Imported recent work in Maneage, minor conflicts fixed

A few minor conflicts came up that were easily fixed.

3 files changed, 19 insertions, 17 deletions

diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 47a01a3..17bb47a 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -33,10 +33,10 @@
 
 
 # Top level environment
+include reproduce/software/config/LOCAL.conf
 include reproduce/software/make/build-rules.mk
-include reproduce/software/config/installation/LOCAL.conf
-include reproduce/software/config/installation/versions.conf
-include reproduce/software/config/installation/checksums.conf
+include reproduce/software/config/versions.conf
+include reproduce/software/config/checksums.conf
 
 lockdir = $(BDIR)/locks
 tdir    = $(BDIR)/software/tarballs
@@ -1334,12 +1334,14 @@ $(ibidir)/gcc: | $(ibidir)/binutils \
 	  && cd ../.. \
 	  && 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 \
 	         isdynamic=$$(file $$f | grep "dynamically linked"); \
 	         if [ x"$$isdynamic" != x ]; then \
 	           cp $$f $$tempname; \
 	           patchelf --set-rpath $(ildir) $$tempname; \
+	           if [ "$$f" = $(ildir)/libstdc++.so ]; then \
+	             patchelf --add-needed $(ildir)/libiconv.so $$tempname; \
+	           fi; \
 	           mv $$tempname $$f; echo "corrected"; \
 	         fi; \
 	       done; \
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index b0847a9..ef4dd4c 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -27,12 +27,12 @@
 
 
 # Top level environment
+include reproduce/software/config/LOCAL.conf
 include reproduce/software/make/build-rules.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
+include reproduce/software/config/TARGETS.conf
+include reproduce/software/config/versions.conf
+include reproduce/software/config/checksums.conf
+include reproduce/software/config/texlive-packages.conf
 
 lockdir = $(BDIR)/locks
 tdir    = $(BDIR)/software/tarballs
@@ -1069,7 +1069,7 @@ $(ibidir)/minizip: $(ibidir)/automake \
 	&& rm $(iidir)/minizip/crypt.h \
 	&& cd ../../.. \
 	&& rm -rf $$unpackdir \
-	&& echo "Minizip $(minizip)" > $@
+	&& echo "Minizip $(minizip-version)" > $@
 
 $(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz
 	$(call gbuild, missfits-$(missfits-version), static) \
@@ -1222,7 +1222,6 @@ $(ibidir)/xlsxio: $(ibidir)/cmake \
 
 
 
-
 # Since we want to avoid complicating the PATH, we are putting a symbolic
 # link of all the TeX Live executables in $(ibdir). But symbolic links are
 # hard to track for Make (as a target). Also, TeX in general is optional
@@ -1242,7 +1241,7 @@ $(ibidir)/xlsxio: $(ibidir)/cmake \
 tlmirror=http://mirrors.rit.edu/CTAN/systems/texlive/tlnet
 
 # The core TeX Live system.
-$(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.conf \
+$(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf \
                                | $(tdir)/install-tl-unx.tar.gz
 
         # Unpack, enter the directory, and install based on the given
@@ -1253,7 +1252,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co
 	tar xf $(tdir)/install-tl-unx.tar.gz
 	cd install-tl-*
 	sed -e's|@installdir[@]|$(idir)|g' \
-	    $$topdir/reproduce/software/config/installation/texlive.conf \
+	    $$topdir/reproduce/software/config/texlive.conf \
 	    > texlive.conf
 
         # TeX Live's installation may fail due to any reason. But TeX Live
@@ -1294,7 +1293,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co
 #else
 #forbiber = $(ibidir)/libnsl
 #endif
-$(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf \
+$(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
                    $(itidir)/texlive-ready-tlmgr \
                    $(forbiber)
 
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index a1d198d..1ef1bf2 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -393,7 +393,7 @@ $(ipydir)/astropy: $(ipydir)/h5py \
         # Currently, when the Expat library is already built in a project
         # (for example as a dependency of another program), Astropy's
         # internal building of Expat will conflict with the project's. So
-        # we have added Expat as a dependency of astropy (so it is always
+        # we have added Expat as a dependency of Astropy (so it is always
         # built before it, and we tell Astropy to use the project's
         # libexpat.
 	pyhook_before () {
@@ -599,7 +599,8 @@ $(ipydir)/numpy: $(ibidir)/unzip \
 	else \
 	  export LDFLAGS="$(LDFLAGS) -shared"; \
 	fi; \
-	conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \
+	export CFLAGS="--std=c99 $$CFLAGS"; \
+	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"; \
 	$(call pybuild, unzip, numpy-$(numpy-version),$$conf, \
 	                Numpy $(numpy-version)) \
 	&& cp $(dtexdir)/numpy.tex $(ictdir)/ \
@@ -678,7 +679,7 @@ $(ipydir)/scipy: $(ipydir)/numpy \
 	else \
 	  export LDFLAGS="$(LDFLAGS) -shared"; \
 	fi; \
-	conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \
+	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"; \
 	$(call pybuild, tar xf, scipy-$(scipy-version),$$conf) \
 	&& cp $(dtexdir)/scipy.tex $(ictdir)/ \
 	&& echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@