IMPORTANT: New software versions (17 basic, 16 high-level and 7 Python)

It was a long time that the Maneage software versions hadn't been updated.

With this commit, the versions of all basic software were checked and 17 of
that had newer versions were updated. Also, 16 high-level programs and
libraries were updated as well as 7 Python modules. The full list is
available below.

Basic Software (affecting all projects)
---------------------------------------
bash            5.0.11 -> 5.0.18
binutils        2.32 -> 2.35
coreutils       8.31 -> 8.32
curl            7.65.3 -> 7.71.1
file            5.36 -> 5.39
gawk            5.0.1 -> 5.1.0
gcc             9.2.0 -> 10.2.0
gettext         0.20.2 -> 0.21
git             2.26.2 -> 2.28.0
gmp             6.1.2 -> 6.2.0
grep            3.3 -> 3.4
libbsd          0.9.1 -> 0.10.0
ncurses         6.1 -> 6.2
perl            5.30.0 -> 5.32.0
sed             4.7 -> 4.8
texinfo         6.6 -> 6.7
xz              5.2.4 -> 5.2.5

Custom programs/libraries
-------------------------
astrometrynet   0.77 -> 0.80
automake        0.16.1 -> 0.16.2
bison           3.6 -> 3.7
cfitsio         3.47 -> 3.48
cmake           3.17.0 -> 3.18.1
freetype        2.9 -> 2.10.2
gdb             8.3 -> 9.2
ghostscript     9.50 -> 9.52
gnuastro        0.11 -> 0.12
libgit2         0.28.2 -> 1.0.1
libidn          1.35 -> 1.36
openmpi         4.0.1 -> 4.0.4
R               3.6.2 -> 4.0.2
python          3.7.4 -> 3.8.5
wcslib          6.4 -> 7.3
yaml            0.2.2 -> 0.2.5

Python modules
--------------
cython          0.29.6 -> 0.29.21
h5py            2.9.0 -> 2.10.0
matplotlib      3.1.1 -> 3.3.0
mpi4py          3.0.2 -> 3.0.3
numpy           1.17.2 -> 1.19.1
pybind11        2.4.3 -> 2.5.0
scipy           1.3.1 -> 1.5.2

4 files changed, 81 insertions, 28 deletions

diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index b9678d0..0b672d8 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -183,6 +183,10 @@ $(ibdir) $(ildir):; mkdir $@
 $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
                            | $(ibdir) $(ildir)
 
+        # Hardware specific
+	$(call makelink,lp)    # For printing, necessary for R.
+	$(call makelink,lpr)   # For printing, necessary for R.
+
         # Mac OS specific
 	$(call makelink,mig)
 	$(call makelink,xcrun)
@@ -922,7 +926,7 @@ $(ibidir)/gettext-$(gettext-version): \
                   $(ibidir)/ncurses-$(ncurses-version) \
                   $(ibidir)/libiconv-$(libiconv-version) \
                   $(ibidir)/libunistring-$(libunistring-version)
-	tarball=gettext-$(gettext-version).tar.xz
+	tarball=gettext-$(gettext-version).tar.lz
 	$(call import-source, $(gettext-url), $(gettext-checksum))
 	$(call gbuild, gettext-$(gettext-version), static,, \
 	               V=1 -j$(numthreads))
@@ -959,7 +963,7 @@ $(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version)
 	$(call import-source, $(libtool-url), $(libtool-checksum))
 	$(call gbuild, libtool-$(libtool-version), static, \
                        --program-prefix=g, V=1 -j$(numthreads))
-	ln -s $(ibdir)/glibtoolize $(ibdir)/libtoolize
+	ln -sf $(ibdir)/glibtoolize $(ibdir)/libtoolize
 	echo "GNU Libtool $(libtool-version)" > $@
 
 $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version)
@@ -1211,6 +1215,7 @@ $(ibidir)/binutils-$(binutils-version): \
 	  $(call makelink,ld)
 	  $(call makelink,nm)
 	  $(call makelink,ps)
+	  $(call makelink,strip)
 	  $(call makelink,ranlib)
 	  echo "" > $@
 	else
@@ -1220,14 +1225,15 @@ $(ibidir)/binutils-$(binutils-version): \
 	                 --with-lib-path=$(sys_library_path), \
 	                 -j$(numthreads) )
 
-          # 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.
+          # The `ld' linker of Binutils needs several `*crt*.o' files from
+          # the host's GNU C Library 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.
 	  if ! [ x"$(sys_library_path)" = x ]; then
 	    for f in $(sys_library_path)/*crt*.o; do
 	      b=$$($(ibdir)/basename $$f)
@@ -1284,9 +1290,9 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
         # built/existing compilers in this project. Note that GCC also
         # installs several executables like this 'x86_64-pc-linux-gnu-gcc',
         # 'x86_64-pc-linux-gnu-gcc-ar' or 'x86_64-pc-linux-gnu-g++'.
+	rm -f $(ibdir)/*g++ $(ibdir)/cpp $(ibdir)/gfortran
 	rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc*
 	rm -f $(ibdir)/*gcc* $(ibdir)/gcov* $(ibdir)/cc $(ibdir)/c++
-	rm -f $(ibdir)/*g++ $(ibdir)/cpp $(ibdir)/gfortran $(ibdir)/strip
 	rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*
 
         # GCC builds is own libraries in '$(idir)/lib64'. But all other
@@ -1315,7 +1321,6 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
           # having GNU CPP in the project build directory is known to cause
           # problems with 'libX11'.
 	  $(call makelink,gfortran)
-	  $(call makelink,strip,mandatory)
 	  if [ x$(on_mac_os) = xyes ]; then
 	    $(call makelink,clang)
 	    $(call makelink,clang++)
diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
index 7471e5b..86370ab 100644
--- a/reproduce/software/make/build-rules.mk
+++ b/reproduce/software/make/build-rules.mk
@@ -170,11 +170,21 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
 	     \
 	 echo; echo "Using '$$confscript' to configure:"; echo; \
 	 echo "$$confscript $(3) $$configop"; echo; \
-	 $$confscript $(3) $$configop; \
-	 make "$$shellop" $(4); \
-	 $$check; \
-	 make "$$shellop" install $(7); \
-	 cd ..; \
+	 if [ x$$configure_in_different_directory = x1 ]; then \
+	   mkdir build; \
+	   cd build; \
+	   ../$$confscript $(3) $$configop; \
+	   make "$$shellop" $(4); \
+	   $$check; \
+	   make "$$shellop" install $(7); \
+	   cd ../..; \
+	 else \
+	   $$confscript $(3) $$configop; \
+	   make "$$shellop" $(4); \
+	   $$check; \
+	   make "$$shellop" install $(7); \
+	   cd ..; \
+	 fi; \
 	 rm -rf $(1)
 
 
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 4052ed4..9f434bc 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -763,8 +763,8 @@ $(ibidir)/libgit2-$(libgit2-version): $(ibidir)/cmake-$(cmake-version)
 	              -DUSE_SSH=OFF -DBUILD_CLAR=OFF \
 	              -DTHREADSAFE=ON -DUSE_ICONV=OFF )
 	if [ x$(on_mac_os) = xyes ]; then
-	  install_name_tool -id $(ildir)/libgit2.28.dylib \
-	                        $(ildir)/libgit2.28.dylib
+	  install_name_tool -id $(ildir)/libgit2.1.0.dylib \
+	                        $(ildir)/libgit2.1.0.dylib
 	fi
 	echo "Libgit2 $(libgit2-version)" > $@
 
@@ -785,8 +785,8 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
                        --with-cfitsioinc=$(idir)/include \
                        --without-pgplot $$fortranopt)
 	if [ x$(on_mac_os) = xyes ]; then
-	  install_name_tool -id $(ildir)/libwcs.6.4.dylib \
-	                        $(ildir)/libwcs.6.4.dylib
+	  install_name_tool -id $(ildir)/libwcs.7.3.dylib \
+	                        $(ildir)/libwcs.7.3.dylib
 	fi
 	echo "WCSLIB $(wcslib-version)" > $@
 
@@ -853,7 +853,7 @@ $(ibidir)/automake-$(automake-version): $(ibidir)/autoconf-$(autoconf-version)
 	echo "GNU Automake $(automake-version)" > $@
 
 $(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version)
-	tarball=bison-$(bison-version).tar.xz
+	tarball=bison-$(bison-version).tar.lz
 	$(call import-source, $(bison-url), $(bison-checksum))
 	$(call gbuild, bison-$(bison-version), static, ,V=1 -j$(numthreads))
 	echo "GNU Bison $(bison-version)" > $@
@@ -916,6 +916,7 @@ $(ibidir)/flex-$(flex-version): $(ibidir)/bison-$(bison-version)
 
 $(ibidir)/gdb-$(gdb-version): $(ibidir)/python-$(python-version)
 	tarball=gdb-$(gdb-version).tar.gz
+	export configure_in_different_directory=1;
 	$(call import-source, $(gdb-url), $(gdb-checksum))
 	$(call gbuild, gdb-$(gdb-version),,,V=1 -j$(numthreads))
 	echo "GNU Project Debugger (GDB) $(gdb-version)" > $@
@@ -1096,10 +1097,17 @@ $(ibidir)/minizip-$(minizip-version): $(ibidir)/automake-$(automake-version)
 	rm -rf $$unpackdir
 	echo "Minizip $(minizip-version)" > $@
 
+# The Astromatic software packages (including missfits, sextractor, swarp
+# and others) need the '-fcommon' flag to compile properly on GCC 10 and
+# after. Previous to GCC 10, it was the default, but from GCC 10, the
+# default is '-fno-common'. This is known by the author (as SExtractor
+# issue 12: https://github.com/astromatic/sextractor/issues/12) and will
+# hopefully be fixed in the future.
 $(ibidir)/missfits-$(missfits-version):
 	tarball=missfits-$(missfits-version).tar.gz
 	$(call import-source, $(missfits-url), $(missfits-checksum))
-	$(call gbuild, missfits-$(missfits-version), static)
+	$(call gbuild, missfits-$(missfits-version), static, \
+	        CFLAGS="-fcommon")
 	cp $(dtexdir)/missfits.tex $(ictdir)/
 	echo "MissFITS $(missfits-version) \citep{missfits}" > $@
 
@@ -1163,11 +1171,25 @@ $(ibidir)/R-$(R-version): \
             $(ibidir)/libpaper-$(libpaper-version)
 	tarball=R-$(R-version).tar.gz
 	$(call import-source, $(R-url), $(R-checksum))
+	cd $(ddir)
+	tar xf $(tdir)/$$tarball
+	cd R-$(R-version)
 
+        # We need to manually remove the lines with '~autodetect~', they
+        # cause the configure script to crash in version 4.0.2. They are
+        # used in relation to Java, and we don't use Java anyway.
+	sed -i -e '/\~autodetect\~/ s/^/#/g' configure
 	export R_SHELL=$(SHELL)
-	$(call gbuild, R-$(R-version), static, \
-                       --without-x --with-readline \
-	               --disable-openmp, -j$(numthreads))
+	./configure --prefix=$(idir) \
+	            --without-x \
+	            --with-pcre1 \
+	            --disable-java \
+	            --with-readline \
+	            --disable-openmp
+	make -j$(numthreads)
+	make install
+	cd ..
+	rm -rf R-$(R-version)
 	echo "R $(R-version)" > $@
 
 # SCAMP documentation says ATLAS is a mandatory prerequisite for using
@@ -1181,7 +1203,10 @@ $(ibidir)/scamp-$(scamp-version): \
                 $(ibidir)/cdsclient-$(cdsclient-version)
 	tarball=scamp-$(scamp-version).tar.lz
 	$(call import-source, $(scamp-url), $(scamp-checksum))
+
+        # See comment above 'missfits' for '-fcommon'.
 	$(call gbuild, scamp-$(scamp-version), static, \
+	           CFLAGS="-fcommon" \
                    --enable-threads \
                    --enable-openblas \
                    --enable-plplot=no \
@@ -1209,13 +1234,20 @@ $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version)
 # libraries. But we can override this issue since we have Openblas
 # installed, it is just necessary to explicity tell sextractor to use it in
 # the configuration step.
+#
+# The '-fcommon' is a necessary C compilation flag for GCC 10 and above. It
+# is necessary for astromatic libraries, otherwise their build will crash.
 $(ibidir)/sextractor-$(sextractor-version): \
                      $(ibidir)/fftw-$(fftw-version) \
                      $(ibidir)/openblas-$(openblas-version)
 	tarball=sextractor-$(sextractor-version).tar.lz
 	$(call import-source, $(sextractor-url), $(sextractor-checksum))
+
+        # See comment above 'missfits' for '-fcommon'.
 	$(call gbuild, sextractor-$(sextractor-version), static, \
-	               --enable-threads --enable-openblas \
+	               CFLAGS="-fcommon" \
+	               --enable-threads \
+	               --enable-openblas \
 	               --with-openblas-libdir=$(ildir) \
 	               --with-openblas-incdir=$(idir)/include)
 	ln -fs $(ibdir)/sex $(ibdir)/sextractor
@@ -1225,7 +1257,10 @@ $(ibidir)/sextractor-$(sextractor-version): \
 $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version)
 	tarball=swarp-$(swarp-version).tar.gz
 	$(call import-source, $(swarp-url), $(swarp-checksum))
+
+        # See comment above 'missfits' for '-fcommon'.
 	$(call gbuild, swarp-$(swarp-version), static, \
+	               CFLAGS="-fcommon" \
                        --enable-threads)
 	cp $(dtexdir)/swarp.tex $(ictdir)/
 	echo "SWarp $(swarp-version) \citep{swarp}" > $@
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 2fede35..d39208f 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -431,6 +431,7 @@ $(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version)
 
 $(ipydir)/numpy-$(numpy-version): \
                 $(ibidir)/unzip-$(unzip-version) \
+                $(ipydir)/cython-$(cython-version) \
                 $(ibidir)/openblas-$(openblas-version) \
                 $(ipydir)/setuptools-$(setuptools-version)
 	tarball=numpy-$(numpy-version).zip
@@ -528,7 +529,9 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
 	$(call pybuild, tar xf, requests-$(requests-version), , \
 	                Requests $(requests-version))
 
-$(ipydir)/scipy-$(scipy-version): $(ipydir)/numpy-$(numpy-version)
+$(ipydir)/scipy-$(scipy-version): \
+                  $(ipydir)/numpy-$(numpy-version) \
+                  $(ipydir)/pybind11-$(pybind11-version)
 	tarball=scipy-$(scipy-version).tar.gz
 	$(call import-source, $(scipy-url), $(scipy-checksum))
 	if [ x$(on_mac_os) = xyes ]; then