Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).

1 files changed, 31 insertions, 24 deletions

diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf
index a311524..7177411 100644
--- a/reproduce/software/config/urls.conf
+++ b/reproduce/software/config/urls.conf
@@ -3,8 +3,8 @@
 # If un-commented the URLs of this file will be used. Otherwise default
 # servers (primarily on 'zenodo.org') will be checked for the tarball.
 #
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2020-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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
@@ -19,15 +19,15 @@
 # -------------------------------------------------------------
 #bash-url = http://akhlaghi.org/src
 #binutils-url = http://ftp.gnu.org/gnu/binutils
-#bzip2-url = http://akhlaghi.org/maneage-software
+#bzip2-url = https://sourceware.org/pub/bzip2
 #cert-url = http://akhlaghi.org/maneage-software
 #coreutils-url = http://ftp.gnu.org/gnu/coreutils
 #curl-url = https://curl.haxx.se/download
-#dash-url = http://akhlaghi.org/maneage-software
+#dash-url = http://gondor.apana.org.au/~herbert/dash/files
 #diffutils-url = http://ftp.gnu.org/gnu/diffutils
 #file-url = ftp://ftp.astron.com/pub/file
 #findutils-url = http://ftp.gnu.org/gnu/findutils
-#flock-url = http://akhlaghi.org/src
+#flock-url = https://github.com/discoteq/flock/releases
 #gawk-url = http://ftp.gnu.org/gnu/gawk
 #gcc-url = http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version)
 #gettext-url = https://ftp.gnu.org/gnu/gettext
@@ -36,8 +36,7 @@
 #grep-url = http://ftp.gnu.org/gnu/grep
 #gzip-url = http://akhlaghi.org/src
 #isl-url = ftp://gcc.gnu.org/pub/gcc/infrastructure
-less-url = http://www.greenwoodsoftware.com/less/
-#libbsd-url = http://libbsd.freedesktop.org/releases
+#less-url = http://www.greenwoodsoftware.com/less/
 #libiconv-url = https://ftp.gnu.org/pub/gnu/libiconv
 #libtool-url = http://ftp.gnu.org/gnu/libtool
 #libunistring-url = http://ftp.gnu.org/gnu/libunistring
@@ -45,15 +44,15 @@ less-url = http://www.greenwoodsoftware.com/less/
 #lzip-url = http://akhlaghi.org/src
 #m4-url = http://akhlaghi.org/maneage-software
 #make-url = http://akhlaghi.org/src
-#metastore-url = http://akhlaghi.org/maneage-software
 #mpc-url = http://ftp.gnu.org/gnu/mpc
 #mpfr-url = http://www.mpfr.org/mpfr-current
 #nano-url = https://www.nano-editor.org/dist/v$(word 1, $(subst ., ,$(nano-version)))
 #ncurses-url = http://ftp.gnu.org/gnu/ncurses
 #openssl-url = http://www.openssl.org/source
-#patchelf-url = http://nixos.org/releases/patchelf/patchelf-$(patchelf-version)
+#patchelf-url = https://github.com/NixOS/patchelf/releases/download/$(patchelf-version)
 #perl-url = $(shell echo https://www.cpan.org/src/$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}'))
 #pkgconfig-url = http://pkg-config.freedesktop.org/releases
+#podlators-url = https://www.eyrie.org/~eagle/software/podlators/
 #readline-url = http://ftp.gnu.org/gnu/readline
 #sed-url = http://ftp.gnu.org/gnu/sed
 #tar-url = http://ftp.gnu.org/gnu/tar
@@ -73,30 +72,31 @@ less-url = http://www.greenwoodsoftware.com/less/
 # ------------------------------------------
 #
 # 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
-# `-url' suffix from the list below.
+# '-url' suffix from the list below.
+
 #apachelog4cxx-url = http://akhlaghi.org/maneage-software
-#apr-url = https://www-us.apache.org/dist/apr
-#apr-util-url = https://www-us.apache.org/dist/apr
+#apr-url = https://archive.apache.org/dist/apr/
+#apr-util-url = https://archive.apache.org/dist/apr/
 #astrometrynet-url = http://astrometry.net/downloads
 #atlas-url = https://sourceforge.net/projects/math-atlas/files/Stable/$(atlas-version)/atlas$(atlas-version).tar.bz2/download
 #autoconf-url = http://akhlaghi.org/maneage-software
 #automake-url = http://ftp.gnu.org/gnu/automake
 #bison-url = http://ftp.gnu.org/gnu/bison
-#boost-url = $(shell vstr=$$(echo $(boost-version) | sed -e's/\./_/g'); echo https://dl.bintray.com/boostorg/release/$(boost-version)/source)
+#boost-url = https://www.boost.org/users/download/
 #cairo-url = https://www.cairographics.org/releases
 #cdsclient-url = http://cdsarc.u-strasbg.fr/ftp/pub/sw
 #cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c
 #cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv)
-#eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz
+#eigen-url = https://eigen.tuxfamily.org
 #emacs-url = http://ftp.gnu.org/gnu/emacs
-#expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz)
-#fftw-url = ftp://ftp.fftw.org/pub/fftw
+#expat-url = https://github.com/libexpat/libexpat/releases
+#fftw-url = https://fftw.org
 #flex-url = https://github.com/westes/flex/files/981163
 #freetype-url = https://download.savannah.gnu.org/releases/freetype
 #gdb-url = http://ftp.gnu.org/gnu/gdb
-#ghostscript-url = $(shell v=$$(echo $(ghostscript-version) | sed -e's/\.//'); echo https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs$$v)
+#ghostscript-url = https://www.ghostscript.com/releases/gsdnld.html
 #gnuastro-url = http://ftp.gnu.org/gnu/gnuastro
 #gperf-url = http://ftp.gnu.org/pub/gnu/gperf
 #gs-fonts-gnu-url = https://downloads.sourceforge.net/gs-fonts
@@ -105,28 +105,33 @@ less-url = http://www.greenwoodsoftware.com/less/
 #hdf5-url = $(shell majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src)
 #healpix-url = http://akhlaghi.org/maneage-software
 #help2man-url = http://ftp.gnu.org/gnu/help2man
-#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/
-#imagemagick-url = http://akhlaghi.org/maneage-software
+#libpaper-url = http://ftp.debian.org/debian/pool/main/libp/libpaper/
+#icu-url = https://github.com/unicode-org/icu/releases
+#imagemagick-url = https://download.imagemagick.org/ImageMagick/download
 #imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit
 #lapack-url = http://www.netlib.org/lapack
-#libffi-url = ftp://sourceware.org/pub/libffi
+#libbsd-url = http://libbsd.freedesktop.org/releases
+#libffi-url = https://sourceware.org/libffi/
 #libgit2-url = http://akhlaghi.org/src
 #libidn-url = https://ftp.gnu.org/gnu/libidn
 #libjpeg-url = http://ijg.org/files
+#libmd-url = https://archive.hadrons.org/software/libmd/
 #libnsl-url = http://akhlaghi.org/maneage-software
+#libpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/
 #libpng-url = https://download.sourceforge.net/libpng
 #libtiff-url = https://download.osgeo.org/libtiff
 #libtirpc-url = https://downloads.sourceforge.net/libtirpc
+#metastore-url = http://akhlaghi.org/maneage-software
 #minizip-url =
 #missfits-url = https://www.astromatic.net/download/missfits
-#netpbm-url = http://akhlaghi.org/maneage-software
+#netpbm-url = https://sourceforge.net/projects/netpbm/files/super_stable/
 #openblas-url = https://github.com/xianyi/OpenBLAS/archive
 #openmpi-url = $(shell majorver=$$(echo $(openmpi-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://download.open-mpi.org/release/open-mpi/v$$majorver)
 #openssh-url = https://artfiles.org/openbsd/OpenSSH/portable
 #patch-url = http://ftp.gnu.org/gnu/patch
 #pixman-url = https://www.cairographics.org/releases
-#python-url = http://akhlaghi.org/src
-#R-url = $(shell majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}'); echo https://cran.r-project.org/src/base/R-$$majver)
+#python-url = https://www.python.org/downloads/
+#r-cran-url = $(shell majver=$$(echo $(r-cran-version) | sed -e's/\./ /g' | awk '{print $$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
 #scons-url = https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download
@@ -149,8 +154,10 @@ less-url = http://www.greenwoodsoftware.com/less/
 #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
+#libice-url = https://www.x.org/archive/individual/lib/
 #util-macros-url = https://www.x.org/pub/individual/util
 #xcb-proto-url = https://xorg.freedesktop.org/archive/individual/proto
+#libxcb-url = https://xcb.freedesktop.org/dist/
 #xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto
 #xtrans-url = https://www.x.org/pub/individual/lib