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

1 files changed, 45 insertions, 10 deletions

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}" > $@