc..c25dfb1 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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
@@ -29,8 +29,13 @@
 # its checksum and if it is correct, remove the extra suffix.
 #
 # Arguments:
-#   1: The optional URL to use for this tarball.
-#   2: The expeced checksum of the tarball.
+#   1: The optional base URL (directory) to use for this tarball.
+#   2: The expected checksum of the tarball.
+#   3: The upstream name of the tarball file, if not automatically derived
+#        from the version number.
+#   4: [Optional]: Alternative upstream base URL (directory) for the
+#        tarball, to be used in preference to user or Maneage backup
+#        servers.
 #
 # Necessary shell variables
 #   'tarball': This is the name of the actual tarball file without a
@@ -56,7 +61,14 @@ import-source = final=$(tdir)/$$tarball; \
 	      tarballurl=$(topbackupserver)/$$tarball; \
 	    else \
 	      bservers="$(backupservers_all)"; \
-	      tarballurl=$$url/$$tarball; \
+	      if [ "x$(strip $(3))" = "x" ]; then \
+	          tarballurl=$$url/$$tarball; \
+	      else \
+	          tarballurl=$$url/$(strip $(3)); \
+	      fi; \
+	    fi; \
+	    if [ x"$(4)" != x ]; then \
+	      bservers="$(strip $(4)) $$bservers"; \
 	    fi; \
 	    if [ -f $(ibdir)/wget ]; then \
 	      downloader="wget --no-use-server-timestamps -O"; \
@@ -89,6 +101,48 @@ import-source = final=$(tdir)/$$tarball; \
 
 
 
+# Double-check an already downloaded R source
+# -------------------------------------------
+#
+# It is probably too late to protect the system if you have already
+# installed an insecure or wrong R package. However, it's still useful
+# to check that the source package is the one that you think it is.
+#
+# Calculate the checksum and exit with a non-zero error code if
+# there's a mismatch, after informing the user.
+#
+# Arguments:
+#   1: The expected checksum of the tarball.
+#
+# Necessary shell variables
+#   'tarball': This is the name of the actual tarball file without a
+#   directory.
+double-check-R-source = final=$(tdir)/R-project/$$tarball; \
+	exp_checksum="$(strip $(1))"; \
+	if [ x"$$exp_checksum" = x"NO-CHECK-SUM" ]; then \
+	  result=0; \
+	else \
+	  if type sha512sum > /dev/null 2>/dev/null; then \
+	    checksum=$$(sha512sum "$$final" | awk '{print $$1}'); \
+	    if [ x"$$checksum" = x"$$exp_checksum" ]; then \
+	      result=0; \
+	    else \
+	      echo "ERROR: Non-matching checksum: $$final"; \
+	      echo "Checksum should be: $$exp_checksum"; \
+	      echo "Checksum is:        $$checksum"; \
+	      result=1; \
+	      exit 1; \
+	    fi; \
+	  else \
+	    echo "ERROR: sha512sum is unavailable."; \
+	    exit 1; \
+	  fi; \
+	fi
+
+
+
+
+
 # Unpack a tarball
 # ----------------
 #
@@ -106,7 +160,7 @@ uncompress = csuffix=$$(echo $$utarball \
 	  intarrm=0; \
 	  intar=$$utarball; \
 	fi; \
-	if tar xf $$intar; then \
+	if tar -xf $$intar; then \
 	  if [ x$$intarrm = x1 ]; then rm $$intar; fi; \
 	else \
 	  echo; echo "Tar error"; exit 1; \
@@ -166,10 +220,13 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
 	 else shellop="SHELL=/bin/sh"; \
 	 fi; \
 	     \
+	 if [ x$$gbuild_prefix = x ]; then prefixdir="$(idir)"; \
+	 else prefixdir="$$gbuild_prefix"; fi; \
+	                                       \
 	 if [ -f "$$confscript" ]; then \
 	   if [ x"$(strip $(1))" = x"zlib-$(zlib-version)" ]; then \
-	     configop="--prefix=$(idir)"; \
-	   else configop="$$shellop --prefix=$(idir)"; \
+	     configop="--prefix=$$prefixdir"; \
+	   else configop="$$shellop --prefix=$$prefixdir"; \
 	   fi; \
 	 fi; \
 	     \
@@ -190,7 +247,7 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
 	   make "$$shellop" install $(7); \
 	   cd ..; \
 	 fi; \
-	 rm -rf $(1)
+	 rm -rf $(1);