diff options
Diffstat (limited to 'reproduce/software/make/high-level.mk')
| -rw-r--r-- | reproduce/software/make/high-level.mk | 233 |
1 files changed, 187 insertions, 46 deletions
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)" > $@ + |