Imported recent important fixes in Maneage, no conflicts

There weren't any conflicts in this merge.

4 files changed, 34 insertions, 15 deletions

diff --git a/project b/project
index 4dc4bd1..3af3d40 100755
--- a/project
+++ b/project
@@ -167,22 +167,22 @@ do
 
 
   # Configure options:
-  -b|--build-dir)        IFS='"' build_dir="$2";                             check_v "$1" "$build_dir";    shift;shift;;
-  -b=*|--build-dir=*)    IFS='"' build_dir="${1#*=}";                        check_v "$1" "$build_dir";    shift;;
-  -b*)                   IFS='"' build_dir=$(echo    "$1" | sed -e's/-b//'); check_v "$1" "$build_dir";    shift;;
+  -b|--build-dir)        build_dir="$2";                                     check_v "$1" "$build_dir";    shift;shift;;
+  -b=*|--build-dir=*)    build_dir="${1#*=}";                                check_v "$1" "$build_dir";    shift;;
+  -b*)                   build_dir=$(echo    "$1" | sed -e's/-b//');         check_v "$1" "$build_dir";    shift;;
   -e|--existing-conf)    existing_conf=1;                                                                  shift;;
   -e*|--existing-conf=*) on_off_option_error --existing-conf -e;;
   --host-cc)             host_cc=1;                                                                        shift;;
   --host-cc=*)           on_off_option_error --host-cc;;
-  -i|--input-dir)        IFS='"' input_dir="$2";                             check_v "$1" "$input_dir";    shift;shift;;
-  -i=*|--input-dir=*)    IFS='"' input_dir="${1#*=}";                        check_v "$1" "$input_dir";    shift;;
+  -i|--input-dir)        input_dir="$2";                                     check_v "$1" "$input_dir";    shift;shift;;
+  -i=*|--input-dir=*)    input_dir="${1#*=}";                                check_v "$1" "$input_dir";    shift;;
   -i*)                   input_dir=$(echo    "$1" | sed -e's/-i//');         check_v "$1" "$input_dir";    shift;;
   -m|--minmapsize)       minmapsize="$2";                                    check_v "$1" "$minmapsize";   shift;shift;;
   -m=*|--minmapsize=*)   minmapsize="${1#*=}";                               check_v "$1" "$minmapsize";   shift;;
   -m*)                   minmapsize=$(echo   "$1" | sed -e's/-m//');         check_v "$1" "$minmapsize";   shift;;
-  -s|--software-dir)     IFS='"' software_dir="$2";                          check_v "$1" "$software_dir"; shift;shift;;
-  -s=*|--software-dir=*) IFS='"' software_dir="${1#*=}";                     check_v "$1" "$software_dir"; shift;;
-  -s*)                   IFS='"' software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;;
+  -s|--software-dir)     software_dir="$2";                                  check_v "$1" "$software_dir"; shift;shift;;
+  -s=*|--software-dir=*) software_dir="${1#*=}";                             check_v "$1" "$software_dir"; shift;;
+  -s*)                   software_dir=$(echo "$1" | sed -e's/-s//');         check_v "$1" "$software_dir"; shift;;
   --check-config)        check_config=1;                                                                   shift;;
   --check-config=*)      on_off_option_error --check-config;;
   --clean-texdir)        clean_texdir=1;                                                                   shift;;
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 3c5e518..c3bda3e 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -1181,6 +1181,24 @@ $(ibidir)/pcre-$(pcre-version):
 	               , V=1 -j$(numthreads))
 	echo "Perl Compatible Regular Expressions $(pcre-version)" > $@
 
+# Comment on building R without GUI support ('--without-tcltlk')
+#
+# Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support
+# in some software. But they are not yet natively built within Maneage,
+# primarily because we have higher-priority work right now (if anyone is
+# interested, they can ofcourse contribute!). GUI tools in general aren't
+# high on our priority list right now because they are generally good for
+# human interaction (which is contrary to the reproducible philosophy:
+# there will always be human-error and frustration, for example in GUI
+# tools the best level of reproducibility is statements like this: "move
+# your mouse to button XXX, then click on menu YYY and etc"). A robust
+# reproducible solution must be done automatically.
+#
+# If someone wants to use R's GUI functionalities while investigating for
+# their analysis, they can do the GUI part on their host OS
+# implementation. Later, they can bring the finalized source into Maneage
+# to be automatically run in Maneage. This will also be the recommended way
+# to deal with GUI tools later when we do install them within Maneage.
 $(ibidir)/R-$(R-version): \
             $(ibidir)/pcre-$(pcre-version) \
             $(ibidir)/cairo-$(cairo-version) \
@@ -1204,6 +1222,7 @@ $(ibidir)/R-$(R-version): \
 	            --with-pcre1 \
 	            --disable-java \
 	            --with-readline \
+	            --without-tcltk \
 	            --disable-openmp
 	make -j$(numthreads)
 	make install
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 0d22dcc..d9a1b46 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -188,7 +188,7 @@ check_permission ()
 free_space_warning()
 {
     fs_threshold=$1
-    IFS='"' fs_destpath="$2"
+    fs_destpath="$2"
     return $(df "$fs_destpath" \
                 | awk 'FNR==2 {if($4>'$fs_threshold') print 1; \
                                else                   print 0; }')
@@ -873,7 +873,7 @@ EOF
 	# 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 ! $(IFS='"' check_permission "$bdir"); then
+            if ! $(check_permission "$bdir"); then
                 # Unable to handle permissions well
                 bdir=
                 echo " ** File permissions can't be modified in this directory"
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index a18966f..4e7d6ad 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -30,11 +30,11 @@ set -e
 
 
 
-# Input arguments (the 'IFS's are to allow space in the name).
-IFS='"' bdir="$1"
-IFS='"' ddir="$2"
-IFS='"' downloader="$3"
-IFS='"' user_backup_urls="$4"
+# Input arguments.
+bdir="$1"
+ddir="$2"
+downloader="$3"
+user_backup_urls="$4"