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-rw-r--r--reproduce/software/make/basic.mk207
-rw-r--r--reproduce/software/make/high-level.mk233
-rw-r--r--reproduce/software/make/python.mk20
3 files changed, 362 insertions, 98 deletions
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index d90d945..14d63cf 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -55,6 +55,7 @@ ddir = $(BDIR)/software/build-tmp
idir = $(BDIR)/software/installed
ibdir = $(BDIR)/software/installed/bin
ildir = $(BDIR)/software/installed/lib
+iidir = $(BDIR)/software/installed/include
ibidir = $(BDIR)/software/installed/version-info/proglib
# Ultimate Makefile target. GNU Nano (a simple and very light-weight text
@@ -87,13 +88,18 @@ export SHELL := $(ibdir)/dash
export PATH := $(ibdir):$(PATH)
export PKG_CONFIG_PATH := $(ildir)/pkgconfig
export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
-export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) \
- -Wno-nullability-completeness
export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
# Disable built-in rules (which are not needed here!)
.SUFFIXES:
+# See description of '-Wno-nullability-completeness' in
+# 'reproduce/software/shell/configure.sh'.
+ifeq ($(on_mac_os),yes)
+ noccwarnings=-Wno-nullability-completeness
+endif
+export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings)
+
# 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,
@@ -202,6 +208,7 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
$(call makelink,xcrun)
$(call makelink,sysctl)
$(call makelink,sw_vers)
+ $(call makelink,codesign)
$(call makelink,dsymutil)
$(call makelink,install_name_tool)
@@ -222,6 +229,10 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
fi
done
+# Useful tools: 'ldd' (list libraries linked by binary on GNU
+# systems)
+ $(call makelink,ldd)
+
# We want this to be empty (so it doesn't interefere with the other
# files in 'ibidir'.
touch $@
@@ -252,10 +263,46 @@ $(ibidir)/gzip-$(gzip-version): | $(ibdir) $(ildir) $(lockdir)
$(call gbuild, gzip-$(gzip-version), static, , V=1)
echo "GNU Gzip $(gzip-version)" > $@
+# 2022-07-14 B Roukema
+#
+# xz-5.2.5 fails on (at least) CentOS 7 (Redhat) systems while trying
+# to compile 'cmake' in Maneage - this is Maneage bug 62700 [1].
+#
+# The fix appears to be just a few lines, although it's not clear
+# how robust or long-term it is. Since we don't yet have 'patch' in
+# 'basic.mk', this file has to be copied into place rather than patched.
+
+# xz-5.2.5_src_liblzma_liblzma.map is a patched
+# version of xz-5.2.5/src/liblzma/liblzma.map based on discussion at
+# [1] + [2] + the patch file [3].
+#
+# [1] https://savannah.nongnu.org/bugs/index.php?62700
+# [2] https://github.com/easybuilders/easybuild-easyconfigs/issues/14991
+# [3] https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/bcebb3320ffb63f9804ca8d4d64d1822ec7c9792/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch
$(ibidir)/xz-$(xz-version): $(ibidir)/gzip-$(gzip-version)
+
+# Prepare the tarball.
tarball=xz-$(xz-version).tar.lz
$(call import-source, $(xz-url), $(xz-checksum))
- $(call gbuild, xz-$(xz-version), static)
+
+# Until the bug mentioned above is fixed, we'll can't use the generic
+# rule.
+# $(call gbuild, xz-$(xz-version), static)
+
+# Configure and build with patched file.
+ srcdir=$$(pwd)
+ unpackdir=xz-$(xz-version)
+ patchedfile=xz-5.2.5_src_liblzma_liblzma.map
+ cd $(ddir)
+ rm -rf $$unpackdir
+ tar -x -f $(tdir)/$$tarball
+ cd $$unpackdir
+ cp -pv $$srcdir/reproduce/software/patches/$$patchedfile \
+ src/liblzma/liblzma.map # copy the fixed file into place
+ ./configure --prefix=$(idir)
+ make install
+ cd ..
+ rm -rf $$unpackdir
echo "XZ Utils $(xz-version)" > $@
$(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
@@ -303,26 +350,6 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
ln -fs libbz2.so.$(bzip2-version) libbz2.so
echo "Bzip2 $(bzip2-version)" > $@
-$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
- tarball=unzip-$(unzip-version).tar.lz
- $(call import-source, $(unzip-url), $(unzip-checksum))
- $(call gbuild, unzip-$(unzip-version), static,, \
- -f unix/Makefile generic \
- CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
- -f unix/Makefile generic \
- BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
- echo "Unzip $(unzip-version)" > $@
-
-$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
- tarball=zip-$(zip-version).tar.lz
- $(call import-source, $(zip-url), $(zip-checksum))
- $(call gbuild, zip-$(zip-version), static,, \
- -f unix/Makefile generic \
- CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
- -f unix/Makefile generic \
- BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
- echo "Zip $(zip-version)" > $@
-
# Some programs (like Wget and CMake) that use zlib need it to be dynamic
# so they use our custom build. So we won't force a static-only build.
#
@@ -341,11 +368,9 @@ $(ibidir)/zlib-$(zlib-version): $(ibidir)/gzip-$(gzip-version)
# software to be built).
$(ibidir)/tar-$(tar-version): \
$(ibidir)/xz-$(xz-version) \
- $(ibidir)/zip-$(zip-version) \
$(ibidir)/gzip-$(gzip-version) \
$(ibidir)/zlib-$(zlib-version) \
- $(ibidir)/bzip2-$(bzip2-version) \
- $(ibidir)/unzip-$(unzip-version)
+ $(ibidir)/bzip2-$(bzip2-version)
# Since all later programs depend on Tar, the configuration will hit
# a bottleneck here: only making Tar. So its more efficient to built
@@ -629,7 +654,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
-Dcccdlflags='-fPIC' \
$(perl-conflddlflags) \
-Dldflags="$$LDFLAGS"
- make -j$(numthreads)
+ make -j$(numthreads) V=1
make install
cd ..
rm -rf perl-$(perl-version)
@@ -807,6 +832,8 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
--without-librtmp \
--without-libidn2 \
--without-wolfssl \
+ --without-nghttp2 \
+ --without-nghttp3 \
--without-brotli \
--without-gnutls \
--without-cyassl \
@@ -814,6 +841,7 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
--without-axtls \
--disable-ldaps \
--disable-ldap \
+ --without-zstd \
--without-nss, V=1)
if [ -f $(ibdir)/patchelf ]; then
@@ -875,6 +903,12 @@ $(ibidir)/wget-$(wget-version): \
# process of the higher-level programs and libraries. Note that during the
# building of those higher-level programs (after this Makefile finishes),
# there is no access to the system's PATH.
+$(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version)
+ 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)" > $@
+
$(ibidir)/diffutils-$(diffutils-version): \
$(ibidir)/coreutils-$(coreutils-version)
tarball=diffutils-$(diffutils-version).tar.lz
@@ -928,6 +962,13 @@ $(ibidir)/gawk-$(gawk-version): \
# Build final target.
echo "GNU AWK $(gawk-version)" > $@
+$(ibidir)/help2man-$(help2man-version): \
+ $(ibidir)/coreutils-$(coreutils-version)
+ tarball=help2man-$(help2man-version).tar.lz
+ $(call import-source, $(help2man-url), $(help2man-checksum))
+ $(call gbuild, help2man-$(help2man-version), static, ,V=1)
+ echo "Help2man $(Help2man-version)" > $@
+
$(ibidir)/libiconv-$(libiconv-version): \
$(ibidir)/pkg-config-$(pkgconfig-version)
tarball=libiconv-$(libiconv-version).tar.lz
@@ -1070,6 +1111,17 @@ $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version)
$(ibidir)/texinfo-$(texinfo-version): \
$(ibidir)/perl-$(perl-version) \
$(ibidir)/gettext-$(gettext-version)
+
+# Setting for the XS sub-package. "This is because in theory, the XS
+# module could be built with a different compiler to the rest of the
+# project, needing completely different flags" (part of [1])
+#
+# [1] https://lists.gnu.org/archive/html/bug-texinfo/2022-08/msg00068.html
+ export PERL="$(ibdir)/perl"
+ export PERL_EXT_LDFLAGS="-L$(ildir)"
+ export PERL_EXT_CPPFLAGS="-I$(iidir)"
+
+# Basic build commands.
tarball=texinfo-$(texinfo-version).tar.lz
$(call import-source, $(texinfo-url), $(texinfo-checksum))
$(call gbuild, texinfo-$(texinfo-version), static)
@@ -1136,6 +1188,7 @@ $(ibidir)/binutils-$(binutils-version): \
$(ibidir)/gawk-$(gawk-version) \
$(ibidir)/grep-$(grep-version) \
$(ibidir)/wget-$(wget-version) \
+ $(ibidir)/bison-$(bison-version) \
$(ibidir)/which-$(which-version) \
$(ibidir)/libtool-$(libtool-version) \
$(ibidir)/texinfo-$(texinfo-version) \
@@ -1164,7 +1217,7 @@ $(ibidir)/binutils-$(binutils-version): \
# Build binutils with the standard 'gbuild' function.
$(call gbuild, binutils-$(binutils-version), static, \
--with-lib-path=$(sys_library_path), \
- -j$(numthreads) )
+ -j$(numthreads) V=1)
# The 'ld' linker of Binutils needs several '*crt*.o' files from
# the host's GNU C Library to run. On some systems these object
@@ -1287,20 +1340,35 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
current_dir=$$(pwd)
# By default 'ddir' (where GCC is decompressed and built) is in the
-# RAM (on systems that support '/dev/shm'). This is done to avoid
-# building so many small/temporary files and possibly harming the
-# hard-drive or SSD. But if the RAM doesn't have enough space, we
-# should use the hard-drive or SSD. During its build GCC's build
-# directory will become about 7GB (multiple of 1024 bytes, for GCC
-# 11.2.0). So at this step, we are making sure we have more than
-# 7.5GiB (multiple of 1000 bytes, which corresponds to 7.32GB)
-# before GCC starts to build. Note that the 4th column of 'df' is
-# the "available" space at the time of running, not the full
-# space. So the background RAM that the OS will be using during
-# Maneage is accounted for. Also consider that GCC is built alone
-# (no other Maneage software is built at the same time as GCC).
- in_ram=$$(df $(ddir) \
- | awk 'NR==2{print ($$4>7500000) ? "yes" : "no"}'); \
+# RAM (on systems that support a '/dev/shm' RAM disk). This is done
+# to avoid building so many small/temporary files and possibly
+# harming the hard-drive or SSD. But if the RAM doesn't have enough
+# space, we should use the hard-drive or SSD. During its build,
+# GCC's build directory will become about 7GiB (in units of 1024^3
+# bytes, for GCC 12.1.0, which corresponds to 7.5GB, in units of
+# 1000^3 bytes). So at this step, we make sure that we have more
+# than 12GiB before GCC starts to build. See the figure in the link
+# below for GCC's RAM consumption as a function of time:
+#
+# https://savannah.nongnu.org/task/?16244#comment12
+#
+# For POSIX portability and longevity (default sizes might change),
+# we use the '-P' option, and we use the environment variable
+# POSIXLY_CORRECT=1, so the 'block size' is 512 bytes. We'll also
+# allow for about ~0.5 GB at the start.
+#
+# So we need 8 GiB * 1024^3 (B/GiB) / 512 blocks/B = 16777216
+# blocks, in blocks of 512 bytes.
+#
+# The 4th column of 'df' is the "available" space at the time of
+# running, not the full space. So the 'RAM disk' that the OS
+# will be using as "pretend" disk space (e.g. using 'tmpfs'; this
+# is physically RAM, but appears as if it is disk space)
+# during this stage of Maneage is accounted for. GCC is built
+# alone - no other Maneage software is built at the same time as
+# GCC - so this amount of RAM should be enough.
+ in_ram=$$(POSIXLY_CORRECT=1 df -P $(ddir) \
+ | awk 'NR==2{print ($$4>16777216) ? "yes" : "no"}'); \
if [ $$in_ram = "yes" ]; then odir=$(ddir)
else
odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space
@@ -1308,9 +1376,11 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
mkdir $$odir
fi
-# Go into the proper directory, unpack GCC and prepare the 'build'
-# directory inside it for all the built files.
+# Go into the directory to uncompress GCC.
cd $$odir
+
+# Unpack GCC and prepare the 'build' directory inside it for all
+# the built files.
rm -rf gcc-$(gcc-version)
tar -xf $(tdir)/$$tarball
if [ $$odir != $(ddir) ]; then
@@ -1318,6 +1388,34 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
fi
cd gcc-$(gcc-version)
+# Unfortunately binutils installs headers like 'ansidecl.h' that
+# have been seen to conflict with GCC's internal versions of those
+# headers. For example in the 'ansidecl.h' of Binutils 2.39, the
+# 'PTR' macro isn't defined, while the same file in GCC 12.1.0 has
+# defined it. Therefore, without this change, GCC will include the
+# file installed from Binutils, not find what it needs and crash!
+# Therefore, with the 'CPPFLAGS' modification below, we tell GCC to
+# first look into its own 'include' directory before anything else.
+ export CPPFLAGS="-I$$(pwd)/include $(CPPFLAGS)"
+
+# In the GNU C Library 2.36 (which is more recent than GCC 12.1.0),
+# the 'linux/mount.h' (loaded by 'linux/fs.h', which is loaded by
+# 'libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp'
+# in GCC) conflicts with 'sys/mount.h' which is directly loaded by
+# the same file! This is a known conflict in glibc 2.36 (see
+# [1]). As described in [1], one solution is the final job done in
+# [2]. We therefore do this process here: 1) Not loading
+# 'linux/fs.h', and adding the necessary macros directly.
+#
+# [1] https://sourceware.org/glibc/wiki/Release/2.36#Usage_of_.3Clinux.2Fmount.h.3E_and_.3Csys.2Fmount.h.3E
+# [2] https://reviews.llvm.org/D129471
+ sed -e's|\#include <linux/fs.h>||' \
+ -e"s|FS_IOC_GETFLAGS;|_IOR('f', 1, long);|" \
+ -e"s|FS_IOC_GETVERSION;|_IOR('v', 1, long);|" \
+ -e"s|FS_IOC_SETFLAGS;|_IOW('f', 2, long);|" \
+ -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \
+ -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
+
# Set the build directory for the processing.
mkdir build
cd build
@@ -1396,6 +1494,25 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
+# Software that need re-compilation (to use our own libraries)
+$(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version)
+ tarball=lzip-$(lzip-version).tar
+ unpackdir=lzip-$(lzip-version)
+ cd $(ddir)
+ rm -rf $$unpackdir
+ tar -xf $(tdir)/$$tarball
+ cd $$unpackdir
+ ./configure --build --check --installdir="$(ibdir)"
+ if [ -f $(ibdir)/patchelf ]; then
+ $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/lzip;
+ fi
+ cd ..
+ rm -rf $$unpackdir
+ echo "Lzip $(lzip-version)" > $@
+
+
+
+
@@ -1418,7 +1535,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
# nano (and use their own optional high-level text editor). To do this, you
# can just have to manually remove 'nano' from 'targets-proglib' above and
# add their optional text editor in 'TARGETS.conf'.
-$(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version)
+$(ibidir)/nano-$(nano-version): $(ibidir)/lzip-$(lzip-version)
tarball=nano-$(nano-version).tar.lz
$(call import-source, $(nano-url), $(nano-checksum))
$(call gbuild, nano-$(nano-version), static)
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 20e758a..a2474af 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -49,6 +49,7 @@ ddir = $(BDIR)/software/build-tmp
idir = $(BDIR)/software/installed
ibdir = $(BDIR)/software/installed/bin
ildir = $(BDIR)/software/installed/lib
+iidir = $(BDIR)/software/installed/include
ibidir = $(BDIR)/software/installed/version-info/proglib
# Basic directories (specific to this Makefile).
@@ -147,7 +148,6 @@ export SHELL := $(ibdir)/bash
.SHELLFLAGS := --noprofile --norc -ec
export LDFLAGS := $(rpath_command) -L$(ildir)
export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
-export CPPFLAGS := -I$(idir)/include -Wno-nullability-completeness
export PKG_CONFIG_PATH := $(ildir)/pkgconfig:$(idir)/share/pkgconfig
# Disable built-in rules (which are not needed here!)
@@ -160,6 +160,13 @@ export F77 := $(ibdir)/gfortran
export LD_RUN_PATH := $(ildir):$(il64dir)
export LD_LIBRARY_PATH := $(ildir):$(il64dir)
+# See description of '-Wno-nullability-completeness' in
+# 'reproduce/software/shell/configure.sh'.
+ifeq ($(on_mac_os),yes)
+ noccwarnings=-Wno-nullability-completeness
+endif
+export CPPFLAGS := -I$(idir)/include $(noccwarnings)
+
# In macOS, if a directory exists in both 'C_INCLUDE_PATH' and 'CPPFLAGS'
# it will be ignored in 'CPPFLAGS' (which has higher precedence). So, we
# should not define 'C_INCLUDE_PATH' on macOS. This happened with clang
@@ -429,6 +436,7 @@ $(ibidir)/cfitsio-$(cfitsio-version):
echo "CFITSIO $(cfitsio-version)" > $@
$(ibidir)/cairo-$(cairo-version): \
+ $(ibidir)/libxt-$(libxt-version) \
$(ibidir)/pixman-$(pixman-version) \
$(ibidir)/libpng-$(libpng-version) \
$(ibidir)/freetype-$(freetype-version)
@@ -448,7 +456,8 @@ $(ibidir)/eigen-$(eigen-version):
topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball
cd eigen-$(eigen-version)
if ! [ -d $(iidir)/eigen3 ]; then mkdir $(iidir)/eigen3; fi
- cp -r Eigen/* $(iidir)/eigen3/
+ cp -r Eigen/* $(iidir)/eigen3/ # Some expect 'eigen3'.
+ ln -s $(iidir)/eigen3 $(iidir)/Eigen # Others expect 'Eigen'.
cd $$topdir
rm -rf $(ddir)/eigen-$(eigen-version)
echo "Eigen $(eigen-version)" > $@
@@ -529,7 +538,7 @@ $(ibidir)/gsl-$(gsl-version):
$(ibidir)/hdf5-$(hdf5-version): $(ibidir)/openmpi-$(openmpi-version)
export CC=mpicc
export FC=mpif90
- tarball=hdf5-$(hdf5-version).tar.gz
+ tarball=hdf5-$(hdf5-version).tar.lz
$(call import-source, $(hdf5-url), $(hdf5-checksum))
$(call gbuild, hdf5-$(hdf5-version), static, \
--enable-parallel \
@@ -919,8 +928,8 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
--with-cfitsioinc=$(idir)/include \
--without-pgplot $$fortranopt)
if [ x$(on_mac_os) = xyes ]; then
- install_name_tool -id $(ildir)/libwcs.7.7.dylib \
- $(ildir)/libwcs.7.7.dylib
+ install_name_tool -id $(ildir)/libwcs.7.11.dylib \
+ $(ildir)/libwcs.7.11.dylib
fi
echo "WCSLIB $(wcslib-version)" > $@
@@ -938,14 +947,42 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
#
# Astrometry-net contains a lot of programs. We need to specify the
# installation directory and the Python executable (by default it will look
-# for /usr/bin/python)
+# for /usr/bin/python).
+#
+# An optional dependency is 'netpbm' but it has many dependencies and a
+# crazy build system. So, it is not in the default preprequisites. If you
+# need it you can add it as a prerequisite and pray that it will work.
+#
+# A consequence of not having 'netpbm' is that for obtaining the
+# astrometric solution of one image using 'solve-field', it is necessary to
+# build a catalog of sources with image coordinates and flux (x,y,flux) in
+# advance. The catalog has to be sorted by flux. Finally, when invoking
+# 'solve-field', the width and heigh of the original image have to be
+# provided.
+#
+# More explicitly, raw basic steps using Gnuastro:
+#
+# - Obtain a catalog with image coordinates and flux (x,y,brightness):
+# $ astnoisechisel img.fits -o det.fits
+# $ astsegment det.fits -o seg.fits
+# $ astmkcatalog seg.fits --clumpscat --x --y --brightness -o cat-raw.fits
+#
+# - Sort by flux:
+# $ asttable cat-raw.fits --hdu 2 --sort brightness --descending \
+# --output cat.fits
+#
+# - Get the x-size and y-size from the header:
+# $ xsize=$(astfits img.fits --keyvalue NAXIS1 --quiet)
+# $ ysize=$(astfits img.fits --keyvalue NAXIS2 --quiet)
+#
+# - Run 'solve-field' to obtain the astrometric solution:
+# $ solve-field cat.fits --width $xsize --height $ysize [--other-parameters]
$(ibidir)/astrometrynet-$(astrometrynet-version): \
$(ibidir)/gsl-$(gsl-version) \
$(ibidir)/swig-$(swig-version) \
$(ipydir)/numpy-$(numpy-version) \
$(ibidir)/cairo-$(cairo-version) \
$(ibidir)/libpng-$(libpng-version) \
- $(ibidir)/netpbm-$(netpbm-version) \
$(ibidir)/wcslib-$(wcslib-version) \
$(ipydir)/astropy-$(astropy-version) \
$(ibidir)/cfitsio-$(cfitsio-version) \
@@ -987,12 +1024,6 @@ $(ibidir)/automake-$(automake-version): $(ibidir)/autoconf-$(autoconf-version)
$(call gbuild, automake-$(automake-version), static, ,V=1)
echo "GNU Automake $(automake-version)" > $@
-$(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version)
- 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)" > $@
-
# cdsclient is a set of software written in c to interact with astronomical
# database servers. It is a dependency of 'scamp' to be able to download
# reference catalogues.
@@ -1049,7 +1080,11 @@ $(ibidir)/cmake-$(cmake-version):
$(ibidir)/flex-$(flex-version): $(ibidir)/bison-$(bison-version)
tarball=flex-$(flex-version).tar.lz
$(call import-source, $(flex-url), $(flex-checksum))
- $(call gbuild, flex-$(flex-version), static, ,V=1 -j$(numthreads))
+ $(call gbuild, flex-$(flex-version), static, \
+ --with-libiconv-prefix=$(idir) \
+ --with-libintl-prefix=$(idir) \
+ --disable-dependency-tracking, \
+ V=1 -j$(numthreads))
echo "Flex $(flex-version)" > $@
$(ibidir)/gdb-$(gdb-version): $(ibidir)/python-$(python-version)
@@ -1128,13 +1163,7 @@ $(ibidir)/gnuastro-$(gnuastro-version): \
$(call gbuild, gnuastro-$(gnuastro-version), static, , \
-j$(numthreads))
cp $(dtexdir)/gnuastro.tex $(ictdir)/
- echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
-
-$(ibidir)/help2man-$(help2man-version):
- tarball=help2man-$(help2man-version).tar.lz
- $(call import-source, $(help2man-url), $(help2man-checksum))
- $(call gbuild, help2man-$(help2man-version), static, ,V=1)
- echo "Help2man $(Help2man-version)" > $@
+ echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro,akhlaghi19}" > $@
$(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version)
@@ -1168,8 +1197,25 @@ $(ibidir)/imagemagick-$(imagemagick-version): \
tarball=ImageMagick-$(imagemagick-version).tar.lz
$(call import-source, $(imagemagick-url), $(imagemagick-checksum))
$(call gbuild, ImageMagick-$(imagemagick-version), static, \
- --with-gslib --without-x --disable-openmp, \
+ --without-x \
+ --with-gslib \
+ --disable-openmp \
+ --with-libstdc=$(ildir), \
V=1 -j$(numthreads))
+
+# On macOS, an executable and several libraries are not properly
+# linked with the Ghostscript library (libgs), so we need to fix it
+# manually.
+ if [ x$(on_mac_os) = xyes ]; then
+ gsversion=$$(echo $(ghostscript-version) \
+ | awk -F'.' '{print $$1"."$$2}')
+ libMagicks=$$(ls -l $(ildir)/libMagick*.dylib \
+ | awk '/^-/{print $$NF}')
+ libMagicks_all="$(ibdir)/magick $$libMagicks"
+ for f in $$libMagicks_all; do \
+ install_name_tool -change libgs.dylib.$$gsversion \
+ $(ildir)/libgs.dylib.$$gsversion $$f; done
+ fi
echo "ImageMagick $(imagemagick-version)" > $@
# 'imfit' doesn't use the traditional 'configure' and 'make' to install
@@ -1281,12 +1327,12 @@ $(ibidir)/missfits-$(missfits-version):
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
-# printf statment. Each '\n' is a new question that the installation process
-# ask to the user. We give all answers with a pipe to the scripts (configure
-# and install). The questions are different depending on the system (tested
-# on GNU/Linux and Mac OS).
+# Netpbm is an optional prerequisite of Astrometry-net, it contains a lot
+# of programs. This program has a crazy dialogue installation which is
+# override using the printf statment. Each '\n' is a new question that the
+# installation process ask to the user. We give all answers with a pipe to
+# the scripts (configure and install). The questions are different
+# depending on the system (tested on GNU/Linux and Mac OS).
$(ibidir)/netpbm-$(netpbm-version): \
$(ibidir)/flex-$(flex-version) \
$(ibidir)/libpng-$(libpng-version) \
@@ -1352,15 +1398,43 @@ $(ibidir)/pcre-$(pcre-version):
, V=1 -j$(numthreads))
echo "Perl Compatible Regular Expressions $(pcre-version)" > $@
-# 2022-01-01 The rules for building R - identified as r-cran to avoid the
-# difficulties in searching text for a one-letter string - were shifted to
-# 'r-cran.mk'.
+# On macOS 12.3 Monterey with AppleClang 13.1.6.13160021, Plplot 5.15.0
+# needs the 'finite' function of 'math.h' which has been deprecated in
+# macOS. By manually adding "#define finite isfinite" in 'math.h' like
+# below, we fixed this problem but still it can't find 'exit' during the
+# configuration phase so we stopped trying to port it to macOS. It means
+# that on macOS Plplot is not available. For other OSs it should be fine.
+# On macOS, the file 'tmath.h' can be found with 'xcrun --show-sdk-path'.
+#
+# cp /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h \
+# $(iidir)/math.h
+# awk '{if($$0 ~ /#define isinf\(x\)/) {print "#define finite isfinite"; print $$0} else print $$0 }' \
+# $(iidir)/math.h > $(iidir)/math-tmp.h
+# mv $(iidir)/math-tmp.h $(iidir)/math.h
+$(ibidir)/plplot-$(plplot-version): \
+ $(ibidir)/cairo-$(cairo-version) \
+ $(ibidir)/freetype-$(freetype-version)
+ tarball=plplot-$(plplot-version).tar.lz
+ $(call import-source, $(plplot-url), $(plplot-checksum))
+ $(call cbuild, plplot-$(plplot-version), static, \
+ -DDEFAULT_NO_BINDINGS:BOOL=ON \
+ -DENABLE_cxx:BOOL=ON \
+ -DENABLE_fortran:BOOL=ON \
+ -DDEFAULT_NO_QT_DEVICES:BOOL=ON)
+ echo "PLplot $(pcre-version)" > $@
# SCAMP documentation says ATLAS is a mandatory prerequisite for using
# SCAMP. We have ATLAS into the project but there are some problems with the
# libraries that are not yet solved. However, we tried to install it with
# the option --enable-openblas and it worked (same issue happened with
# 'sextractor'.
+#
+# Plplot in SCAMP cannot be built for macOS. See comments on top of Plplot.
+# But if you are not using macOS and want to enable plots, follow the
+# steps below:
+#
+# 1. Add '$(ibidir)/plplot-$(plplot-version)' to the prerequisites
+# 2. Remove the option '--enable-plplot=no' from the call of 'gbuild'
$(ibidir)/scamp-$(scamp-version): \
$(ibidir)/fftw-$(fftw-version) \
$(ibidir)/openblas-$(openblas-version) \
@@ -1430,32 +1504,56 @@ $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version)
echo "SCons $(scons-version)" > $@
# Sextractor crashes complaining about not linking with some ATLAS
-# libraries. But we can override this issue since we have Openblas
+# 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)
+# Import the source.
tarball=sextractor-$(sextractor-version).tar.lz
$(call import-source, $(sextractor-url), $(sextractor-checksum))
+# Unpack the tarball and enter the directory.
+ unpackdir=sextractor-$(sextractor-version)
+ cd $(ddir)
+ rm -rf $$unpackdir
+ tar -xf $(tdir)/$$tarball
+ cd $$unpackdir
+
# See comment above 'missfits' for '-fcommon'.
- $(call gbuild, sextractor-$(sextractor-version), static, \
- CFLAGS="-fcommon" \
- --enable-threads \
- --enable-openblas \
- --with-openblas-libdir=$(ildir) \
- --with-openblas-incdir=$(idir)/include)
+ ./configure --prefix="$(idir)" \
+ CFLAGS="-fcommon" \
+ --enable-threads \
+ --enable-openblas \
+ --libdir=$(ildir) \
+ --includedir=$(iidir) \
+ --with-openblas-libdir=$(ildir) \
+ --with-openblas-incdir=$(iidir)
+
+# On macOS we need to manually change 'finite' to 'isfinite' in the
+# header file 'src/levmar/compiler.h'. Until this problem is
+# hopefully fixed in next releases, we are doing it manually using
+# 'sed'. Consequently we are not installing it using 'gbuild'. Once
+# this is fixed upstream, we can use the standard 'gbuild'.
+ sed -i -e's|define LM_FINITE finite |define LM_FINITE isfinite |' \
+ src/levmar/compiler.h
+
+# Build, install and delete the temporary files.
+ make V=1
+ make install
+ cd ..
+ rm -rf $$unpackdir
+
+# Make links for other possibly used names, copy citation and build
+# the final target.
ln -fs $(ibdir)/sex $(ibdir)/sextractor
ln -fs $(ibdir)/sex $(ibdir)/source-extractor
cp $(dtexdir)/sextractor.tex $(ictdir)/
echo "SExtractor $(sextractor-version) \citep{sextractor}" > $@
$(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version)
- tarball=swarp-$(swarp-version).tar.gz
+ tarball=swarp-$(swarp-version).tar.lz
$(call import-source, $(swarp-url), $(swarp-checksum))
# See comment above 'missfits' for '-fcommon'.
@@ -1520,6 +1618,29 @@ $(ibidir)/util-linux-$(util-linux-version): | $(idircustom)
cd $(ddir)
tar -xf $(tdir)/$$tarball
cd util-linux-$(util-linux-version)
+
+# If a patch exists for the current version, apply it.
+ if [ -f $(patchdir)/util-linux-$(util-linux-version)-macos.patch ]; then
+ cp $(patchdir)/util-linux-$(util-linux-version)-macos.patch \
+ util-linux-$(util-linux-version)-macos.patch
+ git apply util-linux-$(util-linux-version)-macos.patch
+ fi
+
+# The 'mkswap' feature needs low-level file system and kernel headers
+# that are not always available (in particular on older Linux
+# kernels). Also, creating SWAP space will need root permissions, so
+# its not something a Maneager may need! Unfortunately there is no
+# configuration option to disable this so we'll have to disable it
+# manually by commenting the relevant files in the
+# 'configure.ac'. Having a more recent 'configure.ac' will trigger
+# the './configure' script to be re-created after the first run, but
+# it is pretty fast and not a problem.
+ sed -e's|UL_BUILD_INIT(\[mkswap\], \[yes\])|UL_BUILD_INIT(\[mkswap\], \[no\])|' \
+ -i configure.ac
+
+
+# Configure Util-linux
+ export CONFIG_SHELL=$(ibdir)/bash
./configure --prefix=$(idircustom)/util-linux \
--disable-dependency-tracking \
--enable-libmount-support-mtab \
@@ -1593,12 +1714,12 @@ $(ibidir)/xlsxio-$(xlsxio-version): \
# useful in projects during its development, for more see the comment above
# GNU Emacs.
$(ibidir)/vim-$(vim-version):
- tarball=vim-$(vim-version).tar.bz2
+ tarball=vim-$(vim-version).tar.lz
$(call import-source, $(vim-url), $(vim-checksum))
cd $(ddir)
tar -xf $(tdir)/$$tarball
- n=$$(echo $(vim-version) | sed -e's|\.||')
- cd $(ddir)/vim$$n
+ unpackdir=vim-$(vim-version)
+ cd $(ddir)/$$unpackdir
./configure --prefix=$(idir) \
--disable-canberra \
--enable-multibyte \
@@ -1611,9 +1732,29 @@ $(ibidir)/vim-$(vim-version):
make -j$(numthreads)
make install
cd ..
- rm -rf vim$$n
+ rm -rf $$unpackdir
echo "VIM $(vim-version)" > $@
+$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
+ tarball=unzip-$(unzip-version).tar.lz
+ $(call import-source, $(unzip-url), $(unzip-checksum))
+ $(call gbuild, unzip-$(unzip-version), static,, \
+ -f unix/Makefile generic \
+ CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
+ -f unix/Makefile generic \
+ BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
+ echo "Unzip $(unzip-version)" > $@
+
+$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
+ tarball=zip-$(zip-version).tar.lz
+ $(call import-source, $(zip-url), $(zip-checksum))
+ $(call gbuild, zip-$(zip-version), static,, \
+ -f unix/Makefile generic \
+ CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
+ -f unix/Makefile generic \
+ BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
+ echo "Zip $(zip-version)" > $@
+
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 6766744..546195b 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -172,8 +172,10 @@ $(ipydir)/astroquery-$(astroquery-version): \
$(call pybuild, tar -xf, astroquery-$(astroquery-version), , \
Astroquery $(astroquery-version))
+# The optional dependency 'h5py' that is necessary for writting tables in
+# HDF5 format has been removed from Astropy because on macOS it cannot be
+# installed.
$(ipydir)/astropy-$(astropy-version): \
- $(ipydir)/h5py-$(h5py-version) \
$(ibidir)/expat-$(expat-version) \
$(ipydir)/scipy-$(scipy-version) \
$(ipydir)/numpy-$(numpy-version) \
@@ -400,7 +402,9 @@ $(ipydir)/lmfit-$(lmfit-version): \
LMFIT $(lmfit-version))
$(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \
- $(ipydir)/cython-$(cython-version)
+ $(ipydir)/cffi-$(cffi-version) \
+ $(ipydir)/numpy-$(numpy-version) \
+ $(ipydir)/future-$(future-version)
tarball=lsstdesccoord-$(lsstdesccoord-version).tar.gz
$(call import-source, $(lsstdesccoord-url), $(lsstdesccoord-checksum))
$(call pybuild, tar -xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \
@@ -455,7 +459,6 @@ $(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version)
mpmath $(mpmath-version))
$(ipydir)/numpy-$(numpy-version): \
- $(ibidir)/unzip-$(unzip-version) \
$(ipydir)/cython-$(cython-version) \
$(ibidir)/openblas-$(openblas-version) \
$(ipydir)/setuptools-$(setuptools-version)
@@ -471,7 +474,7 @@ $(ipydir)/numpy-$(numpy-version): \
$(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \
Numpy $(numpy-version))
cp $(dtexdir)/numpy.tex $(ictdir)/
- echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
+ echo "Numpy $(numpy-version) \citep{numpy2020}" > $@
$(ipydir)/packaging-$(packaging-version): \
$(ipydir)/pyparsing-$(pyparsing-version)
@@ -594,9 +597,12 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
$(call pybuild, tar -xf, requests-$(requests-version), , \
Requests $(requests-version))
+# 'pythran' is disabled in the build of Scipy because of complications it
+# caused on some systems. It is explicitly disabled using the environmental
+# variable. If for some reason it is needed, set the environment variable
+# to 1, and add it as a prerequisite of 'scipy'.
$(ipydir)/scipy-$(scipy-version): \
$(ipydir)/numpy-$(numpy-version) \
- $(ipydir)/pythran-$(pythran-version) \
$(ipydir)/pybind11-$(pybind11-version)
tarball=scipy-$(scipy-version).tar.lz
$(call import-source, $(scipy-url), $(scipy-checksum))
@@ -605,10 +611,11 @@ $(ipydir)/scipy-$(scipy-version): \
else
export LDFLAGS="$(LDFLAGS) -shared"
fi
+ export SCIPY_USE_PYTHRAN=0
conf="$$(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}" > $@
+ echo "Scipy $(scipy-version) \citep{scipy2020}" > $@
$(ipydir)/secretstorage-$(secretstorage-version): \
$(ipydir)/jeepney-$(jeepney-version) \
@@ -619,7 +626,6 @@ $(ipydir)/secretstorage-$(secretstorage-version): \
SecretStorage $(secretstorage-version))
$(ipydir)/setuptools-$(setuptools-version): \
- $(ibidir)/unzip-$(unzip-version) \
$(ibidir)/python-$(python-version)
tarball=setuptools-$(setuptools-version).tar.lz
$(call import-source, $(setuptools-url), $(setuptools-checksum))