diff options
| -rw-r--r-- | reproduce/software/config/TARGETS.conf | 2 | ||||
| -rw-r--r-- | reproduce/software/config/checksums.conf | 80 | ||||
| -rw-r--r-- | reproduce/software/config/urls.conf | 31 | ||||
| -rw-r--r-- | reproduce/software/config/versions.conf | 85 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 29 | ||||
| -rw-r--r-- | reproduce/software/make/build-rules.mk | 20 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 55 | ||||
| -rw-r--r-- | reproduce/software/make/python.mk | 5 | ||||
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 50 |
9 files changed, 187 insertions, 170 deletions
diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf index 8d3bdb0..5f10c96 100644 --- a/reproduce/software/config/TARGETS.conf +++ b/reproduce/software/config/TARGETS.conf @@ -35,7 +35,7 @@ -# Programs and libraries. +# Programs and libraries (for Python modules, add to 'top-level-python'). top-level-programs = gnuastro # Python libraries/modules. diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 62af1e1..b516a61 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -14,26 +14,26 @@ # Basic/low-level programs and libraires (installed in any case) # -------------------------------------------------------------- -bash-checksum = a93f221fe800908e335584837f63d02a350d9c8b2711f1923e946980b960fb2d4a21e4321f722c70e5faf5554991a6b9ef6722d214a1921f71030896cf134639 -binutils-checksum = a5e1f77e985d7d66e3ec6ed62a51a61c82ed0964a5108a1f318bf717f3f2af4dcd018ec3a66c10d6dc7525bad801b118f468eca07b2502c836895f4091bbeed4 +bash-checksum = e210cd63ce1241636fbb14d1a105c83e9481a0312026f746f76f7115b777707170ddfe1840fb4d3a4093613048e2d1eedf926e843ad15ffc8d66f08525e8b04b +binutils-checksum = 5ad795fab0803be83b53aa955fd5414c8408b4cf2a66eba2f8688298312934b4b1b0cbe9cf887d86de77f88adf1333d85fc9f6ab4a530e85a09b9b2dbf6aaf3f bzip2-checksum = 00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12 cert-checksum = a81dfa59c70788126a395c576e54cb8f61c1ea34da69b5cd42e2d83ee6426c2a26941360c7302793774ea98ca16846deb6e683144cc7fb6da6ef87b70447e4c8 -coreutils-checksum = ef8941dae845bbf5ae5838bc49e44554a766302930601aada6fa594e8088f0fbad74e481ee392ff89633e68b99e4da3f761fcb5d31ee3b233d540fe2a2d4e1af -curl-checksum = df8fc6b2cccf100f7479e25cad743964a84066b587da19585b36a788b0041925e33944986d636a451d6bb95a452d5ac6812b2d5fa6631a10e0ac82a2c7821c75 +coreutils-checksum = 1c8f3584efd61b4b02e7ac5db8e103b63cfb2063432caaf1e64cb2dcc56d8c657d1133bbf10bd41468d6a1f31142e6caa81d16ae68fa3e6e84075c253613a145 +curl-checksum = 614f8d67e6ee942cb5e57f2da1a3faaf84ebff549ffe383aaf3751a4de3c8874ff482076afa27a52e910a137dec9b0f6e98265dc7d4ad7c95845b63f39236fd4 dash-checksum = 9d55090115ac04f505d70e6790179331178950f96fe713b33fd698fa8bfa60d4eff1b68cb7b8a2f099d29c587d36034a17dccd6658ba1623ff0a625ac1fb9620 diffutils-checksum = 7b12cf8aea1b9844773748f72272d9c6a38adae9c3c3a8c62048f91fb56c60b76035fa5f51665dceaf2cfbf1d1f4a3efdcc24bf47a5a16ff4350543314b12c9c -file-checksum = 3ec5e51ffb7a82defa74845a90fbc983f6e169fc116606049bc01ff6e720d340c8abf6eb7a08b9ac1099162a5c02deac3633b07b039d486344c8abd9052ca751 +file-checksum = 9cf1a7b769c56eb6f5b25c66ce85fa1300128396e445b2e53dbbd8951e5da973a7a07c4ef9f7ebd1fe945d47bdaf2cd9ef09bd2be6c217a0bcb907d9449835e6 findutils-checksum = 650a24507f8f4ebff83ad28dd27daa4785b4038dcaadc4fe00823b976e848527074cce3f9ec34065b7f037436d2aa6e9ec099bc05d7472c29864ac2c69de7f2e flock-checksum = ddb997174c0653bc3d29410a5a16b6290e737aa40fbf4b746e2d1db1e88e5acb08ec11a25c27c8a5a5fbf5a00fcac17abeaa245e7df27bd975ae86364d400b86 -gawk-checksum = 3734740b7406ddfec9e04bb7774e76c6446cba76642a6180266e7b1822de20aab824c29c4e417256d877762ef04ef3f9df855cd4a3ca414a9225323b49d79195 -gcc-checksum = a12dff52af876aee0fd89a8d09cdc455f35ec46845e154023202392adc164848faf8ee881b59b681b696e27c69fd143a214014db4214db62f9891a1c8365c040 -gettext-checksum = 08d20c659004a77e607af17df15f5ce9bd4fc0feca9436aa206b0cbd2516f9f0c98c7ee1faacf7ff429f9b0dd9de219947b300216887a60727602a688acabc82 -git-checksum = 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pyyaml-checksum = 8f27f92bdfa310a99dd6d83947332cc033fa18f0011998bb585ad5c4340a2da20d8c20bfdb53beaae15651198d1240c986818379b0a05b230f74d1f30f53e7fd requests-checksum = 385e1d80993a21c09e7c4682500ca8c24155962ba41ecd8e73612722b2ff6618b736e827fc48ad1683b0d2bc7a420cfe680f5107860aca52656ef777f1d60104 -scipy-checksum = 672915da782f5a439a3920ad1a200937b8415aeb4f1db2451cf0b5a90ba6e18c69e17e9ff8433f6a7760bbef2434d7b0f6447319faec9bb96fa6841794bfa538 +scipy-checksum = 45463df30a0f6270d9f4cf52235f31607904a6ae1375e12600e7f1ab2d27b1dc25a6211b49dceb71506be22c756890adaf9f81d9e6be7455def86c9caf0dc923 secretstorage-checksum = 295e0f75c772edf153480730dc20051f06e60e040a18f169620cb4aaa37b8c1a254a496464d3794a38cf49fa884a7b561fe364816f0d12a5b2622c77259f03cf setuptools-checksum = 1bed75e7173ea0399f078c96cf5c1818dada7a4b86a93e61ff72da6a25694e321b9047e024617aa775b71a25fe8cb0848323902e1fb9c8c8a1f39434f0de6434 setuptools_scm-checksum = 196d4785a1802875d89b9e54ae788e791a9c5cb685109784059955b691242984e42b96d77075116790935f56be82259bc2588d95d65ecbb101261d76daddb83c diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index 945537d..34c4d89 100644 --- a/reproduce/software/config/urls.conf +++ b/reproduce/software/config/urls.conf @@ -16,8 +16,8 @@ # Basic/low-level programs and libraires (installed in any case) -# -------------------------------------------------------------- -#bash-url = http://akhlaghi.org/maneage-software +# ------------------------------------------------------------- +#bash-url = http://akhlaghi.org/src #binutils-url = http://ftp.gnu.org/gnu/binutils #bzip2-url = http://akhlaghi.org/maneage-software #cert-url = http://akhlaghi.org/maneage-software @@ -86,7 +86,7 @@ #cairo-url = https://www.cairographics.org/releases #cdsclient-url = http://cdsarc.u-strasbg.fr/ftp/pub/sw #cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c -#cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv/cmake-$(cmake-version).tar.gz) +#cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv) #eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz #expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz) #fftw-url = ftp://ftp.fftw.org/pub/fftw @@ -94,22 +94,23 @@ #freetype-url = https://download.savannah.gnu.org/releases/freetype #gdb-url = http://ftp.gnu.org/gnu/gdb #ghostscript-url = $(shell v=$$(echo $(ghostscript-version) | sed -e's/\.//'); echo https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs$$v) -#gs-fonts-std-url = https://downloads.sourceforge.net/gs-fonts -#gs-fonts-gnu-url = https://downloads.sourceforge.net/gs-fonts #gnuastro-url = http://ftp.gnu.org/gnu/gnuastro +#gperf-url = http://ftp.gnu.org/pub/gnu/gperf +#gs-fonts-gnu-url = https://downloads.sourceforge.net/gs-fonts +#gs-fonts-std-url = https://downloads.sourceforge.net/gs-fonts #gsl-url = http://ftp.gnu.org/gnu/gsl #hdf5-url = $(shell majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src) #healpix-url = http://akhlaghi.org/maneage-software #help2man-url = http://ftp.gnu.org/gnu/help2man +#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/ #imagemagick-url = http://akhlaghi.org/maneage-software #imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit #lapack-url = http://www.netlib.org/lapack #libffi-url = ftp://sourceware.org/pub/libffi +#libgit2-url = http://akhlaghi.org/src #libidn-url = https://ftp.gnu.org/gnu/libidn -#libgit2-url = https://github.com/libgit2/libgit2/archive #libjpeg-url = http://ijg.org/files #libnsl-url = http://akhlaghi.org/maneage-software -#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/ #libpng-url = https://download.sourceforge.net/libpng #libtiff-url = https://download.osgeo.org/libtiff #libtirpc-url = https://downloads.sourceforge.net/libtirpc @@ -121,7 +122,7 @@ #openssh-url = https://artfiles.org/openbsd/OpenSSH/portable #patch-url = http://ftp.gnu.org/gnu/patch #pixman-url = https://www.cairographics.org/releases -#python-url = https://www.python.org/ftp/python/$(python-version) +#python-url = http://akhlaghi.org/src #R-url = $(shell majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}'); echo https://cran.r-project.org/src/base/R-$$majver) #rpcsvc-proto-url = https://github.com/thkukuk/rpcsvc-proto/releases/download #scamp-url = http://akhlaghi.org/maneage-software @@ -138,16 +139,16 @@ # Xorg packages # ------------- -#util-macros-url = https://www.x.org/pub/individual/util -#xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto +#fontconfig-url = https://www.freedesktop.org/software/fontconfig/release +#libpthread-stubs-url = https://xcb.freedesktop.org/dist +#libx11-url = https://www.x.org/pub/individual/lib #libxau-url = https://www.x.org/pub/individual/lib #libxdmcp-url = https://www.x.org/pub/individual/lib +#libxext-url = https://www.x.org/pub/individual/lib +#util-macros-url = https://www.x.org/pub/individual/util #xcb-proto-url = https://xorg.freedesktop.org/archive/individual/proto -#fontconfig-url = https://www.freedesktop.org/software/fontconfig/release +#xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto #xtrans-url = https://www.x.org/pub/individual/lib -#libx11-url = https://www.x.org/pub/individual/lib -#libxext-url = https://www.x.org/pub/individual/lib -#libpthread-stubs-url = https://xcb.freedesktop.org/dist @@ -167,7 +168,7 @@ # files" menu, you can download the source '.zip' file. For version 1.18.5, # (with full filename of 'numpy-1.18.5.zip') the link will be like this. # -# numpy-url = https://files.pythonhosted.org/packages/01/1b/d3ddcabd5817be02df0e6ee20d64f77ff6d0d97f83b77f65e98c8a651981/numpy-1.18.5.zip +# numpy-url = https://files.pythonhosted.org/packages/01/1b/d3ddcabd5817be02df0e6ee20d64f77ff6d0d97f83b77f65e98c8a651981 # # Hence, if the version changes, the checksum, and its two top host # directories also change. This is why we aren't putting any URL here by diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 7998345..0a9e21e 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -16,24 +16,24 @@ # -------------------------------------------------------------- # # CLASS:BASIC (important identifier, don't modify this line) -bash-version = 5.0.11 -binutils-version = 2.32 -coreutils-version = 8.31 -curl-version = 7.65.3 +bash-version = 5.0.18 +binutils-version = 2.35 +coreutils-version = 8.32 +curl-version = 7.71.1 dash-version = 0.5.10.2 diffutils-version = 3.7 -file-version = 5.36 +file-version = 5.39 findutils-version = 4.7.0 flock-version = 0.2.3 -gawk-version = 5.0.1 -gcc-version = 9.2.0 -gettext-version = 0.20.2 -git-version = 2.26.2 -gmp-version = 6.1.2 -grep-version = 3.3 +gawk-version = 5.1.0 +gcc-version = 10.2.0 +gettext-version = 0.21 +git-version = 2.28.0 +gmp-version = 6.2.0 +grep-version = 3.4 gzip-version = 1.10 isl-version = 0.18 -libbsd-version = 0.9.1 +libbsd-version = 0.10.0 libiconv-version = 1.16 libtool-version = 2.4.6 libunistring-version = 0.9.10 @@ -44,18 +44,18 @@ make-version = 4.3 metastore-version = 1.1.2-23-fa9170b mpc-version = 1.1.0 mpfr-version = 4.0.2 -ncurses-version = 6.1 +ncurses-version = 6.2 patchelf-version = 0.10 -perl-version = 5.30.0 +perl-version = 5.32.0 pkgconfig-version = 0.29.2 readline-version = 8.0 -sed-version = 4.7 +sed-version = 4.8 tar-version = 1.32 -texinfo-version = 6.6 +texinfo-version = 6.7 unzip-version = 6.0 wget-version = 1.20.3 which-version = 2.21 -xz-version = 5.2.4 +xz-version = 5.2.5 zip-version = 3.0 zlib-version = 1.2.11 @@ -83,35 +83,34 @@ bzip2-version = 1.0.6 apachelog4cxx-version = 0.10.0-603-014954db apr-version = 1.7.0 apr-util-version = 1.6.1 -astrometrynet-version = 0.77 +astrometrynet-version = 0.80 atlas-version = 3.10.3 autoconf-version = 2.69.200-babc -automake-version = 1.16.1 -bison-version = 3.6 +automake-version = 1.16.2 +bison-version = 3.7 boost-version = 1.73.0 cairo-version = 1.16.0 cdsclient-version = 3.84 -cfitsio-version = 3.47 -cmake-version = 3.17.0 +cfitsio-version = 3.48 +cmake-version = 3.18.1 eigen-version = 3.3.7 expat-version = 2.2.9 fftw-version = 3.3.8 flex-version = 2.6.4-91-ga631f5d -freetype-version = 2.9 -gdb-version = 8.3 -ghostscript-version = 9.50 +freetype-version = 2.10.2 +gdb-version = 9.2 +ghostscript-version = 9.52 ghostscript-fonts-gnu-version = 6.0 ghostscript-fonts-std-version = 8.11 -gnuastro-version = 0.11 +gnuastro-version = 0.12 gperf-version = 3.1 gsl-version = 2.6 -hdf5-version = 1.10.5 healpix-version = 3.50 help2man-version = 1.47.11 imagemagick-version = 7.0.8-67 imfit-version = 1.6.1 libffi-version = 3.2.1 -libidn-version = 1.35 +libidn-version = 1.36 libjpeg-version = v9b libnsl-version = 1.2.0-4a062cf libpaper-version = 1.1.28 @@ -120,13 +119,13 @@ libtiff-version = 4.0.10 libtirpc-version = 1.2.6 missfits-version = 2.8.0 openblas-version = 0.3.10 -openmpi-version = 4.0.1 +openmpi-version = 4.0.4 openssh-version = 8.0p1 patch-version = 2.7.6 pcre-version = 8.44 pixman-version = 0.38.0 -python-version = 3.7.4 -R-version = 3.6.2 +python-version = 3.8.5 +R-version = 4.0.2 rpcsvc-proto-version = 1.4 scamp-version = 2.6.7 scons-version = 3.0.5 @@ -136,7 +135,7 @@ swig-version = 3.0.12 tides-version = 2.0 util-linux-version = 2.35 xlsxio-version = 0.2.21 -yaml-version = 0.2.2 +yaml-version = 0.2.5 # Xorg packages util-macros-version = 1.19.2 @@ -157,8 +156,8 @@ libpthread-stubs-version = 0.4 # Version-dependent build # ----------------------- lapack-version = 3.8.0 -libgit2-version = 0.28.2 -wcslib-version = 6.4 +libgit2-version = 1.0.1 +wcslib-version = 7.3 # Netpbm's questions in the configure steps maybe change with different or # new versions. @@ -177,6 +176,9 @@ openssl-version = 1.1.1a # any future release. valgrind-version = 3.15.0 +# Be careful with updateing hdf5 because h5py 2.10.0 doesn't work with +# version 1.12.0. +hdf5-version = 1.10.5 @@ -202,7 +204,7 @@ chardet-version = 3.0.4 corner-version = 2.0.1 cryptography-version = 2.6.1 cycler-version = 0.10.0 -cython-version = 0.29.6 +cython-version = 0.29.21 eigency-version = 1.77 emcee-version = 3.0.1 entrypoints-version = 0.3 @@ -210,7 +212,7 @@ esutil-version = 0.6.4 flake8-version = 3.7.8 future-version = 0.18.1 galsim-version = 2.2.1 -h5py-version = 2.9.0 +h5py-version = 2.10.0 html5lib-version = 1.0.1 idna-version = 2.8 jeepney-version = 0.4 @@ -218,22 +220,22 @@ keyring-version = 18.0.0 kiwisolver-version = 1.0.1 lmfit-version = 0.9.14 lsstdesccoord-version = 1.2.0 -matplotlib-version = 3.1.1 -mpi4py-version = 3.0.2 +matplotlib-version = 3.3.0 +mpi4py-version = 3.0.3 mpmath-version = 1.1.0 -numpy-version = 1.17.2 +numpy-version = 1.19.1 pexpect-version = 4.7.0 pip-version = 19.0.2 pycodestyle-version = 2.5.0 pycparser-version = 2.19 pyflakes-version = 2.1.1 -pybind11-version = 2.4.3 +pybind11-version = 2.5.0 pyparsing-version = 2.3.1 pypkgconfig-version = 1.5.1 python-dateutil-version = 2.8.0 pyyaml-version = 5.1 requests-version = 2.21.0 -scipy-version = 1.3.1 +scipy-version = 1.5.2 secretstorage-version = 3.1.1 setuptools-version = 41.6.0 setuptools_scm-version = 3.3.3 @@ -249,3 +251,4 @@ webencodings-version = 0.5.1 # # Healpy: When any Python module is requested, healpix will also build its # Python module Healpy. +healpy-version = xxxxx diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index b9678d0..0b672d8 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -183,6 +183,10 @@ $(ibdir) $(ildir):; mkdir $@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \ | $(ibdir) $(ildir) + # Hardware specific + $(call makelink,lp) # For printing, necessary for R. + $(call makelink,lpr) # For printing, necessary for R. + # Mac OS specific $(call makelink,mig) $(call makelink,xcrun) @@ -922,7 +926,7 @@ $(ibidir)/gettext-$(gettext-version): \ $(ibidir)/ncurses-$(ncurses-version) \ $(ibidir)/libiconv-$(libiconv-version) \ $(ibidir)/libunistring-$(libunistring-version) - tarball=gettext-$(gettext-version).tar.xz + tarball=gettext-$(gettext-version).tar.lz $(call import-source, $(gettext-url), $(gettext-checksum)) $(call gbuild, gettext-$(gettext-version), static,, \ V=1 -j$(numthreads)) @@ -959,7 +963,7 @@ $(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version) $(call import-source, $(libtool-url), $(libtool-checksum)) $(call gbuild, libtool-$(libtool-version), static, \ --program-prefix=g, V=1 -j$(numthreads)) - ln -s $(ibdir)/glibtoolize $(ibdir)/libtoolize + ln -sf $(ibdir)/glibtoolize $(ibdir)/libtoolize echo "GNU Libtool $(libtool-version)" > $@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) @@ -1211,6 +1215,7 @@ $(ibidir)/binutils-$(binutils-version): \ $(call makelink,ld) $(call makelink,nm) $(call makelink,ps) + $(call makelink,strip) $(call makelink,ranlib) echo "" > $@ else @@ -1220,14 +1225,15 @@ $(ibidir)/binutils-$(binutils-version): \ --with-lib-path=$(sys_library_path), \ -j$(numthreads) ) - # The `ld' linker of Binutils needs several `*crt*.o' file to - # run. On some systems these object files aren't installed in - # standard places. We defined `LIBRARY_PATH' and that fixed the - # problem for many systems. However, some software (for example - # ImageMagick) over-write `LIBRARY_PATH', therefore there is no - # other way than to put a link to these necessary files in our - # local build directory. IMPORTANT NOTE: later, when we build the - # GNU C Library in the project, we should remove this step. + # The `ld' linker of Binutils needs several `*crt*.o' files from + # the host's GNU C Library to run. On some systems these object + # files aren't installed in standard places. We defined + # `LIBRARY_PATH' and that fixed the problem for many + # systems. However, some software (for example ImageMagick) + # over-write `LIBRARY_PATH', therefore there is no other way than + # to put a link to these necessary files in our local build + # directory. IMPORTANT NOTE: later, when we build the GNU C + # Library in the project, we should remove this step. if ! [ x"$(sys_library_path)" = x ]; then for f in $(sys_library_path)/*crt*.o; do b=$$($(ibdir)/basename $$f) @@ -1284,9 +1290,9 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # built/existing compilers in this project. Note that GCC also # installs several executables like this 'x86_64-pc-linux-gnu-gcc', # 'x86_64-pc-linux-gnu-gcc-ar' or 'x86_64-pc-linux-gnu-g++'. + rm -f $(ibdir)/*g++ $(ibdir)/cpp $(ibdir)/gfortran rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc* rm -f $(ibdir)/*gcc* $(ibdir)/gcov* $(ibdir)/cc $(ibdir)/c++ - rm -f $(ibdir)/*g++ $(ibdir)/cpp $(ibdir)/gfortran $(ibdir)/strip rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64* # GCC builds is own libraries in '$(idir)/lib64'. But all other @@ -1315,7 +1321,6 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # having GNU CPP in the project build directory is known to cause # problems with 'libX11'. $(call makelink,gfortran) - $(call makelink,strip,mandatory) if [ x$(on_mac_os) = xyes ]; then $(call makelink,clang) $(call makelink,clang++) diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk index 7471e5b..86370ab 100644 --- a/reproduce/software/make/build-rules.mk +++ b/reproduce/software/make/build-rules.mk @@ -170,11 +170,21 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \ \ echo; echo "Using '$$confscript' to configure:"; echo; \ echo "$$confscript $(3) $$configop"; echo; \ - $$confscript $(3) $$configop; \ - make "$$shellop" $(4); \ - $$check; \ - make "$$shellop" install $(7); \ - cd ..; \ + if [ x$$configure_in_different_directory = x1 ]; then \ + mkdir build; \ + cd build; \ + ../$$confscript $(3) $$configop; \ + make "$$shellop" $(4); \ + $$check; \ + make "$$shellop" install $(7); \ + cd ../..; \ + else \ + $$confscript $(3) $$configop; \ + make "$$shellop" $(4); \ + $$check; \ + make "$$shellop" install $(7); \ + cd ..; \ + fi; \ rm -rf $(1) diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 4052ed4..9f434bc 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -763,8 +763,8 @@ $(ibidir)/libgit2-$(libgit2-version): $(ibidir)/cmake-$(cmake-version) -DUSE_SSH=OFF -DBUILD_CLAR=OFF \ -DTHREADSAFE=ON -DUSE_ICONV=OFF ) if [ x$(on_mac_os) = xyes ]; then - install_name_tool -id $(ildir)/libgit2.28.dylib \ - $(ildir)/libgit2.28.dylib + install_name_tool -id $(ildir)/libgit2.1.0.dylib \ + $(ildir)/libgit2.1.0.dylib fi echo "Libgit2 $(libgit2-version)" > $@ @@ -785,8 +785,8 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version) --with-cfitsioinc=$(idir)/include \ --without-pgplot $$fortranopt) if [ x$(on_mac_os) = xyes ]; then - install_name_tool -id $(ildir)/libwcs.6.4.dylib \ - $(ildir)/libwcs.6.4.dylib + install_name_tool -id $(ildir)/libwcs.7.3.dylib \ + $(ildir)/libwcs.7.3.dylib fi echo "WCSLIB $(wcslib-version)" > $@ @@ -853,7 +853,7 @@ $(ibidir)/automake-$(automake-version): $(ibidir)/autoconf-$(autoconf-version) echo "GNU Automake $(automake-version)" > $@ $(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version) - tarball=bison-$(bison-version).tar.xz + tarball=bison-$(bison-version).tar.lz $(call import-source, $(bison-url), $(bison-checksum)) $(call gbuild, bison-$(bison-version), static, ,V=1 -j$(numthreads)) echo "GNU Bison $(bison-version)" > $@ @@ -916,6 +916,7 @@ $(ibidir)/flex-$(flex-version): $(ibidir)/bison-$(bison-version) $(ibidir)/gdb-$(gdb-version): $(ibidir)/python-$(python-version) tarball=gdb-$(gdb-version).tar.gz + export configure_in_different_directory=1; $(call import-source, $(gdb-url), $(gdb-checksum)) $(call gbuild, gdb-$(gdb-version),,,V=1 -j$(numthreads)) echo "GNU Project Debugger (GDB) $(gdb-version)" > $@ @@ -1096,10 +1097,17 @@ $(ibidir)/minizip-$(minizip-version): $(ibidir)/automake-$(automake-version) rm -rf $$unpackdir echo "Minizip $(minizip-version)" > $@ +# The Astromatic software packages (including missfits, sextractor, swarp +# and others) need the '-fcommon' flag to compile properly on GCC 10 and +# after. Previous to GCC 10, it was the default, but from GCC 10, the +# default is '-fno-common'. This is known by the author (as SExtractor +# issue 12: https://github.com/astromatic/sextractor/issues/12) and will +# hopefully be fixed in the future. $(ibidir)/missfits-$(missfits-version): tarball=missfits-$(missfits-version).tar.gz $(call import-source, $(missfits-url), $(missfits-checksum)) - $(call gbuild, missfits-$(missfits-version), static) + $(call gbuild, missfits-$(missfits-version), static, \ + CFLAGS="-fcommon") cp $(dtexdir)/missfits.tex $(ictdir)/ echo "MissFITS $(missfits-version) \citep{missfits}" > $@ @@ -1163,11 +1171,25 @@ $(ibidir)/R-$(R-version): \ $(ibidir)/libpaper-$(libpaper-version) tarball=R-$(R-version).tar.gz $(call import-source, $(R-url), $(R-checksum)) + cd $(ddir) + tar xf $(tdir)/$$tarball + cd R-$(R-version) + # We need to manually remove the lines with '~autodetect~', they + # cause the configure script to crash in version 4.0.2. They are + # used in relation to Java, and we don't use Java anyway. + sed -i -e '/\~autodetect\~/ s/^/#/g' configure export R_SHELL=$(SHELL) - $(call gbuild, R-$(R-version), static, \ - --without-x --with-readline \ - --disable-openmp, -j$(numthreads)) + ./configure --prefix=$(idir) \ + --without-x \ + --with-pcre1 \ + --disable-java \ + --with-readline \ + --disable-openmp + make -j$(numthreads) + make install + cd .. + rm -rf R-$(R-version) echo "R $(R-version)" > $@ # SCAMP documentation says ATLAS is a mandatory prerequisite for using @@ -1181,7 +1203,10 @@ $(ibidir)/scamp-$(scamp-version): \ $(ibidir)/cdsclient-$(cdsclient-version) tarball=scamp-$(scamp-version).tar.lz $(call import-source, $(scamp-url), $(scamp-checksum)) + + # See comment above 'missfits' for '-fcommon'. $(call gbuild, scamp-$(scamp-version), static, \ + CFLAGS="-fcommon" \ --enable-threads \ --enable-openblas \ --enable-plplot=no \ @@ -1209,13 +1234,20 @@ $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version) # libraries. But we can override this issue since we have Openblas # installed, it is just necessary to explicity tell sextractor to use it in # the configuration step. +# +# The '-fcommon' is a necessary C compilation flag for GCC 10 and above. It +# is necessary for astromatic libraries, otherwise their build will crash. $(ibidir)/sextractor-$(sextractor-version): \ $(ibidir)/fftw-$(fftw-version) \ $(ibidir)/openblas-$(openblas-version) tarball=sextractor-$(sextractor-version).tar.lz $(call import-source, $(sextractor-url), $(sextractor-checksum)) + + # See comment above 'missfits' for '-fcommon'. $(call gbuild, sextractor-$(sextractor-version), static, \ - --enable-threads --enable-openblas \ + CFLAGS="-fcommon" \ + --enable-threads \ + --enable-openblas \ --with-openblas-libdir=$(ildir) \ --with-openblas-incdir=$(idir)/include) ln -fs $(ibdir)/sex $(ibdir)/sextractor @@ -1225,7 +1257,10 @@ $(ibidir)/sextractor-$(sextractor-version): \ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version) tarball=swarp-$(swarp-version).tar.gz $(call import-source, $(swarp-url), $(swarp-checksum)) + + # See comment above 'missfits' for '-fcommon'. $(call gbuild, swarp-$(swarp-version), static, \ + CFLAGS="-fcommon" \ --enable-threads) cp $(dtexdir)/swarp.tex $(ictdir)/ echo "SWarp $(swarp-version) \citep{swarp}" > $@ diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index 2fede35..d39208f 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -431,6 +431,7 @@ $(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version) $(ipydir)/numpy-$(numpy-version): \ $(ibidir)/unzip-$(unzip-version) \ + $(ipydir)/cython-$(cython-version) \ $(ibidir)/openblas-$(openblas-version) \ $(ipydir)/setuptools-$(setuptools-version) tarball=numpy-$(numpy-version).zip @@ -528,7 +529,9 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \ $(call pybuild, tar xf, requests-$(requests-version), , \ Requests $(requests-version)) -$(ipydir)/scipy-$(scipy-version): $(ipydir)/numpy-$(numpy-version) +$(ipydir)/scipy-$(scipy-version): \ + $(ipydir)/numpy-$(numpy-version) \ + $(ipydir)/pybind11-$(pybind11-version) tarball=scipy-$(scipy-version).tar.gz $(call import-source, $(scipy-url), $(scipy-checksum)) if [ x$(on_mac_os) = xyes ]; then diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index b11992e..593b1d9 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -58,9 +58,6 @@ ptconf=$cdir/LOCAL_tmp.conf poconf=$cdir/LOCAL_old.conf depverfile=$cdir/versions.conf depshafile=$cdir/checksums.conf -# --------- Delete for no Gnuastro --------- -glconf=$adir/gnuastro/gnuastro-local.conf -# ------------------------------------------ @@ -634,12 +631,10 @@ EOF # (for example the user might have ran `./project configure' by mistake). printnotice=yes rewritepconfig=yes -rewritegconfig=yes -if [ -f $pconf ] || [ -f $glconf ]; then +if [ -f $pconf ]; then if [ $existing_conf = 1 ]; then printnotice=no if [ -f $pconf ]; then rewritepconfig=no; fi - if [ -f $glconf ]; then rewritegconfig=no; fi fi fi @@ -1010,44 +1005,6 @@ fi -# --------- Delete for no Gnuastro --------- -# Get the version of Gnuastro that must be used. -gversion=$(awk '$1=="gnuastro-version" {print $NF}' $depverfile) - -# Gnuastro's local configuration settings -if [ $rewritegconfig = yes ]; then - create_file_with_notice $glconf - echo "# Minimum number of bytes to use HDD/SSD instead of RAM." >> $glconf - echo " minmapsize $minmapsize" >> $glconf - echo >> $glconf - echo "# Version of Gnuastro that must be used." >> $glconf - echo " onlyversion $gversion" >> $glconf -else - ingversion=$(awk '$1=="onlyversion" {print $NF}' $glconf) - if [ x$ingversion != x$gversion ]; then - cat <<EOF -______________________________________________________ -!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!! - -Gnuastro's version in '$glconf' ($ingversion) doesn't match the tarball -version that this project was designed to use in '$depverfile' -($gversion). Please re-run after removing the former file: - - $ rm $glconf - $ ./project configure -e - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - exit 1 - fi -fi -# ------------------------------------------ - - - - - # Delete final configuration target # --------------------------------- # @@ -1148,12 +1105,15 @@ fi # Note: if we don't delete them first, it can happen that an extra link # will be created in each directory that points to its parent. So to be # safe, we are deleting all the links on each re-configure of the project. -rm -f .build .local .gnuastro +rm -f .build .local + ln -s $bdir .build ln -s $instdir .local ln -s $texdir tex/build ln -s $tikzdir tex/tikz + # --------- Delete for no Gnuastro --------- +rm -f .gnuastro ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro # ------------------------------------------ |