1 files changed, 201 insertions, 110 deletions
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 102ebbd..575cdd6 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -1,7 +1,7 @@
 # Versions of the various dependencies
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
@@ -15,47 +15,47 @@
 # Basic/low-level programs and libraires (installed in any case)
 # --------------------------------------------------------------
 #
-# CLASS:BASIC (important identifier, don't modify this line)
-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 = 5.39
-findutils-version = 4.7.0
-flock-version = 0.2.3
+# CLASS:BASIC (important identifier for 'awk'; don't modify this line)
+bash-version = 5.1.8
+binutils-version = 2.37
+coreutils-version = 9.0
+curl-version = 7.79.1
+dash-version = 0.5.11.5
+diffutils-version = 3.8
+file-version = 5.41
+findutils-version = 4.8.0
+flock-version = 0.4.0
 gawk-version = 5.1.0
-gcc-version = 10.2.0
+gcc-version = 11.2.0
 gettext-version = 0.21
-git-version = 2.28.0
-gmp-version = 6.2.0
-grep-version = 3.4
-gzip-version = 1.10
+git-version = 2.34.0
+gmp-version = 6.2.1
+grep-version = 3.7
+gzip-version = 1.11
 isl-version = 0.18
-less-version = 563
-libbsd-version = 0.10.0
+less-version = 590
 libiconv-version = 1.16
 libtool-version = 2.4.6
-libunistring-version = 0.9.10
-libxml2-version = 2.9.9
-lzip-version = 1.22-rc2
-m4-version = 1.4.18-patched
+libunistring-version = 1.0
+libxml2-version = 2.9.12
+lzip-version = 1.22
+m4-version = 1.4.19
 make-version = 4.3
-metastore-version = 1.1.2-23-fa9170b
-mpc-version = 1.1.0
-mpfr-version = 4.0.2
-nano-version = 5.2
-ncurses-version = 6.2
-patchelf-version = 0.10
-perl-version = 5.32.0
+mpc-version = 1.2.1
+mpfr-version = 4.1.0
+nano-version = 6.0
+ncurses-version = 6.3
+openssl-version = 3.0.0
+patchelf-version = 0.13
+perl-version = 5.34.0
 pkgconfig-version = 0.29.2
-readline-version = 8.0
+podlators-version = 4.14
+readline-version = 8.1.1
 sed-version = 4.8
-tar-version = 1.32
-texinfo-version = 6.7
+tar-version = 1.34
+texinfo-version = 6.8
 unzip-version = 6.0
-wget-version = 1.20.3
+wget-version = 1.21.2
 which-version = 2.21
 xz-version = 5.2.5
 zip-version = 3.0
@@ -67,7 +67,16 @@ zlib-version = 1.2.11
 # When updating the version of these programs/libraries, please look into
 # the build rule first: In one way or another, the version string becomes
 # necessary during their build and must be accounted for.
-bzip2-version = 1.0.6
+bzip2-version = 1.0.8
+
+# PEM Certificate File
+# --------------------
+#
+# This file should be shipped with operating systems and can be found in
+# '/etc/ssl/cert.pem' (which may be a symbolic link to its actual
+# location). The current version was taken from an up-to-date ArchLinux at
+# the date that is also equal to the version.
+certpem-version = 2021-10-15
 
 
 
@@ -77,108 +86,103 @@ bzip2-version = 1.0.6
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/TARGETS.conf' will be built as
+# 'reproduce/software/config/TARGETS.conf' will be built as
 # part of a project. To specify a software there, just remove the
-# `-version' suffix from the list below.
+# '-version' suffix from the list below.
 #
-# CLASS:HIGHLEVEL (important identifier, don't modify this line.)
-apachelog4cxx-version = 0.10.0-603-014954db
+# CLASS:HIGHLEVEL (important identifier for 'awk'; don't modify this line)
+apachelog4cxx-version = 0.12.1
 apr-version = 1.7.0
 apr-util-version = 1.6.1
-astrometrynet-version = 0.80
+astrometrynet-version = 0.85
 atlas-version = 3.10.3
-autoconf-version = 2.69.200-babc
-automake-version = 1.16.2
-bison-version = 3.7
-boost-version = 1.73.0
+autoconf-version = 2.71
+automake-version = 1.16.5
+bison-version = 3.8.2
+boost-version = 1.77.0
 cairo-version = 1.16.0
 cdsclient-version = 3.84
-cfitsio-version = 3.48
-cmake-version = 3.18.1
-eigen-version = 3.3.7
-emacs-version = 27.1
-expat-version = 2.2.9
-fftw-version = 3.3.8
-flex-version = 2.6.4-91-ga631f5d
-freetype-version = 2.10.2
-gdb-version = 9.2
-ghostscript-version = 9.52
+cfitsio-version = 4.0.0
+cmake-version = 3.21.4
+eigen-version = 3.4.0
+emacs-version = 27.2
+expat-version = 2.4.1
+fftw-version = 3.3.10
+flex-version = 2.6.4
+freetype-version = 2.11.0
+gdb-version = 11.1
+ghostscript-version = 9.55.0
 ghostscript-fonts-gnu-version = 6.0
 ghostscript-fonts-std-version = 8.11
-gnuastro-version = 0.12
+gnuastro-version = 0.16.1-e0f1
 gperf-version = 3.1
-gsl-version = 2.6
-healpix-version = 3.50
-help2man-version = 1.47.11
-imagemagick-version = 7.0.8-67
+gsl-version = 2.7
+help2man-version = 1.48.5
+icu-version = 70.1
+imagemagick-version = 7.1.0-13
 imfit-version = 1.6.1
-libffi-version = 3.2.1
-libidn-version = 1.36
-libjpeg-version = v9b
+libbsd-version = 0.11.3
+libffi-version = 3.4.2
+libidn-version = 1.38
+libjpeg-version = 9d
+libmd-version = 1.0.4
 libnsl-version = 1.2.0-4a062cf
 libpaper-version = 1.1.28
 libpng-version = 1.6.37
-libtiff-version = 4.0.10
+libtiff-version = 4.3.0
 libtirpc-version = 1.2.6
+metastore-version = 1.1.2-23-fa9170b
 missfits-version = 2.8.0
-openblas-version = 0.3.10
-openmpi-version = 4.0.4
+openblas-version = 0.3.18
+openmpi-version = 4.1.1
 openssh-version = 8.0p1
 patch-version = 2.7.6
 pcre-version = 8.44
-pixman-version = 0.38.0
-python-version = 3.8.5
-R-version = 4.0.2
+pixman-version = 0.40.0
+python-version = 3.10.0
+r-cran-version = 4.1.2
 rpcsvc-proto-version = 1.4
 scamp-version = 2.6.7
 scons-version = 3.0.5
 sextractor-version = 2.25.0
 swarp-version = 2.38.0
-swig-version = 3.0.12
+swig-version = 4.0.2
 tides-version = 2.0
-util-linux-version = 2.35
+util-linux-version = 2.37.2
+valgrind-version = 3.18.1
 vim-version = 8.2
-xlsxio-version = 0.2.21
 yaml-version = 0.2.5
 
 # Xorg packages
-util-macros-version = 1.19.2
-xorgproto-version = 2020.1
+util-macros-version = 1.19.3
+xorgproto-version = 2021.5
 libxau-version = 1.0.9
 libxdmcp-version = 1.1.3
-xcb-proto-version = 1.14
+xcb-proto-version = 1.14.1
 libxcb-version = 1.14
-fontconfig-version = 2.13.1
+fontconfig-version = 2.13.94
 xtrans-version = 1.4.0
-libx11-version = 1.6.9
+libx11-version = 1.7.2
 libxext-version = 1.3.4
 libice-version = 1.0.10
 libsm-version = 1.2.3
-libxt-version = 1.2.0
+libxt-version = 1.2.1
 libpthread-stubs-version = 0.4
 
 # Version-dependent build
 # -----------------------
 lapack-version = 3.8.0
-libgit2-version = 1.0.1
-wcslib-version = 7.3
+libgit2-version = 1.3.0
+wcslib-version = 7.7
 
 # Netpbm's questions in the configure steps maybe change with different or
 # new versions.
-netpbm-version = 10.86.99
+netpbm-version = 10.73.38
 
-# Minizip is installed with the same `zlib' tarball, and they have the same
+# Minizip is installed with the same 'zlib' tarball, and they have the same
 # version.
 minizip-version = $(zlib-version)
 
-# From version 1.2 OpenSSL may not need a manual addition, as described in
-# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
-# cause problems, put it back in the list of "Basic/low-level" tools.
-openssl-version = 1.1.1a
-
-# Version 3.15.0 needs two patches, please check if they are necessary on
-# 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.
@@ -187,6 +191,7 @@ hdf5-version = 1.10.5
 
 
 
+
 # Python packages
 # ---------------
 #
@@ -194,65 +199,151 @@ hdf5-version = 1.10.5
 #
 # IMPORTANT: If you intend to change the version of any of the Python
 # modules/libraries below, please fix the hash strings of the respective
-# URL in `reproduce/software/make/python.mk'.
+# URL in 'reproduce/software/make/python.mk'.
 #
-# CLASS:PYTHON (important identifier, don't modify this line.)
+# CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line)
 asn1crypto-version = 0.24.0
 asteval-version = 0.9.16
-astropy-version = 4.0
-astroquery-version = 0.4
-beautifulsoup4-version = 4.7.1
+astropy-version = 5.0
+beautifulsoup4-version = 4.10.0
+beniget-version = 0.4.1
 certifi-version = 2018.11.29
-cffi-version = 1.12.2
+cffi-version = 1.15.0
 chardet-version = 3.0.4
 corner-version = 2.0.1
-cryptography-version = 2.6.1
-cycler-version = 0.10.0
-cython-version = 0.29.21
+cycler-version = 0.11.0
+cython-version = 0.29.24
 eigency-version = 1.77
 emcee-version = 3.0.1
 entrypoints-version = 0.3
-esutil-version = 0.6.4
+esutil-version = 0.6.9
+extension-helpers-version = 0.1
 flake8-version = 3.7.8
 future-version = 0.18.1
-galsim-version = 2.2.1
+galsim-version = 2.3.3
+gast-version = 0.5.3
 h5py-version = 2.10.0
 html5lib-version = 1.0.1
 idna-version = 2.8
 jeepney-version = 0.4
-keyring-version = 18.0.0
+jinja2-version = 3.0.3
 kiwisolver-version = 1.0.1
 lmfit-version = 0.9.14
 lsstdesccoord-version = 1.2.0
+markupsafe-version = 2.0.1
 matplotlib-version = 3.3.0
-mpi4py-version = 3.0.3
+mpi4py-version = 3.1.3
 mpmath-version = 1.1.0
-numpy-version = 1.19.1
+numpy-version = 1.21.3
+packaging-version = 21.3
 pexpect-version = 4.7.0
+pillow-version = 8.4.0
 pip-version = 19.0.2
+ply-version = 3.11
 pycodestyle-version = 2.5.0
 pycparser-version = 2.19
+pyerfa-version = 2.0.0.1
 pyflakes-version = 2.1.1
 pybind11-version = 2.5.0
-pyparsing-version = 2.3.1
+pyparsing-version = 3.0.4
 pypkgconfig-version = 1.5.1
 python-dateutil-version = 2.8.0
+pythran-version = 0.11.0
 pyyaml-version = 5.1
 requests-version = 2.21.0
-scipy-version = 1.5.2
-secretstorage-version = 3.1.1
-setuptools-version = 41.6.0
+scipy-version = 1.7.3
+setuptools-version = 58.3.0
 setuptools_scm-version = 3.3.3
 sip_tpv-version = 1.1
-six-version = 1.12.0
+six-version = 1.16.0
 soupsieve-version = 1.8
 sympy-version = 1.4
-uncertainties-version = 3.1.2
+uncertainties-version = 3.1.6
 urllib3-version = 1.24.1
 webencodings-version = 0.5.1
+wheel-version = 0.37.0
+# CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line)
 
 # Special Python modules:
 #
 # Healpy: When any Python module is requested, healpix will also build its
 #         Python module Healpy.
-healpy-version = xxxxx
+#
+# Bug: Healpix 3.50 doesn't yet support Python 3.10, so we are commenting
+# it here. When future versions fix the problem, we'll un-comment it again.
+#healpy-version = xxxxx
+
+
+
+
+
+# Problematic software that are currently ignored:
+
+# Healpix 3.80 has different installation scheme that is not yet
+# implemented here, and unfortunately healpix 3.50 has conflicts with
+# CFITSIO's new version macro and Python 3.10. So for now, we are ignoring
+# it.
+#healpix-version = 3.50
+
+# XLSX I/O (until version 0.2.29) crashes during compilation with GCC
+# 11.1.0, so we are temporarily commenting it.
+#xlsxio-version = 0.2.21
+
+# Setuptools-rust crash (https://savannah.nongnu.org/bugs/index.php?61731),
+# so it and its dependencies are being ignored: 'cryptography', and thus
+# 'secretstorage' and thus 'keyring' and thus 'astroquery'.
+#setuptools-rust-version = 1.1.2
+#cryptography-version = 36.0.1
+#secretstorage-version = 3.1.1
+#keyring-version = 18.0.0
+#astroquery-version = 0.4
+
+
+
+
+
+# R-CRAN (i.e. 'R') packages
+# ------------------
+#
+# Similar to optional programs and libraries above.
+#
+# Notation: The R package and variables associated with it are by default
+# called 'R-CRAN' (or 'r-cran') in Maneage, because searching on a single
+# letter string 'R' is extremely inefficient.
+#
+# IMPORTANT: If you intend to change the version of any of the R-CRAN
+# modules/libraries below, please fix the hash strings of the respective
+# packages in 'reproduce/software/conf/checksums.conf'.
+#
+# CLASS:R-CRAN-START (important identifier for 'awk'; don't modify this line)
+r-cran-cli-version = 2.5.0
+r-cran-colorspace-version = 2.0-1
+r-cran-cowplot-version = 1.1.1
+r-cran-crayon-version = 1.4.1
+r-cran-digest-version = 0.6.27
+r-cran-ellipsis-version = 0.3.2
+r-cran-fansi-version = 0.5.0
+r-cran-farver-version = 2.1.0
+r-cran-ggplot2-version = 3.3.4
+r-cran-glue-version = 1.4.2
+r-cran-gridExtra-version = 2.3
+r-cran-gtable-version = 0.3.0
+r-cran-isoband-version = 0.2.4
+r-cran-labeling-version = 0.4.2
+r-cran-lifecycle-version = 1.0.0
+r-cran-magrittr-version = 2.0.1
+r-cran-MASS-version = 7.3-54
+r-cran-mgcv-version = 1.8-36
+r-cran-munsell-version = 0.5.0
+r-cran-pillar-version = 1.6.1
+r-cran-pkgconfig-version = 2.0.3
+r-cran-R6-version = 2.5.0
+r-cran-RColorBrewer-version = 1.1-2
+r-cran-rlang-version = 0.4.11
+r-cran-scales-version = 1.1.1
+r-cran-tibble-version = 3.1.2
+r-cran-utf8-version = 1.2.1
+r-cran-vctrs-version = 0.3.8
+r-cran-viridisLite-version = 0.4.0
+r-cran-withr-version = 2.4.2
+# CLASS:R-CRAN-END (important identifier for 'awk'; don't modify this line)