From 3c9bf3aff30f02c7d31bd86f36c4db2520f8ffa4 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Fri, 3 May 2024 13:07:41 +0200 Subject: Configuration: no dependency on /bin/sh and useful run-time options SUMMARY: no change necessary in your project, this commit only involves changes in how already-existing software are built. Some handy options have also been added to the top-level project script and the copyright years have been updated. Until now, if the host's '/bin/sh' had conflicts with the Maneage environment, the configuration of Maneage would crash as soon as we entered the building of high-level software. The full scenario is described in the comments of the newly added 'reproduce/software/shell/prep-source.sh'. This is most relevant when building older Maneage'd project in newer environments. With this commit, the following changes were made to avoid the problem above: - Maneage edits the source code of all installed software to replace '/bin/sh' with Maneage's own shell before the programs are built. Through this, we were able to solve the problem described above. - The portable '#!/usr/bin/env sh' shebangs are now used at the start of the scripts that run during configure time so it uses the first available shell that it finds in its PATH (the system's before Dash is built), then Dash, and after Dash is built, Bash. - For TeXLive, since we don't install it from source, it was necessary to add the libraries necessary for the local '/bin/sh' in LD_LIBRARY_PATH. Some high-level options have been added to the './project' script to simplify certain operations: --keep-going: do not stop upon the first crash, but keep going on to build targets until all build-able targets have been built. This is very useful for debugging large pipelines and allows you to isolate the problematic part of your project. --highlight-all: equivalent to calling both '--highlight-new' & '--highlight-notes'. --- README-hacking.md | 8 +- README.md | 2 +- paper.tex | 4 +- project | 28 ++-- reproduce/analysis/bash/download-multi-try | 155 -------------------- reproduce/analysis/bash/download-multi-try.sh | 160 +++++++++++++++++++++ reproduce/analysis/config/INPUTS.conf | 9 +- .../analysis/config/delete-me-squared-num.conf | 2 +- reproduce/analysis/config/metadata.conf | 2 +- reproduce/analysis/config/pdf-build.conf | 2 +- reproduce/analysis/config/verify-outputs.conf | 2 +- reproduce/analysis/make/delete-me.mk | 2 +- reproduce/analysis/make/initialize.mk | 6 +- reproduce/analysis/make/paper.mk | 12 +- reproduce/analysis/make/prepare.mk | 2 +- reproduce/analysis/make/top-make.mk | 2 +- reproduce/analysis/make/top-prepare.mk | 2 +- reproduce/analysis/make/verify.mk | 2 +- reproduce/software/bibtex/astrometrynet.tex | 2 +- reproduce/software/bibtex/astropy.tex | 2 +- reproduce/software/bibtex/corner.tex | 2 +- reproduce/software/bibtex/cython.tex | 2 +- reproduce/software/bibtex/fftw.tex | 2 +- reproduce/software/bibtex/galsim.tex | 2 +- reproduce/software/bibtex/gnuastro.tex | 2 +- reproduce/software/bibtex/healpix.tex | 2 +- reproduce/software/bibtex/imfit.tex | 2 +- reproduce/software/bibtex/matplotlib.tex | 2 +- reproduce/software/bibtex/missfits.tex | 2 +- reproduce/software/bibtex/mpi4py.tex | 2 +- reproduce/software/bibtex/numpy.tex | 2 +- reproduce/software/bibtex/r-cran.tex | 4 +- reproduce/software/bibtex/scamp.tex | 2 +- reproduce/software/bibtex/scipy.tex | 2 +- reproduce/software/bibtex/sextractor.tex | 4 +- reproduce/software/bibtex/sip_tpv.tex | 2 +- reproduce/software/bibtex/swarp.tex | 2 +- reproduce/software/bibtex/sympy.tex | 2 +- reproduce/software/bibtex/tides.tex | 2 +- reproduce/software/config/LOCAL.conf.in | 2 +- reproduce/software/config/TARGETS.conf | 4 +- reproduce/software/config/checksums.conf | 6 +- reproduce/software/config/numpy-scipy.cfg | 4 +- reproduce/software/config/servers-backup.conf | 2 +- .../config/software_acknowledge_context.sh | 4 +- reproduce/software/config/texlive-packages.conf | 59 ++++++-- reproduce/software/config/texlive.conf | 2 +- reproduce/software/config/urls.conf | 4 +- reproduce/software/config/versions.conf | 6 +- reproduce/software/make/README.md | 2 +- reproduce/software/make/atlas-multiple.mk | 2 +- reproduce/software/make/atlas-single.mk | 2 +- reproduce/software/make/basic.mk | 93 +++++++----- reproduce/software/make/build-rules.mk | 35 ++--- reproduce/software/make/high-level.mk | 90 +++++++++--- reproduce/software/make/python.mk | 45 +++++- reproduce/software/make/r-cran.mk | 5 +- reproduce/software/make/xorg.mk | 4 +- reproduce/software/shell/bashrc.sh | 2 +- reproduce/software/shell/configure.sh | 78 ++++++++-- reproduce/software/shell/git-post-checkout | 2 +- reproduce/software/shell/git-pre-commit | 2 +- reproduce/software/shell/pre-make-build.sh | 24 ++-- reproduce/software/shell/prep-source.sh | 94 ++++++++++++ reproduce/software/shell/run-parts.in | 4 +- reproduce/software/shell/tarball-prepare.sh | 4 +- tex/README.md | 2 +- tex/src/delete-me-image-histogram.tex | 2 +- tex/src/delete-me-squared.tex | 2 +- tex/src/preamble-biblatex.tex | 2 +- tex/src/preamble-maneage-default-style.tex | 2 +- tex/src/preamble-maneage.tex | 2 +- tex/src/preamble-pgfplots.tex | 2 +- tex/src/preamble-project.tex | 2 +- tex/src/references.tex | 2 +- 75 files changed, 682 insertions(+), 365 deletions(-) delete mode 100755 reproduce/analysis/bash/download-multi-try create mode 100755 reproduce/analysis/bash/download-multi-try.sh create mode 100755 reproduce/software/shell/prep-source.sh diff --git a/README-hacking.md b/README-hacking.md index 8897333..4c9ff05 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -1,8 +1,8 @@ Maneage: managing data lineage ============================== -Copyright (C) 2018-2023 Mohammad Akhlaghi \ -Copyright (C) 2020-2023 Raul Infante-Sainz \ +Copyright (C) 2018-2025 Mohammad Akhlaghi \ +Copyright (C) 2020-2025 Raul Infante-Sainz \ See the end of the file for license conditions. Maneage is a **fully working template** for doing reproducible research (or @@ -762,8 +762,8 @@ First custom commit and generally, all the files you modified in the previous step. ``` - Copyright (C) 2018-2023 Existing Name - Copyright (C) 2023 YOUR NAME + Copyright (C) 2018-2025 Existing Name + Copyright (C) 2024-2025 YOUR NAME ``` 9. **Configure Git for fist time**: If this is the first time you are diff --git a/README.md b/README.md index 8f827a4..9599c6b 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ Reproducible source for XXXXXXXXXXXXXXXXX ------------------------------------------------------------------------- -Copyright (C) 2018-2023 Mohammad Akhlaghi \ +Copyright (C) 2018-2025 Mohammad Akhlaghi \ See the end of the file for license conditions. This is the reproducible project source for the paper titled "**XXX XXXXX diff --git a/paper.tex b/paper.tex index afb6c0a..2c1a587 100644 --- a/paper.tex +++ b/paper.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2018-2023 Mohammad Akhlaghi +%% Copyright (C) 2018-2025 Mohammad Akhlaghi %% See the end of the file for license conditions. \documentclass[10pt, twocolumn]{article} @@ -200,7 +200,7 @@ The IAC project P/300724, financed by the MCIU, through the Canary Islands Depar \appendix %% Mention all used software in an appendix. -\section{Software acknowledgement} +\section{Software acknowledgment} \label{appendix:software} \input{tex/build/macros/dependencies.tex} diff --git a/project b/project index 0c65211..9d4d6df 100755 --- a/project +++ b/project @@ -3,8 +3,8 @@ # High-level script to manage the project. # Run './project --help' for a description of how to use it. # -# Copyright (C) 2019-2023 Mohammad Akhlaghi -# Copyright (C) 2021-2023 Raul Infante-Sainz +# Copyright (C) 2019-2025 Mohammad Akhlaghi +# Copyright (C) 2021-2025 Raul Infante-Sainz # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -37,6 +37,7 @@ host_cc=0 operation= build_dir= input_dir= +keep_going= check_config= make_targets= software_dir= @@ -118,6 +119,7 @@ Configure options: Configure and Make options: -d, --debug[=FLAGS] In configure: use -j1, no -k, and no Zenodo check. In make: 'FLAGS' will be directly passed to 'make'. + -k, --keep-going Keep going when some targets can't be made. -g, --group=STR Build and run with write permissions for a group. -j, --jobs=INT Number of threads to build/run the software. -?, --help Print this help list. @@ -127,6 +129,7 @@ Make (analysis) options: Make (final PDF) options: --refresh-bib Force refresh the bibliography. + --highlight-all Activate '--highlight-new' & '--highlight-notes'. --highlight-new Highlight '\new' parts of text as green. --highlight-notes Show '\tonote' regions as red text in PDF. @@ -201,15 +204,20 @@ do -j|--jobs) jobs="$2"; check_v jobs "$jobs"; shift;shift;; -j=*|--jobs=*) jobs="${1#*=}"; check_v jobs "$jobs"; shift;; -j*) jobs=$(echo "$1" | sed -e's/-j//'); check_v jobs "$jobs"; shift;; + -k|--keep-going) keep_going="--keep-going"; shift;; + -k=*|--keep-going=*) on_off_option_error --keep-going -k;; + -k*) on_off_option_error --keep-going -k;; -'?'|--help) print_help; exit 0;; -'?'*|--help=*) on_off_option_error --help -?;; - # Make options - # ------------ - # - # Note that Make's 'debug' can take values, but when called without any - # value, it is like giving it a value of 'a'): + # Make options (analysis): + -p|--prepare-redo) prepare_redo=1; shift;; + -p=*|--prepare-redo=*) on_off_option_error --prepare-redo; shift;; + + # Make options (final PDF): --refresh-bib) [ -f tex/src/references.tex ] && touch tex/src/references.tex; shift;; + --highlight-all) highlightnew=1; highlightnotes=1; shift;; + --highlight-all=*) on_off_option_error --highlight-new;; --highlight-new) highlightnew=1; shift;; --highlight-new=*) on_off_option_error --highlight-new;; --highlight-notes) highlightnotes=1; shift;; @@ -218,15 +226,14 @@ do echo "Please set the operation before calling '--debug'"; exit 1 elif [ x$operation = xconfigure ]; then debug=a; shift; elif [ x$operation = xmake ]; then - if [ x"$2" = x ]; then echo "In make-mode, '--debug' needs a value"; exit 1 + if [ x"$2" = x ]; then + echo "In make-mode, '--debug' needs a value; see GNU Make manual"; exit 1 else debug="$2"; check_v debug "$debug"; shift;shift; fi else echo "Operation '$operation' not recognized, please use 'configure' or 'make'" fi;; -d=*|--debug=*) debug="${1#*=}"; check_v debug "$debug"; shift;; -d*) debug=$(echo "$1" | sed -e's/-d//'); check_v debug "$debug"; shift;; - -p|--prepare-redo) prepare_redo=1; shift;; - -p=*|--prepare-redo=*) on_off_option_error --prepare-redo; shift;; # Unrecognized option: -*) echo "$scriptname: unknown option '$1'"; exit 1;; @@ -390,6 +397,7 @@ controlled_env() { envmake="$envmake highlightnew=$highlightnew" envmake="$envmake highlightnotes=$highlightnotes .local/bin/make" envmake="$envmake --no-builtin-rules --no-builtin-variables -f $1" + envmake="$envmake $keep_going" if ! [ x"$debug" = x ]; then envmake="$envmake --debug=$debug"; fi # Set the number of jobs. Note that for the 'configure.sh' script the diff --git a/reproduce/analysis/bash/download-multi-try b/reproduce/analysis/bash/download-multi-try deleted file mode 100755 index d7e9be2..0000000 --- a/reproduce/analysis/bash/download-multi-try +++ /dev/null @@ -1,155 +0,0 @@ -#!/bin/sh -# -# Attempt downloading multiple times before crashing whole project. From -# the top project directory (for the shebang above), this script must be -# run like this: -# -# $ /path/to/download-multi-try downloader lockfile input-url downloaded-name -# -# NOTE: The 'downloader' must contain the option to specify the output name -# in its end. For example "wget -O". Any other option can also be placed in -# the middle. -# -# Due to temporary network problems, a download may fail suddenly, but -# succeed in a second try a few seconds later. Without this script that -# temporary glitch in the network will permanently crash the project and -# it can't continue. The job of this script is to be patient and try the -# download multiple times before crashing the whole project. -# -# LOCK FILE: Since there is usually only one network port to the outside -# world, downloading is done much faster in serial, not in parallel. But -# the project's processing may be done in parallel (with multiple threads -# needing to download different files at the same time). Therefore, this -# script uses the 'flock' program to only do one download at a time. To -# benefit from it, any call to this script must be given the same lock -# file. If your system has multiple ports to the internet, or for any -# reason, you don't want to use a lock file, set the 'lockfile' name to -# 'nolock'. -# -# Copyright (C) 2019-2023 Mohammad Akhlaghi -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . - - - - - -# Script settings -# --------------- -# Stop the script if there are any errors. -set -e - - - - - -# Input arguments and necessary sanity checks. Note that the 5th argument -# (backup servers) isn't mandatory. -inurl="$3" -outname="$4" -lockfile="$2" -downloader="$1" -backupservers="$5" -if [ "x$downloader" = x ]; then - echo "$0: downloader (first argument) not given."; exit 1; -fi -if [ "x$lockfile" = x ]; then - echo "$0: lock file (second argument) not given."; exit 1; -fi -if [ "x$inurl" = x ]; then - echo "$0: full input URL (third argument) not given."; exit 1; -fi -if [ "x$outname" = x ]; then - echo "$0: output name (fourth argument) not given."; exit 1; -fi - - - - - -# Separate the actual filename, to possibly use backup server. -urlfile=$(echo "$inurl" | awk -F "/" '{print $NF}') - - - - - -# Try downloading multiple times before crashing. -counter=0 -maxcounter=10 -while [ ! -f "$outname" ]; do - - # Increment the counter. - counter=$(echo $counter | awk '{print $1+1}') - - # If we have passed a maximum number of trials, just exit with - # a failed code. - reachedmax=$(echo $counter \ - | awk '{if($1>'$maxcounter') print "yes"; else print "no";}') - if [ x$reachedmax = xyes ]; then - echo "" - echo "Failed $maxcounter download attempts: $outname" - echo "" - exit 1 - fi - - # If this isn't the first attempt print a notice and wait a little for - # the next trail. - if [ x$counter = x1 ]; then - just_a_place_holder=1 - else - tstep=$(echo $counter | awk '{print $1*5}') - echo "Download trial $counter for '$outname' in $tstep seconds." - sleep $tstep - fi - - # Attempt downloading the file. Note that the 'downloader' ends with - # the respective option to specify the output name. For example "wget - # -O" (so 'outname', that comes after it) will be the name of the - # downloaded file. - if [ x"$lockfile" = xnolock ]; then - if ! $downloader $outname $inurl; then rm -f $outname; fi - else - # Try downloading from the requested URL. - flock "$lockfile" sh -c \ - "if ! $downloader $outname \"$inurl\"; then rm -f $outname; fi" - fi - - # If the download failed, try the backup server(s). - if [ ! -f "$outname" ]; then - if [ x"$backupservers" != x ]; then - for bs in $backupservers; do - - # Use this backup server. - if [ x"$lockfile" = xnolock ]; then - if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi - else - flock "$lockfile" sh -c \ - "if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi" - fi - - # If the file was downloaded, break out of the loop that - # parses over the backup servers. - if [ -f "$outname" ]; then break; fi - done - fi - fi -done - - - - - -# Return successfully -exit 0 diff --git a/reproduce/analysis/bash/download-multi-try.sh b/reproduce/analysis/bash/download-multi-try.sh new file mode 100755 index 0000000..bea88d5 --- /dev/null +++ b/reproduce/analysis/bash/download-multi-try.sh @@ -0,0 +1,160 @@ +#!/usr/bin/env sh +# +# Attempt downloading multiple times before crashing whole project. From +# the top project directory (for the shebang above), this script must be +# run like this: +# +# $ $SHELL /path/to/download-multi-try.sh downloader lockfile \ +# input-url downloaded-name +# +# NOTE: +# - This script doesn't have a Shebang because in different stages it +# should be built with different shells ('/bin/sh' before Maneage +# installs its own shell and afterwards with Maneage's own shell). +# - The 'downloader' must contain the option to specify the output name +# in its end. For example "wget -O". Any other option can also be placed in +# the middle. +# +# Due to temporary network problems, a download may fail suddenly, but +# succeed in a second try a few seconds later. Without this script that +# temporary glitch in the network will permanently crash the project and +# it can't continue. The job of this script is to be patient and try the +# download multiple times before crashing the whole project. +# +# LOCK FILE: Since there is usually only one network port to the outside +# world, downloading is done much faster in serial, not in parallel. But +# the project's processing may be done in parallel (with multiple threads +# needing to download different files at the same time). Therefore, this +# script uses the 'flock' program to only do one download at a time. To +# benefit from it, any call to this script must be given the same lock +# file. If your system has multiple ports to the internet, or for any +# reason, you don't want to use a lock file, set the 'lockfile' name to +# 'nolock'. +# +# Copyright (C) 2019-2025 Mohammad Akhlaghi +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + + + + + +# Script settings +# --------------- +# Stop the script if there are any errors. +set -e + + + + + +# Input arguments and necessary sanity checks. Note that the 5th argument +# (backup servers) isn't mandatory. +inurl="$3" +outname="$4" +lockfile="$2" +downloader="$1" +backupservers="$5" +if [ "x$downloader" = x ]; then + echo "$0: downloader (first argument) not given."; exit 1; +fi +if [ "x$lockfile" = x ]; then + echo "$0: lock file (second argument) not given."; exit 1; +fi +if [ "x$inurl" = x ]; then + echo "$0: full input URL (third argument) not given."; exit 1; +fi +if [ "x$outname" = x ]; then + echo "$0: output name (fourth argument) not given."; exit 1; +fi + + + + + +# Separate the actual filename, to possibly use backup server. +urlfile=$(echo "$inurl" | awk -F "/" '{print $NF}') + + + + + +# Try downloading multiple times before crashing. +counter=0 +maxcounter=10 +while [ ! -f "$outname" ]; do + + # Increment the counter. + counter=$(echo $counter | awk '{print $1+1}') + + # If we have passed a maximum number of trials, just exit with + # a failed code. + reachedmax=$(echo $counter \ + | awk '{if($1>'$maxcounter') print "yes"; else print "no";}') + if [ x$reachedmax = xyes ]; then + echo "" + echo "Failed $maxcounter download attempts: $outname" + echo "" + exit 1 + fi + + # If this isn't the first attempt print a notice and wait a little for + # the next trail. + if [ x$counter = x1 ]; then + just_a_place_holder=1 + else + tstep=$(echo $counter | awk '{print $1*5}') + echo "Download trial $counter for '$outname' in $tstep seconds." + sleep $tstep + fi + + # Attempt downloading the file. Note that the 'downloader' ends with + # the respective option to specify the output name. For example "wget + # -O" (so 'outname', that comes after it) will be the name of the + # downloaded file. + if [ x"$lockfile" = xnolock ]; then + if ! $downloader $outname $inurl; then rm -f $outname; fi + else + # Try downloading from the requested URL. + flock "$lockfile" sh -c \ + "if ! $downloader $outname \"$inurl\"; then rm -f $outname; fi" + fi + + # If the download failed, try the backup server(s). + if [ ! -f "$outname" ]; then + if [ x"$backupservers" != x ]; then + for bs in $backupservers; do + + # Use this backup server. + if [ x"$lockfile" = xnolock ]; then + if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi + else + flock "$lockfile" sh -c \ + "if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi" + fi + + # If the file was downloaded, break out of the loop that + # parses over the backup servers. + if [ -f "$outname" ]; then break; fi + done + fi + fi +done + + + + + +# Return successfully +exit 0 diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf index 1090e44..5860806 100644 --- a/reproduce/analysis/config/INPUTS.conf +++ b/reproduce/analysis/config/INPUTS.conf @@ -70,9 +70,10 @@ # file). Don't use this if you give the 'fitsdatasum' # keyvalue. # -# INPUT-%-fitsdatasum: The FITS standard DATASUM value for HDU number 1 -# of the FITS file (counting from 0). Don't use this -# if you give the 'sha256' keyword. +# INPUT-%-fitsdatasum: The FITS standard DATASUM value for the HDU given +# to '-fitshdu' (below) of the FITS file (counting +# from 0). Don't use this if you give the 'sha256' +# keyword. # # INPUT-%-fitshdu: The HDU identifier (counter from 0, or name) to use # for the verification. This is only relevant in the @@ -104,7 +105,7 @@ # also called '%' (if your local copy of the input dataset and the only # repository names are the same, be sure to set '%' accordingly). # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/delete-me-squared-num.conf b/reproduce/analysis/config/delete-me-squared-num.conf index c2fa79c..ba8c960 100644 --- a/reproduce/analysis/config/delete-me-squared-num.conf +++ b/reproduce/analysis/config/delete-me-squared-num.conf @@ -1,6 +1,6 @@ # Number of samples in the demonstration analysis (to be deleted). # -# Copyright (C) 2019-2023 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf index 7bafc4b..1ab7de1 100644 --- a/reproduce/analysis/config/metadata.conf +++ b/reproduce/analysis/config/metadata.conf @@ -15,7 +15,7 @@ # and the copyright license name and standard link to the fully copyright # license. # -# Copyright (C) 2020-2023 Mohammad Akhlaghi +# Copyright (C) 2020-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/pdf-build.conf b/reproduce/analysis/config/pdf-build.conf index 2aa2e9a..7821306 100644 --- a/reproduce/analysis/config/pdf-build.conf +++ b/reproduce/analysis/config/pdf-build.conf @@ -12,7 +12,7 @@ # LaTeX. Otherwise, a notice will just printed that, no PDF will be # created. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf index db7751d..031085d 100644 --- a/reproduce/analysis/config/verify-outputs.conf +++ b/reproduce/analysis/config/verify-outputs.conf @@ -1,6 +1,6 @@ # To enable verification of output datasets set this variable to 'yes'. # -# Copyright (C) 2019-2023 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk index 325280d..a20abc6 100644 --- a/reproduce/analysis/make/delete-me.mk +++ b/reproduce/analysis/make/delete-me.mk @@ -1,6 +1,6 @@ # Dummy Makefile to create a random dataset for plotting. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 9e8db4a..92e5eff 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -1,6 +1,6 @@ # Project initialization. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -469,7 +469,7 @@ dist-software: # process with a file and make sure that only one downloading event is in # progress at every moment. $(indir):; mkdir $@ -downloadwrapper = $(bashdir)/download-multi-try +downloadwrapper = $(bashdir)/download-multi-try.sh inputdatasets := $(foreach i, \ $(patsubst INPUT-%-sha256,%, \ $(filter INPUT-%-sha256,$(.VARIABLES))) \ @@ -672,7 +672,7 @@ print-general-metadata = \ # for the final PDF. Since these are not version controlled, it must be # calculated everytime the project is run. So even though this file # actually exists, it is also aded as a '.PHONY' target above. -$(mtexdir)/initialize.tex: | $(mtexdir) +$(mtexdir)/initialize.tex: # Version and title of project. About the starting '@': since these # commands are run every time with './project make', it is annoying diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index 791108b..66c6859 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -1,6 +1,6 @@ # Build the final PDF paper/report. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -128,6 +128,11 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ # use PGFPlots, then you should remove the '-shell-escape' option # for better security. See https://savannah.nongnu.org/task/?15694 # for details. +# +# We need the modification to 'LD_LIBRARY_PATH' because we do not +# build LaTeX from source and it uses '/bin/sh' (among other +# possible system-wide things). + export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex biber paper @@ -158,6 +163,11 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl # See above for a warning and brief discussion on the the pdflatex # option '-shell-escape'. +# +# We need the modification to 'LD_LIBRARY_PATH' because we do not +# build LaTeX from source and it uses '/bin/sh' (among other +# possible system-wide things). + export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex # Come back to the top project directory and copy the built PDF diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk index 36f5294..2cc1187 100644 --- a/reproduce/analysis/make/prepare.mk +++ b/reproduce/analysis/make/prepare.mk @@ -1,6 +1,6 @@ # Basic preparations, called by './project make'. # -# Copyright (C) 2019-2023 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 460433b..2689e64 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -1,6 +1,6 @@ # Top-level Makefile (first to be loaded). # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index 930c2a9..7d92d72 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -4,7 +4,7 @@ # are not included here. Please see that file for thorough comments on each # step. # -# Copyright (C) 2019-2023 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk index aa026b5..c74f8ca 100644 --- a/reproduce/analysis/make/verify.mk +++ b/reproduce/analysis/make/verify.mk @@ -1,6 +1,6 @@ # Verify the project outputs before building the paper. # -# Copyright (C) 2020-2023 Mohammad Akhlaghi +# Copyright (C) 2020-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/bibtex/astrometrynet.tex b/reproduce/software/bibtex/astrometrynet.tex index 10b487e..5697885 100644 --- a/reproduce/software/bibtex/astrometrynet.tex +++ b/reproduce/software/bibtex/astrometrynet.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/astropy.tex b/reproduce/software/bibtex/astropy.tex index f0b8349..3df1aa1 100644 --- a/reproduce/software/bibtex/astropy.tex +++ b/reproduce/software/bibtex/astropy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/corner.tex b/reproduce/software/bibtex/corner.tex index 5eda23d..fd7ea76 100644 --- a/reproduce/software/bibtex/corner.tex +++ b/reproduce/software/bibtex/corner.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/cython.tex b/reproduce/software/bibtex/cython.tex index 6103028..311072d 100644 --- a/reproduce/software/bibtex/cython.tex +++ b/reproduce/software/bibtex/cython.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/fftw.tex b/reproduce/software/bibtex/fftw.tex index e1e9bf8..15c5c62 100644 --- a/reproduce/software/bibtex/fftw.tex +++ b/reproduce/software/bibtex/fftw.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/galsim.tex b/reproduce/software/bibtex/galsim.tex index 6ca9b45..bbfdec1 100644 --- a/reproduce/software/bibtex/galsim.tex +++ b/reproduce/software/bibtex/galsim.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/gnuastro.tex b/reproduce/software/bibtex/gnuastro.tex index 5fd87e4..7d56e3e 100644 --- a/reproduce/software/bibtex/gnuastro.tex +++ b/reproduce/software/bibtex/gnuastro.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/healpix.tex b/reproduce/software/bibtex/healpix.tex index cfb96c0..afdd6a6 100644 --- a/reproduce/software/bibtex/healpix.tex +++ b/reproduce/software/bibtex/healpix.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/imfit.tex b/reproduce/software/bibtex/imfit.tex index f35ee69..1d5270b 100644 --- a/reproduce/software/bibtex/imfit.tex +++ b/reproduce/software/bibtex/imfit.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/matplotlib.tex b/reproduce/software/bibtex/matplotlib.tex index 9873c57..ec7bab4 100644 --- a/reproduce/software/bibtex/matplotlib.tex +++ b/reproduce/software/bibtex/matplotlib.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex index 64704e6..83510dd 100644 --- a/reproduce/software/bibtex/missfits.tex +++ b/reproduce/software/bibtex/missfits.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2020-2023 Surena Fatemi +%% Copyright (C) 2020-2025 Surena Fatemi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/mpi4py.tex b/reproduce/software/bibtex/mpi4py.tex index cc6bcb9..10e0e74 100644 --- a/reproduce/software/bibtex/mpi4py.tex +++ b/reproduce/software/bibtex/mpi4py.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/numpy.tex b/reproduce/software/bibtex/numpy.tex index da54330..fb017c4 100644 --- a/reproduce/software/bibtex/numpy.tex +++ b/reproduce/software/bibtex/numpy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/r-cran.tex b/reproduce/software/bibtex/r-cran.tex index 8d691c1..c58eeeb 100644 --- a/reproduce/software/bibtex/r-cran.tex +++ b/reproduce/software/bibtex/r-cran.tex @@ -1,5 +1,5 @@ -%% Copyright (C) 2022-2023 Boud Roukema -%% Copyright (C) 2022-2023 Mohammad Akhlaghi +%% Copyright (C) 2022-2025 Boud Roukema +%% Copyright (C) 2022-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/scamp.tex b/reproduce/software/bibtex/scamp.tex index 5e5be91..b5c4da9 100644 --- a/reproduce/software/bibtex/scamp.tex +++ b/reproduce/software/bibtex/scamp.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/scipy.tex b/reproduce/software/bibtex/scipy.tex index c92bbec..1296393 100644 --- a/reproduce/software/bibtex/scipy.tex +++ b/reproduce/software/bibtex/scipy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sextractor.tex b/reproduce/software/bibtex/sextractor.tex index cdffe74..818f04a 100644 --- a/reproduce/software/bibtex/sextractor.tex +++ b/reproduce/software/bibtex/sextractor.tex @@ -1,5 +1,5 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sip_tpv.tex b/reproduce/software/bibtex/sip_tpv.tex index d13d7a5..0d52e33 100644 --- a/reproduce/software/bibtex/sip_tpv.tex +++ b/reproduce/software/bibtex/sip_tpv.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/swarp.tex b/reproduce/software/bibtex/swarp.tex index ecac1a7..e0989f9 100644 --- a/reproduce/software/bibtex/swarp.tex +++ b/reproduce/software/bibtex/swarp.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/sympy.tex b/reproduce/software/bibtex/sympy.tex index 27ea9ac..01e481b 100644 --- a/reproduce/software/bibtex/sympy.tex +++ b/reproduce/software/bibtex/sympy.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Raul Infante-Sainz +%% Copyright (C) 2019-2025 Raul Infante-Sainz %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex index dfa8eb8..caf1500 100644 --- a/reproduce/software/bibtex/tides.tex +++ b/reproduce/software/bibtex/tides.tex @@ -1,4 +1,4 @@ -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi %% %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in index 5ee1ff7..341a78e 100644 --- a/reproduce/software/config/LOCAL.conf.in +++ b/reproduce/software/config/LOCAL.conf.in @@ -3,7 +3,7 @@ # This is just a template for the './project configure' script to fill # in. Please don't make any change to this file. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf index 3d35eed..a8b396e 100644 --- a/reproduce/software/config/TARGETS.conf +++ b/reproduce/software/config/TARGETS.conf @@ -1,7 +1,7 @@ # Necessary high-level software to build in this project. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi -# Copyright (C) 2019-2023 Raul Infante-Sainz +# Copyright (C) 2018-2025 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Raul Infante-Sainz # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index e34d9b8..1a81ef1 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -1,8 +1,8 @@ # sha512 checksums of all the necessary software tarballs. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi -# Copyright (C) 2019-2023 Raul Infante-Sainz -# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani +# Copyright (C) 2018-2025 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Raul Infante-Sainz +# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg index 5ad5112..c3cea11 100644 --- a/reproduce/software/config/numpy-scipy.cfg +++ b/reproduce/software/config/numpy-scipy.cfg @@ -7,8 +7,8 @@ # appropriate sections. Not all packages will use all sections so you # should leave out sections that your package does not use. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi -# Copyright (C) 2019-2023 Raul Infante-Sainz +# Copyright (C) 2018-2025 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Raul Infante-Sainz # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf index 67eff44..d4aa25e 100644 --- a/reproduce/software/config/servers-backup.conf +++ b/reproduce/software/config/servers-backup.conf @@ -3,7 +3,7 @@ # is irrelevant). Note that this is not a to be read as a variable but will # be parsed as a list. # -# Copyright (C) 2020-2023 Mohammad Akhlaghi +# Copyright (C) 2020-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/software_acknowledge_context.sh b/reproduce/software/config/software_acknowledge_context.sh index 043d9aa..deae01b 100755 --- a/reproduce/software/config/software_acknowledge_context.sh +++ b/reproduce/software/config/software_acknowledge_context.sh @@ -10,8 +10,8 @@ # your project to make a smoothly readable English text. Afterwards, please # feel free to modify them as you wish. # -# Copyright (C) 2021-2023 Boud Roukema -# Copyright (C) 2021-2023 Mohammad Akhlaghi +# Copyright (C) 2021-2025 Boud Roukema +# Copyright (C) 2021-2025 Mohammad Akhlaghi # # This script is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf index 250a4e6..bb38d5a 100644 --- a/reproduce/software/config/texlive-packages.conf +++ b/reproduce/software/config/texlive-packages.conf @@ -4,23 +4,56 @@ # name to this variable (you can check in 'ctan.org' to find the official # name). # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and # this notice are preserved. This file is offered as-is, without any # warranty. - -# Note on 'tex' and 'fancyhdr': These two packages are installed along with -# the basic installation scheme that we used to install tlmgr, they will be -# ignored in the 'tlmgr install' command, but will be used later when we -# want their versions. +# Notes +# ----- +# +# - tex and fancyhdr: These two packages are installed along with the basic +# installation scheme that we used to install tlmgr, they will be ignored +# in the 'tlmgr install' command, but will be used later when we want +# their versions. # -# fancyvrb: Needed by R. -texlive-packages = tex fancyhdr ec newtx fontaxes xkeyval etoolbox xstring \ - xcolor setspace caption footmisc datetime fmtcount \ - titlesec preprint ulem biblatex biber logreq pgf pgfplots \ - fp courier tex-gyre txfonts times csquotes kastrup \ - trimspaces pdftexcmds pdfescape letltxmacro bitset \ - mweights fancyvrb +# - fancyvrb: needed by R. +texlive-packages = biber \ + biblatex \ + bitset \ + caption \ + courier \ + csquotes \ + datetime \ + ec \ + etoolbox \ + fancyhdr \ + fancyvrb \ + fmtcount \ + fontaxes \ + footmisc \ + fp \ + kastrup \ + letltxmacro \ + logreq \ + mweights \ + newtx \ + pdfescape \ + pdftexcmds \ + pgf \ + pgfplots \ + preprint \ + setspace \ + tex \ + tex-gyre \ + times \ + titlesec \ + trimspaces \ + txfonts \ + ulem \ + xcolor \ + xkeyval \ + xpatch \ + xstring diff --git a/reproduce/software/config/texlive.conf b/reproduce/software/config/texlive.conf index 71878e5..0babd69 100644 --- a/reproduce/software/config/texlive.conf +++ b/reproduce/software/config/texlive.conf @@ -2,7 +2,7 @@ # # installdir: Install directory # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index 3a86d2d..a5998d5 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) 2020-2023 Mohammad Akhlaghi -# Copyright (C) 2020-2023 Raul Infante-Sainz +# Copyright (C) 2020-2025 Mohammad Akhlaghi +# Copyright (C) 2020-2025 Raul Infante-Sainz # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index afb0535..e8b8542 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -1,8 +1,8 @@ # Versions of the various dependencies # -# Copyright (C) 2018-2023 Mohammad Akhlaghi -# Copyright (C) 2019-2023 Raul Infante-Sainz -# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani +# Copyright (C) 2018-2025 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Raul Infante-Sainz +# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md index d2b6952..00afef4 100644 --- a/reproduce/software/make/README.md +++ b/reproduce/software/make/README.md @@ -1,7 +1,7 @@ Software building instructions ------------------------------ -Copyright (C) 2019-2023 Mohammad Akhlaghi \ +Copyright (C) 2019-2025 Mohammad Akhlaghi \ See the end of the file for license conditions. This directory contains Makefiles that are called by the high-level diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk index 5c8f14c..6e7d415 100644 --- a/reproduce/software/make/atlas-multiple.mk +++ b/reproduce/software/make/atlas-multiple.mk @@ -8,7 +8,7 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2023 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/atlas-single.mk b/reproduce/software/make/atlas-single.mk index 4e2b04a..2b68677 100644 --- a/reproduce/software/make/atlas-single.mk +++ b/reproduce/software/make/atlas-single.mk @@ -8,7 +8,7 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2023 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 99e81d2..68c40b3 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -21,9 +21,9 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2018-2023 Mohammad Akhlaghi -# Copyright (C) 2019-2023 Raul Infante-Sainz -# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani +# Copyright (C) 2018-2025 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Raul Infante-Sainz +# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -49,14 +49,15 @@ include reproduce/software/config/checksums.conf include reproduce/software/config/urls.conf # Basic directories -lockdir = $(BDIR)/software/locks -tdir = $(BDIR)/software/tarballs -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 +lockdir = $(BDIR)/software/locks +tdir = $(BDIR)/software/tarballs +ddir = $(BDIR)/software/build-tmp +idir = $(BDIR)/software/installed +ibdir = $(BDIR)/software/installed/bin +ildir = $(BDIR)/software/installed/lib +iidir = $(BDIR)/software/installed/include +shsrcdir = "$(shell pwd)"/reproduce/software/shell +ibidir = $(BDIR)/software/installed/version-info/proglib # Ultimate Makefile target. GNU Nano (a simple and very light-weight text # editor) is installed by default, it is recommended to have it in the @@ -107,6 +108,15 @@ export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings) # 'LD_LIBRARY_PATH', then we'll add our own newly installed libraries. We # will also make sure that there is no "current directory" in it (by # removing a starting or trailing ':' and any occurance of '::'. +# +# But first: in case LD_LIBRARY_PATH is empty, give it the default value of +# $(sys_library_sh_path) (which was the location of the libraries needed by +# the host's shell). This is because after we add the Maneage's library +# path, on some systems, no other libraries will be checked except those +# that are in 'LD_LIBRARY_PATH'. +ifeq ($(strip $(LD_LIBRARY_PATH)),) +export LD_LIBRARY_PATH=$(sys_library_sh_path) +endif export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \ | sed -e's/::/:/g' -e's/^://' -e's/:$$//') @@ -127,7 +137,7 @@ export DYLD_LIBRARY_PATH := # Afer putting everything together, we use the first server as the # reference for all software if their '-url' variable isn't defined (in # 'reproduce/software/config/urls.conf'). -downloadwrapper = ./reproduce/analysis/bash/download-multi-try +downloadwrapper = ./reproduce/analysis/bash/download-multi-try.sh maneage_backup_urls := $(shell awk '!/^#/{printf "%s ", $$1}' \ reproduce/software/config/servers-backup.conf) backupservers_all = $(user_backup_urls) $(maneage_backup_urls) @@ -336,6 +346,7 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version) rm -rf $$tdir tar -xf $(tdir)/$$tarball cd $$tdir + $(shsrcdir)/prep-source.sh $(ibdir) sed -e 's@\(ln -s -f \)$$(PREFIX)/bin/@\1@' Makefile \ > Makefile.sed mv Makefile.sed Makefile @@ -634,6 +645,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) rm -rf perl-$(perl-version) tar -xf $(tdir)/$$tarball cd perl-$(perl-version) + $(shsrcdir)/prep-source.sh $(ibdir) ./Configure -des \ -Dusethreads \ -Duseshrplib \ @@ -691,21 +703,16 @@ $(ibidir)/coreutils-$(coreutils-version): \ $(ibidir)/perl-$(perl-version) \ $(ibidir)/openssl-$(openssl-version) -# Import, unpack and enter the source directory. +# Import the source tarball. tarball=coreutils-$(coreutils-version).tar.lz $(call import-source, $(coreutils-url), $(coreutils-checksum)) + +# Unpack and enter the source. cd $(ddir) rm -rf coreutils-$(coreutils-version) tar -xf $(tdir)/$$tarball cd coreutils-$(coreutils-version) - -# Set the configure script to use our shell, note that we can't -# assume GNU SED here yet (it installs after Coreutils). - sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \ - -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \ - configure > configure-tmp - mv configure-tmp configure - chmod +x configure + $(shsrcdir)/prep-source.sh $(ibdir) # Configure, build and install Coreutils. ./configure --prefix=$(idir) SHELL=$(ibdir)/bash \ @@ -744,6 +751,7 @@ $(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version) rm -rf podlators-$(podlators-version) tar -xf $(tdir)/$$tarball cd podlators-$(podlators-version) + $(shsrcdir)/prep-source.sh $(ibdir) perl Makefile.PL make make install @@ -1030,7 +1038,7 @@ $(ibidir)/gmp-$(gmp-version): \ $(call import-source, $(gmp-url), $(gmp-checksum)) $(call gbuild, gmp-$(gmp-version), static, \ --enable-cxx --enable-fat, \ - -j$(numthreads) ,make check) + -j$(numthreads)) echo "GNU Multiple Precision Arithmetic Library $(gmp-version)" > $@ # Less is useful with Git (to view the diffs within a minimal container) @@ -1070,16 +1078,27 @@ $(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version) $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) tarball=grep-$(grep-version).tar.lz $(call import-source, $(grep-url), $(grep-checksum)) - $(call gbuild, grep-$(grep-version), static,,V=1) + $(call gbuild, grep-$(grep-version), static,, \ + -j$(numthreads) V=1) echo "GNU Grep $(grep-version)" > $@ # M4 doesn't depend on PatchELF, but just to be consistent with the # levels/phases introduced here (where the compressors are level 1, # PatchELF is level 2, and ...), we'll set it as a dependency. +# +# The '--with-syscmd-shell' is used as the default shell and if not given, +# 'm4' will use '/bin/sh' (which is not under Maneage control and can cause +# problems in 'high-level.mk' because it closes off the system's +# LD_LIBRARY_PATH and if the system's '/bin/sh' needs a special system +# library, the high-level programs will not be built). We are setting this +# default shell to Dash because M4 is built before our own Bash. Recall +# that Dash is built before we enter this Makefile. $(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version) tarball=m4-$(m4-version).tar.lz $(call import-source, $(m4-url), $(m4-checksum)) - $(call gbuild, m4-$(m4-version), static,,V=1) + $(call gbuild, m4-$(m4-version), static, \ + --with-syscmd-shell=$(ibdir)/dash, \ + -j$(numthreads) V=1) echo "GNU M4 $(m4-version)" > $@ $(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version) @@ -1169,7 +1188,7 @@ $(ibidir)/mpc-$(mpc-version): $(ibidir)/mpfr-$(mpfr-version) echo "" > $@ else $(call gbuild, mpc-$(mpc-version), static, , \ - -j$(numthreads), make check) + -j$(numthreads)) echo "GNU Multiple Precision Complex library" > $@ fi @@ -1399,6 +1418,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) ln -s $$odir/gcc-$(gcc-version) $(ddir)/gcc-$(gcc-version) fi cd gcc-$(gcc-version) + $(shsrcdir)/prep-source.sh $(ibdir) # Unfortunately binutils installs headers like 'ansidecl.h' that # have been seen to conflict with GCC's internal versions of those @@ -1506,7 +1526,18 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) -# Software that need re-compilation (to use our own libraries) +# Level 6: need re-compilation +# ---------------------------- +# +# The initial build of these was done with the host's settings, which will +# cause problems later when we completely close-off the host environment. +$(ibidir)/make-$(make-version): $(ibidir)/gcc-$(gcc-version) + tarball=make-$(make-version).tar.lz + $(call import-source, $(make-url), $(make-checksum)) + $(call gbuild, make-$(make-version), static, \ + --disable-dependency-tracking --without-guile) + echo "GNU Make $(make-version)" > $@ + $(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version) tarball=lzip-$(lzip-version).tar unpackdir=lzip-$(lzip-version) @@ -1514,6 +1545,7 @@ $(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version) rm -rf $$unpackdir tar -xf $(tdir)/$$tarball cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) ./configure --build --check --installdir="$(ibdir)" if [ -f $(ibdir)/patchelf ]; then $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/lzip; @@ -1526,11 +1558,7 @@ $(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version) - - - - -# Level 6: Basic text editor +# Level 7: Basic text editor # -------------------------- # # If the project is built in a minimal environment, there is no text @@ -1547,7 +1575,8 @@ $(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-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): $(ibidir)/lzip-$(lzip-version) +$(ibidir)/nano-$(nano-version): $(ibidir)/lzip-$(lzip-version) \ + $(ibidir)/make-$(make-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/build-rules.mk b/reproduce/software/make/build-rules.mk index c160d33..62cb6d5 100644 --- a/reproduce/software/make/build-rules.mk +++ b/reproduce/software/make/build-rules.mk @@ -3,7 +3,7 @@ # imported into 'basic.mk' and 'high-level.mk'. They should be activated # with Make's 'Call' function. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -207,17 +207,10 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \ else confscript="$(strip $(6))"; \ fi; \ \ - if [ -f $(ibdir)/bash ]; then \ - if [ -f "$$confscript" ]; then \ - sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \ - -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \ - $$confscript > $$confscript-tmp; \ - mv $$confscript-tmp $$confscript; \ - chmod +x $$confscript; \ - fi; \ + $(shsrcdir)/prep-source.sh $(ibdir); \ + if [ -f $(ibdir)/bash ]; then \ shellop="SHELL=$(ibdir)/bash"; \ - elif [ -f /bin/bash ]; then shellop="SHELL=/bin/bash"; \ - else shellop="SHELL=/bin/sh"; \ + else shellop="SHELL=$(ibdir)/dash"; \ fi; \ \ if [ x$$gbuild_prefix = x ]; then prefixdir="$(idir)"; \ @@ -255,10 +248,7 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \ # CMake # ----- # -# According to the link below, in CMake '/bin/sh' is hardcoded, so there is -# no way to change it unfortunately! -# -# https://stackoverflow.com/questions/21167014/how-to-set-shell-variable-in-makefiles-generated-by-cmake +# Used by packages that are built with CMake. cbuild = if [ x$(static_build) = xyes ] && [ $(2)x = staticx ]; then \ export LDFLAGS="$$LDFLAGS -static"; \ opts="-DBUILD_SHARED_LIBS=OFF"; \ @@ -268,13 +258,18 @@ cbuild = if [ x$(static_build) = xyes ] && [ $(2)x = staticx ]; then \ utarball=$(tdir)/$$tarball; \ $(call uncompress); \ cd $(1); \ - rm -rf project-build; \ - mkdir project-build; \ - cd project-build; \ + $(shsrcdir)/prep-source.sh $(ibdir); \ + if [ -f $(ibdir)/bash ]; then \ + shellop="SHELL=$(ibdir)/bash"; \ + else shellop="SHELL=$(ibdir)/dash"; \ + fi; \ + rm -rf maneage-build; \ + mkdir maneage-build; \ + cd maneage-build; \ cmake .. -DCMAKE_LIBRARY_PATH=$(ildir) \ -DCMAKE_INSTALL_PREFIX=$(idir) \ -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON $$opts $(3); \ - make; \ - make install; \ + make $$shellop; \ + make $$shellop install; \ cd ../..; \ rm -rf $(1) diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 3f9c40c..2274c45 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2018-2023 Mohammad Akhlaghi -# Copyright (C) 2019-2023 Raul Infante-Sainz +# Copyright (C) 2018-2025 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Raul Infante-Sainz # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -64,6 +64,12 @@ ipydir = $(BDIR)/software/installed/version-info/python ircrandir = $(BDIR)/software/installed/version-info/r-cran ilibrcrandir = $(BDIR)/software/installed/lib/R/library +# Special files. +makewshell = $(ibdir)/make-with-shell + + + + # Targets to build. ifeq ($(strip $(all_highlevel)),1) @@ -232,7 +238,7 @@ $(idircustom):; mkdir $@ # Afer putting everything together, we use the first server as the # reference for all software if their '-url' variable isn't defined (in # 'reproduce/software/config/urls.conf'). -downloadwrapper = ./reproduce/analysis/bash/download-multi-try +downloadwrapper = ./reproduce/analysis/bash/download-multi-try.sh maneage_backup_urls := $(shell awk '!/^#/{printf "%s ", $$1}' \ reproduce/software/config/servers-backup.conf) backupservers_all = $(user_backup_urls) $(maneage_backup_urls) @@ -339,6 +345,7 @@ $(ibidir)/atlas-$(atlas-version): cd $(ddir) tar -xf $(tdir)/atlas-$(atlas-version).tar.lz cd ATLAS + $(shsrcdir)/prep-source.sh $(ibdir) rm -rf build mkdir build cd build @@ -395,6 +402,7 @@ $(ibidir)/boost-$(boost-version): \ cd $(ddir) tar -xf $(tdir)/$$tarball cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) ./bootstrap.sh --prefix=$(idir) --with-libraries=all \ --with-python=python3 echo "using mpi ;" > project-config.jam @@ -417,9 +425,7 @@ $(ibidir)/cfitsio-$(cfitsio-version): topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball customtar=cfitsio-$(cfitsio-version)-custom.tar.gz cd cfitsio-$(cfitsio-version) - sed configure -e's|@rpath|$(ildir)|g' > configure_tmp - mv configure_tmp configure - chmod +x configure + sed -i -e's|@rpath|$(ildir)|g' configure cd .. tar cf $$customtar cfitsio-$(cfitsio-version) cd $$topdir @@ -518,6 +524,12 @@ $(ibidir)/fftw-$(fftw-version): echo "FFTW $(fftw-version) \citep{fftw}" > $@ $(ibidir)/freetype-$(freetype-version): $(ibidir)/libpng-$(libpng-version) +# As of version 2.13.2, FreeType doesn't account for the 'SHELL' +# environment variable. The issue has been reported to the +# developers. But until future versions, the work-around was +# discoverd to be setting the 'GNUMAKE' environment variable so it +# includes 'SHELL'. + export GNUMAKE="$(makewshell)" tarball=freetype-$(freetype-version).tar.lz $(call import-source, $(freetype-url), $(freetype-checksum)) $(call gbuild, freetype-$(freetype-version), static) @@ -578,7 +590,9 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \ rm -rf $(ddir)/Healpix_$(healpix-version) topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball - cd Healpix_$(healpix-version)/src/C/autotools/ + cd Healpix_$(healpix-version) + $(shsrcdir)/prep-source.sh $(ibdir) + cd src/C/autotools autoreconf --install ./configure --prefix=$(idir) make V=1 -j$(numthreads) SHELL=$(ibdir)/bash @@ -670,6 +684,7 @@ $(ibidir)/libpaper-$(libpaper-version): \ tar -xf $(tdir)/$$tarball unpackdir=libpaper-$(libpaper-version) cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) autoreconf -fi ./configure --prefix=$(idir) --sysconfdir=$(idir)/etc \ --disable-static @@ -799,6 +814,7 @@ $(ibidir)/openblas-$(openblas-version): cd $(ddir) tar -xf $(tdir)/$$tarball cd OpenBLAS-$(openblas-version) + $(shsrcdir)/prep-source.sh $(ibdir) make -j$(numthreads) make PREFIX=$(idir) install cd .. @@ -1007,6 +1023,7 @@ $(ibidir)/astrometrynet-$(astrometrynet-version): \ rm -rf astrometry.net-$(astrometrynet-version) tar -xf $(tdir)/$$tarball cd astrometry.net-$(astrometrynet-version) + $(shsrcdir)/prep-source.sh $(ibdir) sed -e 's|cat /proc/cpuinfo|echo "Ignoring CPU info"|' \ -e 's|-free|echo "Ignoring RAM info"|' Makefile > Makefile.tmp mv Makefile.tmp Makefile @@ -1045,6 +1062,7 @@ $(ibidir)/cdsclient-$(cdsclient-version): cd $(ddir) tar -xf $(tdir)/$$tarball cd cdsclient-$(cdsclient-version) + $(shsrcdir)/prep-source.sh $(ibdir) touch * ./configure --prefix=$(idir) make @@ -1061,25 +1079,29 @@ $(ibidir)/cmake-$(cmake-version): tarball=cmake-$(cmake-version).tar.lz $(call import-source, $(cmake-url), $(cmake-checksum)) -# After searching in 'bootstrap', I couldn't find 'LIBS', only -# 'LDFLAGS'. So the extra libraries are being added to 'LDFLAGS', not -# 'LIBS'. -# # On Mac systems, the build complains about 'clang' specific # features, so we can't use our own GCC build here. if [ x$(on_mac_os) = xyes ]; then export CC=clang export CXX=clang++ fi + +# CMake wants a single executable for 'MAKE', so we can't use 'make +# SHELL=$(SHELL) and we have defined this script. + export MAKE="$(makewshell)" + +# Go into the unpacked directory and build CMake. cd $(ddir) rm -rf cmake-$(cmake-version) tar -xf $(tdir)/$$tarball cd cmake-$(cmake-version) + $(shsrcdir)/prep-source.sh $(ibdir) ./bootstrap --prefix=$(idir) --system-curl --system-zlib \ --system-bzip2 --system-liblzma --no-qt-gui \ --parallel=$(numthreads) - make -j$(numthreads) LIBS="$$LIBS -lssl -lcrypto -lz" VERBOSE=1 - make install + $(makewshell) VERBOSE=1 LIBS="$$LIBS -lssl -lcrypto -lz" \ + -j$(numthreads) + $(makewshell) install cd .. rm -rf cmake-$(cmake-version) echo "CMake $(cmake-version)" > $@ @@ -1129,6 +1151,7 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ cd $(ddir) tar -xf $(tdir)/$$tarball cd ghostscript-$(ghostscript-version) + $(shsrcdir)/prep-source.sh $(ibdir) ./configure --prefix=$(idir) \ --disable-cups \ --enable-dynamic \ @@ -1170,7 +1193,7 @@ $(ibidir)/gnuastro-$(gnuastro-version): \ $(call gbuild, gnuastro-$(gnuastro-version), static, , \ -j$(numthreads)) cp $(dtexdir)/gnuastro.tex $(ictdir)/ - echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro,akhlaghi19}" > $@ + echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@ $(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version) @@ -1188,7 +1211,9 @@ $(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version) cd $(ddir) tar -xf $(tdir)/$$tarball unpackdir=icu-$(icu-version) - cd $$unpackdir/icu4c/source + cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) + cd icu4c/source ./configure --enable-static --prefix=$(idir) make -j$(numthreads) V=1 make install @@ -1255,6 +1280,7 @@ $(ibidir)/imfit-$(imfit-version): \ rm -rf $$unpackdir tar -xf $(tdir)/$$tarball cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) sed -i 's|/usr/local|$(idir)|g' SConstruct sed -i 's|/usr/include|$(idir)/include|g' SConstruct sed -i 's|.append(|.insert(0,|g' SConstruct @@ -1302,6 +1328,7 @@ $(ibidir)/minizip-$(minizip-version): $(ibidir)/automake-$(automake-version) mkdir $$unpackdir tar -xf $(tdir)/$$tarball -C$$unpackdir --strip-components=1 cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) ./configure --prefix=$(idir) make cd contrib/minizip @@ -1363,6 +1390,7 @@ $(ibidir)/netpbm-$(netpbm-version): \ rm -rf $$unpackdir tar -xf $(tdir)/$$tarball cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) # As of NetPBM 10.73.39 and Flex 2.6.4-410-74a89fd (commit 74a89fd in # Flex's Git that is 410 commits after version 2.6.4), there is the @@ -1482,6 +1510,7 @@ $(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version) rm -rf $$unpackdir tar -xf $(tdir)/$$tarball cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) # Unfortuantely SCons hard-codes its search PATH in its source (to # use POSIX operating system defaults)! So the only way to modify it @@ -1625,8 +1654,9 @@ $(ibidir)/util-linux-$(util-linux-version): | $(idircustom) cd $(ddir) tar -xf $(tdir)/$$tarball cd util-linux-$(util-linux-version) + $(shsrcdir)/prep-source.sh $(ibdir) -# If a patch exists for the current version, apply it. +# If a patch is necessary, apply it. if [ -f $(patchdir)/util-linux-$(util-linux-version)-macos.patch ]; then cp $(patchdir)/util-linux-$(util-linux-version)-macos.patch \ util-linux-$(util-linux-version)-macos.patch @@ -1727,6 +1757,7 @@ $(ibidir)/vim-$(vim-version): tar -xf $(tdir)/$$tarball unpackdir=vim-$(vim-version) cd $(ddir)/$$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) ./configure --prefix=$(idir) \ --disable-canberra \ --enable-multibyte \ @@ -1795,10 +1826,16 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf rm -rf install-tl-* tar -xf $(tdir)/install-tl-unx.tar.gz cd install-tl-* + $(shsrcdir)/prep-source.sh $(ibdir) sed -e's|@installdir[@]|$(idir)|g' \ "$$topdir"/reproduce/software/config/texlive.conf \ > texlive.conf +# We do not build TeXLive from source and for its installation it +# downloads components from the web internally; and those components +# can use '/bin/sh' (which will need '$(sys_library_sh_path)'). + export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" + # TeX Live's installation may fail due to any reason. But TeX Live is # optional (only necessary for building the final PDF). So we don't # want the configure script to fail if it can't run. Possible error @@ -1867,13 +1904,16 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf tarballurl=$$url/install-tl-unx.tar.gz touch $(lockdir)/download downloader="wget --no-use-server-timestamps -O" - if $(downloadwrapper) "$$downloader" $(lockdir)/download \ - $$tarballurl "$(tdir)/install-tl-unx.tar.gz" \ - "$(backupservers)"; then + if $(downloadwrapper) "$$downloader" \ + $(lockdir)/download \ + $$tarballurl \ + "$(tdir)/install-tl-unx.tar.gz" \ + "$(backupservers)"; then cd $(ddir) rm -rf install-tl-* tar -xf $(tdir)/install-tl-unx.tar.gz cd install-tl-* + $(shsrcdir)/prep-source.sh $(ibdir) sed -e's|@installdir[@]|$(idir)|g' \ $$topdir/reproduce/software/config/texlive.conf \ > texlive.conf @@ -1917,6 +1957,11 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ echo "" > $@ else +# We do not build TeXLive from source and for its installation it +# downloads components from the web internally; and those +# components can use '/bin/sh' (which needs 'sys_library_sh_path'). + export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" + # To update itself, tlmgr needs a backup directory. backupdir=$(idir)/texlive/backups mkdir -p $$backupdir @@ -1940,6 +1985,13 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ # directory so we don't have to modify 'PATH'. ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/ +# Correct any reference to '/bin/sh' within the installed LaTeX +# files (this is because we do no yet install LaTeX from source): + cdir=$$(pwd) + cd $(idir)/texlive + $(shsrcdir)/prep-source.sh $(ibdir) + cd $$cdir + # Get all the necessary versions. texlive=$$(pdflatex --version \ | awk 'NR==1' \ diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index 936fab1..deeccf2 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2019-2023 Raul Infante-Sainz -# Copyright (C) 2019-2023 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Raul Infante-Sainz +# Copyright (C) 2019-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -93,13 +93,44 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version) export CC=clang export CXX=clang++ fi - $(call gbuild, python-$(python-version),, \ - --without-ensurepip \ - --with-system-ffi \ - --enable-shared, -j$(numthreads)) + +# Unpack the tarball (see below for the necessary modification). + cd $(ddir) + unpackdir=python-$(python-version) + tar -xf $(tdir)/$$unpackdir.tar.lz + cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) + +# Python's 'setup.py' uses 'os.system' to run shell scripts. On the +# other hand 'os.system' only runs '/bin/sh' (which has its own +# libraries to link to and those are blocked at this level). So we +# need to add an extra line on top of the 'os.system' funciton and +# put '/usr/lib' in 'LD_LIBRARY_PATH' within Python's environment for +# system calls (with 'os.putenv'). + awk '{if(/os.system\(/) \ + { print " os.putenv(\"LD_LIBRARY_PATH\", \"$$LD_LIBRARY_PATH:$(sys_library_sh_path)\");"; \ + print $$0;} \ + else print $$0}' \ + setup.py > setup-tmp.py + mv setup-tmp.py setup.py + +# Do the basic installation and delete the temporary directory. + ./configure SHELL=$(ibdir)/bash \ + --enable-optimizations \ + --without-ensurepip \ + --prefix="$(idir)" \ + --with-system-ffi \ + --enable-shared + $(makewshell) -j$(numthreads) + $(makewshell) install -j$(numthreads) + cd .. + rm -rf $$unpackdir + +# Set the necessary environment variables and finish the build. ln -sf $(ildir)/python$(python-major-version) $(ildir)/python ln -sf $(ibdir)/python$(python-major-version) $(ibdir)/python - ln -sf $(iidir)/python$(python-major-version)m $(iidir)/python$(python-major-version) + ln -sf $(iidir)/python$(python-major-version)m \ + $(iidir)/python$(python-major-version) rm -rf $(ipydir) mkdir $(ipydir) echo "Python $(python-version)" > $@ diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk index 484fe74..7c86c23 100644 --- a/reproduce/software/make/r-cran.mk +++ b/reproduce/software/make/r-cran.mk @@ -12,8 +12,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2022-2023 Boud Roukema -# Copyright (C) 2022-2023 Mohammad Akhlaghi +# Copyright (C) 2022-2025 Boud Roukema +# Copyright (C) 2022-2025 Mohammad Akhlaghi # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -204,6 +204,7 @@ $(ibidir)/r-cran-$(r-cran-version): \ tar -xf $(tdir)/$$tarball unpackdir=R-$(r-cran-version) cd $$unpackdir + $(shsrcdir)/prep-source.sh $(ibdir) # We need to manually remove the lines with '~autodetect~', they # cause the configure script to crash in version 4.0.2. They are used diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk index 1cc87a5..3f99fab 100644 --- a/reproduce/software/make/xorg.mk +++ b/reproduce/software/make/xorg.mk @@ -14,8 +14,8 @@ # # ------------------------------------------------------------------------ # -# Copyright (C) 2021-2023 Mohammad Akhlaghi -# Copyright (C) 2021-2023 Raul Infante-Sainz +# Copyright (C) 2021-2025 Mohammad Akhlaghi +# Copyright (C) 2021-2025 Raul Infante-Sainz # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh index 814de2c..6bbd774 100755 --- a/reproduce/software/shell/bashrc.sh +++ b/reproduce/software/shell/bashrc.sh @@ -34,7 +34,7 @@ # shell'). # # -# Copyright (C) 2019-2023 Mohammad Akhlaghi +# Copyright (C) 2019-2025 Mohammad Akhlaghi # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index 4f71bee..857f3b5 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -2,9 +2,9 @@ # # Necessary preparations/configurations for the reproducible project. # -# Copyright (C) 2018-2023 Mohammad Akhlaghi -# Copyright (C) 2021-2023 Raul Infante-Sainz -# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani +# Copyright (C) 2018-2025 Mohammad Akhlaghi +# Copyright (C) 2021-2025 Raul Infante-Sainz +# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -1252,6 +1252,14 @@ instlibdir="$instdir"/lib if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi ln -fs "$instlibdir" "$instdir"/lib64 +# Wrapper over Make as a single command so it does not default to '/bin/sh' +# during installation (needed by some programs like CMake). +instbindir=$instdir/bin +if ! [ -d $instbindir ]; then mkdir $instbindir; fi +makewshell="$instbindir/make-with-shell" +echo "$instbindir/make SHELL=$instbindir/bash \$@" > $makewshell +chmod +x $makewshell + @@ -1558,6 +1566,35 @@ fi +# Libraries necessary for the system's shell +# ------------------------------------------ +# +# In some cases (mostly the programs that Maneage doesn't yet build by +# itself), the programs may call the system's shell, not Maneage's +# shell. After we close-off the system environment from Maneage, this will +# cause a crash! To avoid such cases, we need to find the locations of the +# libraries that the shell needs and temporarily add them to the library +# search path. +if [ x"$$on_mac_os" != xyes ]; then + sys_library_sh_path=$(otool -L /bin/sh \ + | awk '/\/lib/{print $1}' \ + | sed 's#/[^/]*$##' \ + | sort \ + | uniq \ + | awk '{printf "%s:", $1}END{printf "\b"}') +else + sys_library_sh_path=$(ldd /bin/sh \ + | awk '{if($3!="") print $3}' \ + | sed 's#/[^/]*$##' \ + | sort \ + | uniq \ + | awk '{printf "%s:", $1}END{printf "\b"}') +fi + + + + + # Find Zenodo URL for software downloading # ---------------------------------------- # @@ -1646,6 +1683,7 @@ fi # tools, but we have to be very portable (and use minimal features in all). echo; echo "Building necessary software (if necessary)..." .local/bin/make $keepgoing -f reproduce/software/make/basic.mk \ + sys_library_sh_path=$sys_library_sh_path \ user_backup_urls="$user_backup_urls" \ sys_library_path=$sys_library_path \ rpath_command=$rpath_command \ @@ -1673,17 +1711,29 @@ else numthreads=$jobs fi .local/bin/env -i HOME=$bdir \ - .local/bin/make $keepgoing -f reproduce/software/make/high-level.mk \ - user_backup_urls="$user_backup_urls" \ - sys_library_path=$sys_library_path \ - rpath_command=$rpath_command \ - all_highlevel=$all_highlevel \ - static_build=$static_build \ - numthreads=$numthreads \ - on_mac_os=$on_mac_os \ - sys_cpath=$sys_cpath \ - host_cc=$host_cc \ - -j$numthreads + .local/bin/make $keepgoing \ + -f reproduce/software/make/high-level.mk \ + sys_library_sh_path=$sys_library_sh_path \ + user_backup_urls="$user_backup_urls" \ + sys_library_path=$sys_library_path \ + rpath_command=$rpath_command \ + all_highlevel=$all_highlevel \ + static_build=$static_build \ + numthreads=$numthreads \ + on_mac_os=$on_mac_os \ + sys_cpath=$sys_cpath \ + host_cc=$host_cc \ + -j$numthreads + + + + + +# Delete the temporary Make wrapper +# --------------------------------- +# +# See above for its description. +rm $makewshell diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout index a1340d7..7b521a3 100755 --- a/reproduce/software/shell/git-post-checkout +++ b/reproduce/software/shell/git-post-checkout @@ -4,7 +4,7 @@ # controlled files (with each commit) using the 'metastore' program. # # Copyright (C) 2016 Przemyslaw Pawelczyk -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # This script is taken from the 'examples/hooks/pre-commit' file of the # 'metastore' package (installed within the project, with an MIT license diff --git a/reproduce/software/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit index 02ba488..7b98ad0 100755 --- a/reproduce/software/shell/git-pre-commit +++ b/reproduce/software/shell/git-pre-commit @@ -4,7 +4,7 @@ # controlled files (with each commit) using the 'metastore' program. # # Copyright (C) 2016 Przemyslaw Pawelczyk -# Copyright (C) 2018-2023 Mohammad Akhlaghi +# Copyright (C) 2018-2025 Mohammad Akhlaghi # # WARNING: # diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh index 808429b..93d3266 100755 --- a/reproduce/software/shell/pre-make-build.sh +++ b/reproduce/software/shell/pre-make-build.sh @@ -2,7 +2,7 @@ # # Very basic tools necessary to start Maneage's default building. # -# Copyright (C) 2020-2023 Mohammad Akhlaghi +# Copyright (C) 2020-2025 Mohammad Akhlaghi # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -48,7 +48,7 @@ instdir="$sdir"/installed tmpblddir="$sdir"/build-tmp confdir=reproduce/software/config ibidir="$instdir"/version-info/proglib -downloadwrapper=reproduce/analysis/bash/download-multi-try +downloadwrapper=reproduce/analysis/bash/download-multi-try.sh # Derived directories bindir="$instdir"/bin @@ -123,7 +123,8 @@ download_tarball() { # Make sure this is the correct tarball. if type sha512sum > /dev/null 2> /dev/null; then checksum=$(sha512sum "$ucname" | awk '{print $1}') - expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' "$checksumsfile") + expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' \ + "$checksumsfile") if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar" else echo "ERROR: Non-matching checksum: $tarball" @@ -135,8 +136,10 @@ download_tarball() { fi fi - # If the tarball is newer than the (possibly existing) program (the version - # has changed), then delete the program. + # If the tarball is newer than the (possibly existing) program (the + # version has changed), then delete the program. When the LaTeX name is + # not given here, the software is re-built later (close to the end of + # 'basic.mk') and the name is properly placed there. if [ -f "$ibidir/$progname" ]; then if [ "$maneagetar" -nt "$ibidir/$progname" ]; then rm "$ibidir/$progname" @@ -210,10 +213,15 @@ build_program() { fi fi - # Clean up the source directory + # Clean up the source directory and write the LaTeX name of the + # software (if necessary: otherwise, just make an empty file). cd "$topdir" rm -rf "$tmpblddir/$unpackdir" - echo "$progname_tex $version" > "$ibidir/$progname" + if [ x"$progname_tex" = x ]; then + echo "" > "$ibidir/$progname" + else + echo "$progname_tex $version" > "$ibidir/$progname" + fi fi } @@ -256,7 +264,7 @@ build_program # Make that has a different executable name (using the '--program-prefix=' # configure option) from the "default" make (which is this one!). progname="make" -progname_tex="GNU Make" +progname_tex="" # Make re-built after GCC (empty string to avoid repetition) url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' $versionsfile) tarball=$progname-$version.tar.lz diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh new file mode 100755 index 0000000..dcdc472 --- /dev/null +++ b/reproduce/software/shell/prep-source.sh @@ -0,0 +1,94 @@ +#!/usr/bin/env sh +# +# Necessary corrections in the un-packed source of programs to make them +# portable (for example to not use '/bin/sh'). +# +# Usage: Run in top source directory (will work on all files within the +# directory that it is run in ): +# ./prep-source.sh /FULL/ADDRESS/TO/DESIRED/BIN +# +# Copyright (C) 2024-2025 Mohammad Akhlaghi +# +# This script is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# This script is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this script. If not, see . + + + + + +# Abort the script in case of an error +set -e + + + + +# Read the first argument. +bindir="$1" +if [ x"$bindir" = x ]; then + printf "$0: no argument (location of the 'bin/' directory " + printf "containing the 'bash' executable)\n" + exit 1 +elif ! [ -d "$bindir" ]; then + printf "$0: the directory given as the first argument ('$bindir')" + printf "does not exist" +fi + + + + + +# Find all the files that contain the '/bin/sh' string and correct them to +# Maneage's own Bash. We are using 'while read' to read the file names line +# by line. This is necessary to account file names that include the 'SPACE' +# character (happens in CMake for example!). +# +# Note that dates are important in the source directory (files depend on +# each other), so we should read the original date and after making. We are +# also not using GNU SED's '-i' ('--in-place') option because the host OS +# may not have GNU SED. +# +# Actual situation which prompted the addition of this step: a Maneage'd +# project (with GNU Bash 5.1.8 and Readline 8.1.1) was being built on a +# system where '/bin/sh' was GNU Bash 5.2.26 and had Readline 8.2.010. The +# newer version of Bash needed the newer Readline library function(s) that +# were not available in Maneage's Readline library. Therefore, as soon as +# the basic software were built and Maneage entered the creation of +# high-level software (where we completely close-off the host environment), +# Maneage crashed with the following '/bin/sh' error: +# +# /bin/sh: symbol lookup error: /bin/sh: undefined symbol: rl_trim_arg_from_keyseq +# +# This lead to the discovery that through '/bin/sh' the host operating +# system was leaking into our closed Maneage environment which needs to be +# closed. This needs a source-level correction because '/bin/sh' is +# hard-coded in the source code of almost all programs (their build +# scripts); and in special programs like GNU Make, GNU M4 or CMake it is +# actually hardcoded in the source code (not just build scripts). +if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash +else shpath="$bindir"/dash +fi +grep -I -r -e'/bin/sh' $(pwd)/* \ + | sed -e's|:|\t|' \ + | awk 'BEGIN{FS="\t"}{print $1}' \ + | sort \ + | uniq \ + | while read filename; do \ + tmp="$filename".tmp; \ + origtime="$(date -R -r "$filename")"; \ + origperm=$(stat -c '%a' "$filename"); \ + sed -e's|/bin/sh|'"$shpath"'|g' "$filename" > "$tmp"; \ + mv "$tmp" "$filename"; \ + chmod $origperm "$filename"; \ + touch -d"$origtime" "$filename"; \ + echo "Corrected /bin/sh in $filename"; \ + done diff --git a/reproduce/software/shell/run-parts.in b/reproduce/software/shell/run-parts.in index a7b7705..053f5f3 100755 --- a/reproduce/software/shell/run-parts.in +++ b/reproduce/software/shell/run-parts.in @@ -10,8 +10,8 @@ # However, it didn't have a copyright statement. So one is being added # here. # -# Copyright (C) 2023 Authors mentioned above. -# Copyright (C) 2020-2023 Mohammad Akhlaghi +# Copyright (C) 2025 Authors mentioned above. +# Copyright (C) 2025-2024 Mohammad Akhlaghi # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh index 472b4c0..e12ff98 100755 --- a/reproduce/software/shell/tarball-prepare.sh +++ b/reproduce/software/shell/tarball-prepare.sh @@ -15,8 +15,8 @@ # # Discussion: https://savannah.nongnu.org/task/?15699 # -# Copyright (C) 2022-2023 Mohammad Akhlaghi -# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani +# Copyright (C) 2022-2025 Mohammad Akhlaghi +# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani # Released under GNU GPLv3+ # Abort the script in case of an error. diff --git a/tex/README.md b/tex/README.md index 4963bf5..f100c76 100644 --- a/tex/README.md +++ b/tex/README.md @@ -1,7 +1,7 @@ Directory containing LaTeX-related files ---------------------------------------- -Copyright (C) 2018-2023 Mohammad Akhlaghi \ +Copyright (C) 2018-2025 Mohammad Akhlaghi \ See the end of the file for license conditions. This directory contains directories to various components the LaTeX part of diff --git a/tex/src/delete-me-image-histogram.tex b/tex/src/delete-me-image-histogram.tex index 37618ec..6201c31 100644 --- a/tex/src/delete-me-image-histogram.tex +++ b/tex/src/delete-me-image-histogram.tex @@ -1,6 +1,6 @@ %% Plot the demonstration image and its histogram. % -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/delete-me-squared.tex b/tex/src/delete-me-squared.tex index 968b4d7..51e5f5b 100644 --- a/tex/src/delete-me-squared.tex +++ b/tex/src/delete-me-squared.tex @@ -1,6 +1,6 @@ %% PGFPlots code to plot a random set of numbers as demo %% -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex index fd4bf9d..e80d7d8 100644 --- a/tex/src/preamble-biblatex.tex +++ b/tex/src/preamble-biblatex.tex @@ -12,7 +12,7 @@ %% helps in clearly identifying the files and avoiding places that %% complain about '.bib' files. % -%% Copyright (C) 2018-2023 Mohammad Akhlaghi +%% Copyright (C) 2018-2025 Mohammad Akhlaghi % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-maneage-default-style.tex b/tex/src/preamble-maneage-default-style.tex index f811743..b7aa811 100644 --- a/tex/src/preamble-maneage-default-style.tex +++ b/tex/src/preamble-maneage-default-style.tex @@ -6,7 +6,7 @@ %% style defined here as a preamble. To ignore it, uncomment or delete the %% respective line in 'paper.tex'. % -%% Copyright (C) 2019-2023 Mohammad Akhlaghi +%% Copyright (C) 2019-2025 Mohammad Akhlaghi % %% This file is free software: you can redistribute it and/or modify it %% under the terms of the GNU General Public License as published by the diff --git a/tex/src/preamble-maneage.tex b/tex/src/preamble-maneage.tex index 5dc89fe..9e6cc5a 100644 --- a/tex/src/preamble-maneage.tex +++ b/tex/src/preamble-maneage.tex @@ -1,6 +1,6 @@ %% Preamble for Maneage-related features. % -%% Copyright (C) 2020-2023 Mohammad Akhlaghi +%% Copyright (C) 2020-2025 Mohammad Akhlaghi % %% This LaTeX file is part of Maneage. Maneage is free software: you can %% redistribute it and/or modify it under the terms of the GNU General diff --git a/tex/src/preamble-pgfplots.tex b/tex/src/preamble-pgfplots.tex index 86f649c..74f5290 100644 --- a/tex/src/preamble-pgfplots.tex +++ b/tex/src/preamble-pgfplots.tex @@ -40,7 +40,7 @@ %% hasn't changed since the last build. TiKZ/PGFPlots won't rebuild the %% plot. % -%% Copyright (C) 2018-2023 Mohammad Akhlaghi +%% Copyright (C) 2018-2025 Mohammad Akhlaghi % %% This file is part of Maneage (https://maneage.org). % diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex index 76603f2..adb99b7 100644 --- a/tex/src/preamble-project.tex +++ b/tex/src/preamble-project.tex @@ -4,7 +4,7 @@ %% LaTeX usages. However, if any are not needed in your work, please feel %% free to remove them. % -%% Copyright (C) 2018-2023 Mohammad Akhlaghi +%% Copyright (C) 2018-2025 Mohammad Akhlaghi %% Copyright (C) YYYY Your Name % %% This file is free software: you can redistribute it and/or modify it diff --git a/tex/src/references.tex b/tex/src/references.tex index e4117ae..ae3e5d1 100644 --- a/tex/src/references.tex +++ b/tex/src/references.tex @@ -1,7 +1,7 @@ %% Non-software BibTeX entries. The software-specific BibTeX entries are %% stored in a '*.tex' file under the 'tex/dependencies' directory. % -%% Copyright (C) 2018-2023 Mohammad Akhlaghi +%% Copyright (C) 2018-2025 Mohammad Akhlaghi % %% Copying and distribution of this file, with or without modification, %% are permitted in any medium without royalty provided the copyright -- cgit v1.2.1 From 890858795fd6e0c8c1f3050adec7f4bc78e9e47c Mon Sep 17 00:00:00 2001 From: Giacomo Lorenzetti Date: Tue, 21 Jan 2025 18:57:10 +0100 Subject: IMPORTANT: 73 software upgrades and added offline mode Summary: This is a software update to make Maneage more portable and up to date. It does not involve any Maneage infrastructure changes. You should just re-build your project to make sure the updated software haven't removed/changed any of their features that you were using. Until now, the software in Maneage had not been updated for almost 2.5 years (since August 2022) and were starting to get dated! Also, when no internet is available (for example in a HPC), the Zenodo check would always cause a crash and needed to be commented manually. With this commit, all the basic software that had been updated as well as the dependencies of Gnuastro (which we commit to maintaining) have been updated after a check of their webpage (see the full list below). To fix the offline issue, a new '--offline' option has been added to the project script. The other following changes were made: - tarball-prepare: has become more resilient (for dealing with file name with spaces or Lzip, which should not be compressed). - Readme: improve documentation when used in Docker. Below you can see the list of basic software that have been updated. The only basic software that have not been updated upstream since the previous Maneage software update are 'bison', 'flock', 'm4', 'pkgconfig', 'unzip' and 'zip'. bash 5.2-rc2 5.2.37 binutils 2.39 2.43.1 coreutils 9.1 9.6 curl 7.84.0 8.11.1 dash 0.5.11-057cd65 0.5.12 diffutils 3.8 3.10 file 5.42 5.46 findutils 4.9.0 4.10.0 gawk 5.1.1 5.3.1 gcc 12.1.0 14.2.0 gettext 0.21 0.23.1 git 2.37.1 2.48.1 gmp 6.2.1 6.3.0 grep 3.7 3.11 gzip 1.12 1.13 help2man 1.49.2 1.49.3 isl 0.24 0.27 less 590 668 libiconv 1.17 1.18 libtool 2.4.7 2.5.4 libunistring 1.0 1.3 libxml2 2.9.12 2.13.5 lzip 1.23 1.25 make 4.3 4.4.1 mpc 1.2.1 1.3.1 mpfr 4.1.0 4.2.1 nano 6.4 8.3 ncurses 6.3 6.5 openssl 3.0.5 3.4.0 perl 5.36.0 5.40.1 podlators 4.14 6.0.2 readline 8.2-rc2 8.2.13 sed 4.8 4.9 tar 1.34 1.35 texinfo 6.8 7.2 wget 1.21.2 1.25.0 which 2.21 2.23 xz 5.2.5 5.6.3 zlib 1.2.11 1.3.1 The high-level software that have been updated. autoconf 2.71 2.72 automake 1.16.5 1.17 cfitsio 4.1.0 4.5.0 cmake 3.24.0 3.31.5 expat 2.4.1 2.6.4 fontconfig 2.14.0 2.16.0 freetype 2.11.0 2.13.3 ghostscript 9.56.1 10.04.0 gnuastro 0.18 0.23 gsl 2.7 2.8 libffi 3.4.2 3.4.7 libgit2 1.3.0 1.9.0 libice 1.0.10 1.1.2 libidn 1.38 1.42 libjpeg 9e 9f libpaper 1.1.28 1.1.29 libpng 1.6.37 1.6.46 libpthread-stubs 0.4 0.5 libsm 1.2.3 1.2.5 libtiff 4.4.0 4.7.0 libxau 1.0.9 1.0.12 libxcb 1.15 1.17 libxdmcp 1.1.3 1.1.5 libxext 1.3.4 1.3.6 libxt 1.2.1 1.3.1 python 3.10.6 3.13.12 util-macros 1.19.3 1.20.2 wcslib 7.11 8.4 xcb-proto 1.15 1.17 xorgproto 2022.1 2024.1 xtrans 1.4.0 1.5.2 --- README.md | 32 ++++--- project | 4 + reproduce/software/config/checksums.conf | 144 ++++++++++++++-------------- reproduce/software/config/urls.conf | 11 ++- reproduce/software/config/versions.conf | 144 ++++++++++++++-------------- reproduce/software/make/basic.mk | 2 +- reproduce/software/make/high-level.mk | 46 ++++++--- reproduce/software/make/python.mk | 18 ++-- reproduce/software/make/xorg.mk | 2 +- reproduce/software/shell/configure.sh | 5 +- reproduce/software/shell/tarball-prepare.sh | 26 +++-- 11 files changed, 242 insertions(+), 192 deletions(-) diff --git a/README.md b/README.md index 9599c6b..6e5a2ad 100644 --- a/README.md +++ b/README.md @@ -680,11 +680,11 @@ steps. # If the data or software directories don't exist, put them in the build # directory (they will remain empty, but this helps in simplifiying the # mounting command!). - if ! [ -d $data_dir ]; then + if ! [ x$data_dir = x ]; then data_dir="$build_dir"/data if ! [ -d $data_dir ]; then mkdir $data_dir; fi fi - if ! [ -d $software_dir ]; then + if ! [ x$software_dir = x ]; then software_dir="$build_dir"/tarballs-software if ! [ -d $software_dir ]; then mkdir $software_dir; fi fi @@ -703,7 +703,17 @@ steps. chmod +x docker-run ``` - 8. You can now start the Docker image by executing your newly added + 8. Start the Docker daemon (root permissions required). If the operating + system uses systemd you can use the command below. If you want the + Docker daemon to be available after a reboot also (so you don't have + to restart it after turning off your computer), run this command again + but replacing `start` with `enable`. + + ```shell + systemctl start docker + ``` + + 9. You can now start the Docker image by executing your newly added script like below (it will ask for your root password). You will notice that you are in the Docker container with the changed prompt. @@ -711,7 +721,7 @@ steps. ./docker-run ``` - 9. You are now within the container. First, we'll add the GNU C and C++ + 10. You are now within the container. First, we'll add the GNU C and C++ compilers (which are necessary to build our own programs in Maneage) and the GNU WGet downloader (which may be necessary if you don't have a core software's tarball already). Maneage will build pre-defined @@ -735,7 +745,7 @@ steps. source ~/.bashrc ``` - 10. Now that the compiler is ready, we can start Maneage's + 11. Now that the compiler is ready, we can start Maneage's configuration. So let's go into the project source directory and run these commands to build the software environment. @@ -746,7 +756,7 @@ steps. --software-dir=/home/maneager/tarballs-software ``` - 11. After the configuration finishes successfully, it will say so. It will + 12. After the configuration finishes successfully, it will say so. It will then ask you to run `./project make`. **But don't do that yet**. Keep this Docker container open and don't exit the container or terminal. Open a new terminal, and follow the steps described in the @@ -759,13 +769,13 @@ steps. docker image list # In the other terminal. ``` - 12. Now that you have safely "committed" your current Docker container + 13. Now that you have safely "committed" your current Docker container into a separate Docker image, you can **exit the container** safely with the `exit` command. Don't worry, you won't loose the built software environment: it is all now saved separately within the Docker image. - 13. Re-open your `docker-run` script and change `MANEAGEBASE` to + 14. Re-open your `docker-run` script and change `MANEAGEBASE` to `MY-PROJECT-ENV` (or any other name you set for the environment you committed above). @@ -773,7 +783,7 @@ steps. emacs docker-run ``` - 14. That is it! You can now always easily enter your container (only for + 15. That is it! You can now always easily enter your container (only for the software environemnt) with the command below. Within the container, any file you save/edit in the `source` directory of the docker container is the same file on your host OS and any file you @@ -787,7 +797,7 @@ steps. ./docker-run ``` - 15. In case you want to store the image as a single file as backup or to + 16. In case you want to store the image as a single file as backup or to move to another computer, you can run the commands below. They will produce a single `project-env.tar.gz` file. @@ -796,7 +806,7 @@ steps. gzip --best project-env.tar ``` - 16. To load the tarball above into a clean docker environment (for example + 17. To load the tarball above into a clean docker environment (for example on another system) copy the `my-project-env.tar.gz` file there and run the command below. You can then create the `docker-run` script for that system and run it to enter. Just don't forget that if your diff --git a/project b/project index 9d4d6df..ac801b8 100755 --- a/project +++ b/project @@ -34,6 +34,7 @@ jobs=0 # 0 is for the default for the 'configure.sh' script. group= debug= host_cc=0 +offline= operation= build_dir= input_dir= @@ -184,6 +185,8 @@ do -e*|--existing-conf=*) on_off_option_error --existing-conf -e;; --host-cc) host_cc=1; shift;; --host-cc=*) on_off_option_error --host-cc;; + --offline) offline=1; shift;; + --offline=*) on_off_option_error --offline;; -i|--input-dir) input_dir="$2"; check_v "$1" "$input_dir"; shift;shift;; -i=*|--input-dir=*) input_dir="${1#*=}"; check_v "$1" "$input_dir"; shift;; -i*) input_dir=$(echo "$1" | sed -e's/-i//'); check_v "$1" "$input_dir"; shift;; @@ -455,6 +458,7 @@ case $operation in export jobs=$jobs export debug=$debug export host_cc=$host_cc + export offline=$offline export build_dir=$build_dir export input_dir=$input_dir export scriptname=$scriptname diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 1a81ef1..01ef8c8 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -15,53 +15,53 @@ # Basic/low-level programs and libraires (installed in any case) # -------------------------------------------------------------- -bash-checksum = 2ce67af3ff6b6c9d87b2e98986da937ee100a4cecefd50f01ccdbaeb53e45ff80b1e84d5861619dd3058259223a1f0748e5850aa2dab13b3350fb8a955c3024e -binutils-checksum = 028c64a9ac34def97ddb4ead355776999c4e3376857e865c536ed74593292437f5bd2049c036a506129f596ba78898b0cefec5c677b6cd76e7d18dfac9c64a33 +bash-checksum = 52fa7d14e5f05d7b1b5f64ca110388db119fd6b8d4cc25011e0e25848491507e610259091c56f3ca7a7688ee2547f8a98de2005626b35c29558e71f28e29b848 +binutils-checksum = efbc5957bd22804a860261886598778347e82f9cbc0728d21d26748b7296e34328fdc16252868169594a001a301babbcd0964d9c508523736bc79cac2aff8efc bzip2-checksum = 929cb1b2d0db8a505e2bafe3ce2c893c8f132dd617c0110e86e19f116b570a85de3c8a635483b530456fc8f8b6698c8190d21313e47607f442807b10489ac86e -cert-checksum = 25b689ebac01ebde136bcef1ef4aa18389fcc618375755001f153b37060cfb327fd6d6afac25d4ddfcf78fd6678fa00ce49ba688e725e4a4c657c37cba4ec3ca -coreutils-checksum = 887ca0ea9e6918c9e959033e625537335902a118af8384a050bbdfadf1c7fa30a92521dd4d9714055d869c1619c20f0f6bcecb89a99f22278a74668b393a5cf0 -curl-checksum = 9158e35f1f8bee8236df933b0011bc1865bcf10182725b9578824abbfa9cc4dc1e468ab97a5c30bb791cba23e224e395189a6a70b314a500dac1222e4bf21908 -dash-checksum = 794290f8270f05a134966088af5a7f5abd5c7a06e7057108aa49ad18af43643a038cd926192b81cfc9169d9d419b03c9e815483936bbaf102fe7a462f84f358d -diffutils-checksum = 597cd0a14087722b78469e2238fcee25e78108f53ca43fbff1194d87625b4c7498a205f68c7bb44fcd437b8d642bba263ac40170780aede006076b11956fd06e -file-checksum = 22acda3d760fa19f94c67086ae5ea8243afbc896be10d3905b92610fe58cdc5954ce4f6756a2cc2a2c241572c37a56b4d6813b14a37f51d718314c6dc9b201fb -findutils-checksum = 8f1887781e3f97aec1144dbda6da9590489ffb7dd28e47a5c574c0382398988f015a6f4364b90a66a9e35b3c0e79d8a71c573402b3f95f7f9482f2d47687a4a9 +certpem-checksum = d1198511bf1f61a624691c182ecdd57ff468030a4af8b0f0ef248a5ce1f42ed883c684fc5aafdd791d5d3aa24504fbfbab11043231594b1c4e21fdb7247e5a33 +coreutils-checksum = 2afaee98b305f000ab1c9e25b5fec6413c3e385c685f2afe94e3676593c09efca39d007cfda2b3b122e68e94204d2ebe7f50b39300899d8720518d6f74bce019 +curl-checksum = f391f696d725ace63271fe614ab3067b8d55d04be3a160c70bbca388de93670e5fb986dd5dd45e1b62c0327b2b1374ab229bdb5c9df746f70823e0721c9f048d +dash-checksum = f21a2ac71606a5ae8dbda5639d111f385cc44c357c580a83e453b33faa32c92fd83f8ca6c5d2cf720343f8ab1cfec247ca499596f78ee19f62d67cd1d7ae0c69 +diffutils-checksum = 52582c860a4ce544f0c1a3e61bd9a1ce5f13e1c677b67d3713982439760e40b60267b222de3ef0a27065652822d9880a206899528d7ff8d60c7e64b64721b3e1 +file-checksum = b843b3c25656e8dec52e64eed6f581b29faf36540e0604a803d61c0f0eca830a01a947b81970b0d8a24a1336a37ae5c96bb2ade59daa16c544b1e82fc7db24e8 +findutils-checksum = 826c643e7f5c5d6976a47eabcd9807e51350d09ee8fc7dc931f2d9276f938f65aa0bd97e6213aa979742234784c120e1a6850a52207c327e1c1a465feb374053 flock-checksum = f711815035e21b46572bf80e730a55822e5abf4cb29749e476ee6cf4d5027e9a7deeacf5f6b8c37f18f17a0cc7a6d98fb0be3936e97b122707f1cb2306d1e1d9 -gawk-checksum = 60a9fb36e57c0819576f5b2e48b0cf82210dd0cc45f65529c15d53ae66f8d0674929434bd7ed6fa4beaafc81c6b0ccd8c56d21b5326f7b03dcf958cafca03c3a -gcc-checksum = be8a7e21fb7ee3be80b814708d6ffb63093fa103a51eb736b3717ac506ed4afcc7571bfe0d475f072e82bed439225d20c07e5d1bbf449a9bc4e10b82e4d8dead -gettext-checksum = f3083af79341bfdc849118333c1598812c12bc225d998181694648187088050160deb4777c252f72a7158e914c2967416489bc6167ef8505664497f2fb94ecbf -git-checksum = 2ade8fe6e9bbc88ebfe72348b13e7c68acbd066dfd6bcdd0de4949ec22aa25d02246efb25e7a7868eef1739c8e8cc7bb73c4caffe0060046bbf738f601eac2a7 -gmp-checksum = 2bec8840bceaeac542ce1f7870d5b971b631b055b49751ba4f78f98229d7eb9cd97c0a668f6d7cf81a53bf0b3d5d70e682af523f8f0eee0d7390727ff2bbb271 -grep-checksum = e8c28da23fcef11825c54794b3eebffd0eaf84b7ebf5e187fd06b5d4aeff2af1ac097f0166151b3f11f332dc72abf6097188d578f549496f4c7c96ccf479a61e -gzip-checksum = 43bfed5da4f376f9ee295fb505648e364bd85d38c22f0de79024e5fd2b7e341f7fef8fed0d49a0f0484164fb5c6ce02b1b1951891807bc2b50e1a3e8f7990548 -isl-checksum = e257c19d861da6615c0be303bd8800d5e1a1c71595126da573c7a8d91fea6c41b9cacc2378caf5272949c6719c8835584a6c7fd05246bf4ffe56031543f648e3 -less-checksum = 31f733ecf4170b4f5dcf467b902d0753833f852739b03bf611137aea3672c03e00e9418fd5e289e82624c2dd42b0de06cb65a7a637dae78e7647e5c6ecf9fb57 -libiconv-checksum = 01e1b073ae6a82320d8759c973ca27c217377f2afd7a27f52f944d1d6e9079e407a7a4d2352f6b38541e49a85cb27dd39ce2f5f74f44ff42775901cda72e1159 -libtool-checksum = e0bdf6194e77beff0273a487b6345a0707addf1c7f57c35663550c5ef6f41dfcadaaac9df30ada639f5c066fa17a4ce7155bbfc0c920e1a1eadd55dae8183754 -libunistring-checksum = f1e92717fc043c2d7c454e44700559b0bd75457fdf3da5e803d9d58d8ebdff261bc73f380f6350bb04ce04071687c0317d09b4e8615003187948be1cd4d0bab3 -libxml2-checksum = 0fdc16aa7536adfe1deaadd19cdc20101dd3b081bd0a2e59d8ecc2965b2ef4c30d2e2447ab5b0cdb861c57ddb89ace1bd4ce120d9436b751b37724a90981ba8c -lzip-checksum = 9b18ab9b7ef9a7d1c2da06b48fd018399e94405a5ada457885b778c59caa3faed0e73e1da398516621dc9e721587785b57ef1f8a12c1b0e116ebce5129f0f24d +gawk-checksum = 13cb59a4ef43e5b0d10f13263dcf5ccd72d9344f3ecc512589ed7f6d059baf8a5ae375d38f7654695e29f0694fc33deba3c7c008d61f09e67df57bf81e573f0c +gcc-checksum = 40f239730fc0165a0ef48f252a886e9cbe7a95ed53fe2c7a16531d7f3d6faabecb2d868cc895a25f7561e7bb90892e3372652953efd8ac35359a6ac2e18a4447 +gettext-checksum = c53f3a09cbb62a3ba8870f1310da336c084bfc83534d7e9c236f7660f503d638654a91301558f1e4880ead2d629dcd92f7c3dd7e0d981d445b74215d836d19ea +git-checksum = 6e7ac2188cf3204fceeebffc46f34a8180e53a887987a8e1b9d6c90f84073e4b86d45f39488f69432b1cd0962cd8fbd434c07128fc2e430cd2ec20f1a1fc8b61 +gmp-checksum = ad65de00ecb46cf454ed6c40d2a57ce2528f5fa64df1284dfa15036f1e8cf27760a09a4ecdfcc39048faffb71339bba30d99dd365c54173dbc2ba629bee2fad9 +grep-checksum = b1ad850671290120ca0ced6d1744622d99a903c6e638dd231e89a70a2ab48c382100e218697b6fbbbda8c99316679a7c681383a5e954790bbffb9719bd0d6d8e +gzip-checksum = 19ef6f51ee8274c08aa188ebd26634a40f91c057ff1ad3253719a7fa0c7ac857de5cf289990e0b9fc67d89ca3abb50db6dbaa7664d2c58275c844712834d5e10 +isl-checksum = 615827a86e809c9645e090786008f8b37d7efc7fee6501ff81e937a299a5a72e7998a3965457d1380cb04f7e765b600276d87b7b59cae22d82aa65e71294f499 +less-checksum = 3b52347e1b779a52c89cb18da85a0963eed500e1e94cd3952c0693c56fd0eec4e8606eb02053d451ac92ec8c6e196edd1341eac54515ed84483112513f41f210 +libiconv-checksum = 1f33fcf7f617990812a26e15092dbb2f9e81400cee117eefd40ade813f7ca17c0b9a50a7a9881b4ab0b9c0be8475528204c347d940cbc667a918570e0bde051a +libtool-checksum = 2aa6d535b4d644393d7ca5c8f174b09923dbdb50d947ba40917aad75c8cecf957fec7a54717bd3670c44130331b1f08fae3694e32c79c8e187c31e909b3d401b +libunistring-checksum = 6ca6a2dea2c09b6e8e63eb7ff73ab62b2e2f7c412766209c9f6da5b13a109e3a7cb41e67aaee1fb2b46549965b7df13c508000e40594570abe71819dc9cc2eaf +libxml2-checksum = 7c2c65ae5017be5d695ec5a0e9bf443fe130d33beec97f31bcdbe74c22ac7745ce02524ca603e701035576bdca91c4cb1cbe67ccad5525f9a4566451a8f0c935 +lzip-checksum = 513b7ecdee1d6f12298cbbb025286c887c5e6588e1268b489735955f822a8e305e7a8d4d06054a77b2f4c40f8d82e9e6d779cd73d4227ca3cdfe4002b9e42a98 m4-checksum = 7f8845f99e64d6a45859b9d80b03352a5526b3de0311ca4d6dd6850e504d26dfc90cd21d1640b10382f786213f8fdf20183bff424b3c41ea11432315993ab829 -make-checksum = ddf0fdcb9ee1b182ef294c5da70c1275288c99bef60e63a25c0abed2ddd44aba1770be4aab1db8cac81e5f624576f2127c5d825a1824e1c7a49df4f16445526b -mpc-checksum = 85e044749c2a001a70af2c11fc4bac58709ca7df11bf6da3b03cca852ef336eb37c4fb1dafdffde2d13df35caa7c296a7cba19a4625b82dc3cccc5066ac95774 -mpfr-checksum = 23a30040511809b6a8ed33d5ef83f903e987f0e4b8e87c9bfa627fdf0ca6400330bda4fd727cf1d37f04f7804c77663ed983c6b5ed26f5d5bd772bf13f1f9eb5 -nano-checksum = 0995899c5bae17411461870d5a5fc61da43679938cd2bf909ae96a0e3ecd3f47319f57397983ef53abe076c34147ec77eb87de0167ce17d1933fddd95983e0a9 -ncurses-checksum = 68b7c0388304791ce82ab86ea5c5725357f07bbae0c230af3e4722f75617778b6e28d1f0c1d65871379670e54fcc96ecd54f529a3462d207f3d930e6dad5a2dd -openssl-checksum = 722588b8d9f8b7a1c607475f441c47a7097b12f1885a471767424c7509103589a9e2647b5da35f5218fac6edee5c7946e4f2eb6962b434b14142330cf7403ef1 +make-checksum = 154a0247297a7b0131ff63fa8636d651b33aacc8f4a0dad1db176995b20c2039f4fd58eeb2ec27cc0ca7a95c1853199a4ee35a14afc5084995ecc1d694203412 +mpc-checksum = 76e0720e6287d8b7a3eaa09dc5baa5a2b61dde88198c9e1bc9c458a268a44035d11fbab1c8019501a7ee2d5745c7eddfb0bb3c7297110a0fd9e027acb42d0fc3 +mpfr-checksum = c6013b0f573271a3bc41bc3eb28c61f099c6fc5409096a27624b5ec049e6305a1c48275c6f244d0cbe1fe65f649704c7d5f6487ad24308f6b3becc17032fc222 +nano-checksum = e559c09057ff75cd650f02744dff801750a159785234189e48f976bb4ab90142aca2577a283f80d8eecdc4f2b6c0a55bfe6da69e6aaecc5812f32f923075ca9c +ncurses-checksum = c94eccc1b23a9c6ca9b27881674b19802942802cf21084bd80e45e0b9e50a2d99e0e18a1ecd5cf3e686949982ca93132a7fe2f117a7c4307283db5012b11a2d5 +openssl-checksum = c4c44ab8e4a6d39e6aa69b096a831645c33d5675619d31da6e441452f67e487489b33041a34038a0f8ad596506e17ce8695a8f87bae861700481ecf6b9742b76 patchelf-checksum = f74409c00e7e50a88590267fa0c173f71239f1471985792f7bcdab750d202a9a25383c015987608bbcd6ace5b3642645d46dba63199ba54fabbcb51ae7fca8f6 -perl-checksum = 0cb49a0891ed0b8963093556af232b424d97eea5af659b00a6781c1de446da730a318c5d75d1d8cb7d7572cd4adb1423e4b9019bad96aa17da0de28a19f36399 +perl-checksum = d53da403f2232b487f11df4b0b889babf58350715c7430515ba32e2e7d9996308c5d75ee626906a9f3c56872672c9cfe3880e10c7bb084c178c7c76bb2a5346f pkgconfig-checksum = c37ab9336ac15a73bf5a23101f3fd8a04810f39b0679634e420e5d7bbd60a80cfc919122694cf83965beb071d2780681efc8d954ce99d77eb235a4dc7497e250 -podlators-checksum = c653205fd1e8e570750584cdb3a813a1250ae6f66d4e654b3521b80052867a3a6ba15ad3d7c8a22065f1febc36175257f9b5685570fcf0a87908c2dc9d42cb3d -readline-checksum = e7afacba7da0ec0f98c5cfd1a25873a1803c1beee9f8b2bb603844415466e9406512b69e1624412be3a48dc49ed048433599b0f9693986a5253debbc5631e0ae -sed-checksum = 90d8fa16b2570baee061c128d6db688a3354796a6499014f12dc4c5966b34cbb8a04a47914e4ff8dc1815444ad0235565efef2a327b67c485e3324c2a1d07d78 -tar-checksum = 98d938d76a55dca1d1ba9a13f1aa2a3e8ae25ea422843e93daab98d373f4a72eebf052c88c87122ac16ed629863dc3fdb86dddf18d3ab5a2565b06f49b7d02bd -texinfo-checksum = 6a706bd0f973b9bbe4fdbc3bfd475cc9699eb410d276cbc19a73255924313006e1b80a87803fa30f7245e3fcb610c829da31e38c91e791e19f11ca8b998914c4 +podlators-checksum = 2e1e8547b0c890101a9fb8d80807b164a0a708820617a6826127930f85115285a0e4d62ddf8ce2401df14c021521a1b3ce0cad0d308e08f7b3d0c49d1b0dd36f +readline-checksum = ca08305c5a6d5eb6656a7cdff73aab65c1234de62db8da90335e9ea140b1d4f8a867204bdc49ead3acc5e5236358130e73032bd73de5dfe1eee5bb2c76be5cb2 +sed-checksum = e801dacce45a08671e65897f85be0a37a29d97f61e846ca17ff870d3ab9f5a639dba73457491087ff637df4a81099b864d2496d59acf17a07916b43bfe0ae480 +tar-checksum = f8d0b543dc4a2a57d61d8a183d7a64d611d11f033c64683f022a7f1f956d352d364a959903a2549ab1256c1a068de51052960cf34a70f355b80e237f654bfac7 +texinfo-checksum = 06e7d95d73380c16f064e119bd8717942fb464c1cbc532fb1833d2d5dfc3cbbcab2a9001a1d03721c347f676e1db22c2a0f78d19d22df379d0393527be411ef3 unzip-checksum = 5c1f3c417d5feed64b8c5dbc26b51dd84130b9ea43d77e810cc9e82cee6e965fa76e2636e5ba11a029eae3454a815a6081cc2828079fa3994c511d555b82f12c valgrind-checksum = a99e09e6d957ce435e64f4ce7b1a14e7e266282578171ce4e3bb3f405ce304e4df3b43d2fca59a6024c176f60c2ac82b3992afc810386e8de03c72f262b32702 -wget-checksum = cbce817981864d4dc424b330126b0d06231907004f1fcfc8d105ffc043bab59e93421738d36cf95013cc03b5b9f9813b1c242a3ef3926a907889ca78dfb336d4 -which-checksum = f886f5828359584b204f20a3b712d29c14879288e6255ab612784fce167bc9467c246bf48f9c52780069a95fe25761c3edda358428893967f4a1a1e5e874b2d5 -xz-checksum = a92bc2619f668a9e462945423035a090bc91c010d0788db8fb300851a3f93c04af2d433bc545195979d51312f59667c5814e46dd711b67fa8f89c0864873b81c +wget-checksum = 75ba60150baf673def8ff5f2688af57d89d699f1b5105cb1a6bc0ce88778be191c74757665d773ac84fdab975851ca9015b30f12f31877fd752500efb49e0034 +which-checksum = cbda59450d35c2fa04f9072db43584ff745844cdb129bce1a382eb50bcd19815f0bbf12f2b03f748cb3f585acf0a16eb2e661b71f9066469236d28e9fa40f168 +xz-checksum = d897a55ae5ee7d778c68edff83c53e6624619f233acd529439fade305681d07b7665ba1d370cf84abb38c7f3f8f88c3d127974c4f59667843814211802501080 zip-checksum = 433eda6a27074746a960952fa3b08028d5ba43fe976a1306dbace9209be5f89aa0554b17bba5815cd00984c0f64559c5fa0b754b620f6d646a2b145a8b599acc -zlib-checksum = 97493906504451830655b300b4144deeeb9f41bdb9b3f3a3d5635c2b16bf90d543841dc70d028f1cee6b52ad1c604fdc18b18f559d1e4ed6523e6b3ce76fd8c5 +zlib-checksum = 8f0b28c7d0d5d1906c2c03586f4ad3188a7c7eb73d25295a7acaa88cdf87b7c82ac609282b9b12d2b4d5a368169e4bb5f88ba3b840b57e1cf32c78f2ee3ecd86 @@ -79,44 +79,44 @@ apr-checksum = d0ddf8b10dd8d3a831b94e541d387414cc4d507ad48ff752d3274fb808afe6628 apr-util-checksum = 6589948e3f9daf4ecd700bdbd2053fcb83005cec9d339278dda067996ba696e4a947116f066cee03214458aa15e0cb6f0df0103e7bc6f8f32327722eb7265f35 astrometrynet-checksum = 33bf92ec1d5aad50525739f5afb3abd2abe27c8b0cce35a6923831b7b7c35930cb6f14425df47c60dc5561cd27b4af55ea6ccdabaa2d444c81a6c86c7ef9629c atlas-checksum = 13634a63c686800bef8affcf4e8f5f89d08f485fc557eb1b9ba51a405926014e659e439268f655984bb7f59ffe497d594cd7a607103826f1046325d89796e1b0 -autoconf-checksum = daf3d17178d8c2d0f872a50217ba4d8a1481bad7e70ee5a58c5599717a01209cbd58e6149c72f6c4829b96dcf602bcfb828d47e32a9cfe3e5710c45f4f1736e7 -automake-checksum = 728284b89ab4607b5de5db6b8bf5ad8730cbd8ac094f583b93bb92c59dee35e021e823cddd412b0507b18a12cbbbfbec0fb0447c23d0afd167769641fe0755e5 +autoconf-checksum = 99edec992950b85f7709323247772d1ec0f6ebfd2b066d83af65e856e8ab2facfab257f43d316fc5a8905fec0ce3c24768afd2873a1b85c795c8c120ae5f9277 +automake-checksum = f4b6485c7358554860b370d587bb5cd6c6c1050529eceb2bb0a0aecd408347405b3d1aa2c63e4a0aa38dc394178ea1e05599f1b5b6951c0e3d8f2f85639ffc71 bison-checksum = 08c3e9bcf9fc01bc8b3a6c5e5f8ecdf628e07d6ce0874341e9df6d7b2925db7720a29b3be9a98d644f05a9e55e1130e5d182cb764e1481891414df93aeb2794f boost-checksum = cc7b78311538d6e8a6849d58da3b4d3062dc6b816f91a06b86609e6f1538d87ef9308c27af4db7a644e7c8e2b3de73c9f011a739e75262a0f36affdc313947f3 cairo-checksum = 5de8528196b450d01da5cd4562dec0dd8c31028b77640b6c611172f7c5ad1dc9a4d30bd4e38259344c3ee42b979e29be702a3190aae5fbf47c82c79ee0c14a8e cdsclient-checksum = 24584eedeb84ab4666cbd2ed0b7264c92c63c9cf090595b75b01dd46f848419d6a7e5cff4db3946695f879d0ee2bfbeb527e88c2be85e769b577302d9b2ad2b7 -cfitsio-checksum = 18dcaec9907c0d6d09c28a1238b0ab1425268aa6c83ca163a2ea8df404cc8fcaa5b9a5b17ed585d415d56ee9a2647b0cfcd6e03da91a1a2f75cf0db530287270 -cmake-checksum = 7587ff2bc7f0d75e4a19798081d13f10545fc49fdf06e913fd1606db2056204471f3536c0e2c46924013c4d64ff1f4e0422eff5dd6b911bce65c01e8510d24be +cfitsio-checksum = fd40e0cec22bf3a35a7c48ad61a6ebad5a54d3230606c7492161c067b7ccd303ed34d149427bf1d3365e7a3082d89b51df46fc8a9c3d3c0b1eef8756374d711e +cmake-checksum = 3904964eeb256ae4443d000a24ebdbfd76c677aec08d006f8665020f1ebf2008c65b6a1cffd6fb5b8a29cdb52420415ed2e0e2ea258db2e9888dc48068fc3941 eigen-checksum = 39c1944e0daca50bb01e929edc98e2bfc234accb30ca019dcccfc7b02db5cc81035592be219ae93cc3ec16fe0255e7e4d1f29ca2ad3dfee7e63546c47cb2f807 emacs-checksum = 91313dced8cd74f9e4a996eef42806aad00fb2576fc77b3694bb7b670624b6a1551ff49c2a3326dbeeba916e5732ca5975b5dc40b3b063f6e73a22839009abe9 -expat-checksum = 526f2ec03978f853ff76a911b5a168f58a7eac83b8405536afe2a6acf4611ebcb96acbc5df809fd18e4edeb7ca5059a3ce56dcbd12cb33eecf742c6361d83d19 +expat-checksum = c006dff4ee90ee3722df94ef227cfaab3ee4ebf7ee8193a65b904798b4d185e89c863c75a1e8eae9c120bfbf79336c1e31a8b6aa3042f4131b9a1eb0e97c6643 fftw-checksum = 28bd2f620399a415181027d30d7ea193aa487c7a277c9943d0051488908fd87e2731de0dfc3bebd22a6121d1deaa46037be8296a8a9cdb711f9fde4510c3d368 flex-checksum = a18e0dcdd21bd51779fd70e5efc2d77fa7b2a56d4d0e929d8abb437f86d7fcfa2cd09b8268185698200866dac8bec4444c5a7cff3140c515eaa49fc77c5aea66 -freetype-checksum = b3c7289cda3f89fa6e51143f2d1f1c82fa34808d0caa9262e7be5498c8f0fdb14e88d31ec9928e3add71f03208e40adb2fa94c2a4b4c6b7bfb81daf64b1578cb +freetype-checksum = fb2d89421633a56d4276b192106d930c9f29cf2b70c52d9e13ba0c6a2679b6f69c20ab9f14480522992c263b493f198f24593bdeddb5806a4d801ab7604a5926 gdb-checksum = 4afd6660d2bbc4c48ce726062fb42217bdaa5974774407358b2624036a2ace48ed853746e4d6b83b9a409cd8fefc622b0727c79da8826e28e3d1444fa3a9d148 -ghostscript-checksum = b8ca229c118bd29f0fadb87a65975011d793d8245652eb7e2d2cc1c0e90be1d545b0bfc216703766e35aedd096a1c3ddb6ad9ed8d3c71efa0a9f9904a524e903 +ghostscript-checksum = 2d6422d434cbe6612d4e995022322e17d0167d0d92fe1f6fe122da73558a81fa43025458411e38363a0e30a573cbc6cf997ae7aa562501787d0af88bf1b5b387 ghostscript-fonts-gnu-checksum = d8de17e5d920bd3803ecdc07aca224fa5b9a26db847ddae0ecc79488dc3e867ab3155a8565f20df7855e5228bc7f36a549b082ba0b8b56c9b948d6cfb655fdc0 ghostscript-fonts-std-checksum = 40e01f88dd113c3120686c11da1c4cf4ee77c8db315b21cc936c3ccfb42cad4949e207298ec6d78d03327ff05122fcd75ac82d5e7cdc9698d4bbf1f72b19756a -gnuastro-checksum = 3af26ab271d0015642e7290c96899f433c24ae93685fff3dddcef697acf590981da03a7c598b01f31ff042ec99fc4e4759a5622af73bb6ee989c3c2060be7936 +gnuastro-checksum = d27399993ab65d1864c915fe107efb298c758e1f24e3f300830f8f120768dd3a54daea1d2af5537e9dd3b50a13a51edd237f434bfbb442ab992828b2dab1386a gperf-checksum = 854cdb24337f14b0d4199cc97c4a1d2ec7f953ad8125a47a932d93f79bdc067e2de231859ac0e842f14b1a8d80c5606fdc2c295a370df5e85ea15023b478805b -gsl-checksum = f9b92ef783d922f97fa40e934314648c627002e0b5c8067e6ca9b691cfacd6363efe68216db75ae1a093053c7aa6b56fda2769bd2e10b2c3a373339d7a0fc9c5 +gsl-checksum = 9a46b431eed536182f31e1ecad781ade214ac8bd885ac88bbfd02b6e08482c294775a529e561d358c1f0211d8d20db4ec99b448b9006c3bf7599c076d3fbbcc3 hdf5-checksum = 58d6d9a1c201efa0863d9c31d189b4d40b1a9b1fb1ab9cb3fdeb4463f508c043e467aa4d44484c2af111d4e2fb775223286da69568774e6edef285208290c67b healpix-checksum = c11949e92aae9919fd41de91cbab72beffe2519c1203ab153ba217c6b6c81f2c10ceb07b683da0d04fb53ef5c80a9b208bdbb5379f379b7da9d0611d2430cc8e -help2man-checksum = 94346bed1c6b4f41384a216af55464ee142a47c40fa9d2dcc8bd86a4ecd64afb4ee7c1a06efbc9c6c7f4f275936dc21840ead193a8cc45840808d6d361be5e3d +help2man-checksum = 83dca38c2020c85a66da882cd994b4e291eb6a0584149b7b3a74fec1444399ec5ecfc6296080fbc34071cd9f8ec5c931e249fde1f755c7f40930cecafb3efab0 icu-checksum = ab14b52a3fdf2dcde6b5160ab7218eac381b850d3c278324379741c49d71fa6040fbacca94c6937e6c9fc15843761121deff302ca6854da5ca1cd5b26a34e839 imagemagick-checksum = 2132614540b7422c9772fcebe7e8e358994efcfb53d8e48fa52992313b09b191847e395bad305322c377a4697014353bb8c15adc4edfd712e038504fc7f17c5e imfit-checksum = 15edd2349232c1c8e611b31d3a46b0700112d274515f54d0a0085bb4bfa6d3d5f8a15cd926516e043a29ce841accf3534ae58dbfb952d858dc9445199c957096 lapack-checksum = ff670e194a1d8c998f05e6143e01a09e6b43176c511217ea3c77742afd9f2566251c50fc23aeb916442401f7118c1d1fe21f0172382a7f4f2c516c1d7d873e24 libbsd-checksum = 5c7d98474000af1271a36ab769e54aba41578e0b0f06e47af2986d6821b6586ac430ec04cc51b7836823834dd9d0aec9f4ab3af088b94f963b89729fa2cc95d8 -libffi-checksum = 6a4d46567512c3ce69a11c8d01fa0397cf653ea6207b5a86192a52367006f0f27fc08b9ae3559ef45da69433c7c39818199b29ac06bc2c7dc0fafefe7ae7b32d -libgit2-checksum = 7db8792f4280c484e324aa0f862714cd2ff3ea5c93aaf6953b08f9f2d7423e742d78f6fad11b5e5823747c81188e12432f247ee99dfaf331e4ce293713904ab2 -libidn-checksum = 8606bbdacc48b7fd572104896615acf0ca88f7c11a60c9eafc2ddb8477110a1f62c5684dbd5adf45b6417d9fc04a46add26052f63e464a81b3f4192443d13447 -libjpeg-checksum = 420397a802d81aac7c093aa056bd306f4c617a1deaa42b75179b9497da90568d560624e5423675030fcade69fa2cbca5203060e9fe9f0ef67e5025926b2e1dbc +libffi-checksum = 027416da7066bd36ac0c9ed8228693e5eeeb5e11dc17afcd7ed7faa66a9e57f505e94dffaf18f8978e6b40964938d4289aa3b5fe8778abe8fb97a68138b8b120 +libgit2-checksum = dd8a2acb214a2f6ba05a0a51a05fa7c04e09f482fe166a6d74f072c8335f23a1bbd3358395c3fa6cbb0811369940be26e3463f9c8fe48d70fce062b69ac996b2 +libidn-checksum = 0ffb80ca195ef0b1b4aec7bb45499d64fbf6b45eb0f68c4ea83193148dc3e761a0098d996722c2ac6e54f18d25057fa8c54b55a9d15593924eb733a30cf8137c +libjpeg-checksum = 312b0abf986dc937d57dad31b49472258cb6175f9dbc8796a67ed0971a4410bba40d87fae136e42677521dc14df376771982f9acdccf5143ac7edc9d2e91a34d libmd-checksum = a598b61dcbd7c3daf25a4affccfcdb2f6d58a0d2057b4f24e8fb92cddbeb0d62f1f5e3dd55195dd83be405d187184a331ea080b936b6c336ad4271be03b0beb0 libnsl-checksum = a3c8f674357674b7ed4b26c05adde607f39be8d6dc9ff715448e1fcc5fc23d11fbb4ce85a6e493b79bdb0bb450dc3ffb1fb480715779f738d7bc016fae91621d -libpaper-checksum = e1f37dfbbcc467c2269e228fa71893fd6c4738e1fd6cf24ce6e2ded568cfeeed80da097e51e833aa48e4ab9e1be0a5c75f9f4cf8bf2f050214c85013e9c24043 -libpng-checksum = 8bf8aaccf4b9efe15a18f0c7a0a6a942eba7bcdbaf61313f50af7e04a237ccc12f380b53ed88e5efa2d20b13f1a0f9f365b6bd7824d32350b3b3d9c6fa63eef6 -libtiff-checksum = 4e0da3df4b853f2017d99f23c5ed83d9f0d20743ce4caaf2ab915fa2d392858a7a74f91b1fd8a00055d1e82e26a5eb165aec6411709ea66478dce16062ccb93e +libpaper-checksum = 8532e5e95b53e0dcb2b2c4c161d3840a34087b5870d449950a853dc312a4016fb1443851385ddfaf4196ad3b2d431e0d861efe82e1a0442392c435c4455acd76 +libpng-checksum = c4eff9a427302c6f228b93a5a6b74d1e667439ce77f20c086d91ec6efa932a0e7f5752b976f4af5cd07574c5e4999c86e2b9cae3e82cc448ee61f3d0dde9253d +libtiff-checksum = 72ce12ce317ab2a5c188d3aeb575004eacf890dcb2729e9cb46f73c15cde2132624b4e229539af01626e59ea6a4a7380b4b5f90d5fecad787197b8b901615d20 libtirpc-checksum = bcb6b5c062c1301aa1246ec93ae0a5c1d221b8421126d020863517cb814b43ed038fb6c0c2faf4e68ff133b69abefe4f4d42bfc870671da6c27ca941a30b155a metastore-checksum = ac1230686535a652e95024abaf6c5585bdab36f4e092bee5fa4deff2a913cd60f3a6bd8020c6887ccab97f0da3a284a0d4619fad5464a269e7b2040d6f7e6aaf missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795 @@ -128,7 +128,7 @@ patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187d pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb pixman-checksum = 333732b99994f7ea636d647e0b6123075351b27601b5b6370c9bc821a1ab3921386ddb92b51e015f3fc35104ba09be1e0d7bef47f0b4f73036b01d1d70396dd9 plplot-checksum = 2c5a36d84ebd948402c924d304427b5702bc75bdd22753c9b3b910b382dfdcc26910382aae452f02d86b25c1c813bbe1f40c9305de1d2809d575975f610fdf10 -python-checksum = b3d6b4187b31167b382e195037d7ca01d5e9c112fceb0f12a30c101dbcc91079601c01aa449f9d33d2fc53c795c33305e80c891e986a0e24cbecc14beaf90199 +python-checksum = de940d7eceee69b8a04f12c613753f61db53ddac1c5cde5388dd342e88a09bae8da1f56b71b96f20997f6203d169e92e9e2558c43b38dbc323221d7bb362abfc r-cran-checksum = 54cc07956a70c09b5a533188eb063d2a9dc67a8aa5648ec7f9c107f626220c9f6e17ab7175e65dd54a8d608a1ca4106c8ad2856709eb995ab66439b5f033e725 rpcsvc-proto-checksum = c3011d7d7ef97a4a751f6921df1a23e1dd8ac50fb0690c759d37010ed7be27968a2130e3b8872cb48d5914216f9d539096a424f1ec38a75f7ed899748151c6f4 scamp-checksum = c7a192f357c6808acd16d1c5d2657c5c8c2f61e4fecb8a4b18d39b07f4c444f85d5029c21571d41ec3ba9c8d075de8bd660b0e029bf5dd63e3819e963430a938 @@ -137,27 +137,27 @@ sextractor-checksum = 4035710f9b8a20a0bb1a3913dab2dadd8444c179bf6dee425e0e8bb66a swarp-checksum = 810af6ea0a2dfc7b78b0f6aaa486b80c29f517b90c29f5037d05f31f761e96a55c8b5dcc259e1b435b25f45f01dac45ddba61da84000a69676cce119880bb05d swig-checksum = ecb1d940f584c23df036a8f77288916003f861851dfdf836ddc5bc45b95312f9259150084191c1d9f086c006e64e12a4db22f7ea382fbb71667b811b8f99995d tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108 -util-linux-checksum = 5f2534266a71cf61373d5b79f5a130191a06e5a3cc025982747be0d336b7ff60bded56cb1e0b42705f01dbd3ff8634928760554c53fef10045e68775c945854f +util-linux-checksum = 9d421976a344f982f2bd910f0c888a7df4370a1e367c7d2582d03a58cb8500f1fe65cf6a7164c492a9ebd76bff04560c344b3a0f63ecdb372bfea2379b383030 vim-checksum = 85d083fcf3638f2c3a049b88da46d569d6a250ae132f3821d440c07c4792befffc09e4235241ca96d7b0307a1bb96cd2222ac8a63fb41c6add8c2bdc6c17aabb -wcslib-checksum = f2ee5b0b6aa8e6ef2923a85d0213e7d66c54b6cdee5c6843abc97436b699215479815db2766ae76af1f1bd6eef4f46cd8510dd87bae8272a4a7c770c32ab7535 +wcslib-checksum = cc72804611df1b0087faed2ec19edbc17352cc631559edc8ceb03792162837cdaa6bbf144897c69a58c9fab7e569a1958149be7eaea6552d72190406e4755d12 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02 # Xorg related packages -fontconfig-checksum = 4786b8419bdead24fe16cdb152b898d2676a59c534fd301f02e5343fd4fe54780fea06521e7c0bf45b794dbb08b0f17359eb5c6f1fe4e31d71dfd952c8fa3da2 -libice-checksum = 9e3488abaff115ac919e5df85479044579802b38a10597425e13466c22c149ef56a8adba77e2adbbcccb8d2e72e23976313f4af3dcee66128b768c971c513932 -libpthread-stubs-checksum = a99695c007e17d81879d5c113652c5e1edab2d63aac9b2984c4f334d85e2cebc1d0b4e8134d6196ed8eea4d4da41972fca27bb8a0c76c2946460f785233a2c03 -libsm-checksum = b9eec391f0438e85e32cf771afbb35bf215119ec31d9e31be40c1b653f2c3e894c2d19add0d6ff69e944d1230f681275e8abad86a8912ec37c1c41e0f1ce4d00 +fontconfig-checksum = e71c684ffcc75015b1aa13918d6598a213b926630317e4babf876fc503e0444ed3211277080a08505cc26da033ee8e673bf5e246cb9d75d2fbe18a43160a0dad +libice-checksum = c38b5f14d8ac92c5c2507f4369a70c5e2738ee547765ea7a160fc6a0ebc217deb042bad65e16b76a1874ebd131eacc5f53e9630bded5ae1805a7c4c61ff5f357 +libpthread-stubs-checksum = 7895a95e4674fb0c4f206abf744818f58272597f0dd84480a1a217cb4358ff413d153f5e13f748867904e104cf26c43ff8d59a33e0f0a7cfaa81ee21d5d847fd +libsm-checksum = 7b03a81ae81704ed97426e596849ec1209771f6ca4db296aedd7a698750b586cd56d149690922686c52c64c1c582672474fce00816dddca2c90ad9bded51a269 libx11-checksum = c5ee35af06a90bfa0e9c5f42feea9887c5beb88960a7658f8465524a360e400a5640e5dcda741549d7ecf470e7142d3728a32659e12f95a316203655a408db42 -libxau-checksum = bdca8935aa1a52bcd2748004d26c7405725c18021a4d9a67604c98c1ec3957cc85b5d987d2fcd9fa4ae5e59b6bbd6ab75712beee2d448bd733a7e3ffeb18e62f -libxcb-checksum = 85effa5ac6c158df2affbe1a9085ebd2c52ddceaa8d972035afaea2a1f1d3031357bac2586237438cfc20a51468e620b0ff8775d057446ce2ef0768d947e9f25 -libxdmcp-checksum = cb1d4650f97d66e73acd2465ec7d757b9b797cce2f85e301860a44997a461837eea845ec9bd5b639ec5ca34c804f8bdd870697a5ce3f4e270b687c9ef74f25ec -libxext-checksum = 58f4e87f200bfde2b9a2cd85c1c39d5462b702e12274ffa5fae5bd3a08b3dfab1290b399c31224c86627d927106e4dbfcdec6152c11b169834442008228796d4 -libxt-checksum = 9ec0f95ae073360ea7a80ffca2dcd998c991363b79696550c4f88edf2c9cbf740caca23929660b77fffca4ca292465a101398e9e891cd00db85f8eceaa78cde0 -util-macros-checksum = b29c388c60b8318a478656f0552210b2194ee302c082f694e5426ac5c3f4b97fc3e377cd6a7b2b97c3da3442cfb4a5e42dbae18e151ae39f5f84554016a01155 -xcb-proto-checksum = b1e2c12c9d66e729815e782af47cfd50ede4c771fe0d0607a423a3bcddfb5f2fdf5c8b58b17cfccf508104cf5ad6cc05be8bad5f96807538322050ecd65fa320 -xorgproto-checksum = 32852ca4d682207dd1399274714f26da6a995c3f4a20c3ef197e8dfd637f6782d4ce02cb8721ca0179e4618a585beacc53e74537869434dc3096d4ad47e10c26 -xtrans-checksum = 1c2fdd7cb906f012f7db5d42466734f89608bf3376b6bf4b115c2efbf71c4247587cc218ccfcfaa6d50f0cf336865d10fc604515b25bc6e95917db8acb7e3000 +libxau-checksum = db9c8ce453a650a493f83e30d4fa3b50aabaf01e98b5e24f666c32238f46a8c2c120cd18ac8fda447c3c7f9bf300f9e3a08a1cd2bd1c4ef4ace72a54cfb8243c +libxcb-checksum = e360337777e578c76251b793dc4e7e9203271f4dd0e1032abbc092f96fa228717fbb702965dff061264cca52f2540c983f4085fa486ced0145ebcc4b9e5b766a +libxdmcp-checksum = 3c25a8d37f2ea553ebadfd9d886592f9c181e7da0a73b5e7bc853f15f0cddbae39483e55dc417c47ed55b45b8401e633efcb02d692af715b1ec1549b75a67378 +libxext-checksum = 99b2dc7b1e65e78b3335138176a1031a8259820b60abe0ebc87b0c8cc1d3bc9f65aca8b43942811ff78b4e85640e0d4cd63b092423b1351daf32bc4109debf88 +libxt-checksum = 776457c702a8685cdda0c2c0b1d1c441f8e20513b89f83b031c3037ae132b56dec53027465c15b2c2d7d5dd0e6933840b5325de8a7242ef0daa76ae5f28016a5 +util-macros-checksum = a9facbdcf973bfb202832b57207731152e7d58ca4ba034b4de31b931256af55daa651d0463309bed5ad84ed892b19b319c919aab77c849e08deac083d1445529 +xcb-proto-checksum = ea92650cacf0a864381fa29ec5e0c9562435cdbd8604ada5639a79e6aa359b3ef0d7ad0a10c5b1599fa1ddd49d86fade4048526445a9525c2978fa984a34f7fb +xorgproto-checksum = 1b52be01bea4c22c0bd92ea073d1a11e08e9233e93e28d578a7cb247385f3a270b4fb4ce463cb853f3e1a9c6acb45da456e5f6caf4cfa7676a9e316e98bd22cc +xtrans-checksum = 84f1142994f93882c9c68a4a85a218290c1c979162dbd4c5ee6b6becf0f96b69685d292cae1793ce65db8d7f1fe3f8955499f4b2ced771081894921512e2e16a # Python packages # --------------- diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index a5998d5..b742fb1 100644 --- a/reproduce/software/config/urls.conf +++ b/reproduce/software/config/urls.conf @@ -20,7 +20,7 @@ #bash-url = http://akhlaghi.org/src #binutils-url = http://ftp.gnu.org/gnu/binutils #bzip2-url = https://sourceware.org/pub/bzip2 -#cert-url = http://akhlaghi.org/maneage-software +#certpem-url = http://akhlaghi.org/maneage-software #coreutils-url = http://ftp.gnu.org/gnu/coreutils #curl-url = https://curl.haxx.se/download #dash-url = http://gondor.apana.org.au/~herbert/dash/files @@ -62,7 +62,7 @@ #which-url = http://ftp.gnu.org/gnu/which #xz-url = http://tukaani.org/xz #zip-url = $(shell echo ftp://ftp.info-zip.org/pub/infozip/src/zip$$(echo $(zip-version) | sed -e's/\.//').tgz) -#zlib-url = http://www.zlib.net +#zlib-url = https://zlib.net/current/zlib.tar.gz # The version is in the tar @@ -111,13 +111,13 @@ #imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit #lapack-url = http://www.netlib.org/lapack #libbsd-url = http://libbsd.freedesktop.org/releases -#libffi-url = https://sourceware.org/libffi/ +#libffi-url = https://github.com/libffi/libffi #libgit2-url = http://akhlaghi.org/src #libidn-url = https://ftp.gnu.org/gnu/libidn #libjpeg-url = http://ijg.org/files #libmd-url = https://archive.hadrons.org/software/libmd/ #libnsl-url = http://akhlaghi.org/maneage-software -#libpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/ +#libpaper-url = http://ftp.debian.org/debian/pool/main/libp/libpaper/ #libpng-url = https://download.sourceforge.net/libpng #libtiff-url = https://download.osgeo.org/libtiff #libtirpc-url = https://downloads.sourceforge.net/libtirpc @@ -139,7 +139,7 @@ #swarp-url = https://www.astromatic.net/download/swarp #swig-url = https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version) #tides-url = http://akhlaghi.org/maneage-software -#util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.35/ +#util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.40 #valgrind-url = https://sourceware.org/pub/valgrind #vim-url = ftp://ftp.vim.org/pub/vim/unix #wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib @@ -158,6 +158,7 @@ #libxdmcp-url = https://www.x.org/pub/individual/lib #libxext-url = https://www.x.org/pub/individual/lib #libxext-url = https://www.x.org/archive/individual/lib/ +#libxt-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 #xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index e8b8542..07bdb9e 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -17,51 +17,51 @@ # -------------------------------------------------------------- # # CLASS:BASIC (important identifier for 'awk'; don't modify this line) -bash-version = 5.2-rc2 -binutils-version = 2.39 +bash-version = 5.2.37 +binutils-version = 2.43.1 bison-version = 3.8.2 -coreutils-version = 9.1 -curl-version = 7.84.0 -dash-version = 0.5.11-057cd65 -diffutils-version = 3.8 -file-version = 5.42 -findutils-version = 4.9.0 +coreutils-version = 9.6 +curl-version = 8.11.1 +dash-version = 0.5.12 +diffutils-version = 3.10 +file-version = 5.46 +findutils-version = 4.10.0 flock-version = 0.4.0 -gawk-version = 5.1.1 -gcc-version = 12.1.0 -gettext-version = 0.21 -git-version = 2.37.1 -gmp-version = 6.2.1 -grep-version = 3.7 -gzip-version = 1.12 -help2man-version = 1.49.2 -isl-version = 0.24 -less-version = 590 -libiconv-version = 1.17 -libtool-version = 2.4.7 -libunistring-version = 1.0 -libxml2-version = 2.9.12 -lzip-version = 1.23 +gawk-version = 5.3.1 +gcc-version = 14.2.0 +gettext-version = 0.23.1 +git-version = 2.48.1 +gmp-version = 6.3.0 +grep-version = 3.11 +gzip-version = 1.13 +help2man-version = 1.49.3 +isl-version = 0.27 +less-version = 668 +libiconv-version = 1.18 +libtool-version = 2.5.4 +libunistring-version = 1.3 +libxml2-version = 2.13.5 +lzip-version = 1.25 m4-version = 1.4.19 -make-version = 4.3 -mpc-version = 1.2.1 -mpfr-version = 4.1.0 -nano-version = 6.4 -ncurses-version = 6.3 -openssl-version = 3.0.5 -perl-version = 5.36.0 +make-version = 4.4.1 +mpc-version = 1.3.1 +mpfr-version = 4.2.1 +nano-version = 8.3 +ncurses-version = 6.5 +openssl-version = 3.4.0 +perl-version = 5.40.1 pkgconfig-version = 0.29.2 -podlators-version = 4.14 -readline-version = 8.2-rc2 -sed-version = 4.8 -tar-version = 1.34 -texinfo-version = 6.8 +podlators-version = 6.0.2 +readline-version = 8.2.13 +sed-version = 4.9 +tar-version = 1.35 +texinfo-version = 7.2 unzip-version = 6.0 -wget-version = 1.21.2 -which-version = 2.21 -xz-version = 5.2.5 +wget-version = 1.25.0 +which-version = 2.23 +xz-version = 5.6.3 zip-version = 3.0 -zlib-version = 1.2.11 +zlib-version = 1.3.1 # Version-dependent build # ----------------------- @@ -78,7 +78,7 @@ bzip2-version = 1.0.8 # '/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 +certpem-version = 2025-02-10 # PatchELF # -------- @@ -107,38 +107,38 @@ apr-util-version = 1.6.1 apr-version = 1.7.0 astrometrynet-version = 0.91 atlas-version = 3.10.3 -autoconf-version = 2.71 -automake-version = 1.16.5 +autoconf-version = 2.72 +automake-version = 1.17 boost-version = 1.77.0 cairo-version = 1.16.0 cdsclient-version = 3.84 -cfitsio-version = 4.1.0 -cmake-version = 3.24.0 +cfitsio-version = 4.5.0 +cmake-version = 3.31.5 eigen-version = 3.4.0 emacs-version = 28.1 -expat-version = 2.4.1 +expat-version = 2.6.4 fftw-version = 3.3.10 flex-version = 2.6.4-410-74a89fd -freetype-version = 2.11.0 +freetype-version = 2.13.3 gdb-version = 11.1 ghostscript-fonts-gnu-version = 6.0 ghostscript-fonts-std-version = 8.11 -ghostscript-version = 9.56.1 -gnuastro-version = 0.18 +ghostscript-version = 10.04.0 +gnuastro-version = 0.23 gperf-version = 3.1 -gsl-version = 2.7 +gsl-version = 2.8 icu-version = 70.1 imagemagick-version = 7.1.0-13 imfit-version = 1.6.1 libbsd-version = 0.11.3 -libffi-version = 3.4.2 -libidn-version = 1.38 -libjpeg-version = 9e +libffi-version = 3.4.7 +libidn-version = 1.42 +libjpeg-version = 9f libmd-version = 1.0.4 libnsl-version = 1.2.0-4a062cf -libpaper-version = 1.1.28 -libpng-version = 1.6.37 -libtiff-version = 4.4.0 +libpaper-version = 1.1.29 +libpng-version = 1.6.46 +libtiff-version = 4.7.0 libtirpc-version = 1.2.6 metastore-version = 1.1.2-23-fa9170b missfits-version = 2.8.0 @@ -149,7 +149,7 @@ patch-version = 2.7.6 pcre-version = 8.44 pixman-version = 0.40.0 plplot-version = 5.15.0 -python-version = 3.10.6 +python-version = 3.13.2 r-cran-version = 4.1.2 rpcsvc-proto-version = 1.4 scamp-version = 2.10.0 @@ -158,33 +158,33 @@ sextractor-version = 2.25.0 swarp-version = 2.41.5 swig-version = 4.0.2 tides-version = 2.0 -util-linux-version = 2.38.1 +util-linux-version = 2.40.4 valgrind-version = 3.18.1 vim-version = 9.0 -wcslib-version = 7.11 +wcslib-version = 8.4 xlsxio-version = 0.2.21 yaml-version = 0.2.5 # Xorg packages -fontconfig-version = 2.14.0 -libice-version = 1.0.10 -libpthread-stubs-version = 0.4 -libsm-version = 1.2.3 +fontconfig-version = 2.16.0 +libice-version = 1.1.2 +libpthread-stubs-version = 0.5 +libsm-version = 1.2.5 libx11-version = 1.8 -libxau-version = 1.0.9 -libxcb-version = 1.15 -libxdmcp-version = 1.1.3 -libxext-version = 1.3.4 -libxt-version = 1.2.1 -util-macros-version = 1.19.3 -xcb-proto-version = 1.15 -xorgproto-version = 2022.1 -xtrans-version = 1.4.0 +libxau-version = 1.0.12 +libxcb-version = 1.17.0 +libxdmcp-version = 1.1.5 +libxext-version = 1.3.6 +libxt-version = 1.3.1 +util-macros-version = 1.20.2 +xcb-proto-version = 1.17.0 +xorgproto-version = 2024.1 +xtrans-version = 1.5.2 # Version-dependent build # ----------------------- lapack-version = 3.8.0 -libgit2-version = 1.3.0 +libgit2-version = 1.9.0 # Netpbm's questions in the configure steps maybe change with different or # new versions. diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 68c40b3..628a0e2 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -774,7 +774,7 @@ $(ibidir)/openssl-$(openssl-version): $(ibidir)/podlators-$(podlators-version) \ # First download the certificates and copy them into the # installation directory. tarball=cert.pem-$(certpem-version) - $(call import-source, $(cert-url), $(cert-checksum)) + $(call import-source, $(certpem-url), $(certpem-checksum)) cp $(tdir)/cert.pem-$(certpem-version) $(idir)/etc/ssl/cert.pem # Now download the OpenSSL tarball. diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 2274c45..fdab193 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -118,11 +118,16 @@ else endif +# Disable the TeXLive target if `--offline` +ifneq ($(strip $(offline)),1) + target-texlive := $(itidir)/texlive +endif + # Ultimate Makefile target. all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \ $(foreach p, $(targets-python), $(ipydir)/$(p)) \ $(foreach p, $(targets-r-cran), $(ircrandir)/$(p)) \ - $(itidir)/texlive + $(target-texlive) # Define the shell environment # ---------------------------- @@ -433,11 +438,14 @@ $(ibidir)/cfitsio-$(cfitsio-version): # Continue the standard build on the customized tarball. Note that # with the installation of CFITSIO, 'fpack' and 'funpack' are not # installed by default. Because of that, they are added explicity. +# +# Note that older versions of CFITSIO (before 4.4.0) require a +# specific 'shared' target for the building of the shared libraries. export gbuild_tar=$(ddir)/$$customtar $(call gbuild, cfitsio-$(cfitsio-version), , \ --enable-sse2 --enable-reentrant \ --with-bzip2=$(idir), , \ - make shared fpack funpack) + make fpack funpack) rm $$customtar echo "CFITSIO $(cfitsio-version)" > $@ @@ -921,8 +929,8 @@ $(ibidir)/libgit2-$(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)/libgit2.1.3.dylib \ - $(ildir)/libgit2.1.3.dylib + install_name_tool -id $(ildir)/libgit2.1.9.dylib \ + $(ildir)/libgit2.1.9.dylib fi echo "Libgit2 $(libgit2-version)" > $@ @@ -1156,7 +1164,9 @@ $(ibidir)/ghostscript-$(ghostscript-version): \ --disable-cups \ --enable-dynamic \ --disable-compile-inits \ - CFLAGS="-DPNG_ARM_NEON_OPT=0" + --disable-hidden-visibility \ + CFLAGS="-DPNG_ARM_NEON_OPT=0" \ + LDFLAGS=-Wl,--copy-dt-needed-entries # Build and install the program and the shared libraries. make V=1 -j$(numthreads) @@ -1642,7 +1652,10 @@ $(ibidir)/swig-$(swig-version): # '$(ibdir)'. If any program does need 'util-linux' libraries, they can # simply add the proper directories to the environment variables, see # 'fontconfig' for example. -$(ibidir)/util-linux-$(util-linux-version): | $(idircustom) +$(ibidir)/util-linux-$(util-linux-version): \ + $(ibidir)/autoconf-$(autoconf-version) \ + $(ibidir)/automake-$(automake-version) \ + | $(idircustom) # Import the source. tarball=util-linux-$(util-linux-version).tar.lz @@ -1663,18 +1676,20 @@ $(ibidir)/util-linux-$(util-linux-version): | $(idircustom) git apply util-linux-$(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. +# 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'. sed -e's|UL_BUILD_INIT(\[mkswap\], \[yes\])|UL_BUILD_INIT(\[mkswap\], \[no\])|' \ -i configure.ac +# Having updated 'configure.ac', we need to re-generate the +# './configure' script with 'autoreconf' (which is part of Autoconf +# and needs Automake; hence why they are dependencies. + autoreconf -f # Configure Util-linux export CONFIG_SHELL=$(ibdir)/bash @@ -1682,6 +1697,7 @@ $(ibidir)/util-linux-$(util-linux-version): | $(idircustom) --disable-dependency-tracking \ --enable-libmount-support-mtab \ --disable-silent-rules \ + --disable-liblastlog2 \ --disable-mountpoint \ --disable-libmount \ --disable-unshare \ diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk index deeccf2..43e2e77 100644 --- a/reproduce/software/make/python.mk +++ b/reproduce/software/make/python.mk @@ -106,13 +106,17 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version) # libraries to link to and those are blocked at this level). So we # need to add an extra line on top of the 'os.system' funciton and # put '/usr/lib' in 'LD_LIBRARY_PATH' within Python's environment for -# system calls (with 'os.putenv'). - awk '{if(/os.system\(/) \ - { print " os.putenv(\"LD_LIBRARY_PATH\", \"$$LD_LIBRARY_PATH:$(sys_library_sh_path)\");"; \ - print $$0;} \ - else print $$0}' \ - setup.py > setup-tmp.py - mv setup-tmp.py setup.py +# system calls (with 'os.putenv'). As of Python 3.13.2 the tarball no +# longer has an 'setup.py'. But when it did, the change below was +# necessary. + if [ -f setup.py ]; then + awk '{if(/os.system\(/) \ + { print " os.putenv(\"LD_LIBRARY_PATH\", \"$$LD_LIBRARY_PATH:$(sys_library_sh_path)\");"; \ + print $$0;} \ + else print $$0}' \ + setup.py > setup-tmp.py + mv setup-tmp.py setup.py + fi # Do the basic installation and delete the temporary directory. ./configure SHELL=$(ibdir)/bash \ diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk index 3f99fab..864c32a 100644 --- a/reproduce/software/make/xorg.mk +++ b/reproduce/software/make/xorg.mk @@ -79,7 +79,7 @@ $(ibidir)/libxau-$(libxau-version): $(ibidir)/xorgproto-$(xorgproto-version) # Library implementing the X Display Manager Control Protocol. $(ibidir)/libxdmcp-$(libxdmcp-version): $(ibidir)/libxau-$(libxau-version) - tarball=libXdmcp-$(libxdmcp-version).tar.bz2 + tarball=libXdmcp-$(libxdmcp-version).tar.lz $(call import-source, $(libxdmcp-url), $(libxdmcp-checksum)) $(call gbuild, libXdmcp-$(libxdmcp-version),,$(XORG_CONFIG), V=1) echo "libXdmcp (Xorg) $(libxdmcp-version)" > $@ diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index 857f3b5..f226ced 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -1612,11 +1612,11 @@ fi # which will download the DOI-resolved webpage, and extract the Zenodo-URL # of the most recent version from there (using the 'coreutils' tarball as # an example, the directory part of the URL for all the other software are -# the same). This is not done if the option '--debug' is used. +# the same). This is not done if the options '--debug' or `--offline` are used. zenodourl="" user_backup_urls="" zenodocheck=.build/software/zenodo-check.html -if [ x$debug = x ]; then +if [ x$debug = x ] && [ x$offline = x ]; then if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \ | sed -n -e'/http/p' \ @@ -1723,6 +1723,7 @@ fi on_mac_os=$on_mac_os \ sys_cpath=$sys_cpath \ host_cc=$host_cc \ + offline=$offline \ -j$numthreads diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh index e12ff98..09e1c89 100755 --- a/reproduce/software/shell/tarball-prepare.sh +++ b/reproduce/software/shell/tarball-prepare.sh @@ -159,12 +159,19 @@ for f in $allfiles; do name=$(echo $(basename $f) \ | sed -e 's/.tar.*//' -e's/_/-/') + # Lzip will not be available to unpack Lzip itself, so just use Tar. + if [[ $name =~ ^lzip ]]; then + outname=$name.tar + else + outname=$name.tar.lz + fi + # Skip previously packed files - if [ -f $odir/$name.tar.lz ]; then + if [ -f $odir/$outname ]; then # Print the info message if not in quiet mode if [ -z $quiet ]; then - echo "$scriptname: $odir/$name.tar.lz: already present in output directory" + echo "$scriptname: $odir/$outname: already present in output directory" fi # skip this file @@ -206,19 +213,26 @@ for f in $allfiles; do # Put the current date on all the files because some packagers will not # add dates to their release tarballs, resulting in dates of the # Unix-time zero'th second (1970-01-01 at 00:00:00)! - touch $(find "$name"/ -type f) + # -print0 is needed for those tarballs that has paths with spaces. For + # the same reason it's needed also `xargs -0`. (`xargs` is needed also + # for large tarballs such as gcc's) + find "$name"/ -type f -print0 | xargs -0 touch # Pack with recommended options tar -c -Hustar --owner=root --group=root \ -f $name.tar $name/ - lzip -9 $name.tar + + # Lzip will not be available when unpacking Lzip, so we just use Tar. + if [[ ! $name =~ ^lzip ]]; then + lzip -9 $name.tar + fi # Move the compressed file from the temporary directory to the target # output directory - mv $name.tar.lz $odir/ + mv $outname $odir/ # Print the sha512sum along with the filename for a quick reference - echo $(sha512sum $odir/$name.tar.lz) + echo $(sha512sum $odir/$outname) # Clean up the temporary directory rm -rf $tmpdir -- cgit v1.2.1 From a55a407c1f2a1b280be78f24abd1fe6d4a8032e2 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Thu, 13 Feb 2025 19:27:57 +0100 Subject: Configuration: new server for tarballs and portability fixed SUMMARY: no change is necessary for your pipeline after upgrading to this commit. Until this commit, the following noteworthy portability problems existed that have been fixed as described in each item. - In commit 8908587 (titled "IMPORTANT: 73 software upgrades and added offline mode"; committed on 2025-02-11); the versions of all (except those that were not updated upstream) basic software as well as the high-level software necessary for Gnuastro were updated. This included Python. However, the update of Python could cause crashes in the Python-related software that are also in Maneage but not tested for that commit. -- With this commit, Python has been revered back to 3.10.6 (from 3.13.2) and it has been taken to a dedicated part of 'versions.conf' (reminding the reader that the version of Python should only be updated by the Python maintainer: to ensure it doesn't conflict with Python-based builds). - Following the update of XZ Utils in 8908587, the custom build recipe that was necessary is no longer necessary. This was reported by Boud Roukema (see https://savannah.nongnu.org/bugs/index.php?62700). -- With this commit, XZ Utils uses our basic high-level build scripts. - CMake could use out-of-Maneage libraries for those that we already had in Maneage on some systems. This was reported by Boud Roukema (see https://savannah.nongnu.org/bugs/?63043) -- With this commit, CMake is built with '--no-system-libs'; so it builds and statically links to all its necessary libraries internally (not confusing between Maneage and the host). - Building Binutils 2.39 was likely to fail on older GCC versions due to special features (such as the 'gprofng' feature when building with GCC 6.2.0). This was reported by Boud Roukema in https://savannah.nongnu.org/bugs/index.php?63242. -- With this commit, the 'gprofng' feature of Binutils has been disabled by default to allow reproducibility on older systems. If you need it, remove the '--enable-gprofng=no' option in the build recipe of Binutils. - The Maneage tarball repository is now also kept in 'gitlab.cefca.es'. -- With this commit, a new server URL has been added for this. - The list of TeXLive packages included some packages that get installed in the basic scheme that we do for the initial setup of TeXLive. -- With this commit, the extra packages have been removed. --- reproduce/software/config/checksums.conf | 2 +- reproduce/software/config/servers-backup.conf | 2 +- reproduce/software/config/texlive-packages.conf | 18 +++--- reproduce/software/config/versions.conf | 5 +- reproduce/software/make/basic.mk | 77 +++++++++---------------- reproduce/software/make/high-level.mk | 33 ++++++++--- reproduce/software/shell/configure.sh | 11 +++- 7 files changed, 78 insertions(+), 70 deletions(-) diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 01ef8c8..130c116 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -128,7 +128,7 @@ patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187d pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb pixman-checksum = 333732b99994f7ea636d647e0b6123075351b27601b5b6370c9bc821a1ab3921386ddb92b51e015f3fc35104ba09be1e0d7bef47f0b4f73036b01d1d70396dd9 plplot-checksum = 2c5a36d84ebd948402c924d304427b5702bc75bdd22753c9b3b910b382dfdcc26910382aae452f02d86b25c1c813bbe1f40c9305de1d2809d575975f610fdf10 -python-checksum = de940d7eceee69b8a04f12c613753f61db53ddac1c5cde5388dd342e88a09bae8da1f56b71b96f20997f6203d169e92e9e2558c43b38dbc323221d7bb362abfc +python-checksum = b3d6b4187b31167b382e195037d7ca01d5e9c112fceb0f12a30c101dbcc91079601c01aa449f9d33d2fc53c795c33305e80c891e986a0e24cbecc14beaf90199 r-cran-checksum = 54cc07956a70c09b5a533188eb063d2a9dc67a8aa5648ec7f9c107f626220c9f6e17ab7175e65dd54a8d608a1ca4106c8ad2856709eb995ab66439b5f033e725 rpcsvc-proto-checksum = c3011d7d7ef97a4a751f6921df1a23e1dd8ac50fb0690c759d37010ed7be27968a2130e3b8872cb48d5914216f9d539096a424f1ec38a75f7ed899748151c6f4 scamp-checksum = c7a192f357c6808acd16d1c5d2657c5c8c2f61e4fecb8a4b18d39b07f4c444f85d5029c21571d41ec3ba9c8d075de8bd660b0e029bf5dd63e3819e963430a938 diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf index d4aa25e..f0e040e 100644 --- a/reproduce/software/config/servers-backup.conf +++ b/reproduce/software/config/servers-backup.conf @@ -9,6 +9,6 @@ # permitted in any medium without royalty provided the copyright notice and # this notice are preserved. This file is offered as-is, without any # warranty. +http://gitlab.cefca.es/maneage/tarballs-software/-/raw/master/ http://gitlab.com/maneage/tarballs-software/-/raw/master http://git.maneage.org/tarballs-software.git/plain -http://akhlaghi.org/maneage-software diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf index bb38d5a..e68a771 100644 --- a/reproduce/software/config/texlive-packages.conf +++ b/reproduce/software/config/texlive-packages.conf @@ -5,14 +5,20 @@ # name). # # Copyright (C) 2018-2025 Mohammad Akhlaghi +# Copyright (C) 2022-2025 Boud Roukema # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and # this notice are preserved. This file is offered as-is, without any # warranty. -# Notes -# ----- +# Hints: +# +# - For debugging: after a partial or successful build, look through +# '.build/software/installed/texlive/maneage/tlpkg/texlive.tlpdb.main.*' +# to see what packages and files were looked at during the install. + +# Notes: # # - tex and fancyhdr: These two packages are installed along with the basic # installation scheme that we used to install tlmgr, they will be ignored @@ -22,31 +28,23 @@ # - fancyvrb: needed by R. texlive-packages = biber \ biblatex \ - bitset \ caption \ courier \ csquotes \ datetime \ - ec \ - etoolbox \ - fancyhdr \ fancyvrb \ fmtcount \ fontaxes \ footmisc \ fp \ kastrup \ - letltxmacro \ logreq \ mweights \ newtx \ - pdfescape \ - pdftexcmds \ pgf \ pgfplots \ preprint \ setspace \ - tex \ tex-gyre \ times \ titlesec \ diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 07bdb9e..861b5c5 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -149,7 +149,6 @@ patch-version = 2.7.6 pcre-version = 8.44 pixman-version = 0.40.0 plplot-version = 5.15.0 -python-version = 3.13.2 r-cran-version = 4.1.2 rpcsvc-proto-version = 1.4 scamp-version = 2.10.0 @@ -186,6 +185,10 @@ xtrans-version = 1.5.2 lapack-version = 3.8.0 libgit2-version = 1.9.0 +# Python should only be updated by the maintainer for Python packages; see +# https://savannah.nongnu.org/task/?16622. +python-version = 3.10.6 + # Netpbm's questions in the configure steps maybe change with different or # new versions. netpbm-version = 10.73.39 diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 628a0e2..cf155f0 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -273,46 +273,10 @@ $(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)) - -# 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 + $(call gbuild, xz-$(xz-version), static) echo "XZ Utils $(xz-version)" > $@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version) @@ -1247,7 +1211,8 @@ $(ibidir)/binutils-$(binutils-version): \ # Build binutils with the standard 'gbuild' function. $(call gbuild, binutils-$(binutils-version), static, \ - --with-lib-path=$(sys_library_path), \ + --with-lib-path=$(sys_library_path) \ + --enable-gprofng=no, \ -j$(numthreads) V=1) # The 'ld' linker of Binutils needs several '*crt*.o' files from @@ -1375,21 +1340,35 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # 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: +# GCC's build directory will become several gigabytes and the build +# also needs RAM. You can track the RAM usage of the system with a +# 1-second resolution (if no other RAM consuming program is running +# while building GCC) with the command below (example outputs can +# be seen in https://savannah.nongnu.org/task/index.php?16623). # -# https://savannah.nongnu.org/task/?16244#comment12 +# c=1; while true; do POSIXLY_CORRECT=1 df -P /dev/shm/maneage-* | awk 'NR==2{print '$c', $3}'; c=$((c+1)); sleep 1; done > mem-usage.txt +# asttable mem-usage.txt -c1,'arith $2 512 x 1024 / 1024 / 1024 /' -o mem.fits # # 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. +# POSIXLY_CORRECT=1, so the 'block size' is 512 bytes. In this way, +# to get the actual GiB amount, multiply the value returned above +# by 512 (B/block), then divide by 1024^3 (B/GiB). +# +# To get the final value to use here, get the maximum used value +# after GCC is fully built and you have stopped the 'while true' +# command above. You can do this with the command below (assumes +# you have Gnuastro). +# +# aststatistics mem-usage.txt -c2 --maximum | asttable -c'arith $1 7000000 +' -Afixed -B0 +# +# The extra space is because we will assume an extra 3 GiB = 3GiB * +# 1024^3 (B/GiB) / 512 (B/block) = 6291456 blocks are necessary for +# the building (let's round it to 7000000!). # -# So we need 8 GiB * 1024^3 (B/GiB) / 512 blocks/B = 16777216 -# blocks, in blocks of 512 bytes. +# Therefore, we need to make sure that the running system more than +# the necessary amount of space in the RAM. To do this, we use 'df' +# below. # # 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 @@ -1399,7 +1378,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # 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"}'); \ + | awk 'NR==2{print ($$4>26613216) ? "yes" : "no"}'); \ if [ $$in_ram = "yes" ]; then odir=$(ddir) else odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index fdab193..928d0a2 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -1098,18 +1098,28 @@ $(ibidir)/cmake-$(cmake-version): # SHELL=$(SHELL) and we have defined this script. export MAKE="$(makewshell)" -# Go into the unpacked directory and build CMake. +# Go into the unpacked directory and prepare CMake. cd $(ddir) rm -rf cmake-$(cmake-version) tar -xf $(tdir)/$$tarball cd cmake-$(cmake-version) $(shsrcdir)/prep-source.sh $(ibdir) - ./bootstrap --prefix=$(idir) --system-curl --system-zlib \ - --system-bzip2 --system-liblzma --no-qt-gui \ + +# Bootstrap, build and install CMake: +# - With the '--no-system-libs' option, CMake builds and statically +# links all the libraries it needs. Even though some of those (like +# liblzma, libcurl, zlib or bzip2) are within Maneage, we +# discovered that CMake can get confused and use out-of-Maneage +# libraries (https://savannah.nongnu.org/bugs/?63043). + ./bootstrap --no-qt-gui \ + --prefix=$(idir) \ + --no-system-libs \ --parallel=$(numthreads) $(makewshell) VERBOSE=1 LIBS="$$LIBS -lssl -lcrypto -lz" \ -j$(numthreads) $(makewshell) install + +# Clean up. cd .. rm -rf cmake-$(cmake-version) echo "CMake $(cmake-version)" > $@ @@ -1960,10 +1970,19 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf # Live itself (only very basic TeX and LaTeX) and the installation of its # necessary packages into two packages. # -# Note that Biber needs to link with libraries like libnsl. However, we -# don't currently build biber from source. So we can't choose the library -# version. But we have the source and build instructions for the 'nsl' -# library. When we later build biber from source, we can easily use them. +# Note that we do not build the TeXLive executables (like Biber) from +# source. So in case they need special libraries, we can't choose the +# library version here (for example see [1] and [2]). In such cases there +# is no solution but to manually add the location necessary library to +# LD_LIBRARY_PATH when calling the respective LaTeX command in +# 'reproduce/analysis/make/paper.mk'. Fortunately as of Biber 2.20, it does +# not depend on anything except the C library (all dependencies are now +# statically linked), so problems [1] and [2] will not happen. But this can +# generally happen for any other tool/OS, so it is important to build +# TeXLive from source as soon as possible [3]. +# [1] https://github.com/plk/biber/issues/445 +# [2] https://savannah.nongnu.org/bugs/index.php?63175 +# [3] https://savannah.nongnu.org/task/?15267 $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ $(itidir)/texlive-ready-tlmgr diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index f226ced..d58a829 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -1439,6 +1439,15 @@ fi +# Make sure the temporary build directory is empty (un-finished +# source/build files from previous builds can remain there during debugging +# or software updates). +rm -rf $tmpblddir/* + + + + + # Inform the user that the build process is starting # ------------------------------------------------- # @@ -1575,7 +1584,7 @@ fi # cause a crash! To avoid such cases, we need to find the locations of the # libraries that the shell needs and temporarily add them to the library # search path. -if [ x"$$on_mac_os" != xyes ]; then +if [ x"$on_mac_os" != xyes ]; then sys_library_sh_path=$(otool -L /bin/sh \ | awk '/\/lib/{print $1}' \ | sed 's#/[^/]*$##' \ -- cgit v1.2.1