Imported recent changes in Maneage, minor conflicts fixed

A few small conflicts showed up here and there. They are fixed with this
merge.

10 files changed, 292 insertions, 166 deletions

diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index 37fe64d..b173589 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -2,18 +2,15 @@
 #
 # Copyright (C) 2018-2020 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This Makefile is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This Makefile is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
 
 
 
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 0c2cd0b..d19f095 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -3,18 +3,15 @@
 # Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 # Copyright (C) 2019-2020 Raul Infante-Sainz <infantesainz@gmail.com>
 #
-# 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This Makefile is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This Makefile is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
 
 
 
@@ -46,7 +43,6 @@ metastore-version = 1.1.2-23-fa9170b
 mpc-version = 1.1.0
 mpfr-version = 4.0.2
 ncurses-version = 6.1
-openssl-version = 1.1.1a
 patchelf-version = 0.10
 perl-version = 5.30.0
 pkgconfig-version = 0.29.2
@@ -216,6 +212,11 @@ libgit2-version = 0.28.2
 netpbm-version = 10.86.99
 wcslib-version = 6.4
 
-# Minizip is installed as a part of `zlib', and they have the same version.
-zlib-version = 1.2.11
+# Minizip is installed with the same `zlib' tarball, and they have the same
+# version.
 minizip-version = $(zlib-version)
+
+# From version 1.2 OpenSSL may not need a manual addition, as described in
+# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
+# cause problems, put it back in the list of "Basic/low-level" tools.
+openssl-version = 1.1.1a
\ No newline at end of file
diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk
index b05d3f8..c98130d 100755
--- a/reproduce/software/make/atlas-multiple.mk
+++ b/reproduce/software/make/atlas-multiple.mk
@@ -10,18 +10,15 @@
 #
 # Copyright (C) 2019-2020 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This Makefile is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This Makefile is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
 
 ORIGLDFLAGS := $(LDFLAGS)
 
diff --git a/reproduce/software/make/atlas-single.mk b/reproduce/software/make/atlas-single.mk
index 61ae9a1..82eade9 100755
--- a/reproduce/software/make/atlas-single.mk
+++ b/reproduce/software/make/atlas-single.mk
@@ -10,18 +10,15 @@
 #
 # Copyright (C) 2019-2020 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This Makefile is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This Makefile is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
 
 ORIGLDFLAGS := $(LDFLAGS)
 
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index d1fbc3f..0bec163 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -18,18 +18,15 @@
 # Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 # Copyright (C) 2019-2020 Raul Infante-Sainz <infantesainz@gmail.com>
 #
-# 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This Makefile is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This Makefile is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
 
 
 # Top level environment
@@ -159,14 +156,18 @@ tarballs = $(foreach t, bash-$(bash-version).tar.lz \
                       , $(tdir)/$(t) )
 $(tarballs): $(tdir)/%: | $(lockdir)
 
-	n=$$(echo $* | sed -e's/[0-9\-]/ /g' \
-	                   -e's/\./ /g' \
+        # Remove the version numbers and suffix from the tarball name so we
+        # can search more easily only with the program name. This requires
+        # the first character of the version to be a digit: packages such
+        # as `foo' and `foo-3' will not be distinguished, but `foo' and
+        # `foo2' will be distinguished.
+	n=$$(echo $* | sed -e's/-[0-9]/ /' -e's/\./ /g' \
 	             | awk '{print $$1}' ); \
 	                                    \
 	mergenames=1; \
 	if   [ $$n = bash      ]; then c=$(bash-checksum); w=http://akhlaghi.org/maneage-software; \
 	elif [ $$n = binutils  ]; then c=$(binutils-checksum); w=http://ftp.gnu.org/gnu/binutils; \
-	elif [ $$n = bzip      ]; then c=$(bzip2-checksum); w=http://akhlaghi.org/maneage-software; \
+	elif [ $$n = bzip2     ]; then c=$(bzip2-checksum); w=http://akhlaghi.org/maneage-software; \
 	elif [ $$n = cert      ]; then c=$(cert-checksum); w=http://akhlaghi.org/maneage-software; \
 	elif [ $$n = coreutils ]; then c=$(coreutils-checksum); w=http://ftp.gnu.org/gnu/coreutils;\
 	elif [ $$n = curl      ]; then c=$(curl-checksum); w=https://curl.haxx.se/download; \
@@ -184,7 +185,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	elif [ $$n = libiconv  ]; then c=$(libiconv-checksum); w=https://ftp.gnu.org/pub/gnu/libiconv; \
 	elif [ $$n = libtool   ]; then c=$(libtool-checksum); w=http://ftp.gnu.org/gnu/libtool; \
 	elif [ $$n = lzip      ]; then c=$(lzip-checksum); w=http://download.savannah.gnu.org/releases/lzip; \
-	elif [ $$n = m         ]; then \
+	elif [ $$n = m4        ]; then \
 	  mergenames=0; \
 	  c=$(m4-checksum); \
 	  w=http://akhlaghi.org/maneage-software/m4-1.4.18-patched.tar.gz; \
@@ -199,7 +200,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  c=$(perl-checksum); \
 	  v=$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}'); \
 	  w=https://www.cpan.org/src/$$v; \
-	elif [ $$n = pkg       ]; then c=$(pkgconfig-checksum); w=http://pkg-config.freedesktop.org/releases; \
+	elif [ $$n = pkg-config ]; then c=$(pkgconfig-checksum); w=http://pkg-config.freedesktop.org/releases; \
 	elif [ $$n = readline  ]; then c=$(readline-checksum); w=http://ftp.gnu.org/gnu/readline; \
 	elif [ $$n = sed       ]; then c=$(sed-checksum); w=http://ftp.gnu.org/gnu/sed; \
 	elif [ $$n = tar       ]; then c=$(tar-checksum); w=http://ftp.gnu.org/gnu/tar; \
@@ -804,6 +805,14 @@ $(ibidir)/openssl: $(tdir)/cert.pem \
         # environment variable.
         #
         # https://wiki.openssl.org/index.php/Compilation_and_Installation
+        #
+        # Bug 58263 (https://savannah.nongnu.org/bugs/?58263): In OpenSSL
+        # Version 1.1.1a (also checked in 1.1.1g), `openssl/ec.h' fails to
+        # include `openssl/openconf.h' on some OSs. The SED hack below
+        # inserts a hardwired element of `openssl/openconf.h' that is
+        # needed to include sections of code `f` that are deprecated in
+        # 1.2.0, but not yet in 1.1.1. This problem may be solved in
+        # version 1.2.x, so please check again in that bug.
 	if [ x$(on_mac_os) = xyes ]; then \
 	  export KERNEL_BITS=64; \
 	  copt="shared no-ssl2 no-ssl3 enable-ec_nistp_64_gcc_128";  \
@@ -816,6 +825,9 @@ $(ibidir)/openssl: $(tdir)/cert.pem \
 	               --with-zlib-lib=$(ildir) \
 	               --with-zlib-include=$(idir)/include, \
 	               -j$(numthreads), , ./config ) \
+	&& mv -v $(idir)/include/openssl/ec.h $(idir)/include/openssl/ec.h.orig \
+	&& sed -e 's,\(# include .openssl/opensslconf\.h.\),\1\n#ifndef DEPRECATEDIN_1_2_0\n#define DEPRECATEDIN_1_2_0(f)   f;\n#endif\n,' \
+	   $(idir)/include/openssl/ec.h.orig > $(idir)/include/openssl/ec.h \
 	&& cp $(tdir)/cert.pem $(idir)/etc/ssl/cert.pem \
 	&& if [ $$? = 0 ]; then \
 	     if [ x$(on_mac_os) = xyes ]; then \
@@ -1296,8 +1308,8 @@ $(ibidir)/gcc: | $(ibidir)/binutils \
 	  tar xf $(word 1,$(filter $(tdir)/%,$|)); \
 	  if [ $$odir != $(ddir) ]; then \
 	    ln -s $$odir/gcc-$(gcc-version) $(ddir)/gcc-$(gcc-version); \
-	  fi \
-	  && cd gcc-$(gcc-version) \
+	  fi; \
+	  if cd gcc-$(gcc-version) \
 	  && mkdir build \
 	  && cd build \
 	  && ../configure SHELL=$(ibdir)/bash \
@@ -1346,6 +1358,25 @@ $(ibidir)/gcc: | $(ibidir)/binutils \
 	       rm -rf $$odir; \
 	       rm $(ddir)/gcc-$(gcc-version); \
 	     fi \
-	  && ln -sf $(ibdir)/gcc $(ibdir)/cc \
-	  && echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@; \
+	  && ln -sf $(ibdir)/gcc $(ibdir)/cc; \
+	  then \
+	    echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@; \
+	  else echo; echo; echo; \
+	    echo "_________________________________________________"; \
+	    echo "!!!!!!!!       Warning from Maneage      !!!!!!!!"; \
+	    echo; \
+	    echo "Unfortunately building of GCC failed on this system!"; \
+	    echo "Can you please copy the last ~500 lines above and post it"; \
+	    echo "as a bug here (as an attached file):"; \
+	    echo "  https://sv.nongnu.org/support/?func=additem&group=reproduce"; \
+	    echo; \
+	    echo "In the meantime, please re-configure Maneage with '--host-cc'"; \
+	    echo "like below so it uses your own C compiler for building the"; \
+	    echo "high-level software ('-e' is to use the existing configuration):"; \
+	    echo; \
+	    echo "  ./project configure -e --host-cc"; \
+	    echo; \
+	    echo "__________ SEE NOTE FROM MANEAGE ABOVE __________"; \
+	    echo; exit 1; \
+	  fi; \
 	fi
diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
index f3ca7d2..8d78ce3 100644
--- a/reproduce/software/make/build-rules.mk
+++ b/reproduce/software/make/build-rules.mk
@@ -5,18 +5,15 @@
 #
 # Copyright (C) 2018-2020 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This Makefile is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This Makefile is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
 
 
 
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index ce617af..ffab19c 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -11,18 +11,15 @@
 # Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 # Copyright (C) 2019-2020 Raul Infante-Sainz <infantesainz@gmail.com>
 #
-# 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This Makefile is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This Makefile is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
 
 
 
@@ -206,17 +203,19 @@ tarballs = $(foreach t, apachelog4cxx-$(apachelog4cxx-version).tar.lz \
                       , $(tdir)/$(t) )
 $(tarballs): $(tdir)/%: | $(lockdir)
 
-        # Remove all numbers, `-' and `.' from the tarball name so we can
-        # search more easily only with the program name.
-	@n=$$(echo $* | sed -e's/[0-9\-]/ /g' -e's/\./ /g' \
-	             | awk '{print $$1}' )
+        # Remove the version numbers and suffix from the tarball name so we
+        # can search more easily only with the program name. This requires
+        # the first character of the version to be a digit: packages such
+        # as `foo' and `foo-3' will not be distinguished, but `foo' and
+        # `foo2' will be distinguished.
+	@n=$$(echo $* | sed -e's/-[0-9]/ /' -e's/\./ /g' \
+	              | awk '{print $$1}' )
 
         # Set the top download link of the requested tarball.
 	mergenames=1
-	if   [ $$n = apachelog   ]; then c=$(apachelog4cxx-checksum); w=http://akhlaghi.org/maneage-software
-	elif [ $* = apr-util-$(apr-util-version).tar.gz ]; then
-	  c=$(apr-util-checksum); w=https://www-us.apache.org/dist/apr
+	if   [ $$n = apachelog4cxx ]; then c=$(apachelog4cxx-checksum); w=http://akhlaghi.org/maneage-software
 	elif [ $$n = apr         ]; then c=$(apr-checksum); w=https://www-us.apache.org/dist/apr
+	elif [ $$n = apr-util    ]; then c=$(apr-util-checksum); w=https://www-us.apache.org/dist/apr
 	elif [ $$n = astrometry  ]; then c=$(astrometrynet-checksum); w=http://astrometry.net/downloads
 	elif [ $$n = atlas       ]; then
 	  mergenames=0
@@ -259,29 +258,29 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  w=https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs$$v
 	elif [ $$n = gnuastro    ]; then c=$(gnuastro-checksum); w=http://ftp.gnu.org/gnu/gnuastro
 	elif [ $$n = gsl         ]; then c=$(gsl-checksum); w=http://ftp.gnu.org/gnu/gsl
-	elif [ $$n = hdf         ]; then
+	elif [ $$n = hdf5        ]; then
 	  mergenames=0
 	  c=$(hdf5-checksum)
 	  majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}')
 	  w=https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src/$*
 	elif [ $$n = healpix     ]; then c=$(healpix-checksum); w=http://akhlaghi.org/maneage-software
-	elif [ $$n = help        ]; then c=$(help2man-checksum); w=http://ftp.gnu.org/gnu/help2man
+	elif [ $$n = help2man    ]; then c=$(help2man-checksum); w=http://ftp.gnu.org/gnu/help2man
 	elif [ $$n = imagemagick ]; then c=$(imagemagick-checksum); w=http://akhlaghi.org/maneage-software
 	elif [ $$n = imfit       ]; then
 	  mergenames=0
 	  c=$(imfit-checksum)
 	  w=http://www.mpe.mpg.de/~erwin/resources/imfit/imfit-$(imfit-version)-source.tar.gz
-	elif [ $$n = install     ]; then c=NO-CHECK-SUM; w=http://mirror.ctan.org/systems/texlive/tlnet
+	elif [ $$n = install-tl-unx ]; then c=NO-CHECK-SUM; w=http://mirror.ctan.org/systems/texlive/tlnet
 	elif [ $$n = jpegsrc     ]; then c=$(libjpeg-checksum); w=http://ijg.org/files
 	elif [ $$n = lapack      ]; then c=$(lapack-checksum); w=http://www.netlib.org/lapack
 	elif [ $$n = libnsl      ]; then c=$(libnsl-checksum); w=http://akhlaghi.org/maneage-software
 	elif [ $$n = libpng      ]; then c=$(libpng-checksum); w=https://download.sourceforge.net/libpng
-	elif [ $$n = libgit      ]; then
+	elif [ $$n = libgit2     ]; then
 	  mergenames=0
 	  c=$(libgit2-checksum)
 	  w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz
 	elif [ $$n = libtirpc    ]; then c=$(libtirpc-checksum); w=https://downloads.sourceforge.net/libtirpc
-	elif [ $$n = libxml      ]; then c=$(libxml2-checksum); w=ftp://xmlsoft.org/libxml2
+	elif [ $$n = libxml2     ]; then c=$(libxml2-checksum); w=ftp://xmlsoft.org/libxml2
 	elif [ $$n = missfits    ]; then c=$(missfits-checksum); w=https://www.astromatic.net/download/missfits
 	elif [ $$n = netpbm      ]; then c=$(netpbm-checksum); w=http://akhlaghi.org/maneage-software
 	elif [ $$n = openblas    ]; then
@@ -298,7 +297,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	elif [ $$n = R           ]; then c=$(R-checksum);
 	  majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}')
 	  w=https://cran.r-project.org/src/base/R-$$majver
-	elif [ $$n = rpcsvc      ]; then c=$(rpcsvc-proto-checksum); w=https://github.com/thkukuk/rpcsvc-proto/releases/download/v$(rpcsvc-proto-version)
+	elif [ $$n = rpcsvc-proto ]; then c=$(rpcsvc-proto-checksum); w=https://github.com/thkukuk/rpcsvc-proto/releases/download/v$(rpcsvc-proto-version)
 	elif [ $$n = scamp       ]; then c=$(scamp-checksum); w=http://akhlaghi.org/maneage-software
 	elif [ $$n = scons       ]; then
 	  mergenames=0
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 1ef1bf2..f378650 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -11,18 +11,15 @@
 # Copyright (C) 2019-2020 Raul Infante-Sainz <infantesainz@gmail.com>
 # Copyright (C) 2019-2020 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This Makefile is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This Makefile is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
 
 
 
@@ -134,16 +131,18 @@ $(pytarballs): $(tdir)/%:
         # first string.
 	@if [ $* = python-dateutil-$(python-dateutil-version).tar.gz ]; then
 	  n=dateutil
-	elif [ $* = h5py-$(h5py-version).tar.gz ]; then
-	  n=h5py
 
         # elif [ $* = strange-tarball5name-version.tar.gz ]; then
         #  n=strange5-name
 	else
-          # Remove all numbers, `-' and `.' from the tarball name so we can
-          # search more easily only with the program name.
-	  n=$$(echo $* | sed -e's/[0-9\-]/ /g' -e's/\./ /g'           \
-	            | awk '{print $$1}')
+          # Remove the version numbers and suffix from the tarball name so
+          # we can search more easily only with the program name. This
+          # requires the first character of the version to be a digit:
+          # packages such as `foo' and `foo-3' will not be distinguished,
+          # but `foo' and `foo2' will be distinguished.
+	  n=$$(echo $* | sed -e's/-[0-9]/ /' -e's/\./ /g' \
+	               | awk '{print $$1}' )
+
 	fi
 
         # Set the top download link of the requested tarball. The ones
@@ -183,11 +182,11 @@ $(pytarballs): $(tdir)/%:
 	  c=$(secretstorage-checksum)
 	  hash=a6/89/df343dbc2957a317127e7ff2983230dc5336273be34f2e1911519d85aeb5
 	  h=$(pytopurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz
-	elif [ $$n = asn            ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4; c=$(asn1crypto-checksum)
+	elif [ $$n = asn1crypto     ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4; c=$(asn1crypto-checksum)
 	elif [ $$n = asteval        ]; then h=50/3f/29b7935c6dc09ee96dc347edc66c57e8ef68d595dd35b763a36a117acc8c; c=$(asteval-checksum)
 	elif [ $$n = astroquery     ]; then h=e2/af/a3cd3b30745832a0e81f5f13327234099aaf5d03b7979ac947a888e68e91; c=$(astroquery-checksum)
 	elif [ $$n = astropy        ]; then h=de/96/7feaca4b9be134128838395a9d924ea0b389ed4381702dcd9d11ae31789f; c=$(astropy-checksum)
-	elif [ $$n = beautifulsoup  ]; then h=80/f2/f6aca7f1b209bb9a7ef069d68813b091c8c3620642b568dac4eb0e507748; c=$(beautifulsoup4-checksum)
+	elif [ $$n = beautifulsoup4 ]; then h=80/f2/f6aca7f1b209bb9a7ef069d68813b091c8c3620642b568dac4eb0e507748; c=$(beautifulsoup4-checksum)
 	elif [ $$n = certifi        ]; then h=55/54/3ce77783acba5979ce16674fc98b1920d00b01d337cfaaf5db22543505ed; c=$(certifi-checksum)
 	elif [ $$n = cffi           ]; then h=64/7c/27367b38e6cc3e1f49f193deb761fe75cda9f95da37b67b422e62281fcac; c=$(cffi-checksum)
 	elif [ $$n = chardet        ]; then h=fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d; c=$(chardet-checksum)
@@ -198,23 +197,23 @@ $(pytarballs): $(tdir)/%:
 	elif [ $$n = emcee          ]; then h=f0/c0/cd433f2aedeef9b1e5ed7d236c82564f7518fe7fe2238fa141ea9ce08e73; c=$(emcee-checksum)
 	elif [ $$n = entrypoints    ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c; c=$(entrypoints-checksum)
 	elif [ $$n = esutil         ]; then h=5b/91/77e38282fd3d47b55e351544ab179eb209b309a8d2d40f8cdb6241beda00; c=$(esutil-checksum)
-	elif [ $$n = flake          ]; then h=8d/a7/99222c9200af533c1ecb1120d99adbd1c033b57296ac5cb39d121db007a8; c=$(flake8-checksum)
+	elif [ $$n = flake8         ]; then h=8d/a7/99222c9200af533c1ecb1120d99adbd1c033b57296ac5cb39d121db007a8; c=$(flake8-checksum)
 	elif [ $$n = future         ]; then h=3f/bf/57733d44afd0cf67580658507bd11d3ec629612d5e0e432beb4b8f6fbb04; c=$(future-checksum)
 	elif [ $$n = h5py           ]; then h=43/27/a6e7dcb8ae20a4dbf3725321058923fec262b6f7835179d78ccc8d98deec; c=$(h5py-checksum)
-	elif [ $$n = html           ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f; c=$(html5lib-checksum)
+	elif [ $$n = html5lib       ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f; c=$(html5lib-checksum)
 	elif [ $$n = idna           ]; then h=ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7; c=$(idna-checksum)
 	elif [ $$n = jeepney        ]; then h=16/1d/74adf3b164a8d19a60d0fcf706a751ffa2a1eaa8e5bbb1b6705c92a05263; c=$(jeepney-checksum)
 	elif [ $$n = keyring        ]; then h=15/88/c6ce9509438bc02d54cf214923cfba814412f90c31c95028af852b19f9b2; c=$(keyring-checksum)
 	elif [ $$n = kiwisolver     ]; then h=31/60/494fcce70d60a598c32ee00e71542e52e27c978e5f8219fae0d4ac6e2864; c=$(kiwisolver-checksum)
 	elif [ $$n = lmfit          ]; then h=59/6e/117794cf85b7345361877e49245870490ae438f1981dea3c6af1316b30e7; c=$(lmfit-checksum)
 	elif [ $$n = matplotlib     ]; then h=12/d1/7b12cd79c791348cb0c78ce6e7d16bd72992f13c9f1e8e43d2725a6d8adf; c=$(matplotlib-checksum)
-	elif [ $$n = mpi            ]; then h=04/f5/a615603ce4ab7f40b65dba63759455e3da610d9a155d4d4cece1d8fd6706; c=$(mpi4py-checksum)
+	elif [ $$n = mpi4py         ]; then h=04/f5/a615603ce4ab7f40b65dba63759455e3da610d9a155d4d4cece1d8fd6706; c=$(mpi4py-checksum)
 	elif [ $$n = mpmath         ]; then h=ca/63/3384ebb3b51af9610086b23ea976e6d27d6d97bf140a76a365bd77a3eb32; c=$(mpmath-checksum)
 	elif [ $$n = numpy          ]; then h=ac/36/325b27ef698684c38b1fe2e546e2e7ef9cecd7037bcdb35c87efec4356af; c=$(numpy-checksum)
 	elif [ $$n = pexpect        ]; then h=1c/b1/362a0d4235496cb42c33d1d8732b5e2c607b0129ad5fdd76f5a583b9fcb3; c=$(pexpect-checksum)
 	elif [ $$n = pip            ]; then h=4c/4d/88bc9413da11702cbbace3ccc51350ae099bb351febae8acc85fec34f9af; c=$(pip-checksum)
 	elif [ $$n = pkgconfig      ]; then h=6e/a9/ff67ef67217dfdf2aca847685fe789f82b931a6957a3deac861297585db6; c=$(pypkgconfig-checksum)
-	elif [ $$n = pybind         ]; then h=aa/91/deb6743e79e22ab01502296570b39b8404f10cc507a6692d612a7fee8d51; c=$(pybind11-checksum)
+	elif [ $$n = pybind11       ]; then h=aa/91/deb6743e79e22ab01502296570b39b8404f10cc507a6692d612a7fee8d51; c=$(pybind11-checksum)
 	elif [ $$n = pycodestyle    ]; then h=1c/d1/41294da5915f4cae7f4b388cea6c2cd0d6cd53039788635f6875dfe8c72f; c=$(pycodestyle-checksum)
 	elif [ $$n = pycparser      ]; then h=68/9e/49196946aee219aead1290e00d1e7fdeab8567783e83e1b9ab5585e6206a; c=$(pycparser-checksum)
 	elif [ $$n = pyflakes       ]; then h=52/64/87303747635c2988fcaef18af54bfdec925b6ea3b80bcd28aaca5ba41c9e; c=$(pyflakes-checksum)
@@ -230,7 +229,7 @@ $(pytarballs): $(tdir)/%:
 	elif [ $$n = soupsieve      ]; then h=0c/52/e9088bb9b96e2d39fc3b33fcda5b4fde9d71473536ac660a1ca9a0958a2f; c=$(soupsieve-checksum)
 	elif [ $$n = sympy          ]; then h=54/2e/6adb11fe599d4cfb7e8833753350ac51aa2c0603c226b36f9051cc9d2425; c=$(sympy-checksum)
 	elif [ $$n = uncertainties  ]; then h=2a/c2/babbe5b16141859dd799ed31c03987100a7b6d0ca7c0ed4429c96ce60fdf; c=$(uncertainties-checksum)
-	elif [ $$n = urllib         ]; then h=b1/53/37d82ab391393565f2f831b8eedbffd57db5a718216f82f1a8b4d381a1c1; c=$(urllib3-checksum)
+	elif [ $$n = urllib3        ]; then h=b1/53/37d82ab391393565f2f831b8eedbffd57db5a718216f82f1a8b4d381a1c1; c=$(urllib3-checksum)
 	elif [ $$n = virtualenv     ]; then h=51/aa/c395a6e6eaaedfa5a04723b6446a1df783b16cca6fec66e671cede514688; c=$(virtualenv-checksum)
 	elif [ $$n = webencodings   ]; then h=0b/02/ae6ceac1baeda530866a85075641cec12989bd8d31af6d5ab4a3e8c92f47; c=$(webencodings-checksum)
 #	elif [ $$n = strange5-name  ]; then h=XXXXX; c=$(XXXXX-checksum)
diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh
index b2a151f..69bbba6 100755
--- a/reproduce/software/shell/bashrc.sh
+++ b/reproduce/software/shell/bashrc.sh
@@ -31,15 +31,12 @@
 #
 # Copyright (C) 2019-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
-# 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
-#
-# This script is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# This script is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
+#
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index dc93d80..71b07cc 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -4,18 +4,18 @@
 #
 # Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
-# 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 the
-# Free Software Foundation, either version 3 of the License, or (at your
-# option) any later version.
+# This script is part of Maneage. Maneage is free software: you can
+# redistribute it and/or modify it under the terms of the GNU General
+# Public License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
 #
-# This script is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# <http://www.gnu.org/licenses/>.
+# Maneage is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
+# more details. See <http://www.gnu.org/licenses/>.
+
+
+
 
 
 # Script settings
@@ -93,6 +93,64 @@ absolute_dir ()
 
 
 
+# Check file permission handling (POSIX-compatibility)
+# ----------------------------------------------------
+#
+# 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
+# function receives the directory as an argument and then, creates a dummy
+# 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
+# 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
+# minimal example:
+#
+#     if $(check_permission $some_directory) ; then
+#       echo "yay"; else "nay";
+#     fi ;
+check_permission ()
+{
+    # Make a `junk' file, activate its executable flag and record its
+    # permissions generally.
+    local junkfile=$1/check_permission_tmp_file
+    rm -f $junkfile
+    echo "Don't let my short life go to waste" > $junkfile
+    chmod +x $junkfile
+    local perm_before=$(ls -l $junkfile | awk '{print $1}')
+
+    # Now, remove the executable flag and record the permissions.
+    chmod -x $junkfile
+    local perm_after=$(ls -l $junkfile | awk '{print $1}')
+
+    # Clean up before leaving the function
+    rm -f $junkfile
+
+    # If the permissions are equal, the filesystem doesn't allow
+    # permissions.
+    if [ $perm_before = $perm_after ]; then
+        # Setting permission FAILED
+        return 1
+    else
+        # Setting permission SUCCESSFUL
+	return 0
+    fi
+}
+
+
+
+
+
+
 # Check for C/C++ compilers
 # -------------------------
 #
@@ -241,7 +299,7 @@ rm -f $testprog $testsource
 
 # See if the C compiler can build static libraries
 # ------------------------------------------------
-
+#
 # We are manually only working with shared libraries: because some
 # high-level programs like Wget and cURL need dynamic linking and if we
 # build the libraries statically, our own builds will be ignored and these
@@ -258,6 +316,44 @@ static_build=no
 
 
 
+# Check for GNU gettext
+# ---------------------
+#
+# Some of the basic sofware need GNU gettext which we don't yet install.
+has_gettext=0
+if type msgfmt > /dev/null 2>/dev/null; then has_gettext=1; fi
+if [ $has_gettext = 0 ]; then
+    cat <<EOF
+______________________________________________________
+!!!!!!!          GNU gettext NOT FOUND         !!!!!!!
+
+Some of the core programs in Maneage require a running GNU gettext on the
+host. Unfortuantely we haven't had the time yet to include its installation
+in Maneage, but it is defined as task #15616 so we don't forget. Generally,
+GNU gettext is already available on many systems, so it hasn't been
+reported too commonly. But please consider helping in this if you have
+time and interest.
+
+Until we include gettext's installation in Maneage, please use your package
+manager to install GNU gettext, then re-run the configuration to
+continue. Here are the relevant commands on some common GNU/Linux
+distributions (you'll only need one of them, or a similar command, if you
+use another package manager):
+
+  apt install gettext
+  yum install gettext
+  pacman -S gettext
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    exit 1
+fi
+
+
+
+
+
 # If we are on a Mac OS system
 # ----------------------------
 #
@@ -287,7 +383,6 @@ ______________________________________________________
 EOF
     sleep 5
 else
-    host_cc=0
     on_mac_os=no
 fi
 
@@ -653,21 +748,20 @@ EOF
                 bdir=$(absolute_dir $build_dir)
                 rm -rf $build_dir/$junkname
             else
-                echo " -- Can't write in '$build_dir'"; echo
+                echo " ** Can't write in '$build_dir'"; echo
             fi
         else
             if mkdir $build_dir 2> /dev/null; then
                 instring="the newly created"
                 bdir=$(absolute_dir $build_dir)
             else
-                echo " -- Can't create '$build_dir'"; echo
+                echo " ** Can't create '$build_dir'"; echo
             fi
         fi
 
         # If its given, make sure it isn't a subdirectory of the source
         # directory.
         if ! [ x"$bdir" = x ]; then
-            echo "Given build directory: $bdir"
             if echo "$bdir/" \
                     | grep '^'$currentdir 2> /dev/null > /dev/null; then
 
@@ -676,17 +770,30 @@ EOF
 
                 # Inform the user that this is not acceptable and reset `bdir'.
                 bdir=
-                echo " -- The build-directory cannot be under the source-directory."
-                echo "    Please specify another build-directory that is outside of the source."
-                echo ""
-            else
-                echo " -- Build directory set to ($instring): '$bdir'"
+                echo " ** The build-directory cannot be under the source-directory."
+            fi
+        fi
+
+	# If everything is fine until now, see if we're able to manipulate
+	# file permissions.
+	if ! [ x"$bdir" = x ]; then
+            if ! $(check_permission $bdir); then
+                bdir=
+                echo " ** File permissions can't be modified in this directory"
             fi
         fi
 
-        # Reset `build_dir' to blank, so it continues asking when the
-        # previous value wasn't usable.
-        build_dir=
+        # If the build directory was good, the loop will stop, if not,
+        # 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$bdir = x ]; then
+            build_dir=
+            echo " ** Please select another directory."
+            echo ""
+        else
+            echo " -- Build directory set to ($instring): '$bdir'"
+        fi
     done
 fi
 
@@ -1405,12 +1512,16 @@ cat <<EOF
 ----------------
 The project and its environment are configured with no errors.
 
-Please run the following command to start.
+To change the configuration later, you can re-run './project configure' or
+manually edit 'reproduce/software/config/LOCAL.conf'. Just be careful with
+the build-directory: its location is hard-coded in the installed software
+so if you change it manually, many of the project's software will crash. If
+you have to use another built-directory, just re-configure a clean project
+there.
+
+Please run the following command to start the project.
 (Replace '8' with the number of CPU threads on your system)
 
     $buildcommand
 
-To change the configuration later, please re-run './project configure', DO
-NOT manually edit the relevant files.
-
 EOF