Imported recent work on Maneage, minor conflicts fixed

A few minor conflicts occurred and were fixed.
author: Mohammad Akhlaghi <mohammad@akhlaghi.org> 2020-04-02 15:51:28 +0100
committer: Mohammad Akhlaghi <mohammad@akhlaghi.org> 2020-04-02 16:05:03 +0100
commit: de3842a14e36b2debb3ad375d95411d15d45dc84 (patch)
tree: 86ae571f85c639c616cf8939cbcec7f1c1be4c9c /reproduce
parent: 646756675566a0907edf143c6b6950e0479d9e7e (diff)
parent: cbf177e09af6b9d240388d148b0cb5e3488d8b09 (diff)
24 files changed, 752 insertions, 607 deletions
diff --git a/reproduce/analysis/bash/download-multi-try b/reproduce/analysis/bash/download-multi-try
index dec2539..7a5f8f2 100755
--- a/reproduce/analysis/bash/download-multi-try
+++ b/reproduce/analysis/bash/download-multi-try
@@ -51,11 +51,13 @@ set -e
 
 
 
-# Input arguments and necessary sanity checks.
+# Input arguments and necessary sanity checks. Note that the 5th argument
+# (backup servers) isn't mandatory.
 inurl="$3"
 outname="$4"
 lockfile="$2"
 downloader="$1"
+backupservers="$5"
 if [ "x$downloader" = x ]; then
     echo "$0: downloader (first argument) not given."; exit 1;
 fi
@@ -73,6 +75,13 @@ fi
 
 
 
+# Separate the actual filename, to possibly use backup server.
+urlfile=$(echo "$inurl" | awk -F "/" '{print $NF}')
+
+
+
+
+
 # Try downloading multiple times before crashing.
 counter=0
 maxcounter=10
@@ -107,8 +116,19 @@ while [ ! -f "$outname" ]; do
     if [ x"$lockfile" = xnolock ]; then
         if ! $downloader $outname $inurl; then rm -f $outname; fi
     else
+        # Try downloading from the requested URL.
         flock "$lockfile" bash -c \
               "if ! $downloader $outname $inurl; then rm -f $outname; fi"
+
+        # If it failed, try the backup server(s).
+        if [ ! -f "$outname" ]; then
+            if [ x"$backupservers" != x ]; then
+                for bs in "$backupservers"; do
+                    flock "$lockfile" bash -c \
+                          "if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi"
+                done
+            fi
+        fi
     fi
 
 done
diff --git a/reproduce/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf
index e580e04..0542c53 100644
--- a/reproduce/analysis/config/verify-outputs.conf
+++ b/reproduce/analysis/config/verify-outputs.conf
@@ -1,3 +1,2 @@
 # To disable verification of output datasets set this variable to yes
-
 verify-outputs =
diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk
index e4f2ccd..cf5bfa4 100644
--- a/reproduce/analysis/make/download.mk
+++ b/reproduce/analysis/make/download.mk
@@ -24,9 +24,10 @@
 # Download input data
 # --------------------
 #
-# The input dataset properties are defined in `$(pconfdir)/INPUTS.mk'. For
-# this template we only have one dataset to enable easy processing, so all
-# the extra checks in this rule may seem redundant.
+# The input dataset properties are defined in
+# `$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to
+# enable easy processing, so all the extra checks in this rule may seem
+# redundant.
 #
 # In a real project, you will need more than one dataset. In that case,
 # just add them to the target list and add an `elif' statement to define it
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index a4acff7..ce4e488 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -141,6 +141,12 @@ export SHELL := $(installdir)/bin/bash
 export CPPFLAGS := -I$(installdir)/include
 export LD_LIBRARY_PATH := $(installdir)/lib
 
+# Until we build our own C library, without this, the project's GCC won't
+# be able to compile anything if the host C library isn't in a standard
+# place: in particular Debian-based operatings sytems. On other systems, it
+# will be empty.
+export CPATH := $(SYS_CPATH)
+
 # RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
 # ultimately redundant. But on some systems, even having a single value
 # causes crashs (see bug #56682). So we'll just give it no value at all.
@@ -151,9 +157,9 @@ export DYLD_LIBRARY_PATH :=
 # remote-shell accesss through this environment variable.
 export OMPI_MCA_plm_rsh_agent=/bin/false
 
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# Recipe startup script.
 export PROJECT_STATUS := make
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
 
 
 
@@ -242,7 +248,7 @@ distclean: clean
         # `rm', not our own.
 	$$sys_rm -rf $(BDIR)
 	$$sys_rm -f Makefile .gnuastro .local .build
-	$$sys_rm -f $(pconfdir)/LOCAL.mk $(gconfdir)/gnuastro-local.conf
+	$$sys_rm -f $(pconfdir)/LOCAL.conf $(gconfdir)/gnuastro-local.conf
 
 
 
@@ -299,10 +305,11 @@ $(packagecontents): paper.pdf | $(texdir)
         # directories (when building in a group structure, there will be
         # `build-user1', `build-user2' and etc), are just temporary LaTeX
         # build files and don't have any relevant/hand-written files in
-        # them. 2) The `LOCAL.mk' and `gnuastro-local.conf' files just have
-        # this machine's local settings and are irrelevant for anyone else.
+        # them. 2) The `LOCAL.conf' and `gnuastro-local.conf' files just
+        # have this machine's local settings and are irrelevant for anyone
+        # else.
 	rm -rf $$dir/tex/build/build*
-	rm $$dir/reproduce/software/config/installation/LOCAL.mk
+	rm $$dir/reproduce/software/config/installation/LOCAL.conf
 	rm $$dir/reproduce/software/config/gnuastro/gnuastro-local.conf
 
         # When submitting to places like arXiv, they will just run LaTeX
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index af6bdc5..67db364 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -38,7 +38,7 @@
 #
 # Note that if you don't want the final PDF and just want the processing
 # and file outputs, you can remove the value of `pdf-build-final' in
-# `reproduce/analysis/config/pdf-build.mk'.
+# `reproduce/analysis/config/pdf-build.conf'.
 $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 
         # If no PDF is requested, or if LaTeX isn't available, don't
@@ -62,7 +62,7 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 	    echo "can check by running './.local/bin/latex --version'), _AND_"
 	    echo "make sure that the 'pdf-build-final' variable has a value."
 	    echo "'pdf-build-final' is defined in: "
-	    echo     "'reproduce/analysis/config/pdf-build.mk'."
+	    echo     "'reproduce/analysis/config/pdf-build.conf'."
 	    echo
 	    echo "If you don't have LaTeX within the project, please re-run"
 	    echo "'./project configure -e' when you have internet access."
diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk
index 1f0613c..36f25e7 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -19,7 +19,9 @@
 # Final-target
 #
 # Without this file, `./project make' won't work.
-$(BDIR)/software/preparation-done.mk:
+prepare-dep = $(subst prepare, ,$(makesrc))
+$(BDIR)/software/preparation-done.mk: \
+                $(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex)
 
         # If you need to add preparations define targets above to do the
         # preparations, then set the value below to `yes'. Recall that just
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 000c1fd..30d537a 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -21,7 +21,7 @@
 
 # Load the local configuration (created after running
 # `./project configure').
-include reproduce/software/config/installation/LOCAL.mk
+include reproduce/software/config/installation/LOCAL.conf
 
 
 
@@ -50,7 +50,7 @@ include reproduce/software/config/installation/LOCAL.mk
 #
 # Controlling this requires two variables that are available at this stage:
 #
-#   - `GROUP-NAME': from `LOCAL.mk' (which was built by `./project configure').
+#   - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure').
 #   - `reproducible_paper_group_name': value to the `--group' option.
 #
 # The analysis is only done when both have the same group name. Note that
@@ -63,7 +63,7 @@ include reproduce/software/config/installation/LOCAL.mk
 #
 # If you are just interested in the processing and don't want to build the
 # PDF, you can skip the creatation of the final PDF by removing the value
-# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.mk'.
+# of `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
 ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
 all: paper.pdf
 else
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index 5ce120d..1778c6b 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -25,7 +25,7 @@
 
 # Load the local configuration (created after running
 # `./project configure').
-include reproduce/software/config/installation/LOCAL.mk
+include reproduce/software/config/installation/LOCAL.conf
 
 
 
@@ -37,19 +37,7 @@ include reproduce/software/config/installation/LOCAL.mk
 # See `top-make.mk' for complete explanation.
 ifeq (x$(reproducible_paper_group_name),x$(GROUP-NAME))
 all: $(BDIR)/software/preparation-done.mk
-	@echo "";
-	echo "----------------"
-	echo "Project preparation has been completed without any errors."
-	echo ""
-	echo "Please run the following command to start building the project."
-	echo "(Replace '8' with the number of CPU threads on your system)"
-	echo ""
-	if [ "x$(GROUP-NAME)" = x ]; then \
-	  echo "   $$ ./project make"; \
-	else \
-	  echo "   $$ ./project make --group=$(GROUP-NAME) -j8"; \
-	fi
-	echo ""
+	@echo "Project preparation is complete.";
 else
 all:
 	@if [ "x$(GROUP-NAME)" = x ]; then \
@@ -59,6 +47,7 @@ all:
 	  echo "Project is configured for groups, please run"; \
 	  echo "   $$ ./project prepare --group=$(GROUP-NAME) -j8"; \
 	fi
+	exit 1
 endif
 
 
@@ -87,5 +76,5 @@ makesrc = initialize \
 #
 # See `top-make.mk' for complete explanation.
 project-phase = prepare
-include reproduce/analysis/config/*.mk
+include reproduce/analysis/config/*.conf
 include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk)
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index a04bce4..f0bcf10 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -33,7 +33,7 @@ verify-print-tips = \
   echo "If you are still developing your project, you can disable"; \
   echo "verification by removing the value of the variable in the"; \
   echo "following file (from the top project source directory):"; \
-  echo "    reproduce/analysis/config/verify-outputs.mk"; \
+  echo "    reproduce/analysis/config/verify-outputs.conf"; \
   echo; \
   echo "If this is the final version of the file, you can just copy"; \
   echo "and paste the calculated checksum (above) for the file in"; \
diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex
new file mode 100644
index 0000000..85a1645
--- /dev/null
+++ b/reproduce/software/bibtex/missfits.tex
@@ -0,0 +1,18 @@
+%% Copyright (C) 2020 Surena Fatemi <surena.fatemi@ipm.ir>
+%%
+%% Copying and distribution of this file, with or without modification,
+%% are permitted in any medium without royalty provided the copyright
+%% notice and this notice are preserved.  This file is offered as-is,
+%% without any warranty.
+
+@ARTICLE{missfits,
+       author = {{Marmo}, C. and {Bertin}, E.},
+        title = "{MissFITS and WeightWatcher: Two Optimised Tools for Managing FITS Data.}",
+      journal = {Astronomical Data Analysis Software and Systems XVII},
+         year = 2008,
+       volume = {394},
+       series = {Astronomical Society of the Pacific Conference Series},
+        pages = {619},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2008ASPC..394..619M},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+\ No newline at end of file
diff --git a/reproduce/software/config/installation/LOCAL.mk.in b/reproduce/software/config/installation/LOCAL.conf.in
index 1045f72..0579218 100644
--- a/reproduce/software/config/installation/LOCAL.mk.in
+++ b/reproduce/software/config/installation/LOCAL.conf.in
@@ -12,5 +12,6 @@
 BDIR             = @bdir@
 INDIR            = @indir@
 DEPENDENCIES-DIR = @ddir@
+SYS_CPATH        = @sys_cpath@
 DOWNLOADER       = @downloader@
 GROUP-NAME       = @groupname@
diff --git a/reproduce/software/config/installation/TARGETS.mk b/reproduce/software/config/installation/TARGETS.conf
index 0352d53..bb402be 100644
--- a/reproduce/software/config/installation/TARGETS.mk
+++ b/reproduce/software/config/installation/TARGETS.conf
@@ -18,17 +18,17 @@
 # All software that are currently available for installation can be seen in
 # the following file.
 #
-#     reproduce/software/config/installation/versions.mk
+#     reproduce/software/config/installation/versions.conf
 #
 # Please add any software that you need for your project in the respective
-# part below (using its name in `versions.mk', but without the `-version'
+# part below (using its name in `versions.conf', but without the `-version'
 # part). Just note that if a program/library is a dependency of another,
 # you don't need to include it here (it will be installed before the
 # higher-level software anyway).
 #
 # Note that many low-level software will be installed before those that are
 # installed in this step. They are clearly distinguished from the
-# higher-level (optional) software in `versions.mk'. These low-level
+# higher-level (optional) software in `versions.conf'. These low-level
 # software MUST NOT be added here.
 
 
diff --git a/reproduce/software/config/installation/checksums.mk b/reproduce/software/config/installation/checksums.conf
index a1a3767..4a5d8aa 100644
--- a/reproduce/software/config/installation/checksums.mk
+++ b/reproduce/software/config/installation/checksums.conf
@@ -43,7 +43,7 @@ libiconv-checksum = 365dac0b34b4255a0066e8033a8b3db4bdb94b9b57a9dca17ebf2d779139
 libtool-checksum = a6eef35f3cbccf2c9e2667f44a476ebc80ab888725eb768e91a3a6c33b8c931afc46eb23efaee76c8696d3e4eed74ab1c71157bcb924f38ee912c8a90a6521a4
 lzip-checksum= 0349b4c6c0b41e601b7ee381c3254d741397beb3ef9354c08162f346f131f4f48f6613ee0a610cdc6d827530df634f884ecfeee35215b10045a40fee76f8e938
 m4-checksum = a92cad4441b3fd7c033837389ca3499494523d364a5fda043d92c517051510f1758b3b837f0477f42d2258a179ab79a4993e5d1694ef2673db6d96d1faff84fe
-make-checksum = 6ebf886a394c61eea53dc0fa277b00cda263861e8e647608e0fce549cd619946981224408ee519bbd71068e9424798d3c5791451f60ff06d766f563142703d32
+make-checksum = 9a1185cc468368f4ec06478b1cfa343bf90b5cd7c92c0536567db0315b0ee909af53ecce3d44cfd93dd137dbca1ed13af5713e8663590c4fdd21ea635d78496b
 metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a
 mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628
 mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88
@@ -71,9 +71,9 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/installation/TARGETS.mk' will be built as part
-# of a project. To specify a software there, just remove the `-checksum'
-# suffix from the list below.
+# `reproduce/software/config/installation/TARGETS.conf' will be built as
+# part of a project. To specify a software there, just remove the
+# `-checksum' suffix from the list below.
 apachelog4cxx-checksum = aa59ce549c2c5cbeec031361dfce09cdfc3e62ee3bc9ecbc809507b7ec878c14409b98536b7d13c27690809c8e9d5ebafc3589c9fb5e4aecd5cc064943ae7d6b
 apr-checksum = daa140c83c7e2c45c3980d9dc81d34fa662bebd050653562c39572d0ddf2eaedb71767c518a59d77f59db9b32e00221ef48b9f72ec3666c4521dd511969f3706
 apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536
@@ -111,6 +111,7 @@ libtiff-checksum = d213e5db09fd56b8977b187c5a756f60d6e3e998be172550c2892dbdb4b2a
 libtirpc-checksum = 392f391f9fc1bd68d81dc44e4058831a64b32790b5c8c37338b0ab416fad2ae4d16389e632596734dba09780347918cc65c6f134e0c1afd09e81ec250785ed23
 libxml2-checksum = cb7784ba4e72e942614e12e4f83f4ceb275f3d738b30e3b5c1f25edf8e9fa6789e854685974eed95b362049dbf6c8e7357e0327d64c681ed390534ac154e6810
 minizip-checksum = 56b5443f79d1a0a5f563a563f7b1c27b0b0fc5ba5b37248367b204a89a9373df7d12ea802c678f3f39c987d5f1766003eac3dd31b643773afa4463a3f6406628
+missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795
 netpbm-checksum = 064720f8a9d0a502488e1af4daecdbf3936910996507ca6f311073a0ad842346692a148eb1ddf7b717f7b108f60500246cb4b83f4d3665f5fc285a84ae1d63d6
 openblas-checksum = 91b3074eb922453bf843158b4281cde65db9e8bbdd7590e75e9e6cdcb486157f7973f2936f327bb3eb4f1702ce0ba51ae6729d8d4baf2d986c50771e8f696df0
 openmpi-checksum = 760716974cb6b25ad820184622e1ee7926bc6fda87db6b574f76792bc1ca99522e52195866c14b7cb2df5a4981efdaf9f71d2c5533cc0e8e45c2c4b3b74cbacc
@@ -144,7 +145,7 @@ yaml-checksum = 13d2197135946204323dbfccafa0ac7b3d05437e920545a56f46811fd7319c01
 asn1crypto-checksum = 44d442a6ddfa971e31e24712fe084368356deb5e1c4c3b3e813e0910931860215bc1c4f9eb2c4bd4fdef607c324086c096e9357068646efd28c97f2d4f85c62f
 asteval-checksum = 4d64900b2f7dfdd098d6c8c102f9d9fd46f9ec265a54330e7d94479ba41f0ee0698855658e18b8b32b9c255159eb9a085af5f0306eb6508663d3fea7d2e00b4a
 astropy-checksum = c32e874d208f312f894643ab5b3d71dc37630e544da0ceb5ee998d752f9a055d32f6e4319f2cb6928637aaf8573bac58d2882bd636b6a89f5501e3ac7e5ab681
-astroquery-checksum = 0da57f687ac0aa7611cd97085771d79c99e9ac8c11f0828fcbc7390faf24e1e87d86812020e0ae8be1749f5f2ae9cb3733e5922d38a897a9e212247175c28e52
+astroquery-checksum = 43846791d8469a26cf6bb8819db58b830cfe50a34bc0091c2e843dd7dc78b1317530855d432a3a567a9f6a6f4d2682382a32edc91ea01716246b99b3625ec521
 beautifulsoup4-checksum = 7aa77bc6008bbcbbbe91b0a850007ab237d2832b63a787fbd94b7cbf47d4276b185e0c61c134df73221406458edff2b75b6b8c2b53b543aa3bb1b0e2202dac5a
 certifi-checksum = 6a6bf1ff98caefcdbf78a8c83e11e155368bacdd806f0ae0c6afa8f513667df6598e594b3584de61acdca3d6049f4a776937f2aa8672b602bd6db7b737f6074e
 cffi-checksum = af4fe47cf5d6f1126222898365cfa21e9f11d0e71b87d869014dbb37af30dca9ddf50c989030d0f610f50e8099e8dfd08a688d8c3629abbcc4f0294f5f91b817
diff --git a/reproduce/software/config/installation/texlive.mk b/reproduce/software/config/installation/texlive-packages.conf
index 6760eba..6760eba 100644
--- a/reproduce/software/config/installation/texlive.mk
+++ b/reproduce/software/config/installation/texlive-packages.conf
diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.conf
index 988f668..1b678ad 100644
--- a/reproduce/software/config/installation/versions.mk
+++ b/reproduce/software/config/installation/versions.conf
@@ -41,7 +41,7 @@ libiconv-version = 1.16
 libtool-version = 2.4.6
 lzip-version= 1.20
 m4-version = 1.4.18
-make-version = 4.2.90
+make-version = 4.3
 metastore-version = 1.1.2-23-fa9170b
 mpc-version = 1.1.0
 mpfr-version = 4.0.2
@@ -69,9 +69,9 @@ zlib-version = 1.2.11
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/installation/TARGETS.mk' will be built as part
-# of a project. To specify a software there, just remove the `-version'
-# suffix from the list below.
+# `reproduce/software/config/installation/TARGETS.conf' will be built as
+# part of a project. To specify a software there, just remove the
+# `-version' suffix from the list below.
 apachelog4cxx-version = 0.10.0-603-014954db
 apr-version = 1.7.0
 apr-util-version = 1.6.1
@@ -108,6 +108,7 @@ libtiff-version = 4.0.10
 libtirpc-version = 1.1.4
 libxml2-version = 2.9.9
 minizip-version = 2.9.2
+missfits-version = 2.8.0
 openblas-version = 0.3.5
 openmpi-version = 4.0.1
 openssh-version = 8.0p1
@@ -139,7 +140,7 @@ yaml-version = 0.2.2
 asn1crypto-version = 0.24.0
 asteval-version = 0.9.16
 astropy-version = 4.0
-astroquery-version = 0.3.9
+astroquery-version = 0.4
 beautifulsoup4-version = 4.7.1
 certifi-version = 2018.11.29
 cffi-version = 1.12.2
diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md
index fc04dfb..d71a3d5 100644
--- a/reproduce/software/make/README.md
+++ b/reproduce/software/make/README.md
@@ -2,7 +2,7 @@ Software building instructions
 ==============================
 
 This directory contains Makefiles that are called by the high-level
-`reproduce/software/bash/configure.sh` script. The main target for the
+`reproduce/software/shell/configure.sh` script. The main target for the
 installation of each software is a simple plain text file that contains the
 name of the software and its version (which is put in the paper in the
 end). Once built, these plain-text files are all put in the proper
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index e7d00df..212c738 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -34,9 +34,9 @@
 
 # Top level environment
 include reproduce/software/make/build-rules.mk
-include reproduce/software/config/installation/LOCAL.mk
-include reproduce/software/config/installation/versions.mk
-include reproduce/software/config/installation/checksums.mk
+include reproduce/software/config/installation/LOCAL.conf
+include reproduce/software/config/installation/versions.conf
+include reproduce/software/config/installation/checksums.conf
 
 lockdir = $(BDIR)/locks
 tdir    = $(BDIR)/software/tarballs
@@ -48,7 +48,7 @@ ibidir  = $(BDIR)/software/installed/version-info/proglib
 
 # We'll need the system's PATH for making links to low-level programs we
 # won't be building ourselves.
-syspath         := $(PATH)
+syspath := $(PATH)
 
 # As we build more programs, we want to use this project's built programs
 # and libraries, not the host's.
@@ -58,7 +58,15 @@ export PKG_CONFIG_PATH := $(ildir)/pkgconfig
 export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
 export CPPFLAGS := -I$(idir)/include $(CPPFLAGS)
 export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
-export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH) \
+
+# This is the "basic" tools where we are relying on the host operating
+# system, but are slowly populating our basic software envirnoment. To run
+# (system or template) programs, `LD_LIBRARY_PATH' is necessary, so here,
+# we'll first tell the programs to look into any possible pre-defined
+# `LD_LIBRARY_PATH', then we'll add our own newly installed libraries.  We
+# will also make sure that there is no "current directory" in it (by
+# removing a starting or trailing `:' and any occurance of `::'.
+export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \
                                   | sed -e's/::/:/g' -e's/^://' -e's/:$$//')
 
 # RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
@@ -66,14 +74,18 @@ export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH) \
 # causes crashs (see bug #56682). So we'll just give it no value at all.
 export DYLD_LIBRARY_PATH :=
 
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# Recipe startup script.
 export PROJECT_STATUS := configure_basic
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
 
 # Define the top-level basic programs (that don't depend on any other).
 top-level-programs = low-level-links gcc
 all: $(foreach p, $(top-level-programs), $(ibidir)/$(p))
 
+# Servers to use as backup, later this should go in a file that is not
+# under version control (the actual server that the tarbal comes from is
+# irrelevant).
+backupservers = http://akhlaghi.org/reproduce-software
 
 
 
@@ -176,7 +188,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  mergenames=0; \
 	  c=$(m4-checksum); \
 	  w=http://akhlaghi.org/reproduce-software/m4-1.4.18-patched.tar.gz; \
-	elif [ $$n = make      ]; then c=$(make-checksum); w=https://alpha.gnu.org/gnu/make; \
+	elif [ $$n = make      ]; then c=$(make-checksum); w=https://ftp.gnu.org/gnu/make; \
 	elif [ $$n = metastore ]; then c=$(metastore-checksum); w=http://akhlaghi.org/reproduce-software; \
 	elif [ $$n = mpc       ]; then c=$(mpc-checksum); w=http://ftp.gnu.org/gnu/mpc; \
 	elif [ $$n = mpfr      ]; then c=$(mpfr-checksum); w=http://www.mpfr.org/mpfr-current;\
@@ -228,15 +240,19 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	      \
 	  touch $(lockdir)/download; \
 	  $(downloadwrapper) "$$downloader" $(lockdir)/download \
-	                     $$tarballurl "$@.unchecked"; \
+	                     $$tarballurl "$@.unchecked" "$(backupservers)"; \
 	fi; \
 	                                                \
 	                                                \
 	if type sha512sum > /dev/null 2>/dev/null; then \
 	  checksum=$$(sha512sum "$@.unchecked" | awk '{print $$1}'); \
-	  echo "$*: should be '$$c', is '$$checksum'"; \
-	  if [ x$$checksum = x$$c ]; then mv "$@.unchecked" "$@"; \
-	  else echo "ERROR: Non-matching checksum for '$*'."; exit 1; \
+	  if [ x"$$checksum" = x"$$c" ]; then \
+	    mv "$@.unchecked" "$@"; \
+	  else \
+	    echo "ERROR: Non-matching checksum for '$*'."; \
+	    echo "Checksum should be: $$c"; \
+	    echo "Checksum is:        $$checksum"; \
+	    exit 1; \
 	  fi; \
 	else mv "$@.unchecked" "$@"; \
 	fi;
@@ -658,6 +674,66 @@ $(ibidir)/bash: $(ibidir)/readline \
 
 
 
+# The `-shared' flag will cause problems while building Perl on macOS, so
+# we'll only use this configuration option when we are GNU/Linux
+# systems. However, since the whole option must be used (which includes `='
+# and empty space), its easier to define the variable as a Make variable
+# outside the recipe, not as a shell variable inside it.
+ifeq ($(on_mac_os),yes)
+perl-conflddlflags =
+else
+perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS"
+endif
+$(ibidir)/perl: | $(ibidir)/bash \
+                  $(tdir)/perl-$(perl-version).tar.gz
+	major_version=$$(echo $(perl-version) \
+	                     | sed -e's/\./ /g' \
+	                     | awk '{printf("%d", $$1)}'); \
+	base_version=$$(echo $(perl-version) \
+	                     | sed -e's/\./ /g' \
+	                     | awk '{printf("%d.%d", $$1, $$2)}'); \
+	cd $(ddir) \
+	&& rm -rf perl-$(perl-version) \
+	&& if ! tar xf $(word 1,$(filter $(tdir)/%,$|)); then \
+	      echo; echo "Tar error"; exit 1; \
+	   fi \
+	&& cd perl-$(perl-version) \
+	&& sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \
+	       -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \
+	       Configure > Configure-tmp \
+	&& mv -f Configure-tmp Configure \
+	&& chmod +x Configure \
+	&& ./Configure -des \
+	               -Dusethreads \
+	               -Duseshrplib \
+	               -Dprefix=$(idir) \
+	               -Dvendorprefix=$(idir) \
+	               -Dprivlib=$(idir)/share/perl$$major_version/core_perl \
+	               -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \
+	               -Dsitelib=$(idir)/share/perl$$major_version/site_perl \
+	               -Dsitearch=$(idir)/lib/perl$$major_version/$$basever/site_perl \
+	               -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \
+	               -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \
+	               -Dscriptdir=$(idir)/bin/core_perl \
+	               -Dsitescript=$(idir)/bin/site_perl \
+	               -Dvendorscript=$(idir)/bin/vendor_perl \
+	               -Dinc_version_list=none \
+	               -Dman1ext=1perl \
+	               -Dman3ext=3perl \
+	               -Dcccdlflags='-fPIC' \
+	               $(perl-conflddlflags) \
+	               -Dldflags="$$LDFLAGS" \
+	&& make SHELL=$(ibdir)/bash -j$(numthreads) \
+	&& make SHELL=$(ibdir)/bash install \
+	&& cd .. \
+	&& rm -rf perl-$(perl-version) \
+	&& cd $$topdir \
+	&& echo "Perl $(perl-version)" > $@
+
+
+
+
+
 # Coreutils
 # ---------
 #
@@ -677,8 +753,10 @@ $(ibidir)/bash: $(ibidir)/readline \
 # The echo after the PatchELF loop is to avoid a crash if the last
 # file that PatchELF encounters is not usable (and it returns with
 # an error).
+#
+# Coreutils uses Perl to create man pages!
 $(ibidir)/coreutils: $(ibidir)/openssl \
-	             | $(ibidir)/bash \
+	             | $(ibidir)/perl \
                        $(tdir)/coreutils-$(coreutils-version).tar.xz
 	cd $(ddir) \
 	&& rm -rf coreutils-$(coreutils-version) \
@@ -847,17 +925,17 @@ $(ibidir)/wget: $(ibidir)/libiconv \
 # there is no access to the system's PATH.
 $(ibidir)/diffutils: | $(ibidir)/coreutils \
                        $(tdir)/diffutils-$(diffutils-version).tar.xz
-	$(call gbuild, diffutils-$(diffutils-version), static, , V=1) \
+	$(call gbuild, diffutils-$(diffutils-version), static,,V=1) \
 	&& echo "GNU Diffutils $(diffutils-version)" > $@
 
 $(ibidir)/file: | $(ibidir)/coreutils \
                   $(tdir)/file-$(file-version).tar.gz
-	$(call gbuild, file-$(file-version), static) \
+	$(call gbuild, file-$(file-version), static,,V=1) \
 	&& echo "File $(file-version)" > $@
 
 $(ibidir)/findutils: | $(ibidir)/coreutils \
                        $(tdir)/findutils-$(findutils-version).tar.xz
-	$(call gbuild, findutils-$(findutils-version), static, , V=1) \
+	$(call gbuild, findutils-$(findutils-version), static,,V=1) \
 	&& echo "GNU Findutils $(findutils-version)" > $@
 
 $(ibidir)/gawk: $(ibidir)/gmp \
@@ -910,13 +988,13 @@ $(ibidir)/gmp: | $(ibidir)/m4 \
 $(ibidir)/glibtool: | $(ibidir)/m4 \
                       $(tdir)/libtool-$(libtool-version).tar.xz
 	$(call gbuild, libtool-$(libtool-version), static, \
-                       --program-prefix=g) \
+                       --program-prefix=g, V=1) \
 	&& ln -s $(ibdir)/glibtoolize $(ibdir)/libtoolize \
 	&& echo "GNU Libtool $(libtool-version)" > $@
 
 $(ibidir)/grep: | $(ibidir)/coreutils \
                   $(tdir)/grep-$(grep-version).tar.xz
-	$(call gbuild, grep-$(grep-version), static) \
+	$(call gbuild, grep-$(grep-version), static,,V=1) \
 	&& echo "GNU Grep $(grep-version)" > $@
 
 $(ibidir)/libbsd: | $(ibidir)/coreutils \
@@ -927,7 +1005,7 @@ $(ibidir)/libbsd: | $(ibidir)/coreutils \
 $(ibidir)/m4: | $(ibidir)/coreutils \
                 $(ibidir)/texinfo \
                 $(tdir)/m4-$(m4-version).tar.gz
-	$(call gbuild, m4-$(m4-version), static) \
+	$(call gbuild, m4-$(m4-version), static,,V=1) \
 	&& echo "GNU M4 $(m4-version)" > $@
 
 # Metastore is used (through a Git hook) to restore the source modification
@@ -997,7 +1075,7 @@ $(ibidir)/metastore: $(needlibbsd) \
 	           -e's|@GROUP[@]|'$$group'|g' \
 	           -e's|@BINDIR[@]|$(ibdir)|g' \
 	           -e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \
-	           reproduce/software/bash/git-$$f > .git/hooks/$$f \
+	           reproduce/software/shell/git-$$f > .git/hooks/$$f \
 	       && chmod +x .git/hooks/$$f; \
 	    done; \
 	  fi \
@@ -1020,63 +1098,6 @@ $(ibidir)/mpfr: $(ibidir)/gmp \
 	$(call gbuild, mpfr-$(mpfr-version), static, , , make check)  \
 	&& echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@
 
-# The `-shared' flag will cause problems while building Perl on macOS, so
-# we'll only use this configuration option when we are GNU/Linux
-# systems. However, since the whole option must be used (which includes `='
-# and empty space), its easier to define the variable as a Make variable
-# outside the recipe, not as a shell variable inside it.
-ifeq ($(on_mac_os),yes)
-perl-conflddlflags =
-else
-perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS"
-endif
-$(ibidir)/perl: | $(ibidir)/coreutils \
-                  $(tdir)/perl-$(perl-version).tar.gz
-	major_version=$$(echo $(perl-version) \
-	                     | sed -e's/\./ /g' \
-	                     | awk '{printf("%d", $$1)}'); \
-	base_version=$$(echo $(perl-version) \
-	                     | sed -e's/\./ /g' \
-	                     | awk '{printf("%d.%d", $$1, $$2)}'); \
-	cd $(ddir) \
-	&& rm -rf perl-$(perl-version) \
-	&& if ! tar xf $(word 1,$(filter $(tdir)/%,$|)); then \
-	      echo; echo "Tar error"; exit 1; \
-	   fi \
-	&& cd perl-$(perl-version) \
-	&& sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \
-	       -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \
-	       Configure > Configure-tmp \
-	&& mv -f Configure-tmp Configure \
-	&& chmod +x Configure \
-	&& ./Configure -des \
-	               -Dusethreads \
-	               -Duseshrplib \
-	               -Dprefix=$(idir) \
-	               -Dvendorprefix=$(idir) \
-	               -Dprivlib=$(idir)/share/perl$$major_version/core_perl \
-	               -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \
-	               -Dsitelib=$(idir)/share/perl$$major_version/site_perl \
-	               -Dsitearch=$(idir)/lib/perl$$major_version/$$basever/site_perl \
-	               -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \
-	               -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \
-	               -Dscriptdir=$(idir)/bin/core_perl \
-	               -Dsitescript=$(idir)/bin/site_perl \
-	               -Dvendorscript=$(idir)/bin/vendor_perl \
-	               -Dinc_version_list=none \
-	               -Dman1ext=1perl \
-	               -Dman3ext=3perl \
-	               -Dcccdlflags='-fPIC' \
-	               $(perl-conflddlflags) \
-	               -Dldflags="$$LDFLAGS" \
-	&& make SHELL=$(ibdir)/bash -j$(numthreads) \
-	&& make SHELL=$(ibdir)/bash install \
-	&& cd .. \
-	&& rm -rf perl-$(perl-version) \
-	&& cd $$topdir \
-	&& echo "Perl $(perl-version)" > $@
-
-
 $(ibidir)/pkg-config: | $(ibidir)/coreutils \
                         $(tdir)/pkg-config-$(pkgconfig-version).tar.gz
         # An existing `libiconv' can cause a conflict with `pkg-config',
@@ -1101,7 +1122,7 @@ $(ibidir)/pkg-config: | $(ibidir)/coreutils \
 
 $(ibidir)/sed: | $(ibidir)/coreutils \
                  $(tdir)/sed-$(sed-version).tar.xz
-	$(call gbuild, sed-$(sed-version), static) \
+	$(call gbuild, sed-$(sed-version), static,,V=1) \
 	&& echo "GNU Sed $(sed-version)" > $@
 
 $(ibidir)/texinfo: | $(ibidir)/perl \
@@ -1111,7 +1132,7 @@ $(ibidir)/texinfo: | $(ibidir)/perl \
 	     $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/info; \
 	     $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/install-info; \
 	   fi \
-	&& echo "GNU Texinfo $(sed-version)" > $@
+	&& echo "GNU Texinfo $(texinfo-version)" > $@
 
 $(ibidir)/which: | $(ibidir)/coreutils \
                    $(tdir)/which-$(which-version).tar.gz
@@ -1161,6 +1182,15 @@ endif
 # programs (http://savannah.nongnu.org/bugs/?56294). Therefore, we'll set
 # all other basic programs as Binutils prerequisite and GCC (the final
 # basic target) ultimately just depends on Binutils.
+#
+# The `ld' linker of Binutils needs several `*crt*.o' file to run. On some
+# systems these object files aren't installed in standard places. We
+# defined `LIBRARY_PATH' and that fixed the problem for many
+# systems. However, some software (for example ImageMagick) over-write
+# `LIBRARY_PATH', therefore there is no other way than to put a link to
+# these necessary files in our local build directory. IMPORTANT NOTE:
+# later, when we build the GNU C Library in the project, we should remove
+# this step.
 $(ibidir)/binutils: | $(ibidir)/sed \
                       $(ibidir)/wget \
                       $(ibidir)/grep \
@@ -1174,6 +1204,7 @@ $(ibidir)/binutils: | $(ibidir)/sed \
                       $(ibidir)/diffutils \
                       $(ibidir)/coreutils \
                       $(gcc-prerequisites)
+
 	if [ x$(on_mac_os) = xyes ]; then \
 	  $(call makelink,as); \
 	  $(call makelink,ar); \
@@ -1181,9 +1212,17 @@ $(ibidir)/binutils: | $(ibidir)/sed \
 	  $(call makelink,nm); \
 	  $(call makelink,ps); \
 	  $(call makelink,ranlib); \
-          echo "" > $@; \
+	  echo "" > $@; \
 	else \
-	  $(call gbuild, binutils-$(binutils-version), static) \
+	  $(call gbuild, binutils-$(binutils-version), static, \
+	                 --with-lib-path=$(sys_library_path), \
+	                 -j$(numthreads) ) \
+	  && if ! [ x"$(sys_library_path)" = x ]; then \
+	       for f in $(sys_library_path)/*crt*.o; do \
+	         b=$$($(ibdir)/basename $$f); \
+	         ln -s $$f $(ildir)/$$b; \
+	       done; \
+	     fi \
 	  && echo "GNU Binutils $(binutils-version)" > $@; \
 	fi
 
@@ -1222,15 +1261,27 @@ $(ibidir)/gcc: | $(ibidir)/binutils \
 	  ccinfo=$$(gcc --version | awk 'NR==1'); \
 	  echo "C compiler (""$$ccinfo"")" > $@; \
 	else \
+	  current_dir=$$(pwd); \
 	  rm -f $(ibdir)/gcc* $(ibdir)/g++ $(ibdir)/gfortran $(ibdir)/gcov*;\
 	  rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc*; \
 	  rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*;\
 	                                 \
 	  ln -fs $(ildir) $(idir)/lib64; \
-	                                 \
-	  cd $(ddir); \
+	                       \
+	  in_ram=$$(df $(ddir) \
+	               | awk 'NR==2{print ($$4>10000000) ? "yes" : "no"}'); \
+	  if [ $$in_ram = "yes" ]; then odir=$(ddir); \
+	  else \
+	    odir=$(BDIR)/software/build-tmp-gcc; \
+	    if [ -d $$odir ]; then rm -rf $$odir; fi; \
+	    mkdir $$odir; \
+	  fi; \
+	  cd $$odir; \
 	  rm -rf gcc-$(gcc-version); \
-	  tar xf $(word 1,$(filter $(tdir)/%,$|)) \
+	  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) \
 	  && mkdir build \
 	  && cd build \
@@ -1257,15 +1308,24 @@ $(ibidir)/gcc: | $(ibidir)/binutils \
 	  && make SHELL=$(ibdir)/bash -j$(numthreads) \
 	  && make SHELL=$(ibdir)/bash install \
 	  && cd ../.. \
-	  && rm -rf gcc-$(gcc-version) \
+	  && tempname=$$odir/gcc-$(gcc-version)/build/rpath-temp-copy \
 	  && if [ "x$(on_mac_os)" != xyes ]; then \
 	       patchelf --add-needed $(ildir)/libiconv.so $(ildir)/libstdc++.so; \
 	       for f in $$(find $(idir)/libexec/gcc) $(ildir)/libstdc++*; do \
-	         if ldd $$f &> /dev/null; then \
-	           patchelf --set-rpath $(ildir) $$f; \
+	         isdynamic=$$(file $$f | grep "dynamically linked"); \
+	         if [ x"$$isdynamic" != x ]; then \
+	           cp $$f $$tempname; \
+	           patchelf --set-rpath $(ildir) $$tempname; \
+	           mv $$tempname $$f; echo "corrected"; \
 	         fi; \
 	       done; \
 	     fi \
+	  && rm -rf gcc-$(gcc-version) \
+	  && cd $$current_dir \
+	  && if [ "$$odir" != "$(ddir)" ]; then \
+	       rm -rf $$odir; \
+	       rm $(ddir)/gcc-$(gcc-version); \
+	     fi \
 	  && ln -sf $(ibdir)/gcc $(ibdir)/cc \
 	  && echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@; \
 	fi
diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
index cbde70b..f3ca7d2 100644
--- a/reproduce/software/make/build-rules.mk
+++ b/reproduce/software/make/build-rules.mk
@@ -1,7 +1,7 @@
 # Generic configurable recipes to build packages with GNU Build system or
 # CMake. This is Makefile is not intended to be run directly, it will be
-# imported into `dependencies-basic.mk' and `dependencies.mk'. They should
-# be activated with Make's `Call' function.
+# imported into `basic.mk' and `high-level.mk'. They should be activated
+# with Make's `Call' function.
 #
 # Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index ac46f3a..5f1d2b2 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -28,11 +28,11 @@
 
 # Top level environment
 include reproduce/software/make/build-rules.mk
-include reproduce/software/config/installation/LOCAL.mk
-include reproduce/software/config/installation/TARGETS.mk
-include reproduce/software/config/installation/texlive.mk
-include reproduce/software/config/installation/versions.mk
-include reproduce/software/config/installation/checksums.mk
+include reproduce/software/config/installation/LOCAL.conf
+include reproduce/software/config/installation/TARGETS.conf
+include reproduce/software/config/installation/versions.conf
+include reproduce/software/config/installation/checksums.conf
+include reproduce/software/config/installation/texlive-packages.conf
 
 lockdir = $(BDIR)/locks
 tdir    = $(BDIR)/software/tarballs
@@ -70,8 +70,8 @@ all: $(foreach p, $(top-level-programs),  $(ibidir)/$(p)) \
 .SHELLFLAGS := --noprofile --norc -ec
 export CCACHE_DISABLE := 1
 export PATH := $(ibdir)
-export CXX := $(ibdir)/g++
 export CC := $(ibdir)/gcc
+export CXX := $(ibdir)/g++
 export SHELL := $(ibdir)/bash
 export F77 := $(ibdir)/gfortran
 export LD_RUN_PATH := $(ildir):$(il64dir)
@@ -79,14 +79,31 @@ export PKG_CONFIG_PATH := $(ildir)/pkgconfig
 export LD_LIBRARY_PATH := $(ildir):$(il64dir)
 export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
 
+# Until we build our own C library, without this, our GCC won't be able to
+# compile anything! Note that on most systems (in particular
+# non-Debian-based), `sys_cpath' will be empty.
+export CPATH := $(sys_cpath)
+
 # RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
 # ultimately redundant. But on some systems, even having a single value
 # causes crashs (see bug #56682). So we'll just give it no value at all.
 export DYLD_LIBRARY_PATH :=
 
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# On Debian-based OSs, the basic C libraries are in a target-specific
+# location, not in standard places. Until we merge the building of the C
+# library, it is thus necessary to include this location here. On systems
+# that don't need it, `sys_library_path' is just empty. This is necessary
+# for `ld'.
+export LIBRARY_PATH := $(sys_library_path)
+
+# Recipe startup script, see `reproduce/software/shell/bashrc.sh'.
 export PROJECT_STATUS := configure_highlevel
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
+
+# Servers to use as backup, later this should go in a file that is not
+# under version control (the actual server that the tarbal comes from is
+# irrelevant).
+backupservers = http://akhlaghi.org/reproduce-software
 
 # Building flags:
 #
@@ -168,6 +185,7 @@ tarballs = $(foreach t, apachelog4cxx-$(apachelog4cxx-version).tar.lz \
                         libtirpc-$(libtirpc-version).tar.bz2 \
                         libxml2-$(libxml2-version).tar.gz \
                         minizip-$(minizip-version).tar.gz \
+                        missfits-$(missfits-version).tar.gz \
                         netpbm-$(netpbm-version).tar.gz \
                         openblas-$(openblas-version).tar.gz \
                         openmpi-$(openmpi-version).tar.gz \
@@ -268,6 +286,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  mergenames=0
 	  c=$(minizip-checksum);
 	  w=https://github.com/nmoinvaz/minizip/archive/$(minizip-version).tar.gz
+	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/reproduce-software
 	elif [ $$n = openblas    ]; then
 	  mergenames=0
@@ -325,7 +344,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  touch $(lockdir)/download
 	  downloader="wget --no-use-server-timestamps -O"
 	  $(downloadwrapper) "$$downloader" $(lockdir)/download \
-	                     $$tarballurl "$@.unchecked"
+	                     $$tarballurl "$@.unchecked" "$(backupservers)"
 	fi
 
         # Make sure this is the expected tarball. Note that we now have a
@@ -601,7 +620,7 @@ $(ibidir)/hdf5: $(ibidir)/openmpi \
 # HEALPix includes the source of its C, C++, Python (and several other
 # languages) libraries within one tarball. We will include the Python
 # installation only when any other Python module is requested (in
-# `TARGETS.mk').
+# `TARGETS.conf').
 #
 # Note that the default `./configure' script is an interactive script which
 # is hard to automate. So we need to go into the `autotools' directory of
@@ -647,7 +666,7 @@ $(ibidir)/healpix: $(ibidir)/cfitsio \
 	&& echo "HEALPix $(healpix-version) \citep{healpix}" > $@
 
 $(ibidir)/libjpeg: | $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
-	$(call gbuild, jpeg-9b, static) \
+	$(call gbuild, jpeg-9b, static,,V=1) \
 	&& echo "Libjpeg $(libjpeg-version)" > $@
 
 $(ibidir)/libnsl: $(ibidir)/libtirpc \
@@ -1017,12 +1036,15 @@ $(ibidir)/imfit: $(ibidir)/gsl \
 	   fi \
 	&& echo "Imfit $(imfit-version) \citep{imfit2015}" > $@
 
-
 $(ibidir)/minizip: $(ibidir)/cmake \
                    | $(tdir)/minizip-$(minizip-version).tar.gz
 	$(call cbuild, minizip-$(minizip-version), static) \
 	&& echo "minizip $(minizip-version)" > $@
 
+$(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz
+	$(call gbuild, missfits-$(missfits-version), static) \
+	&& cp $(dtexdir)/missfits.tex $(ictdir)/ \
+	&& echo "MissFITS $(missfits-version) \citep{missfits}" > $@
 
 # Netpbm is a prerequisite of Astrometry-net, it contains a lot of programs.
 # This program has a crazy dialogue installation which is override using the
@@ -1135,7 +1157,10 @@ $(ibidir)/xlsxio: $(ibidir)/expat \
                   | $(tdir)/xlsxio-$(xlsxio-version).tar.gz
 	export LDFLAGS="-lbz2 -lbsd"; \
 	$(call cbuild, xlsxio-$(xlsxio-version), static) \
-	&& echo "XLSX I/O $(xlsxio-version)" > $@
+	&& echo "XLSX I/O $(xlsxio-version)" > $
+
+
+
 
 
 
@@ -1216,7 +1241,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co
 #else
 #forbiber = $(ibidir)/libnsl
 #endif
-$(itidir)/texlive: reproduce/software/config/installation/texlive.mk \
+$(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf \
                    $(itidir)/texlive-ready-tlmgr \
                    $(forbiber)
 
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 8c7b6f0..fef1605 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -185,7 +185,7 @@ $(pytarballs): $(tdir)/%:
 	  h=$(pytopurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz
 	elif [ $$n = asn            ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4; c=$(asn1crypto-checksum)
 	elif [ $$n = asteval        ]; then h=50/3f/29b7935c6dc09ee96dc347edc66c57e8ef68d595dd35b763a36a117acc8c; c=$(asteval-checksum)
-	elif [ $$n = astroquery     ]; then h=61/50/a7a08f9e54d7d9d97e69433cd88231e1ad2901811c9d1ae9ac7ccaef9396; c=$(astroquery-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 = certifi        ]; then h=55/54/3ce77783acba5979ce16674fc98b1920d00b01d337cfaaf5db22543505ed; c=$(certifi-checksum)
@@ -259,7 +259,7 @@ $(pytarballs): $(tdir)/%:
 	  touch $(lockdir)/download
 	  downloader="wget --no-use-server-timestamps -O"
 	  $(downloadwrapper) "$$downloader" $(lockdir)/download \
-	                     $$tarballurl "$@.unchecked"
+	                     $$tarballurl "$@.unchecked" "$(backupservers)"
 	fi
 
         # Make sure this is the expected tarball. Note that we now have a
@@ -373,12 +373,9 @@ $(ipydir)/asteval: $(ipydir)/numpy \
 	$(call pybuild, tar xf, asteval-$(asteval-version), , \
 	                ASTEVAL $(asteval-version))
 
-$(ipydir)/astroquery: $(ipydir)/numpy \
-                      $(ipydir)/astropy \
+$(ipydir)/astroquery: $(ipydir)/astropy \
                       $(ipydir)/keyring \
-                      $(ipydir)/html5lib \
                       $(ipydir)/requests \
-                      $(ipydir)/beautifulsoup4 \
                       | $(tdir)/astroquery-$(astroquery-version).tar.gz
 	$(call pybuild, tar xf, astroquery-$(astroquery-version), ,\
 	                Astroquery $(astroquery-version))
@@ -386,6 +383,9 @@ $(ipydir)/astroquery: $(ipydir)/numpy \
 $(ipydir)/astropy: $(ipydir)/h5py \
                    $(ipydir)/scipy \
                    $(ipydir)/numpy \
+                   $(ipydir)/pyyaml \
+                   $(ipydir)/html5lib \
+                   $(ipydir)/beautifulsoup4 \
                    | $(tdir)/astropy-$(astropy-version).tar.gz
 	$(call pybuild, tar xf, astropy-$(astropy-version)) \
 	&& cp $(dtexdir)/astropy.tex $(ictdir)/ \
diff --git a/reproduce/software/bash/bashrc.sh b/reproduce/software/shell/bashrc.sh
index b2a151f..b2a151f 100755
--- a/reproduce/software/bash/bashrc.sh
+++ b/reproduce/software/shell/bashrc.sh
diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/shell/configure.sh
index f7fa9c8..6e1b5fb 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -1,4 +1,4 @@
-#! /bin/bash
+#! /bin/sh
 #
 # Necessary preparations/configurations for the reproducible project.
 #
@@ -38,11 +38,11 @@ cdir=reproduce/software/config
 
 sbdir=$cdir/installation
 
-pconf=$sbdir/LOCAL.mk
-ptconf=$sbdir/LOCAL_tmp.mk
-poconf=$sbdir/LOCAL_old.mk
-depverfile=$cdir/installation/versions.mk
-depshafile=$cdir/installation/checksums.mk
+pconf=$sbdir/LOCAL.conf
+ptconf=$sbdir/LOCAL_tmp.conf
+poconf=$sbdir/LOCAL_old.conf
+depverfile=$cdir/installation/versions.conf
+depshafile=$cdir/installation/checksums.conf
 # --------- Delete for no Gnuastro ---------
 glconf=$cdir/gnuastro/gnuastro-local.conf
 # ------------------------------------------
@@ -57,7 +57,8 @@ glconf=$cdir/gnuastro/gnuastro-local.conf
 # In case someone opens the files output from the configuration scripts in
 # a text editor and wants to edit them, it is important to let them know
 # that their changes are not going to be permenant.
-function create_file_with_notice() {
+create_file_with_notice ()
+{
     if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1"
     then
         echo "#"                                                      >> "$1"
@@ -81,7 +82,8 @@ function create_file_with_notice() {
 #
 # Since the build directory will go into a symbolic link, we want it to be
 # an absolute address. With this function we can make sure of that.
-function absolute_dir() {
+absolute_dir ()
+{
     if stat "$1" 1> /dev/null; then
         echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
     else
@@ -93,6 +95,415 @@ function absolute_dir() {
 
 
 
+# Check for C/C++ compilers
+# -------------------------
+#
+# To build the software, we'll need some basic tools (the compilers in
+# particular) to be present.
+hascc=0;
+if type cc > /dev/null 2>/dev/null; then
+    if type c++ > /dev/null 2>/dev/null; then export CC=cc; hascc=1; fi
+else
+    if type gcc > /dev/null 2>/dev/null; then
+        if type g++ > /dev/null 2>/dev/null; then export CC=gcc; hascc=1; fi
+    else
+        if type clang > /dev/null 2>/dev/null; then
+            if type clang++ > /dev/null 2>/dev/null; then export CC=clang; hascc=1; fi
+        fi
+    fi
+fi
+if [ $hascc = 0 ]; then
+    cat <<EOF
+______________________________________________________
+!!!!!!!       C/C++ Compiler NOT FOUND         !!!!!!!
+
+To build the project's software, the host system needs to have basic C and
+C++ compilers. The executables that were checked are 'cc', 'gcc' and
+'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++
+compiler. If you have a relevant compiler that is not checked, please get
+in touch with us (with the form below) so we add it:
+
+  https://savannah.nongnu.org/support/?func=additem&group=reproduce
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    exit 1
+fi
+
+
+
+
+
+# Special directory for compiler testing
+# --------------------------------------
+#
+# This directory will be deleted when the compiler testing is finished.
+compilertestdir=.compiler_test_dir_please_delete
+if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi
+
+
+
+
+
+# Check C compiler
+# ----------------
+gcc_works=0
+testprog=$compilertestdir/test
+testsource=$compilertestdir/test.c
+echo; echo; echo "Checking host C compiler...";
+cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+int main(void){printf("...C compiler works.\n");
+               return EXIT_SUCCESS;}
+EOF
+if $CC $testsource -o$testprog && $testprog; then
+    rm $testsource $testprog
+else
+    rm $testsource
+    cat <<EOF
+
+______________________________________________________
+!!!!!!!        C compiler doesn't work         !!!!!!!
+
+Host C compiler ('gcc') can't build a simple program.
+
+A working C compiler is necessary for building the project's software.
+Please use the error message above to find a good solution and re-run the
+project configuration.
+
+If you can't find a solution, please send the error message above to the
+link below and we'll try to help
+
+https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+TIP: Once you find the solution, you can use the '-e' option to use
+existing configuration:
+
+   $ ./project configure -e
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    exit 1
+fi
+
+
+
+
+
+# See if the linker accepts -Wl,-rpath-link
+# -----------------------------------------
+#
+# `-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.
+cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+int main(void) {return EXIT_SUCCESS;}
+EOF
+if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then
+    export rpath_command="-Wl,-rpath-link=$instdir/lib"
+else
+    export rpath_command=""
+fi
+rm -f $testprog $testsource
+
+
+
+
+
+# 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
+# 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
+#include <stdio.h>
+#include <dlfcn.h>
+int
+main(void) {
+    void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
+    return 0;
+}
+EOF
+if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then
+    needs_ldl=no;
+else
+    needs_ldl=yes;
+fi
+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
+# 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
+# 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.
+static_build=no
+
+
+
+
+
+# If we are on a Mac OS system
+# ----------------------------
+#
+# For the time being, we'll use the existance of `otool' to see if we are
+# on a Mac OS system or not. Some tools (for example OpenSSL) need to know
+# this.
+#
+# On Mac OS, the building of GCC crashes sometimes while building libiberty
+# with CLang's `g++'. Until we find a solution, we'll just use the host's C
+# compiler.
+if type otool > /dev/null 2>/dev/null; then
+    host_cc=1
+    on_mac_os=yes
+    cat <<EOF
+
+______________________________________________________
+!!!!!!!!!!!!!!!        Warning        !!!!!!!!!!!!!!!!
+
+The GNU Compiler Collection (GCC, including compilers for C, C++, Fortran
+and etc) is currently not built on macOS systems for this project. To build
+the project's necessary software on this system, we need to use your
+system's C compiler.
+
+Project's configuration will continue in 5 seconds.
+______________________________________________________
+
+EOF
+    sleep 5
+else
+    host_cc=0
+    on_mac_os=no
+fi
+
+
+
+
+
+# Necessary C library element positions
+# -------------------------------------
+#
+# 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
+# similarly different location.
+sys_cpath=""
+sys_library_path=""
+if [ x"$$on_mac_os" != xyes ]; then
+
+    # Get the GCC target name of the compiler, when its given, special
+    # C libraries and headers are in a sub-directory of the host.
+    gcctarget=$(gcc -v 2>&1 \
+                    | tr ' ' '\n' \
+                    | awk '/\-\-target/' \
+                    | sed -e's/\-\-target=//')
+    if [ x"$gcctarget" != x ]; then
+        if [ -f /usr/lib/$gcctarget/libc.a ]; then
+            export sys_library_path=/usr/lib/$gcctarget
+            export sys_cpath=/usr/include/$gcctarget
+        fi
+    fi
+
+    # For a check:
+    #echo "sys_library_path: $sys_library_path"
+    #echo "sys_cpath: $sys_cpath"
+fi
+
+
+
+
+
+# See if a link-able static C library exists
+# ------------------------------------------
+#
+# After building GCC, we must use PatchELF to correct its RPATHs. However,
+# PatchELF links internally with `libstdc++'. So a dynamicly linked
+# PatchELF cannot be used to correct the links to `libstdc++' in general
+# (on some systems this causes no problem, but on others it doesn't!).
+#
+# However, to build a Static PatchELF, we need to be able to link with the
+# static C library, which is not always available on some GNU/Linux
+# systems. Therefore we need to check this here. If we can't build a static
+# PatchELF, we won't build any GCC either.
+if [ x"$host_cc" = x0 ]; then
+    echo; echo; echo "Checking if static C library is available...";
+    cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/cdefs.h>
+int main(void){printf("...yes\n");
+               return EXIT_SUCCESS;}
+EOF
+    cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc"
+    if $cc_call && $testprog; then
+        gccwarning=0
+        good_static_libc=1
+        rm $testsource $testprog
+    else
+        echo; echo "Compilation command:"; echo "$cc_call"
+        good_static_libc=0
+        rm $testsource
+        gccwarning=1
+        host_cc=1
+        cat <<EOF
+
+_______________________________________________________
+!!!!!!!!!!!!            Warning            !!!!!!!!!!!!
+
+The 'sys/cdefs.h' header cannot be included, or a usable static C library
+('libc.a', in any directory) cannot be used with the current settings of
+this system. SEE THE ERROR MESSAGE ABOVE.
+
+Because of this, we can't build GCC. You either 1) don't have them, or 2)
+the default system environment aren't enough to find them.
+
+1) If you don't have them, your operating system provides them as separate
+packages that you must manually install. Please look into your operating
+system documentation or contact someone familiar with it. For example on
+some Redhat-based GNU/Linux distributions, the static C library package can
+be installed with this command:
+
+    $ sudo yum install glibc-static
+
+2) If you have 'libc.a' and 'sys/cdefs.h', but in a non-standard location (for
+example in '/PATH/TO/STATIC/LIBC/libc.a' and
+'/PATH/TO/SYS/CDEFS_H/sys/cdefs.h'), please run the commands below, then
+re-configure the project to fix this problem.
+
+    $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
+    $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS"
+
+_______________________________________________________
+
+EOF
+    fi
+fi
+
+# Print a warning if GCC is not meant to be built.
+if [ x"$gccwarning" = x1 ]; then
+        cat <<EOF
+
+PLEASE SEE THE WARNINGS ABOVE.
+
+Since GCC is pretty low-level, this configuration script will continue in 5
+seconds and use your system's C compiler (it won't build a custom GCC). But
+please consider installing the necessary package(s) to complete your C
+compiler, then re-run './project configure'.
+
+Project's configuration will continue in 5 seconds.
+
+EOF
+        sleep 5
+fi
+
+
+
+
+
+# Fortran compiler
+# ----------------
+#
+# If GCC is ultimately build within the project, the user won't need to
+# have a fortran compiler, we'll build it internally for high-level
+# programs. However, when the host C compiler is to be used, the user needs
+# to have a Fortran compiler available.
+if [ $host_cc = 1 ]; then
+
+    # See if a Fortran compiler exists.
+    hasfc=0;
+    if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
+    if [ $hasfc = 0 ]; then
+        cat <<EOF
+______________________________________________________
+!!!!!!!      Fortran Compiler NOT FOUND        !!!!!!!
+
+The project won't be building its own GCC (which includes a Fortran
+compiler) on this system. If you need software that need a Fortran
+compiler, it will crash with an error. Fortran is necessary for many
+lower-level scientific programs, hence this warning. Currently we search
+for 'gfortran'. If you have a Fortran compiler that is not checked, please
+get in touch with us (with the form below) so we add it:
+
+  https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+Project's configuration will continue in 5 seconds.
+______________________________________________________
+
+EOF
+        sleep 5
+    else
+
+        # See if the Fortran compiler works
+        testsource=$compilertestdir/test.f
+        echo; echo; echo "Checking host Fortran compiler...";
+        echo "      PRINT *, \"... Fortran Compiler works.\""  > $testsource
+        echo "      END"                                      >> $testsource
+        if gfortran $testsource -o$testprog && $testprog; then
+            rm $testsource $testprog
+        else
+            rm $testsource
+            cat <<EOF
+
+______________________________________________________
+!!!!!!!     Fortran compiler doesn't work      !!!!!!!
+
+Host Fortran compiler ('gfortran') can't build a simple program.
+
+A working Fortran compiler is necessary for building some of the project's
+software.  Please use the error message above to find a good solution and
+re-run the project configuration.
+
+If you can't find a solution, please send the error message above to the
+link below and we'll try to help
+
+https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+TIP: Once you find the solution, you can use the '-e' option to use
+existing configuration:
+
+   $ ./project configure -e
+
+Project's configuration will continue in 5 seconds.
+______________________________________________________
+
+EOF
+            sleep 5
+        fi
+    fi
+fi
+
+
+
+
+
+# Delete the compiler testing directory
+# -------------------------------------
+#
+# This directory was made above to make sure the necessary compilers can be
+# run.
+rm -rf $compilertestdir
+
+
+
+
+
 # Inform the user
 # ---------------
 #
@@ -117,7 +528,7 @@ EOF
 # What to do with possibly existing configuration file
 # ----------------------------------------------------
 #
-# `LOCAL.mk' is the top-most local configuration for the project. If it
+# `LOCAL.conf' is the top-most local configuration for the project. If it
 # already exists when this script is run, we'll make a copy of it as backup
 # (for example the user might have ran `./project configure' by mistake).
 printnotice=yes
@@ -239,7 +650,7 @@ EOF
     bdir=
     currentdir=$(pwd)
     junkname=pure-junk-974adfkj38
-    while [ x$bdir == x ]
+    while [ x$bdir = x ]
     do
         # Ask the user (if not already set on the command-line).
         if [ x"$build_dir" = x ]; then
@@ -264,10 +675,12 @@ EOF
             fi
         fi
 
-        # Make sure the given directory is not a subdirectory of the
-        # source directory.
+        # If its given, make sure it isn't a subdirectory of the source
+        # directory.
         if ! [ x"$bdir" = x ]; then
-            if [[ $bdir == $currentdir* ]]; then
+            echo "Given build directory: $bdir"
+            if echo "$bdir/" \
+                    | grep '^'$currentdir 2> /dev/null > /dev/null; then
 
                 # If it was newly created, it will be empty, so delete it.
                 if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
@@ -299,10 +712,10 @@ if [ x"$input_dir" = x ]; then
 else
     indir=$input_dir
 fi
-mk20name=$(awk '!/^#/ && $1=="MK20DATA" {print $3}' $adir/INPUTS.mk)
-mk20md5=$(awk  '!/^#/ && $1=="MK20MD5"  {print $3}' $adir/INPUTS.mk)
-mk20size=$(awk '!/^#/ && $1=="MK20SIZE" {print $3}' $adir/INPUTS.mk)
-mk20url=$(awk  '!/^#/ && $1=="MK20URL"  {print $3}' $adir/INPUTS.mk)
+mk20name=$(awk '!/^#/ && $1=="MK20DATA" {print $3}' $adir/INPUTS.conf)
+mk20md5=$(awk  '!/^#/ && $1=="MK20MD5"  {print $3}' $adir/INPUTS.conf)
+mk20size=$(awk '!/^#/ && $1=="MK20SIZE" {print $3}' $adir/INPUTS.conf)
+mk20url=$(awk  '!/^#/ && $1=="MK20URL"  {print $3}' $adir/INPUTS.conf)
 if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
     cat <<EOF
 
@@ -387,6 +800,7 @@ if [ $rewritepconfig = yes ]; then
     sed -e's|@bdir[@]|'"$bdir"'|' \
         -e's|@indir[@]|'"$indir"'|' \
         -e's|@ddir[@]|'"$ddir"'|' \
+        -e's|@sys_cpath[@]|'"$sys_cpath"'|' \
         -e's|@downloader[@]|'"$downloader"'|' \
         -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
         $pconf.in >> $pconf
@@ -630,195 +1044,7 @@ fi
 
 
 
-# Check for C/C++ compilers
-# -------------------------
-#
-# To build the software, we'll need some basic tools (the compilers in
-# particular) to be present.
-hascc=0;
-if type cc > /dev/null 2>/dev/null; then
-    if type c++ > /dev/null 2>/dev/null; then hascc=1; fi
-else
-    if type gcc > /dev/null 2>/dev/null; then
-        if type g++ > /dev/null 2>/dev/null; then hascc=1; fi
-    else
-        if type clang > /dev/null 2>/dev/null; then
-            if type clang++ > /dev/null 2>/dev/null; then hascc=1; fi
-        fi
-    fi
-fi
-if [ $hascc = 0 ]; then
-    cat <<EOF
-______________________________________________________
-!!!!!!!       C/C++ Compiler NOT FOUND         !!!!!!!
-
-To build the project's software, the host system needs to have basic C and
-C++ compilers. The executables that were checked are 'cc', 'gcc' and
-'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++
-compiler. If you have a relevant compiler that is not checked, please get
-in touch with us (with the form below) so we add it:
-
-  https://savannah.nongnu.org/support/?func=additem&group=reproduce
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-    exit 1
-fi
-
-
-
-
-
-# Check C compiler
-# ----------------
-gcc_works=0
-testprog=$tmpblddir/test-c
-testsource=$tmpblddir/test.c
-echo; echo; echo "Checking host C compiler...";
-echo "#include <stdio.h>"                                  > $testsource
-echo "#include <stdlib.h>"                                >> $testsource
-echo "int main(void){printf(\"...C compiler works.\n\");" >> $testsource
-echo "               return EXIT_SUCCESS;}"               >> $testsource
-if gcc $testsource -o$testprog && $testprog; then
-    rm $testsource $testprog
-else
-    rm $testsource
-    cat <<EOF
-
-______________________________________________________
-!!!!!!!        C compiler doesn't work         !!!!!!!
-
-Host C compiler ('gcc') can't build a simple program.
-
-A working C compiler is necessary for building the project's software.
-Please use the error message above to find a good solution and re-run the
-project configuration.
-
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
-
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
-
-   $ ./project configure -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-    exit 1
-fi
-
-
-
-
-
-# See if the linker accepts -Wl,-rpath-link
-# -----------------------------------------
-#
-# `-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.
-oprog=$sdir/rpath-test
-cprog=$sdir/rpath-test.c
-echo "#include <stdio.h>"          > $cprog
-echo "int main(void) {return 0;}" >> $cprog
-if [ x$CC = x ]; then CC=gcc; fi;
-if $CC $cprog -o$oprog -Wl,-rpath-link &> /dev/null; then
-    export rpath_command="-Wl,-rpath-link=$instdir/lib"
-else
-    export rpath_command=""
-fi
-rm -f $oprog $cprog
-
-
-
-
-
-# See if we need the dynamic-linker (-ldl)
-# ----------------------------------------
-#
-# Some programs (like Wget) need dynamic loading (using `libdl'). On
-# GNU/Linux systems, we'll need the `-ldl' flag to link such programs.  But
-# Mac OS doesn't need any explicit linking. So we'll check here to see if
-# it is present (thus necessary) or not.
-oprog=$sdir/ldl-test
-cprog=$sdir/ldl-test.c
-cat > $cprog <<EOF
-#include <stdio.h>
-#include <dlfcn.h>
-int
-main(void) {
-    void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
-    return 0;
-}
-EOF
-if gcc $cprog -o$oprog &> /dev/null; then needs_ldl=no; else needs_ldl=yes; fi
-rm -f $oprog $cprog
-
-
-
-
-
-# See if the C compiler can build static libraries
-# ------------------------------------------------
-
-# We are manually only working with shared libraries: because some
-# high-level programs like Wget and cURL need dynamic linking and if we
-# build the libraries statically, our own builds will be ignored and these
-# programs will go and find their necessary libraries on the host system.
-#
-# Another good advantage of shared libraries is that we can actually use
-# the shared library tool of the system (`ldd' with GNU C Library) and see
-# exactly where each linked library comes from. But in static building,
-# unless you follow the build closely, its not easy to see if the source of
-# the library came from the system or our build.
-static_build=no
-
-#oprog=$sdir/static-test
-#cprog=$sdir/static-test.c
-#echo "#include <stdio.h>"          > $cprog
-#echo "int main(void) {return 0;}" >> $cprog
-#if [ x$CC = x ]; then CC=gcc; fi;
-#if $CC $cprog -o$oprog -static &> /dev/null; then
-#    export static_build="yes"
-#else
-#    export static_build="no"
-#fi
-#rm -f $oprog $cprog
-#if [ $printnotice = yes ] && [ $static_build = "no" ]; then
-#    cat <<EOF
-#_________________________________________________________________________
-#!!!!!!!!!!!!!!!!!!!!!!!!!!!!      WARNING      !!!!!!!!!!!!!!!!!!!!!!!!!!
-#
-#Your system's C compiler ('$CC') doesn't support building static
-#libraries. Therefore the dependencies will be built dynamically. This means
-#that they will depend more strongly on changes/updates in the host
-#system. For high-level applications (like most research projects in natural
-#sciences), this shouldn't be a significant problem.
-#
-#But generally, for reproducibility, its better to build static libraries
-#and programs. For more on their difference (and generally an introduction
-#on linking), please see the link below:
-#
-#https://www.gnu.org/software/gnuastro/manual/html_node/Linking.html
-#
-#If you have other compilers on your system, you can select a different
-#compiler by setting the 'CC' environment variable before running
-#'./project configure'.
-#
-#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-#
-#EOF
-#    sleep 5
-#fi
-
-
-
-
-
-# inform the user that the build process is starting
+# Inform the user that the build process is starting
 # -------------------------------------------------
 if [ $printnotice = yes ]; then
     tsec=10
@@ -839,12 +1065,13 @@ will be installed in:
 **TIP**: you can see which software is being installed at every moment with
 the following command. See "Inspecting status" section of
 'README-hacking.md' for more. In short, run it while the project is being
-configured (in another terminal, but on this same directory: '`pwd`'):
+configured (in another terminal, but on this same directory: 'pwd'):
 
-  $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done
+  $ ./project --check-config
 
--------------------------
+Project's configuration will continue in $tsec seconds.
 
+-------------------------
 
 EOF
     sleep $tsec
@@ -854,241 +1081,6 @@ fi
 
 
 
-# If we are on a Mac OS system
-# ----------------------------
-#
-# For the time being, we'll use the existance of `otool' to see if we are
-# on a Mac OS system or not. Some tools (for example OpenSSL) need to know
-# this.
-#
-# On Mac OS, the building of GCC crashes sometimes while building libiberty
-# with CLang's `g++'. Until we find a solution, we'll just use the host's C
-# compiler.
-if type otool > /dev/null 2>/dev/null; then
-    host_cc=1
-    on_mac_os=yes
-else
-    on_mac_os=no
-fi
-
-
-
-
-
-# See if GCC can be built
-# -----------------------
-#
-# On some GNU/Linux distros, the C compiler is broken into `multilib' (for
-# 32-bit and 64-bit support, with their own headers). On these systems,
-# `/usr/include/sys/cdefs.h' and `/usr/lib/libc.a' are not available by
-# default. So GCC will crash with different ugly errors! The only solution
-# is that user manually installs the `multilib' part as root, before
-# running the configure script.
-#
-# Note that `sys/cdefs.h' may be available in other directories (for
-# example `/usr/include/x86_64-linux-gnu/') that are automatically included
-# in an installed GCC. HOWEVER during the build of GCC, all those other
-# directories are ignored. So even if they exist, they are useless.
-gccwarning=0
-if [ $host_cc = 0 ]; then
-    if ! [ -f /usr/include/sys/cdefs.h ]; then
-        host_cc=1
-        gccwarning=1
-        cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-This system doesn't have '/usr/include/sys/cdefs.h'. Because of this, the
-project can't build its custom GCC to ensure better reproducibility. We
-strongly recommend installing the proper package (for your operating
-system) that installs this necessary file. For example on some Debian-based
-GNU/Linux distros, you need these two packages: 'gcc-multilib' and
-'g++-multilib'.
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-    fi
-
-    if [ -f /usr/lib/libc.a ] || [ -f /usr/lib64/libc.a ]; then
-        # This is just a place holder
-        host_cc=$host_cc
-    else
-        host_cc=1
-        gccwarning=1
-        cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-This system doesn't have '/usr/lib/libc.a' or '/usr/lib64/libc.a'. Because
-of this, the project can't build its custom GCC to ensure better
-reproducibility. We recommend installing the proper package (for your
-operating system) that installs this necessary file.
-
-Some possible solutions:
-  1. On some Debian-based GNU/Linux distros, these two packages may fix the
-     problem: 'gcc-multilib' and 'g++-multilib'.
-  2. (BE CAREFUL!) If you have '/usr/lib/x86_64-linux-gnu' but don't have
-     '/usr/lib64', then running the following command might fix this
-     particular problem by making a symbolic link.
-         $ sudo ln -s /usr/lib/x86_64-linux-gnu /usr/lib64
-     After the configure script is finished, delete the link with 'rm
-     /usr/lib64' (you won't need it any more as far as this project is
-     concerned).
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-    fi
-fi
-
-# See if a link-able static C library exists
-# ------------------------------------------
-#
-# After building GCC, we must use PatchELF to correct its RPATHs. However,
-# PatchELF links internally with `libstdc++'. So a dynamicly linked
-# PatchELF cannot be used to correct the links to `libstdc++' in general
-# (on some systems this causes no problem, but on others it doesn't!).
-#
-# However, to build a Static PatchELF, we need to be able to link with the
-# static C library, which is not always available on some GNU/Linux
-# systems. Therefore we need to check this here. If we can't build a static
-# PatchELF, we won't build any GCC either.
-if [ $host_cc = 0 ]; then
-    testprog=$tmpblddir/test-c
-    testsource=$tmpblddir/test.c
-    echo; echo; echo "Checking if static C library is available...";
-    echo "#include <stdio.h>"                       > $testsource
-    echo "#include <stdlib.h>"                     >> $testsource
-    echo "int main(void){printf(\"...yes\");"      >> $testsource
-    echo "               return EXIT_SUCCESS;}"    >> $testsource
-    if gcc $testsource -o$testprog -static -lc && $testprog; then
-        good_static_libc=1
-        rm $testsource $testprog
-    else
-        good_static_libc=0
-        rm $testsource
-        gccwarning=1
-        host_cc=1
-        cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-A usable static C library ('libc.a', in any directory) cannot be linked in
-the current settings of this system. Because of this we can't build a
-static PatchELF, hence we can't build GCC.
-
-If you have 'libc.a', but in a non-standard location (for example in
-'/PATH/TO/STATIC/LIBC/libc.a'), please run this command, then re-configure
-the project to fix this problem.
-
-export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-    fi
-fi
-
-# Print a warning if GCC is not meant to be built.
-if [ $gccwarning = 1 ]; then
-        cat <<EOF
-
-PLEASE SEE THE WARNINGS ABOVE.
-
-Since GCC is pretty low-level, this configuration script will continue in 5
-seconds and use your system's C compiler (it won't build a custom GCC). But
-please consider installing the necessary package(s) to complete your C
-compiler, then re-run './project configure'.
-
-EOF
-        sleep 5
-fi
-
-
-
-
-
-# Fortran compiler
-# ----------------
-#
-# If GCC is ultimately build within the project, the user won't need to
-# have a fortran compiler, we'll build it internally for high-level
-# programs. However, when the host C compiler is to be used, the user needs
-# to have a Fortran compiler available.
-if [ $host_cc = 1 ]; then
-
-    # See if a Fortran compiler exists.
-    hasfc=0;
-    if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
-    if [ $hasfc = 0 ]; then
-        cat <<EOF
-______________________________________________________
-!!!!!!!      Fortran Compiler NOT FOUND        !!!!!!!
-
-Because the project won't be building its own GCC (which includes a Fortran
-compiler), you need to have a Fortran compiler available. Fortran is
-commonly necessary for many lower-level scientific programs. Currently we
-search for 'gfortran'. If you have a Fortran compiler that is not checked,
-please get in touch with us (with the form below) so we add it:
-
-  https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-Note: GCC will not be built because you are either using the '--host-cc'
-option, or you are using an operating system that currently has bugs when
-building GCC.
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-        exit 1
-    fi
-
-    # See if the Fortran compiler works
-    testprog=$tmpblddir/test-f
-    testsource=$tmpblddir/test.f
-    echo; echo; echo "Checking host Fortran compiler...";
-    echo "      PRINT *, \"... Fortran Compiler works.\"" > $testsource
-    echo "      END"                                      >> $testsource
-    if gfortran $testsource -o$testprog && $testprog; then
-        rm $testsource $testprog
-    else
-        rm $testsource
-        cat <<EOF
-
-______________________________________________________
-!!!!!!!     Fortran compiler doesn't work      !!!!!!!
-
-Host Fortran compiler ('gfortran') can't build a simple program.
-
-A working Fortran compiler is necessary for building some of the project's
-software.  Please use the error message above to find a good solution and
-re-run the project configuration.
-
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
-
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
-
-   $ ./project configure -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-        exit 1
-    fi
-fi
-
-
-
-
-
 # Number of threads for basic builds
 # ----------------------------------
 #
@@ -1181,6 +1173,32 @@ fi
 
 
 
+# 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
+# operating systems use. We thus need to tell the intermediate compiler
+# where its necessary libraries and headers are.
+if [ x"$sys_library_path" != x ]; then
+    if [ x"$LIBRARY_PATH" = x ]; then
+        export LIBRARY_PATH="$sys_library_path"
+    else
+        export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path"
+    fi
+    if [ x"$CPATH" = x ]; then
+        export CPATH="$sys_cpath"
+    else
+        export CPATH="$CPATH:$sys_cpath"
+    fi
+fi
+
+
+
+
+
 # Build basic software
 # --------------------
 #
@@ -1188,13 +1206,14 @@ fi
 # Bash, Make, or AWK. In this step, we'll install such low-level basic
 # tools, but we have to be very portable (and use minimal features in all).
 echo; echo "Building necessary software (if necessary)..."
-make -f reproduce/software/make/basic.mk \
+make -k -f reproduce/software/make/basic.mk \
+     sys_library_path=$sys_library_path \
      good_static_libc=$good_static_libc \
      rpath_command=$rpath_command \
      static_build=$static_build \
+     numthreads=$numthreads \
      needs_ldl=$needs_ldl \
      on_mac_os=$on_mac_os \
-     numthreads=$numthreads \
      host_cc=$host_cc \
      -j$numthreads
 
@@ -1215,11 +1234,13 @@ else
     numthreads=$jobs
 fi
 .local/bin/env -i HOME=$bdir \
-    .local/bin/make -f reproduce/software/make/high-level.mk \
+    .local/bin/make -k -f reproduce/software/make/high-level.mk \
+                    sys_library_path=$sys_library_path \
                     rpath_command=$rpath_command \
                     static_build=$static_build \
                     numthreads=$numthreads \
                     on_mac_os=$on_mac_os \
+                    sys_cpath=$sys_cpath \
                     host_cc=$host_cc \
                     -j$numthreads
 
@@ -1279,8 +1300,8 @@ fi
 # After everything is installed, we'll put all the names and versions in a
 # human-readable paragraph and also prepare the BibTeX citation for the
 # software.
-function prepare_name_version() {
-
+prepare_name_version ()
+{
     # 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).
@@ -1385,9 +1406,9 @@ echo `.local/bin/date` > $finaltarget
 # The configuration is now complete, we can inform the user on the next
 # step(s) to take.
 if [ x$reproducible_paper_group_name = x ]; then
-    buildcommand="./project prepare -j8"
+    buildcommand="./project make -j8"
 else
-    buildcommand="./project prepare --group=$reproducible_paper_group_name -j8"
+    buildcommand="./project make --group=$reproducible_paper_group_name -j8"
 fi
 cat <<EOF
 
diff --git a/reproduce/software/bash/git-post-checkout b/reproduce/software/shell/git-post-checkout
index f6366dc..f6366dc 100755
--- a/reproduce/software/bash/git-post-checkout
+++ b/reproduce/software/shell/git-post-checkout
diff --git a/reproduce/software/bash/git-pre-commit b/reproduce/software/shell/git-pre-commit
index 9d550db..9d550db 100755
--- a/reproduce/software/bash/git-pre-commit
+++ b/reproduce/software/shell/git-pre-commit
author	Mohammad Akhlaghi <mohammad@akhlaghi.org>	2020-04-02 15:51:28 +0100
committer	Mohammad Akhlaghi <mohammad@akhlaghi.org>	2020-04-02 16:05:03 +0100
commit	de3842a14e36b2debb3ad375d95411d15d45dc84 (patch)
tree	86ae571f85c639c616cf8939cbcec7f1c1be4c9c /reproduce
parent	646756675566a0907edf143c6b6950e0479d9e7e (diff)
parent	cbf177e09af6b9d240388d148b0cb5e3488d8b09 (diff)