diff options
Diffstat (limited to 'reproduce/software/make')
| -rw-r--r-- | reproduce/software/make/basic.mk | 207 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 233 | ||||
| -rw-r--r-- | reproduce/software/make/python.mk | 20 |
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)) |