Imported recent important fixes in Maneage, no conflicts

There weren't any conflicts in this merge.

3 files changed, 26 insertions, 7 deletions

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"