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-rwxr-xr-xreproduce/analysis/bash/download-multi-try14
-rw-r--r--reproduce/analysis/config/INPUTS.conf2
-rw-r--r--reproduce/analysis/config/delete-me-squared-num.conf2
-rw-r--r--reproduce/analysis/config/metadata.conf2
-rw-r--r--reproduce/analysis/config/pdf-build.conf2
-rw-r--r--reproduce/analysis/config/verify-outputs.conf2
-rw-r--r--reproduce/analysis/make/delete-me.mk64
-rw-r--r--reproduce/analysis/make/download.mk26
-rw-r--r--reproduce/analysis/make/initialize.mk204
-rw-r--r--reproduce/analysis/make/paper.mk83
-rw-r--r--reproduce/analysis/make/prepare.mk47
-rw-r--r--reproduce/analysis/make/top-make.mk20
-rw-r--r--reproduce/analysis/make/top-prepare.mk20
-rw-r--r--reproduce/analysis/make/verify.mk40
-rw-r--r--reproduce/software/bibtex/astrometrynet.tex2
-rw-r--r--reproduce/software/bibtex/astropy.tex2
-rw-r--r--reproduce/software/bibtex/corner.tex2
-rw-r--r--reproduce/software/bibtex/cython.tex2
-rw-r--r--reproduce/software/bibtex/fftw.tex2
-rw-r--r--reproduce/software/bibtex/galsim.tex2
-rw-r--r--reproduce/software/bibtex/gnuastro.tex2
-rw-r--r--reproduce/software/bibtex/healpix.tex2
-rw-r--r--reproduce/software/bibtex/imfit.tex2
-rw-r--r--reproduce/software/bibtex/matplotlib.tex2
-rw-r--r--reproduce/software/bibtex/missfits.tex2
-rw-r--r--reproduce/software/bibtex/mpi4py.tex2
-rw-r--r--reproduce/software/bibtex/numpy.tex2
-rw-r--r--reproduce/software/bibtex/r-cran.tex19
-rw-r--r--reproduce/software/bibtex/scamp.tex2
-rw-r--r--reproduce/software/bibtex/scipy.tex2
-rw-r--r--reproduce/software/bibtex/sextractor.tex4
-rw-r--r--reproduce/software/bibtex/sip_tpv.tex2
-rw-r--r--reproduce/software/bibtex/swarp.tex2
-rw-r--r--reproduce/software/bibtex/sympy.tex2
-rw-r--r--reproduce/software/bibtex/tides.tex2
-rw-r--r--reproduce/software/config/LOCAL.conf.in4
-rw-r--r--reproduce/software/config/TARGETS.conf14
-rw-r--r--reproduce/software/config/checksums.conf315
-rw-r--r--reproduce/software/config/numpy-scipy.cfg6
-rw-r--r--reproduce/software/config/servers-backup.conf2
-rwxr-xr-xreproduce/software/config/software_acknowledge_context.sh4
-rw-r--r--reproduce/software/config/texlive-packages.conf12
-rw-r--r--reproduce/software/config/texlive.conf2
-rw-r--r--reproduce/software/config/urls.conf55
-rw-r--r--reproduce/software/config/versions.conf311
-rw-r--r--reproduce/software/make/README.md2
-rw-r--r--reproduce/software/make/atlas-multiple.mk4
-rw-r--r--reproduce/software/make/atlas-single.mk4
-rw-r--r--reproduce/software/make/basic.mk780
-rw-r--r--reproduce/software/make/build-rules.mk73
-rw-r--r--reproduce/software/make/high-level.mk881
-rw-r--r--reproduce/software/make/python.mk313
-rw-r--r--reproduce/software/make/r-cran.mk487
-rw-r--r--reproduce/software/make/xorg.mk33
-rw-r--r--reproduce/software/patches/README.md6
-rw-r--r--reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch37
-rw-r--r--reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch23
-rwxr-xr-xreproduce/software/shell/bashrc.sh6
-rwxr-xr-xreproduce/software/shell/configure.sh134
-rwxr-xr-xreproduce/software/shell/git-post-checkout10
-rwxr-xr-xreproduce/software/shell/git-pre-commit10
-rwxr-xr-xreproduce/software/shell/pre-make-build.sh30
-rwxr-xr-xreproduce/software/shell/run-parts.in4
63 files changed, 2481 insertions, 1670 deletions
diff --git a/reproduce/analysis/bash/download-multi-try b/reproduce/analysis/bash/download-multi-try
index 76eb859..994a8fa 100755
--- a/reproduce/analysis/bash/download-multi-try
+++ b/reproduce/analysis/bash/download-multi-try
@@ -6,7 +6,7 @@
#
# $ /path/to/download-multi-try downloader lockfile input-url downloaded-name
#
-# NOTE: The `downloader' must contain the option to specify the output 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.
#
@@ -20,13 +20,13 @@
# 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
+# 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'.
+# reason, you don't want to use a lock file, set the 'lockfile' name to
+# 'nolock'.
#
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -114,9 +114,9 @@ while [ ! -f "$outname" ]; do
sleep $tstep
fi
- # Attempt downloading the file. Note that the `downloader' ends with
+ # Attempt downloading the file. Note that the 'downloader' ends with
# the respective option to specify the output name. For example "wget
- # -O" (so `outname', that comes after it) will be the name of the
+ # -O" (so 'outname', that comes after it) will be the name of the
# downloaded file.
if [ x"$lockfile" = xnolock ]; then
if ! $downloader $outname $inurl; then rm -f $outname; fi
diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf
index b969945..936f5f9 100644
--- a/reproduce/analysis/config/INPUTS.conf
+++ b/reproduce/analysis/config/INPUTS.conf
@@ -36,7 +36,7 @@
# (including the file-name) that can be used to download the dataset
# when necessary. Also, see the description above on local filename.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 13068e4..4df2101 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) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 aaf2ca0..0241136 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) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 015bf2e..a57b529 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 d96f293..37fc43c 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) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 c160e51..f4c8600 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -30,16 +30,16 @@
dm-squared = $(tex-publish-dir)/squared.txt
$(dm-squared): $(pconfdir)/delete-me-squared-num.conf | $(tex-publish-dir)
- # When the plotted values are re-made, it is necessary to also
- # delete the TiKZ externalized files so the plot is also re-made by
- # PGFPlots.
+# When the plotted values are re-made, it is necessary to also delete
+# the TiKZ externalized files so the plot is also re-made by
+# PGFPlots.
rm -f $(tikzdir)/delete-me-squared.pdf
- # Write the column metadata in a temporary file name (appending
- # '.tmp' to the actual target name). Once all steps are done, it is
- # renamed to the final target. We do this because if there is an
- # error in the middle, Make will not consider the job to be
- # complete and will stop here.
+# Write the column metadata in a temporary file name (appending
+# '.tmp' to the actual target name). Once all steps are done, it is
+# renamed to the final target. We do this because if there is an
+# error in the middle, Make will not consider the job to be complete
+# and will stop here.
echo "# Data for demonstration plot of default Maneage (MANaging data linEAGE)." > $@.tmp
echo "# It is a simple plot, showing the power of two: y=x^2! " >> $@.tmp
echo "# " >> $@.tmp
@@ -50,11 +50,11 @@ $(dm-squared): $(pconfdir)/delete-me-squared-num.conf | $(tex-publish-dir)
echo "# " >> $@.tmp
$(call print-general-metadata, $@.tmp)
- # Generate the table of random values.
+# Generate the table of random values.
awk 'BEGIN {for(i=1;i<=$(delete-me-squared-num);i+=0.5) \
printf("%-8.1f%.2f\n", i, i*i); }' >> $@.tmp
- # Write it into the final target
+# Write it into the final target
mv $@.tmp $@
@@ -71,11 +71,11 @@ $(dm-histdir): | $(texdir); mkdir $@
dm-img-pdf = $(dm-histdir)/wfpc2.pdf
$(dm-img-pdf): $(dm-histdir)/%.pdf: $(indir)/%.fits | $(dm-histdir)
- # When the plotted values are re-made, it is necessary to also
- # delete the TiKZ externalized files so the plot is also re-made.
+# When the plotted values are re-made, it is necessary to also
+# delete the TiKZ externalized files so the plot is also re-made.
rm -f $(tikzdir)/delete-me-image-histogram.pdf
- # Convert the dataset to a PDF.
+# Convert the dataset to a PDF.
astconvertt --colormap=gray --fluxhigh=4 $< -h0 -o$@
@@ -92,15 +92,15 @@ dm-img-histogram = $(tex-publish-dir)/wfpc2-histogram.txt
$(dm-img-histogram): $(tex-publish-dir)/%-histogram.txt: $(indir)/%.fits \
| $(tex-publish-dir)
- # When the plotted values are re-made, it is necessary to also
- # delete the TiKZ externalized files so the plot is also re-made.
+# When the plotted values are re-made, it is necessary to also delete
+# the TiKZ externalized files so the plot is also re-made.
rm -f $(tikzdir)/delete-me-image-histogram.pdf
- # Generate the pixel value histogram.
+# Generate the pixel value histogram.
aststatistics --lessthan=5 $< -h0 --histogram -o$@.data
- # Put a two-line description of the dataset, copy the column
- # metadata from '$@.data', and add copyright.
+# Put a two-line description of the dataset, copy the column metadata
+# from '$@.data', and add copyright.
echo "# Histogram of example image to demonstrate Maneage (MANaging data linEAGE)." \
> $@.tmp
echo "# Example image URL: $(DEMO-URL)" >> $@.tmp
@@ -109,8 +109,8 @@ $(dm-img-histogram): $(tex-publish-dir)/%-histogram.txt: $(indir)/%.fits \
echo "# " >> $@.tmp
$(call print-general-metadata, $@.tmp)
- # Add the column numbers in a formatted manner, rename it to the
- # output and clean up.
+# Add the column numbers in a formatted manner, rename it to the
+# output and clean up.
awk '!/^#/{printf("%-15.4f%d\n", $$1, $$2)}' $@.data >> $@.tmp
mv $@.tmp $@
rm $@.data
@@ -123,7 +123,7 @@ $(dm-img-histogram): $(tex-publish-dir)/%-histogram.txt: $(indir)/%.fits \
# ----------------
#
# This is just as a demonstration on how to get analysic configuration
-# parameters from variables defined in `reproduce/analysis/config/'.
+# parameters from variables defined in 'reproduce/analysis/config/'.
dm-img-stats = $(dm-histdir)/wfpc2-stats.txt
$(dm-img-stats): $(dm-histdir)/%-stats.txt: $(indir)/%.fits \
| $(dm-histdir)
@@ -143,17 +143,17 @@ $(dm-img-stats): $(dm-histdir)/%-stats.txt: $(indir)/%.fits \
$(mtexdir)/delete-me.tex: $(dm-squared) $(dm-img-pdf) $(dm-img-histogram) \
$(dm-img-stats)
- # Write the number of random values used.
+# Write the number of random values used.
echo "\newcommand{\deletemenum}{$(delete-me-squared-num)}" > $@
- # Note that since Make variables start with a `$(', if you want to
- # use `$' within the shell (not Make), you have to quote any
- # occurance of `$' with another `$'. That is why there are `$$' in
- # the AWK command below.
- #
- # Here, we are first using AWK to find the minimum and maximum
- # values, then using it again to read each separately to use in the
- # macro definition.
+# Note that since Make variables start with a '$(', if you want to
+# use '$' within the shell (not Make), you have to quote any
+# occurance of '$' with another '$'. That is why there are '$$' in
+# the AWK command below.
+#
+# Here, we are first using AWK to find the minimum and maximum
+# values, then using it again to read each separately to use in the
+# macro definition.
mm=$$(awk 'BEGIN{min=99999; max=-min}
!/^#/{if($$2>max) max=$$2; if($$2<min) min=$$2;}
END{print min, max}' $(dm-squared));
@@ -162,7 +162,7 @@ $(mtexdir)/delete-me.tex: $(dm-squared) $(dm-img-pdf) $(dm-img-histogram) \
v=$$(echo "$$mm" | awk '{printf "%.3f", $$2}');
echo "\newcommand{\deletememax}{$$v}" >> $@
- # Write the statistics of the demo image as a macro.
+# Write the statistics of the demo image as a macro.
mean=$$(awk '{printf("%.2f", $$1)}' $(dm-img-stats))
echo "\newcommand{\deletemewfpctwomean}{$$mean}" >> $@
median=$$(awk '{printf("%.2f", $$2)}' $(dm-img-stats))
diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk
index 0ea3432..e652c17 100644
--- a/reproduce/analysis/make/download.mk
+++ b/reproduce/analysis/make/download.mk
@@ -5,7 +5,7 @@
# recipes in this Makefile all use a single file lock to have one download
# script running at every instant.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# This Makefile is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -28,12 +28,12 @@
# --------------------
#
# The input dataset properties are defined in
-# `$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to
+# '$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to
# enable easy processing, so all the extra checks in this rule may seem
# redundant.
#
# In a real project, you will need more than one dataset. In that case,
-# just add them to the target list and add an `elif' statement to define it
+# just add them to the target list and add an 'elif' statement to define it
# in the recipe.
#
# Files in a server usually have very long names, which are mainly designed
@@ -48,7 +48,7 @@
# internet, therefore downloading is inherently done in series. As a
# result, when more than one dataset is necessary for download, if they are
# done in parallel, the speed will be slower than downloading them in
-# series. We thus use the `flock' program to tie/lock the downloading
+# series. We thus use the 'flock' program to tie/lock the downloading
# process with a file and make sure that only one downloading event is in
# progress at every moment.
$(indir):; mkdir $@
@@ -56,7 +56,7 @@ downloadwrapper = $(bashdir)/download-multi-try
inputdatasets = $(foreach i, wfpc2, $(indir)/$(i).fits)
$(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir)
- # Set the necessary parameters for this input file.
+# Set the necessary parameters for this input file.
if [ $* = wfpc2 ]; then
localname=$(DEMO-DATA); url=$(DEMO-URL); mdf=$(DEMO-MD5);
else
@@ -64,13 +64,13 @@ $(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir)
echo; echo; exit 1
fi
- # Download (or make the link to) the input dataset. If the file
- # exists in `INDIR', it may be a symbolic link to some other place
- # in the filesystem. To avoid too many links when using these files
- # during processing, we'll use `readlink -f' so the link we make
- # here points to the final file directly (note that `readlink' is
- # part of GNU Coreutils). If its not a link, the `readlink' part
- # has no effect.
+# Download (or make the link to) the input dataset. If the file
+# exists in 'INDIR', it may be a symbolic link to some other place in
+# the filesystem. To avoid too many links when using these files
+# during processing, we'll use 'readlink -f' so the link we make here
+# points to the final file directly (note that 'readlink' is part of
+# GNU Coreutils). If its not a link, the 'readlink' part has no
+# effect.
unchecked=$@.unchecked
if [ -f $(INDIR)/$$localname ]; then
ln -fs $$(readlink -f $(INDIR)/$$localname) $$unchecked
@@ -80,7 +80,7 @@ $(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir)
$(lockdir)/download $$url $$unchecked
fi
- # Check the md5 sum to see if this is the proper dataset.
+# Check the md5 sum to see if this is the proper dataset.
sum=$$(md5sum $$unchecked | awk '{print $$1}')
if [ $$sum = $$mdf ]; then
mv $$unchecked $@
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 744ecbf..4823e3a 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -1,6 +1,6 @@
# Project initialization.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -25,10 +25,10 @@
# Basic directories that are used throughout the project.
#
# Locks are used to make sure that an operation is done in series not in
-# parallel (even if Make is run in parallel with the `-j' option). The most
+# parallel (even if Make is run in parallel with the '-j' option). The most
# common case is downloads which are better done in series and not in
# parallel. Also, some programs may not be thread-safe, therefore it will
-# be necessary to put a lock on them. This project uses the `flock' program
+# be necessary to put a lock on them. This project uses the 'flock' program
# to achieve this.
#
# To help with modularity and clarity of the build directory (not mixing
@@ -56,10 +56,10 @@ pconfdir = reproduce/analysis/config
# Preparation phase
# -----------------
#
-# This Makefile is loaded both for the `prepare' phase and the `make'
+# This Makefile is loaded both for the 'prepare' phase and the 'make'
# phase. But the preparation files should be dealt with differently
-# (depending on the phase). In the `prepare' phase, the main directory
-# should be created, and in the `make' phase, its contents should be
+# (depending on the phase). In the 'prepare' phase, the main directory
+# should be created, and in the 'make' phase, its contents should be
# loaded.
#
# If you don't need any preparation, please simply comment these lines.
@@ -89,9 +89,9 @@ endif
# create a separate LaTeX build directory for each user.
#
# The same logic applies to the final paper PDF: each user will create a
-# separte final PDF (for example `paper-user1.pdf' and `paper-user2.pdf')
-# and no `paper.pdf' will be built. This isn't a problem because
-# `initialize.tex' is a .PHONY prerequisite, so the rule to build the final
+# separte final PDF (for example 'paper-user1.pdf' and 'paper-user2.pdf')
+# and no 'paper.pdf' will be built. This isn't a problem because
+# 'initialize.tex' is a .PHONY prerequisite, so the rule to build the final
# paper is always executed (even if it is present and nothing has
# changed). So in terms of over-all efficiency and processing steps, this
# doesn't change anything.
@@ -114,7 +114,7 @@ tikzdir = $(texbdir)/tikz
# ---------------------------
#
# Before defining the local sub-environment here, we'll need to save the
-# system's environment for some scenarios (for example after `clean'ing the
+# system's environment for some scenarios (for example after 'clean'ing the
# built programs).
curdir := $(shell echo $$(pwd))
@@ -127,16 +127,16 @@ curdir := $(shell echo $$(pwd))
#
# We want the full recipe to be executed in one call to the shell. Also we
# want Make to run the specific version of Bash that we have installed
-# during `./project configure' time.
+# during './project configure' time.
#
# Regarding the directories, this project builds its major dependencies
# itself and doesn't use the local system's default tools. With these
# environment variables, we are setting it to prefer the software we have
# build here.
#
-# `TEXINPUTS': we have to remove all possible user-specified directories to
-# avoid conflicts with existing TeX Live solutions. Later (in `paper.mk'),
-# we are also going to overwrite `TEXINPUTS' just before `pdflatex'.
+# 'TEXINPUTS': we have to remove all possible user-specified directories to
+# avoid conflicts with existing TeX Live solutions. Later (in 'paper.mk'),
+# we are also going to overwrite 'TEXINPUTS' just before 'pdflatex'.
.ONESHELL:
.SHELLFLAGS = -ec
export TEXINPUTS :=
@@ -153,12 +153,12 @@ export LD_LIBRARY_PATH := $(installdir)/lib
# will be empty.
export CPATH := $(SYS_CPATH)
-# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
+# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
# ultimately redundant. But on some systems, even having a single value
# causes crashs (see bug #56682). So we'll just give it no value at all.
export DYLD_LIBRARY_PATH :=
-# OpenMPI can depend on an existing `ssh' or `rsh' binary. However, because
+# OpenMPI can depend on an existing 'ssh' or 'rsh' binary. However, because
# of security reasons, its best to not install them, disable any
# remote-shell accesss through this environment variable.
export OMPI_MCA_plm_rsh_agent=/bin/false
@@ -172,7 +172,7 @@ export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
# Python enviroment
# -----------------
#
-# The main Python environment variable is `PYTHONPATH'. However, so far we
+# The main Python environment variable is 'PYTHONPATH'. However, so far we
# have found several other Python-related environment variables on some
# systems which might interfere. To be safe, we are removing all their
# values.
@@ -196,10 +196,10 @@ export MPI_PYTHON3_SITEARCH :=
# directories (or possible sub-directories) for individual steps will be
# defined and added within their own Makefiles.
#
-# The `.SUFFIXES' rule with no prerequisite is defined to eliminate all the
+# The '.SUFFIXES' rule with no prerequisite is defined to eliminate all the
# default implicit rules. The default implicit rules are to do with
-# programming (for example converting `.c' files to `.o' files). The
-# problem they cause is when you want to debug the make command with `-d'
+# programming (for example converting '.c' files to '.o' files). The
+# problem they cause is when you want to debug the make command with '-d'
# option: they add too many extra checks that make it hard to find what you
# are looking for in the outputs.
.SUFFIXES:
@@ -222,10 +222,10 @@ project-package-contents = $(texdir)/$(project-package-name)
# High-level Makefile management
# ------------------------------
#
-# About `.PHONY': these are targets that must be built even if a file with
+# About '.PHONY': these are targets that must be built even if a file with
# their name exists.
#
-# Only `$(mtexdir)/initialize.tex' corresponds to a file. This is because
+# Only '$(mtexdir)/initialize.tex' corresponds to a file. This is because
# we want to ensure that the file is always built in every run: it contains
# the project version which may change between two separate runs, even when
# no file actually differs.
@@ -238,14 +238,14 @@ texclean:
mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist.
clean:
- # Delete the top-level PDF file.
+# Delete the top-level PDF file.
rm -f *.pdf
- # Delete all the built outputs except the dependency
- # programs. We'll use Bash's extended options builtin (`shopt') to
- # enable "extended glob" (for listing of files). It allows extended
- # features like ignoring the listing of a file with `!()' that we
- # are using afterwards.
+# Delete all the built outputs except the dependency programs. We'll
+# use Bash's extended options builtin ('shopt') to enable "extended
+# glob" (for listing of files). It allows extended features like
+# ignoring the listing of a file with '!()' that we are using
+# afterwards.
shopt -s extglob
rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex)
rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir))
@@ -253,14 +253,13 @@ clean:
rm -rf $(bsdir)/preparation-done.mk
distclean: clean
- # Without cleaning the Git hooks, we won't be able to easily
- # commit or checkout after this task is done. So we'll remove them
- # first.
+# Without cleaning the Git hooks, we won't be able to easily commit
+# or checkout after this task is done. So we'll remove them first.
rm -f .git/hooks/post-checkout .git/hooks/pre-commit
- # We'll be deleting the built environent programs and just need the
- # `rm' program. So for this recipe, we'll use the host system's
- # `rm', not our own.
+# We'll be deleting the built environent programs and just need the
+# 'rm' program. So for this recipe, we'll use the host system's 'rm',
+# not our own.
$$sys_rm -rf $(BDIR)
$$sys_rm -f .local .build $(pconfdir)/LOCAL.conf
@@ -277,14 +276,14 @@ distclean: clean
# without having to worry about the technicalities of the analysis.
$(project-package-contents): paper.pdf | $(texdir)
- # Set up the output directory, delete it if it exists and remake it
- # to fill with new contents.
+# Set up the output directory, delete it if it exists and remake it
+# to fill with new contents.
dir=$@
rm -rf $$dir
mkdir $$dir
- # Build a small Makefile to help in automatizing the paper building
- # (including the bibliography).
+# Build a small Makefile to help in automatizing the paper building
+# (including the bibliography).
m=$$dir/Makefile
echo "paper.pdf: paper.tex paper.bbl" > $$m
printf "\tpdflatex -shell-escape -halt-on-error paper\n" >> $$m
@@ -296,91 +295,89 @@ $(project-package-contents): paper.pdf | $(texdir)
printf "\trm -f *.aux *.auxlock *.bbl *.bcf\n" >> $$m
printf "\trm -f *.blg *.log *.out *.run.xml\n" >> $$m
- # Copy the top-level contents (see next step for `paper.tex').
+# Copy the top-level contents (see next step for 'paper.tex').
cp COPYING project README.md README-hacking.md $$dir/
- # Since the packaging is mainly intended for high-level building of
- # the PDF with LaTeX, we'll comment the `makepdf' LaTeX macro in
- # the paper. This will disable usage of TiKZ.
+# Since the packaging is mainly intended for high-level building of
+# the PDF with LaTeX, we'll comment the 'makepdf' LaTeX macro in the
+# paper. This will disable usage of TiKZ.
sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \
paper.tex > $$dir/paper.tex
- # Copy ONLY the version-controlled files in 'reproduce' and
- # 'tex/src'. This is important because files like 'LOCAL.conf' (in
- # 'reproduce/software/config') should not be archived, they contain
- # information about the host computer and are irrelevant for
- # others. Also some project authors may have temporary files here
- # that are not under version control and thus shouldn't be archived
- # (although this is bad practice, but that is up to the user).
- #
- # To keep the sub-directory structure, we are packaging the files
- # with Tar, piping it, and unpacking it in the archive
- # directory. So afterwards we need to come back to the current
- # directory.
+# Copy ONLY the version-controlled files in 'reproduce' and
+# 'tex/src'. This is important because files like 'LOCAL.conf' (in
+# 'reproduce/software/config') should not be archived, they contain
+# information about the host computer and are irrelevant for
+# others. Also some project authors may have temporary files here
+# that are not under version control and thus shouldn't be archived
+# (although this is bad practice, but that is up to the user).
+#
+# To keep the sub-directory structure, we are packaging the files
+# with Tar, piping it, and unpacking it in the archive directory. So
+# afterwards we need to come back to the current directory.
tar -c -f - $$(git ls-files reproduce tex/src) \
| (cd $$dir ; tar -x -f -)
cd $(curdir)
- # Build the other two subdirectories of 'tex/' that we need in the
- # archive (in the actual project, these are symbolic links to the
- # build directory).
+# Build the other two subdirectories of 'tex/' that we need in the
+# archive (in the actual project, these are symbolic links to the
+# build directory).
mkdir $$dir/tex/tikz $$dir/tex/build
- # Copy the 'tex/build' directory into the archive (excluding the
- # temporary archive directory that we are now copying to). We will
- # be using Bash's extended globbing ('extglob') for excluding this
- # directory.
+# Copy the 'tex/build' directory into the archive (excluding the
+# temporary archive directory that we are now copying to). We will be
+# using Bash's extended globbing ('extglob') for excluding this
+# directory.
shopt -s extglob
cp -r tex/build/!($(project-package-name)) $$dir/tex/build
- # Clean up the $(texdir)/build* directories in the archive (when
- # building in a group structure, there will be `build-user1',
- # `build-user2' and etc). These are just temporary LaTeX build
- # files and don't have any relevant/hand-written files in them.
+# Clean up the $(texdir)/build* directories in the archive (when
+# building in a group structure, there will be 'build-user1',
+# 'build-user2' and etc). These are just temporary LaTeX build files
+# and don't have any relevant/hand-written files in them.
rm -rf $$dir/tex/build/build*
- # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
- # PGFPlots was used to generate them), copy them too.
+# If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
+# PGFPlots was used to generate them), copy them too.
if ls tex/tikz/*.pdf &> /dev/null; then
cp tex/tikz/*.pdf $$dir/tex/tikz
fi
- # When submitting to places like arXiv, they will just run LaTeX
- # once and won't run `biber'. So we need to also keep the `.bbl'
- # file into the distributing tarball. However, BibLaTeX is
- # particularly sensitive to versioning (a `.bbl' file has to be
- # read by the same BibLaTeX version that created it). This is hard
- # to do with non-up-to-date places like arXiv. Therefore, we thus
- # just copy the whole of BibLaTeX's source (the version we are
- # using) into the top tarball directory. In this way, arXiv's LaTeX
- # engine will use the same BibLaTeX version to interpret the `.bbl'
- # file. TIP: you can use the same strategy for other LaTeX packages
- # that may cause problems on the arXiv server.
+# When submitting to places like arXiv, they will just run LaTeX once
+# and won't run 'biber'. So we need to also keep the '.bbl' file into
+# the distributing tarball. However, BibLaTeX is particularly
+# sensitive to versioning (a '.bbl' file has to be read by the same
+# BibLaTeX version that created it). This is hard to do with
+# non-up-to-date places like arXiv. Therefore, we thus just copy the
+# whole of BibLaTeX's source (the version we are using) into the top
+# tarball directory. In this way, arXiv's LaTeX engine will use the
+# same BibLaTeX version to interpret the '.bbl' file. TIP: you can
+# use the same strategy for other LaTeX packages that may cause
+# problems on the arXiv server.
cp tex/build/build/paper.bbl $$dir/
tltopdir=.local/texlive/maneage/texmf-dist/tex/latex
find $$tltopdir/biblatex/ -maxdepth 1 -type f -print0 \
| xargs -0 cp -t $$dir
- # Just in case the package users want to rebuild some of the
- # figures (manually un-comment the `makepdf' command we commented
- # above), correct the TikZ external directory, so the figures can
- # be rebuilt.
+# Just in case the package users want to rebuild some of the figures
+# (manually un-comment the 'makepdf' command we commented above),
+# correct the TikZ external directory, so the figures can be rebuilt.
pgfsettings="$$dir/tex/src/preamble-pgfplots.tex"
sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new
mv $$pgfsettings.new $$pgfsettings
- # PROJECT SPECIFIC
- # ----------------
- # Put any project-specific distribution steps here.
+# PROJECT SPECIFIC
+# ----------------
+# Put any project-specific distribution steps here.
- # ----------------
+# ----------------
- # Clean temporary files that may have been created by text editors.
+# Clean temporary files that may have been created by text editors.
cd $(texdir)
find $(project-package-name) -name \*~ -delete
find $(project-package-name) -name \*.swp -delete
-# Package into `.tar.gz' or '.tar.lz'.
+# Package into '.tar.gz' or '.tar.lz'.
dist dist-lzip: $(project-package-contents)
curdir=$$(pwd)
cd $(texdir)
@@ -396,7 +393,7 @@ dist dist-lzip: $(project-package-contents)
cd $$curdir
mv $(texdir)/$(project-package-name).tar.$$suffix ./
-# Package into `.zip'.
+# Package into '.zip'.
dist-zip: $(project-package-contents)
curdir=$$(pwd)
cd $(texdir)
@@ -497,13 +494,13 @@ print-general-metadata = \
# This file will store some basic info about the project that is necessary
# 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.
+# actually exists, it is also aded as a '.PHONY' target above.
$(mtexdir)/initialize.tex: | $(mtexdir)
- # Version and title of project. About the starting '@': since these
- # commands are run every time with './project make', it is annoying
- # to print them on the standard output every time. With the '@',
- # make will not print the commands that it runs in this recipe.
+# Version and title of project. About the starting '@': since these
+# commands are run every time with './project make', it is annoying
+# to print them on the standard output every time. With the '@', make
+# will not print the commands that it runs in this recipe.
@d=$$(git show -s --format=%aD HEAD | awk '{print $$2, $$3, $$4}')
echo "\newcommand{\projectdate}{$$d}" > $@
echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@
@@ -511,16 +508,15 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
echo "\newcommand{\projectgitrepo}{$(metadata-git-repository)}" >> $@
echo "\newcommand{\projectcopyrightowner}{$(metadata-copyright-owner)}" >> $@
- # Calculate the latest Maneage commit used to build this
- # project:
- # - The project may not have the 'maneage' branch (for example
- # after cloning from a fork that didn't include it!). In this
- # case, we'll print a descriptive warning, telling the user what
- # should be done (reporting the last merged commit and its date
- # is very useful for the future).
- # - The '--dirty' option (used in 'project-commit-hash') isn't
- # applicable to "commit-ishes" (direct quote from Git's error
- # message!).
+# Calculate the latest Maneage commit used to build this project:
+# - The project may not have the 'maneage' branch (for example
+# after cloning from a fork that didn't include it!). In this
+# case, we'll print a descriptive warning, telling the user what
+# should be done (reporting the last merged commit and its date
+# is very useful for the future).
+# - The '--dirty' option (used in 'project-commit-hash') isn't
+# applicable to "commit-ishes" (direct quote from Git's error
+# message!).
if git log maneage -1 &> /dev/null; then
c=$$(git merge-base HEAD maneage)
v=$$(git describe --always --long $$c)
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index b5b5b29..740dc7d 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -23,14 +23,14 @@
#
# To report the input settings and results, the final report's PDF (final
# target of this project) uses macros generated from various steps of the
-# project. All these macros are defined through `$(mtexdir)/project.tex'.
+# project. All these macros are defined through '$(mtexdir)/project.tex'.
#
-# `$(mtexdir)/project.tex' is actually just a combination of separate files
+# '$(mtexdir)/project.tex' is actually just a combination of separate files
# that keep the LaTeX macros related to each workhorse Makefile (in
-# `reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
-# `$(mtexdir)/verify.tex' which will check them before starting to build
+# 'reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
+# '$(mtexdir)/verify.tex' which will check them before starting to build
# the paper. The only workhorse Makefile that doesn't need to produce LaTeX
-# macros is this Makefile (`reproduce/src/make/paper.mk').
+# macros is this Makefile ('reproduce/src/make/paper.mk').
#
# This file is thus the interface between the analysis/processing steps and
# the final PDF: when we get to this point, all the processing has been
@@ -38,33 +38,33 @@
#
# Note that if you don't want the final PDF and just want the processing
# and file outputs, you can give any value other than 'yes' to
-# 'pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
$(mtexdir)/project.tex: $(mtexdir)/verify.tex
- # If no PDF is requested, or if LaTeX isn't available, don't
- # continue to building the final PDF. Otherwise, merge all the TeX
- # macros into one for building the PDF.
+# If no PDF is requested, or if LaTeX isn't available, don't continue
+# to building the final PDF. Otherwise, merge all the TeX macros into
+# one for building the PDF.
@if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; then
- # Put a LaTeX input command for all the necessary macro files.
- # 'hardware-parameters.tex' is created in 'configure.sh'.
+# Put a LaTeX input command for all the necessary macro files.
+# 'hardware-parameters.tex' is created in 'configure.sh'.
projecttex=$(mtexdir)/project.tex
rm -f $$projecttex
for t in $(subst paper,,$(makesrc)) hardware-parameters; do
echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex
done
- # Possibly highlight the '\new' parts of the text.
+# Possibly highlight the '\new' parts of the text.
if [ x"$(highlightnew)" = x1 ]; then
echo "\newcommand{\highlightnew}{}" >> $$projecttex
fi
- # Possibly show the text within '\tonote'.
+# Possibly show the text within '\tonote'.
if [ x"$(highlightnotes)" = x1 ]; then
echo "\newcommand{\highlightnotes}{}" >> $$projecttex
fi
- # The paper shouldn't be built.
+# The paper shouldn't be built.
else
echo
echo "-----"
@@ -95,39 +95,39 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
# The bibliography
# ----------------
#
-# We need to run the `biber' program on the output of LaTeX to generate the
+# We need to run the 'biber' program on the output of LaTeX to generate the
# necessary bibliography before making the final paper. So we'll first have
-# one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
+# one run of LaTeX (similar to the 'paper.pdf' recipe), then 'biber'.
#
-# NOTE: `$(mtexdir)/project.tex' is an order-only-prerequisite for
-# `paper.bbl'. This is because we need to run LaTeX in both the `paper.bbl'
-# recipe and the `paper.pdf' recipe. But if `tex/src/references.tex' hasn't
+# NOTE: '$(mtexdir)/project.tex' is an order-only-prerequisite for
+# 'paper.bbl'. This is because we need to run LaTeX in both the 'paper.bbl'
+# recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't
# been modified, we don't want to re-build the bibliography, only the final
# PDF.
$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
| $(mtexdir)/project.tex
- # If `$(mtexdir)/project.tex' is empty, don't build PDF.
+# If '$(mtexdir)/project.tex' is empty, don't build PDF.
@macros=$$(cat $(mtexdir)/project.tex)
if [ x"$$macros" != x ]; then
- # We'll run LaTeX first to generate the `.bcf' file (necessary
- # for `biber') and then run `biber' to generate the `.bbl' file.
+# We'll run LaTeX first to generate the '.bcf' file (necessary for
+# 'biber') and then run 'biber' to generate the '.bbl' file.
p=$$(pwd)
export TEXINPUTS=$$p:
cd $(texbdir);
- # Delete any possibly existing target (a '.bbl' file) to avoid
- # complications with LaTeX being run before the command that
- # generates it. Otherwise users will have to manually delete
- # it. It will be built anyway once this rule is done.
+# Delete any possibly existing target (a '.bbl' file) to avoid
+# complications with LaTeX being run before the command that
+# generates it. Otherwise users will have to manually delete it. It
+# will be built anyway once this rule is done.
rm -f $@
- # The pdflatex option '-shell-escape' is "normally disallowed for
- # security reasons" according to the `info pdflatex' manual, but
- # is enabled here in order to allow the use of PGFPlots. If you
- # do not use PGFPlots, then you should remove the `-shell-escape'
- # option for better security. See
- # https://savannah.nongnu.org/task/?15694 for details.
+# The pdflatex option '-shell-escape' is "normally disallowed for
+# security reasons" according to the 'info pdflatex' manual, but is
+# enabled here in order to allow the use of PGFPlots. If you do not
+# use PGFPlots, then you should remove the '-shell-escape' option
+# for better security. See https://savannah.nongnu.org/task/?15694
+# for details.
pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
biber paper
@@ -140,27 +140,28 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
# The final paper
# ---------------
#
-# Run LaTeX in the `$(texbdir)' directory so all the intermediate and
+# Run LaTeX in the '$(texbdir)' directory so all the intermediate and
# auxiliary files stay there and keep the top directory clean. To be able
# to run everything cleanly from there, it is necessary to add the current
-# directory (top project directory) to the `TEXINPUTS' environment
+# directory (top project directory) to the 'TEXINPUTS' environment
# variable.
paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
- # If `$(mtexdir)/project.tex' is empty, don't build the PDF.
+# If '$(mtexdir)/project.tex' is empty, don't build the PDF.
@macros=$$(cat $(mtexdir)/project.tex)
if [ x"$$macros" != x ]; then
- # Go into the top TeX build directory and make the paper.
+# Go into the top TeX build directory and make the paper.
p=$$(pwd)
export TEXINPUTS=$$p:
cd $(texbdir)
- # See above for a warning and brief discussion on the the
- # pdflatex option `-shell-escape'.
+
+# See above for a warning and brief discussion on the the pdflatex
+# option '-shell-escape'.
pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
- # Come back to the top project directory and copy the built PDF
- # file here.
+# Come back to the top project directory and copy the built PDF
+# file here.
cd "$$p"
cp $(texbdir)/$@ $(final-paper)
diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk
index d0b61d9..ecb6842 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -1,6 +1,6 @@
-# Basic preparations, called by `./project prepare'.
+# Basic preparations, called by './project prepare'.
#
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -21,30 +21,29 @@
# Final-target
#
-# Without this file, `./project make' won't work.
+# Without this file, './project make' won't work.
prepare-dep = $(subst prepare, ,$(makesrc))
$(bsdir)/preparation-done.mk: \
$(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex)
- # If you need to add preparations define targets above to do the
- # preparations, then set the value below to `yes'. Recall that just
- # like `./project make', before loading this file, `./project
- # prepare' loads loads `initialize.mk' and `download.mk', so you
- # can safely assume everything that is defined there in the
- # preparation phase also.
- #
- # TIP: the targets can actually be automatically generated
- # Makefiles that are used by `./project make'. They can include
- # variables, or automatically generated rules. Just make sure that
- # those Makefiles aren't written in the source directory. Even
- # though they are Makefiles, they are automatically built, so they
- # don't belong in the source. `$(prepdir)' has been defined for
- # this purpose (see `initialize.mk'), we recommend that you put all
- # automatically generated Makefiles under this directory. In the
- # `make' phase, `initialize.mk' will automatically load all the
- # `*.mk' files. If you need to load your generated
- # configuration-makefiles before automatically generated Makefiles
- # containing rules, you can use some naming convension like
- # `conf-*.mk' and `rule-*.mk', or you can put them in
- # subdirectories.
+# If you need to add preparations define targets above to do the
+# preparations, then set the value below to 'yes'. Recall that just
+# like './project make', before loading this file, './project
+# prepare' loads loads 'initialize.mk' and 'download.mk', so you can
+# safely assume everything that is defined there in the preparation
+# phase also.
+#
+# TIP: the targets can actually be automatically generated Makefiles
+# that are used by './project make'. They can include variables, or
+# automatically generated rules. Just make sure that those Makefiles
+# aren't written in the source directory. Even though they are
+# Makefiles, they are automatically built, so they don't belong in
+# the source. '$(prepdir)' has been defined for this purpose (see
+# 'initialize.mk'), we recommend that you put all automatically
+# generated Makefiles under this directory. In the 'make' phase,
+# 'initialize.mk' will automatically load all the '*.mk' files. If
+# you need to load your generated configuration-makefiles before
+# automatically generated Makefiles containing rules, you can use
+# some naming convension like 'conf-*.mk' and 'rule-*.mk', or you can
+# put them in subdirectories.
@echo "include-prepare-results = no" > $@
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 596cc0d..4e95c54 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -20,7 +20,7 @@
# Load the local configuration (created after running
-# `./project configure').
+# './project configure').
include reproduce/software/config/LOCAL.conf
@@ -30,7 +30,7 @@ include reproduce/software/config/LOCAL.conf
# Ultimate target of this project
# -------------------------------
#
-# The final paper/report (`paper.pdf') is the main target of this
+# The final paper/report ('paper.pdf') is the main target of this
# project. As defined in the Make paradigm, it must be the first target
# that Make encounters (immediately after loading the local configuration
# settings, necessary for a group building scenario mentioned next).
@@ -50,8 +50,8 @@ include reproduce/software/config/LOCAL.conf
#
# Controlling this requires two variables that are available at this stage:
#
-# - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure').
-# - `maneage_group_name': value to the `--group' option.
+# - 'GROUP-NAME': from 'LOCAL.conf' (which was built by './project configure').
+# - 'maneage_group_name': value to the '--group' option.
#
# The analysis is only done when both have the same group name. Note that
# when the project isn't being built for a group, both variables will be an
@@ -63,7 +63,7 @@ include reproduce/software/config/LOCAL.conf
#
# If you are just interested in the processing and don't want to build the
# PDF, you can skip the creation of the final PDF by giving a value of
-# `yes' to `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# 'yes' to 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
ifeq (x$(maneage_group_name),x$(GROUP-NAME))
all: paper.pdf
else
@@ -87,13 +87,13 @@ endif
# To keep things clean, managable and readable, each set of operations
# is (and must be) classified (modularized) by context into separate
# Makefiles: the more the better. These modular steps are then
-# included in this top-level Makefile through the `include' command of
+# included in this top-level Makefile through the 'include' command of
# the next step. Each Makefile should also produce a LaTeX macro file
# with the same fixed name (used to keep all the parameters and
# relevant outputs of the steps in it for the final paper).
#
# In the rare case that no special LaTeX macros are necessary in a
-# workhorse Makefile, you can simply make an empty file with `touch
+# workhorse Makefile, you can simply make an empty file with 'touch
# $@'. This will not add any lines to the final combined LaTeX macros
# file, but will create the file that is a prerequisite to the final
# paper generation.
@@ -107,7 +107,7 @@ endif
# IMPORTANT NOTE: order matters in the inclusion of the processing
# Makefiles. As the project grows, some Makefiles will define
# variables/dependencies that later Makefiles need. Therefore we are using
-# a `foreach' loop in the next step to explicitly request loading them in
+# a 'foreach' loop in the next step to explicitly request loading them in
# the same order that they are defined here (we aren't just using a
# wild-card like the configuration Makefiles).
makesrc = initialize \
@@ -130,7 +130,7 @@ makesrc = initialize \
# contain rules to actually do this project's processing.
#
# But before that, we need to identify the phase for the Makefiles that are
-# run both in `./project prepare' and `./project make'.
+# run both in './project prepare' and './project make'.
project-phase = make
include reproduce/analysis/config/*.conf
include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk)
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index fb5700e..3950bf1 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -1,10 +1,10 @@
# Do basic preparations to optimize the project's running.
#
-# NOTE: This file is very similar to `top-make.mk', so the large comments
+# NOTE: This file is very similar to 'top-make.mk', so the large comments
# are not included here. Please see that file for thorough comments on each
# step.
#
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# This Makefile is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -24,7 +24,7 @@
# Load the local configuration (created after running
-# `./project configure').
+# './project configure').
include reproduce/software/config/LOCAL.conf
@@ -34,7 +34,7 @@ include reproduce/software/config/LOCAL.conf
# Ultimate target of this project
# -------------------------------
#
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
ifeq (x$(maneage_group_name),x$(GROUP-NAME))
all: $(BDIR)/software/preparation-done.mk
@echo "Project preparation is complete.";
@@ -57,12 +57,12 @@ endif
# Define source Makefiles
# -----------------------
#
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
#
-# To ensure that `prepare' and `make' have the same basic definitions and
-# environment and that all `downloads' are managed in one place, both
-# `./project prepare' and `./project make' will first read `initialize.mk'
-# and `downloads.mk'.
+# To ensure that 'prepare' and 'make' have the same basic definitions and
+# environment and that all 'downloads' are managed in one place, both
+# './project prepare' and './project make' will first read 'initialize.mk'
+# and 'downloads.mk'.
makesrc = initialize \
download \
prepare
@@ -74,7 +74,7 @@ makesrc = initialize \
# Include all analysis Makefiles
# ------------------------------
#
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
project-phase = prepare
include reproduce/analysis/config/*.conf
include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk)
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index 7e16add..d3f3282 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) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -94,7 +94,7 @@ verify-txt-no-comments-no-space = \
# (generated in various stages of the analysis.
#
# Since each analysis step's data files are already prerequisites of their
-# respective TeX macro file, its enough for `verify.tex' to depend on the
+# respective TeX macro file, its enough for 'verify.tex' to depend on the
# final TeX macro.
#
# USEFUL TIP: during the early phases of your research (when you are
@@ -103,40 +103,40 @@ verify-txt-no-comments-no-space = \
#
# Here is a description of the variables defined here.
#
-# verify-dep: The major step dependencies of `verify.tex', this includes
+# verify-dep: The major step dependencies of 'verify.tex', this includes
# all the steps that must be finished before it.
#
# verify-changes: The files whose contents are important. This is
-# essentially the same as `verify-dep', but it has removed
-# the `initialize' step (which is information about the
+# essentially the same as 'verify-dep', but it has removed
+# the 'initialize' step (which is information about the
# pipeline, not the results).
verify-dep = $(subst verify,,$(subst paper,,$(makesrc)))
verify-check = $(subst initialize,,$(verify-dep))
$(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
- # Make sure that verification is actually requested, the '@' at the
- # start of the recipe is added so Make doesn't print the commands
- # on the standard output because this recipe is run on every call
- # to the project and can be annoying (get mixed in the middle of
- # the analysis outputs or the LaTeX outputs).
+# Make sure that verification is actually requested, the '@' at the
+# start of the recipe is added so Make doesn't print the commands on
+# the standard output because this recipe is run on every call to the
+# project and can be annoying (get mixed in the middle of the
+# analysis outputs or the LaTeX outputs).
@if [ x"$(verify-outputs)" = xyes ]; then
- # Make sure the temporary output doesn't exist (because we want
- # to append to it). We are making a temporary output target so if
- # there is a crash in the middle, Make will not continue. If we
- # write in the final target progressively, the file will exist,
- # and its date will be more recent than all prerequisites, so
- # next time the project is run, Make will continue and ignore the
- # rest of the checks.
+# Make sure the temporary output doesn't exist (because we want to
+# append to it). We are making a temporary output target so if
+# there is a crash in the middle, Make will not continue. If we
+# write in the final target progressively, the file will exist, and
+# its date will be more recent than all prerequisites, so next time
+# the project is run, Make will continue and ignore the rest of the
+# checks.
rm -f $@.tmp
- # Verify the figure datasets.
+# Verify the figure datasets.
$(call verify-txt-no-comments-no-space, \
$(dm-squared), 6b6d3b0f9c351de53606507b59bca5d1, $@.tmp)
$(call verify-txt-no-comments-no-space, \
$(dm-img-histogram), b1f9c413f915a1ad96078fee8767b16c, $@.tmp)
- # Verify TeX macros (the values that go into the PDF text).
+# Verify TeX macros (the values that go into the PDF text).
for m in $(verify-check); do
file=$(mtexdir)/$$m.tex
if [ $$m == download ]; then s=49e4e9f049aa9da0453a67203d798587
@@ -146,7 +146,7 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
$(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp)
done
- # Move temporary file to final target.
+# Move temporary file to final target.
mv $@.tmp $@
else
echo "% Verification was DISABLED!" > $@
diff --git a/reproduce/software/bibtex/astrometrynet.tex b/reproduce/software/bibtex/astrometrynet.tex
index 15d4829..26d211b 100644
--- a/reproduce/software/bibtex/astrometrynet.tex
+++ b/reproduce/software/bibtex/astrometrynet.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/astropy.tex b/reproduce/software/bibtex/astropy.tex
index c25803b..2041fc3 100644
--- a/reproduce/software/bibtex/astropy.tex
+++ b/reproduce/software/bibtex/astropy.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%%
%% 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 b2e0e25..f6b4f22 100644
--- a/reproduce/software/bibtex/corner.tex
+++ b/reproduce/software/bibtex/corner.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%%
%% 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 88a5c4e..30a0713 100644
--- a/reproduce/software/bibtex/cython.tex
+++ b/reproduce/software/bibtex/cython.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/fftw.tex b/reproduce/software/bibtex/fftw.tex
index 7f525c9..1186efa 100644
--- a/reproduce/software/bibtex/fftw.tex
+++ b/reproduce/software/bibtex/fftw.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%%
%% 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 3646639..8fceda8 100644
--- a/reproduce/software/bibtex/galsim.tex
+++ b/reproduce/software/bibtex/galsim.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%%
%% 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 1470a00..018a35b 100644
--- a/reproduce/software/bibtex/gnuastro.tex
+++ b/reproduce/software/bibtex/gnuastro.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%%
%% 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 08bef90..77471c5 100644
--- a/reproduce/software/bibtex/healpix.tex
+++ b/reproduce/software/bibtex/healpix.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%%
%% 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 3822fd4..167586d 100644
--- a/reproduce/software/bibtex/imfit.tex
+++ b/reproduce/software/bibtex/imfit.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/matplotlib.tex b/reproduce/software/bibtex/matplotlib.tex
index c35f682..aab2c04 100644
--- a/reproduce/software/bibtex/matplotlib.tex
+++ b/reproduce/software/bibtex/matplotlib.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex
index 9fb0f54..470cf8a 100644
--- a/reproduce/software/bibtex/missfits.tex
+++ b/reproduce/software/bibtex/missfits.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2020-2021 Surena Fatemi <surena.fatemi@ipm.ir>
+%% Copyright (C) 2020-2022 Surena Fatemi <surena.fatemi@ipm.ir>
%%
%% 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 9a99803..598bbda 100644
--- a/reproduce/software/bibtex/mpi4py.tex
+++ b/reproduce/software/bibtex/mpi4py.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/numpy.tex b/reproduce/software/bibtex/numpy.tex
index 07101cf..0dee489 100644
--- a/reproduce/software/bibtex/numpy.tex
+++ b/reproduce/software/bibtex/numpy.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/r-cran.tex b/reproduce/software/bibtex/r-cran.tex
new file mode 100644
index 0000000..cf74a8e
--- /dev/null
+++ b/reproduce/software/bibtex/r-cran.tex
@@ -0,0 +1,19 @@
+%% Copyright (C) 2022 Boud Roukema <boud@cosmo.torun.pl>
+%% Copyright (C) 2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%%
+%% 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.
+
+@ARTICLE{RIhakaGentleman1996,
+ author = {{Ihaka}, Ross and {Gentleman}, Robert},
+ title = "{R: A language for data analysis and graphics}",
+ journal = {J.Comput.Graph.Stat.},
+ year = {1996},
+ volume = {5},
+ number = {3},
+ pages = {299-314},
+ DOI = {10.1080/10618600.1996.10474713},
+ ISSN = {10618600},
+}
diff --git a/reproduce/software/bibtex/scamp.tex b/reproduce/software/bibtex/scamp.tex
index ab68dd6..62e910c 100644
--- a/reproduce/software/bibtex/scamp.tex
+++ b/reproduce/software/bibtex/scamp.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/scipy.tex b/reproduce/software/bibtex/scipy.tex
index 71b0caa..4b1292d 100644
--- a/reproduce/software/bibtex/scipy.tex
+++ b/reproduce/software/bibtex/scipy.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/sextractor.tex b/reproduce/software/bibtex/sextractor.tex
index 0c91a3d..8905be8 100644
--- a/reproduce/software/bibtex/sextractor.tex
+++ b/reproduce/software/bibtex/sextractor.tex
@@ -1,5 +1,5 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%%
%% 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 02dfec0..2a5b68b 100644
--- a/reproduce/software/bibtex/sip_tpv.tex
+++ b/reproduce/software/bibtex/sip_tpv.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/swarp.tex b/reproduce/software/bibtex/swarp.tex
index 7636f1c..f645bb3 100644
--- a/reproduce/software/bibtex/swarp.tex
+++ b/reproduce/software/bibtex/swarp.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/sympy.tex b/reproduce/software/bibtex/sympy.tex
index 1d07846..3ce064a 100644
--- a/reproduce/software/bibtex/sympy.tex
+++ b/reproduce/software/bibtex/sympy.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+%% Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
%%
%% Copying and distribution of this file, with or without modification,
%% are permitted in any medium without royalty provided the copyright
diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex
index f3b5490..b97762a 100644
--- a/reproduce/software/bibtex/tides.tex
+++ b/reproduce/software/bibtex/tides.tex
@@ -1,4 +1,4 @@
-%% Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%% Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
%%
%% 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 132c3f7..a7434ea 100644
--- a/reproduce/software/config/LOCAL.conf.in
+++ b/reproduce/software/config/LOCAL.conf.in
@@ -1,9 +1,9 @@
# Local project configuration.
#
-# This is just a template for the `./project configure' script to fill
+# This is just a template for the './project configure' script to fill
# in. Please don't make any change to this file.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 bec3adb..ef95f57 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice and
@@ -21,22 +21,26 @@
# reproduce/software/config/versions.conf
#
# Please add any software that you need for your project in the respective
-# part below (using its name in `versions.conf', but without the `-version'
+# part below (using its name in 'versions.conf', but without the '-version'
# part). Just note that if a program/library is a dependency of another,
# you don't need to include it here (it will be installed before the
# higher-level software anyway).
#
# Note that many low-level software will be installed before those that are
# installed in this step. They are clearly distinguished from the
-# higher-level (optional) software in `versions.conf'. These low-level
+# higher-level (optional) software in 'versions.conf'. These low-level
# software MUST NOT be added here.
-# Programs and libraries (for Python modules, add to 'top-level-python').
+# Programs and libraries (for Python or R modules, use respective variable).
top-level-programs = gnuastro
# Python libraries/modules.
top-level-python =
+
+# R libraries/modules
+# [For developers 2022-01-02: 'r-cran-cowplot r-cran-gridExtra' for all]
+top-level-r-cran =
diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index 0e21912..d8b3a96 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -1,7 +1,7 @@
# sha512 checksums of all the necessary software tarballs.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice and
@@ -14,54 +14,53 @@
# Basic/low-level programs and libraires (installed in any case)
# --------------------------------------------------------------
-bash-checksum = e210cd63ce1241636fbb14d1a105c83e9481a0312026f746f76f7115b777707170ddfe1840fb4d3a4093613048e2d1eedf926e843ad15ffc8d66f08525e8b04b
-binutils-checksum = 5ad795fab0803be83b53aa955fd5414c8408b4cf2a66eba2f8688298312934b4b1b0cbe9cf887d86de77f88adf1333d85fc9f6ab4a530e85a09b9b2dbf6aaf3f
-bzip2-checksum = 00ace5438cfa0c577e5f578d8a808613187eff5217c35164ffe044fbafdfec9e98f4192c02a7d67e01e5a5ccced630583ad1003c37697219b0f147343a3fdd12
-cert-checksum = a81dfa59c70788126a395c576e54cb8f61c1ea34da69b5cd42e2d83ee6426c2a26941360c7302793774ea98ca16846deb6e683144cc7fb6da6ef87b70447e4c8
-coreutils-checksum = 1c8f3584efd61b4b02e7ac5db8e103b63cfb2063432caaf1e64cb2dcc56d8c657d1133bbf10bd41468d6a1f31142e6caa81d16ae68fa3e6e84075c253613a145
-curl-checksum = 614f8d67e6ee942cb5e57f2da1a3faaf84ebff549ffe383aaf3751a4de3c8874ff482076afa27a52e910a137dec9b0f6e98265dc7d4ad7c95845b63f39236fd4
-dash-checksum = 9d55090115ac04f505d70e6790179331178950f96fe713b33fd698fa8bfa60d4eff1b68cb7b8a2f099d29c587d36034a17dccd6658ba1623ff0a625ac1fb9620
-diffutils-checksum = 7b12cf8aea1b9844773748f72272d9c6a38adae9c3c3a8c62048f91fb56c60b76035fa5f51665dceaf2cfbf1d1f4a3efdcc24bf47a5a16ff4350543314b12c9c
-file-checksum = 9cf1a7b769c56eb6f5b25c66ce85fa1300128396e445b2e53dbbd8951e5da973a7a07c4ef9f7ebd1fe945d47bdaf2cd9ef09bd2be6c217a0bcb907d9449835e6
-findutils-checksum = 650a24507f8f4ebff83ad28dd27daa4785b4038dcaadc4fe00823b976e848527074cce3f9ec34065b7f037436d2aa6e9ec099bc05d7472c29864ac2c69de7f2e
-flock-checksum = ddb997174c0653bc3d29410a5a16b6290e737aa40fbf4b746e2d1db1e88e5acb08ec11a25c27c8a5a5fbf5a00fcac17abeaa245e7df27bd975ae86364d400b86
+bash-checksum = 409843172032fbe7ef50004ddc30934e12d864e30935fa501dd8a2792c0c12c9c00e1108c05a95ba84b5ab4dd146d92e793b684df1f49ba51eba40f39d47f14d
+binutils-checksum = f3c10d8aeb50872278ece6ad31f7369bf12b2d09618812322b35e6750024b45f77fc32d498a9c579df3c152ce3da382f480281743eb5b53639aa287b7166aba3
+bzip2-checksum = 929cb1b2d0db8a505e2bafe3ce2c893c8f132dd617c0110e86e19f116b570a85de3c8a635483b530456fc8f8b6698c8190d21313e47607f442807b10489ac86e
+cert-checksum = 25b689ebac01ebde136bcef1ef4aa18389fcc618375755001f153b37060cfb327fd6d6afac25d4ddfcf78fd6678fa00ce49ba688e725e4a4c657c37cba4ec3ca
+coreutils-checksum = efdffdeec139e4a7e4033472197145d25400c4cbf6380cb63b18a748934021a977e613a75f018fff23bf506ebdb876b1d79166ba8d3b6077dd1c0a338ef5bff6
+curl-checksum = af977f4ea4b096d3de8d116cfe4f8abbfe5dad487745b6fbc1b13c2669d2bcfdcafa44c9c4cf89c4fb413b3c0986d4e25ae107d461e6295bf469ae3cbc31bb67
+dash-checksum = d8533e3fb29ab00369ee0e4f700a2e5ac2fc11a7c51d83fb93dbbe25d1e06b73718f6f583e368bd232edde41b03b53493657e81dc2e0ce439a9da8e1ed627923
+diffutils-checksum = 597cd0a14087722b78469e2238fcee25e78108f53ca43fbff1194d87625b4c7498a205f68c7bb44fcd437b8d642bba263ac40170780aede006076b11956fd06e
+file-checksum = f1cc951f8972073aa8d29842858d653ecf890e18840d29b848e3b7ac717b2cebe41091415f38cfda1e0d8d066d9e8200ca8a94b5a77f96b8a9b952a9a567284c
+findutils-checksum = a330ace9e7af668b5294c231f9fb45f23c1345d770d67d047d280cd1c6c0fe01f248ccd9877c170bebe8471618261e09a3d64909bb094c73584928005027d58e
+flock-checksum = f711815035e21b46572bf80e730a55822e5abf4cb29749e476ee6cf4d5027e9a7deeacf5f6b8c37f18f17a0cc7a6d98fb0be3936e97b122707f1cb2306d1e1d9
gawk-checksum = 682fadd3630d51d13d19443a9a93d4cba1bd6802dd078f1366f17f39d3fa5800f47037b103d742be9254475fdc251d90626f95a2e04b5ace117cfaecebca2281
-gcc-checksum = 42ae38928bd2e8183af445da34220964eb690b675b1892bbeb7cd5bb62be499011ec9a93397dba5e2fb681afadfc6f2767d03b9035b44ba9be807187ae6dc65e
+gcc-checksum = 7f9605b9527799f92b3251968f63e53bd0b74880952f0cbc58ade9b4eee60bac4990ad408c1a6067f7aa36225709061106f0d93bc581ec97711fc5ff6ae15127
gettext-checksum = f3083af79341bfdc849118333c1598812c12bc225d998181694648187088050160deb4777c252f72a7158e914c2967416489bc6167ef8505664497f2fb94ecbf
-git-checksum = a6159c0a15e3c5f9603157d4010664a6d74e7d65b9fe97a03b36fac12607248ed57980d96565841e88eae343001c167222232737d3af812608c8db011941df1a
-gmp-checksum = 9975e8766e62a1d48c0b6d7bbdd2fccb5b22243819102ca6c8d91f0edd2d3a1cef21c526d647c2159bb29dd2a7dcbd0d621391b2e4b48662cf63a8e6749561cd
-grep-checksum = 0f1506bd19971fbdcb47a111277ca63e8ad045456f096980852fd0a61c860f29f4b369bbaaa5cbce4b0a81718e3e3274d9a078b491f2109baa9a02ce600ee206
-gzip-checksum = 753fbcf5eb104bfc8a8eb81b69b8701f757b5158e6333b17438574169a4662642a122e1fdbd920a536edbcb77253d65fa571e4f507dbe72a70fee5eb161d6324
-isl-checksum = 85d0b40f4dbf14cb99d17aa07048cdcab2dc3eb527d2fbb1e84c41b2de5f351025370e57448b63b2b8a8cf8a0843a089c3263f9baee1542d5c2e1cb37ed39d94
-less-checksum = 79384ff3faa33aeb86da6027c8b264df78f9f8c799af43dc5340e2ca3d86053c9be168140bfa05734a4217e65ef9939652b004d6a536f64b2e0ef3b74b07f535
-libbsd-checksum = b75529785b16c93d31401187f8a58258fbebe565dac071c8311775c913af989f62cd29d5ce2651af3ea6221cffd31cf04826577d3e546ab9ca14340f297777b9
-libiconv-checksum = 365dac0b34b4255a0066e8033a8b3db4bdb94b9b57a9dca17ebf2d779139fe935caf51a465d17fd8ae229ec4b926f3f7025264f37243432075e5583925bb77b7
-libtool-checksum = a6eef35f3cbccf2c9e2667f44a476ebc80ab888725eb768e91a3a6c33b8c931afc46eb23efaee76c8696d3e4eed74ab1c71157bcb924f38ee912c8a90a6521a4
-libunistring-checksum = 01dcab6e05ea4c33572bf96cc0558bcffbfc0e62fc86410cef06c1597a0073d5750525fe2dee4fdb39c9bd704557fcbab864f9645958108a2e07950bc539fe54
-libxml2-checksum = cb7784ba4e72e942614e12e4f83f4ceb275f3d738b30e3b5c1f25edf8e9fa6789e854685974eed95b362049dbf6c8e7357e0327d64c681ed390534ac154e6810
-lzip-checksum = e2e229899002072322a5bf7fb7ef37ff7cc2d0ded7d6525679ac29cec5c1534de89f76bc01e15c3d76584099957d596b9e5b32d3f9cbfc6bc8d6370fc67d7d96
-m4-checksum = a92cad4441b3fd7c033837389ca3499494523d364a5fda043d92c517051510f1758b3b837f0477f42d2258a179ab79a4993e5d1694ef2673db6d96d1faff84fe
+git-checksum = 4556c6e4ee5a2f583109c8b8811ca7bc66b1c717be4ffbdec77b6c9da49b2eb3a77fef538ee9a2dc599bfdb2baa0e436ca61f5601225cf80d16333a82ef79d51
+gmp-checksum = 2bec8840bceaeac542ce1f7870d5b971b631b055b49751ba4f78f98229d7eb9cd97c0a668f6d7cf81a53bf0b3d5d70e682af523f8f0eee0d7390727ff2bbb271
+grep-checksum = e8c28da23fcef11825c54794b3eebffd0eaf84b7ebf5e187fd06b5d4aeff2af1ac097f0166151b3f11f332dc72abf6097188d578f549496f4c7c96ccf479a61e
+gzip-checksum = 48db13116543ffff39ce03a058e5ca279d93581b8aead3b857c41b0aa3028aa787d5bb21ee18d002565ba3e016fed60d55062b3fd91c41a9877f9f7febc6ae27
+isl-checksum = 00821ccdde36540869b47b1f68837183dfc8eb0ae580a36ba92c25308618a25680adc8de7b9df4d93851b300d7e457c931e7ff3a40fa90e336c74bcab3504e41
+less-checksum = 31f733ecf4170b4f5dcf467b902d0753833f852739b03bf611137aea3672c03e00e9418fd5e289e82624c2dd42b0de06cb65a7a637dae78e7647e5c6ecf9fb57
+libiconv-checksum = 396be5305f899619596b72ccc8a192c5fcc8e12163fd23376833c957ee44dbf3d39461360bf7e32a049f9f12a851da7836bfc8a62842114fc10717ac92762987
+libtool-checksum = 379a16baf2123d3cdd28cf8e35e4bb1e0326ae7f431c42ab2a3bd42ccac99a622e5ff0a68703b81614c147bc02178612a5cecb105b8943937a05c0b3ec91fea0
+libunistring-checksum = f1e92717fc043c2d7c454e44700559b0bd75457fdf3da5e803d9d58d8ebdff261bc73f380f6350bb04ce04071687c0317d09b4e8615003187948be1cd4d0bab3
+libxml2-checksum = 0fdc16aa7536adfe1deaadd19cdc20101dd3b081bd0a2e59d8ecc2965b2ef4c30d2e2447ab5b0cdb861c57ddb89ace1bd4ce120d9436b751b37724a90981ba8c
+lzip-checksum = 8d063a5f0609caa4d568f7bad4c67fcdee70a16c37e67b9d3cccbae53f09c14fa8590816aeb37a3fe0bc71a642c55e9fb4b371c0f68585be9564af22584d5c99
+m4-checksum = 7f8845f99e64d6a45859b9d80b03352a5526b3de0311ca4d6dd6850e504d26dfc90cd21d1640b10382f786213f8fdf20183bff424b3c41ea11432315993ab829
make-checksum = ddf0fdcb9ee1b182ef294c5da70c1275288c99bef60e63a25c0abed2ddd44aba1770be4aab1db8cac81e5f624576f2127c5d825a1824e1c7a49df4f16445526b
-metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a
-mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628
-mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88
-nano-checksum = d101e7f4802c079254e79340b433749dcd699fa9adec3f96e4218ec12f066a1f6b0954c27254bb6f019bc370ee2116817717870f4e2bc782c552442f2cc75195
-ncurses-checksum = 4c1333dcc30e858e8a9525d4b9aefb60000cfc727bc4a1062bace06ffc4639ad9f6e54f6bdda0e3a0e5ea14de995f96b52b3327d9ec633608792c99a1e8d840d
-openssl-checksum = 1523985ba90f38aa91aa6c2d57652f4e243cb2a095ce6336bf34b39b5a9b5b876804299a6825c758b65990e57948da532cca761aa12b10958c97478d04dd6d34
-patchelf-checksum = 39745662651cf0a9915685b2767a611ceab4286f8fa57eace342b3f44248431616e8563d4ac6709c97d8534229c73c05470239e462b7e74b36bf629a876dfbad
-perl-checksum = b00f3482f6961be043349a09445227e99472a8ae804919bfa0641de5bbd683249deb607f3b5c6c44ccfcf916408eac125132f9660191d574de0a9d1f17892bc1
-pkgconfig-checksum = 4861ec6428fead416f5cbbbb0bbad10b9152967e481d4b0ff2eb396a9f297f552984c9bb72f6864a37dcd8fca1d9ccceda3ef18d8f121938dbe4fdf2b870fe75
-readline-checksum = 41759d27bc3a258fefd7f4ff3277fa6ab9c21abb7b160e1a75aa8eba547bd90b288514e76264bd94fb0172da8a4faa54aab2c07b68a0356918ecf7f1969e866f
-sed-checksum = 7de25d9bc2981c63321c2223f3fbcab61d7b0df4fcf7d4394b72400b91993e1288d8bf53948ed5fffcf5a98c75265726a68ad4fb98e1d571bf768603a108c1c8
-tar-checksum = 4be18afeac54aec4af074cf2358cfade5aaebe2041c5075c5764a81114df4d002e90b28f4444bd1430783e7d6bed82abd0440ef5cb244695f2e56a9a41b42fbc
-texinfo-checksum = da55a0d0a760914386393c5e8e864540265d8550dc576f784781a6d72501918e8afce716ff343e5c2a0ce09cf921bfaf0a48ecb49f6182a7d10e920ae3ea17e7
-unzip-checksum = 0694e403ebc57b37218e00ec1a406cae5cc9c5b52b6798e0d4590840b6cdbf9ddc0d9471f67af783e960f8fa2e620394d51384257dca23d06bcd90224a80ce5d
-valgrind-checksum = 5695d1355226fb63b0c80809ed43bb077b6eed4d427792d9d7ed944c38b557a84fe3c783517b921e32f161228e10e4625bea0550faa4685872bb4454450cfa7f
-wget-checksum = 95fb064f0d79b0a3178a83322f58a85a3a036fb300ed759eb67a538f0bbacdd552f6cbeb60d63b4f0113e8467d923a5ce7ac5570b7a4ce1733b3dfd559bb33b2
-which-checksum = d2f04a5c5291f2d7d1226982da7cf999d36cfe24d3f7bda145508efcfb359511251d3c68b860c0ddcedd66b15a0587b648a35ab6d1f173707565305c506dfc61
-xz-checksum = 7443674247deda2935220fbc4dfc7665e5bb5a260be8ad858c8bd7d7b9f0f868f04ea45e62eb17c0a5e6a2de7c7500ad2d201e2d668c48ca29bd9eea5a73a3ce
-zip-checksum = c1c3d62bf1426476c0f9919b568013d6d7b03514912035f09ee283226d94c978791ad2af5310021e96c4c2bf320bfc9d0b8f4045c48e4667e034d98197e1a9b3
-zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae
+mpc-checksum = 85e044749c2a001a70af2c11fc4bac58709ca7df11bf6da3b03cca852ef336eb37c4fb1dafdffde2d13df35caa7c296a7cba19a4625b82dc3cccc5066ac95774
+mpfr-checksum = 23a30040511809b6a8ed33d5ef83f903e987f0e4b8e87c9bfa627fdf0ca6400330bda4fd727cf1d37f04f7804c77663ed983c6b5ed26f5d5bd772bf13f1f9eb5
+nano-checksum = e1ae28710ce05ef9c73357b9fb556fa6a7e670ae6fd786339677cb8a154446029dd9c4ead4eeab014691e941211a2d2c9faefc7695d1b97c2b8b445ba77ff067
+ncurses-checksum = 68b7c0388304791ce82ab86ea5c5725357f07bbae0c230af3e4722f75617778b6e28d1f0c1d65871379670e54fcc96ecd54f529a3462d207f3d930e6dad5a2dd
+openssl-checksum = f913eb1f654f702161e524a02ccdd028e26d418f26e334069d77ee0134f094809d5c86bfd65e8d05c9bf3d4f10d58a9f3c4452c8d6120741a90541114d82d5b6
+patchelf-checksum = f74409c00e7e50a88590267fa0c173f71239f1471985792f7bcdab750d202a9a25383c015987608bbcd6ace5b3642645d46dba63199ba54fabbcb51ae7fca8f6
+perl-checksum = 47c37f2698d7f46d2bd8a19abfd329ed58509a9eeb6c9ddb32e435434fcacd5b70419c01d0fa10d1c599cf43248ebc1538076e6bdedc56624fac887d480b8b8d
+pkgconfig-checksum = c37ab9336ac15a73bf5a23101f3fd8a04810f39b0679634e420e5d7bbd60a80cfc919122694cf83965beb071d2780681efc8d954ce99d77eb235a4dc7497e250
+podlators-checksum = c653205fd1e8e570750584cdb3a813a1250ae6f66d4e654b3521b80052867a3a6ba15ad3d7c8a22065f1febc36175257f9b5685570fcf0a87908c2dc9d42cb3d
+readline-checksum = 90d9571609b90f07573f831878f5131df17f1baabc064398c95915f13d44ea0907e41218be089377523751ca5b02a8486b5306ef6d0245432a0c224b7aa7fb94
+sed-checksum = 90d8fa16b2570baee061c128d6db688a3354796a6499014f12dc4c5966b34cbb8a04a47914e4ff8dc1815444ad0235565efef2a327b67c485e3324c2a1d07d78
+tar-checksum = 98d938d76a55dca1d1ba9a13f1aa2a3e8ae25ea422843e93daab98d373f4a72eebf052c88c87122ac16ed629863dc3fdb86dddf18d3ab5a2565b06f49b7d02bd
+texinfo-checksum = 6a706bd0f973b9bbe4fdbc3bfd475cc9699eb410d276cbc19a73255924313006e1b80a87803fa30f7245e3fcb610c829da31e38c91e791e19f11ca8b998914c4
+unzip-checksum = 5c1f3c417d5feed64b8c5dbc26b51dd84130b9ea43d77e810cc9e82cee6e965fa76e2636e5ba11a029eae3454a815a6081cc2828079fa3994c511d555b82f12c
+valgrind-checksum = a99e09e6d957ce435e64f4ce7b1a14e7e266282578171ce4e3bb3f405ce304e4df3b43d2fca59a6024c176f60c2ac82b3992afc810386e8de03c72f262b32702
+wget-checksum = cbce817981864d4dc424b330126b0d06231907004f1fcfc8d105ffc043bab59e93421738d36cf95013cc03b5b9f9813b1c242a3ef3926a907889ca78dfb336d4
+which-checksum = f886f5828359584b204f20a3b712d29c14879288e6255ab612784fce167bc9467c246bf48f9c52780069a95fe25761c3edda358428893967f4a1a1e5e874b2d5
+xz-checksum = a92bc2619f668a9e462945423035a090bc91c010d0788db8fb300851a3f93c04af2d433bc545195979d51312f59667c5814e46dd711b67fa8f89c0864873b81c
+zip-checksum = 433eda6a27074746a960952fa3b08028d5ba43fe976a1306dbace9209be5f89aa0554b17bba5815cd00984c0f64559c5fa0b754b620f6d646a2b145a8b599acc
+zlib-checksum = 97493906504451830655b300b4144deeeb9f41bdb9b3f3a3d5635c2b16bf90d543841dc70d028f1cee6b52ad1c604fdc18b18f559d1e4ed6523e6b3ce76fd8c5
@@ -71,150 +70,208 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff
# ------------------------------------------
#
# These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/TARGETS.conf' will be built as part of a
-# project. To specify a software there, just remove the `-checksum' suffix
+# 'reproduce/software/config/TARGETS.conf' will be built as part of a
+# project. To specify a software there, just remove the '-checksum' suffix
# from the list below.
-apachelog4cxx-checksum = aa59ce549c2c5cbeec031361dfce09cdfc3e62ee3bc9ecbc809507b7ec878c14409b98536b7d13c27690809c8e9d5ebafc3589c9fb5e4aecd5cc064943ae7d6b
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-apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536
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-atlas-checksum = bf17306f09f2aa973cb776e2c9eacfb2409ad4d95d19802e1c4e0597d0a099fccdb5eaafe273c2682a41e41a3c6fabc8bbba4ce03180cffea40ede5df1d1f56e
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-cdsclient-checksum = 2d7abf0079189b9dd19cb8919061445fd19ea9f7dfd54e8ceee26b743218cf62ab00eba0147abe82d9294223927f04b4cc3328620dfc9184a7049f8d515b29e4
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-gsl-checksum = 0be8240715f0b86aba2c63d9f12da4dba4719d4e350e9308d279e0dd3b2f0519ea26fd2e38a17f3e8cf43aacbaa2455207a7ca0d6c305f3b8725e8ece2250a74
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+openmpi-checksum = 88c73fd708dd5fe3a893d5517425a8a4c3e252fae4715df9a9b0f2311abe94cf5f71be92f153820fbaeb32c7d0ac0175d5165bdadcadc731427309102182c1bd
openssh-checksum = e280fa2d56f550efd37c5d2477670326261aa8b94d991f9eb17aad90e0c6c9c939efa90fe87d33260d0f709485cb05c379f0fd1bd44fc0d5190298b6398c9982
patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187dad77d1413f0eb3319b3fe4df076714615c98b29df06af052bb65960fa8b0c86bf
pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb
-pixman-checksum = 1b0205dbe9d9185c68813ce577a889f3c83e83fbd9955c3a72d411c3b476e6be93fc246b5b6ef4ee17e2bb8eb6fb5559e01dff7feb6a6c4c6314f980e960d690
-python-checksum = 392459354b8438f76670ec2086b4618ee21f615ca4b22e5dbb366273665a470de5047a3f241925a62b60bf3cddde5984a05144a55d0c5ced43342f5b94576952
-R-checksum = b7330613ee9795f54cde3dd9f7509be83d9156fb8577c17179727ee01450db27704249f68bd48e0331e2df09c2d9833d8bb019c4f9ce9ba669df74650ff2e842
+pixman-checksum = 333732b99994f7ea636d647e0b6123075351b27601b5b6370c9bc821a1ab3921386ddb92b51e015f3fc35104ba09be1e0d7bef47f0b4f73036b01d1d70396dd9
+python-checksum = 30cc55a4ca7d65c55a967d9c43e2ebeeed2905f2fab01540140537e0384f943b6ab6699b1c2b91cb2b3834fe7d3d1976aec58ba4c5b9f209bc0ea9a0ff248332
+r-cran-checksum = 54cc07956a70c09b5a533188eb063d2a9dc67a8aa5648ec7f9c107f626220c9f6e17ab7175e65dd54a8d608a1ca4106c8ad2856709eb995ab66439b5f033e725
rpcsvc-proto-checksum = c3011d7d7ef97a4a751f6921df1a23e1dd8ac50fb0690c759d37010ed7be27968a2130e3b8872cb48d5914216f9d539096a424f1ec38a75f7ed899748151c6f4
scamp-checksum = 35034a367d2cd09dc51e727e0f23ef6234edc0d978fd71cda1e80391d86af160138cb57281f7f7f9047e35b1246a0de6b235414086a62524413ed423f498583f
scons-checksum = 0477038b014674049f12899b64584d44a85283d521b2422561e42020a5ae296a5af005684087c3ff410ed3fcbdcc5ff61998bc429eb29513f2a864138ffc4945
sextractor-checksum = 4035710f9b8a20a0bb1a3913dab2dadd8444c179bf6dee425e0e8bb66a772944ea189bfce89fd791d316a790fc4b2cb15a62633b19d1d5331b1803dec2e70af7
swarp-checksum = 80f4ade59738df3d4c9b47bda04148b53c6ba995d523fa8d1e02fb5d952b6078a53cc7d273849a033505de127a4f318b95adf2bf5a2dc38e8cc9bdaf5658487a
-swig-checksum = 5eaa2e06d8e4197fd02194051db1e518325dbb074a4c55a91099ad9c55193874f577764afc9029409a41bd520a95154095f26e33ef5add5c102bb2c1d98d33eb
+swig-checksum = ecb1d940f584c23df036a8f77288916003f861851dfdf836ddc5bc45b95312f9259150084191c1d9f086c006e64e12a4db22f7ea382fbb71667b811b8f99995d
tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108
-util-linux-checksum = c95d26b9037d6b877a247e6aeb58d17aa80f7e1bd6b523a4e0fde559fe07b3d924ece6d373300fefb65d1f206b3f990aeddb3a03605040e72ce6d6ee88591021
+util-linux-checksum = 2e07b4765482182112c424cbfe5af0dc9c9a50918e335bf99846f3017b291f5df23e95c77942f2265e9b0d471201a0d53d3c79d916df1c61cf044a80e37f85ee
vim-checksum = 06ba43386fcf308520d88d7a68e9bc1fabd824b05078b8f9112500a2ad4e50a91f1a1c2925889b7c06dbce34307f12abf508e2172b05fd283f965cc06552eb6d
-wcslib-checksum = 8c98c4b575056e2d966b77a4bc951256d02ecee3a11847e140fd38d93afd0f76b3e906d590c952dc9fc58ceeb1ba062b19d8e1e676ee0032f5b7ed13a9dfa892
+wcslib-checksum = 008bb069bcc21f7944b37ca44e85aa5d343d44aeb24ad3920c2db716a984e3fb63cdad8fe05ae63b8850c5ce4ce5f81c524dfd14958ae38fcaef32f893814b45
xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c
yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02
-zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff229713bd197d203edfa17c2727700fce65a2a235f07568212d820dca88b528ae
# Xorg related packages
-util-macros-checksum = 3f51504b27f0478c136126f15110cf3cdbba218c4d74a8e974cca1381c6e8364609bd0c444f2fb19aa86a7f4e848dfce4f4da940463b224036f75a60b3d88619
-xorgproto-checksum = 2d10533e54987f293e1c8578aa742c38cf2fac8551db1d317cf5ee4a6a9600eced50f59c57c38b35dd210fe02d350294c967512f04cb9876d6c0c1f7e89cb199
-libxau-checksum = 3ca454ba466a807ea28b0f715066d73dc76ad312697b121d43e4d5766215052e9b7ffb8fe3ed3e496fa3f2a13f164ac692ff85cc428e26731b679f0f06a1d562
+util-macros-checksum = b29c388c60b8318a478656f0552210b2194ee302c082f694e5426ac5c3f4b97fc3e377cd6a7b2b97c3da3442cfb4a5e42dbae18e151ae39f5f84554016a01155
+xorgproto-checksum = b9471ce92f2a5fee9d32710191d7df63799027214ceace60fb2ae8616c888ad142d2a131dea5acc768e86bc71719873c72c20a2863fa821790b96faef44f603f
+libxau-checksum = bdca8935aa1a52bcd2748004d26c7405725c18021a4d9a67604c98c1ec3957cc85b5d987d2fcd9fa4ae5e59b6bbd6ab75712beee2d448bd733a7e3ffeb18e62f
libxdmcp-checksum = cb1d4650f97d66e73acd2465ec7d757b9b797cce2f85e301860a44997a461837eea845ec9bd5b639ec5ca34c804f8bdd870697a5ce3f4e270b687c9ef74f25ec
-xcb-proto-checksum = de66d568163b6da2be9d6c59984f3afa3acd119a781378638045fd68018665ef5c9af98f024e9962ba3eb7c7a4d85c27ba70ffafceb2324ccc6940f34de16690
-libxcb-checksum = b90a23204b0d2c29d8b115577edb01df0465e02d6a8876550fecd62375d24a5d5f872ddd5946772ddba077cadce75b12c7a6d218469dc30b5b92bc82188e8bc6
-fontconfig-checksum = f97f2a9db294fd72d416a7d76dd7db5934ade2cf76903764b09e7decc33e0e2eed1a1d35c5f1c7fd9ea39e2c7653b9e65365f0c6205e047e95e38ba5000dd100
-xtrans-checksum = 4fea89a3455c0e13321cbefa43340016dbb59bdd0dbdb5b796c1a6d2a6b1fd63cf1327b769ab426286b9c54b32ec764a50cd2b46228e4e43b841bda6b94de214
-libx11-checksum = fc18f0dc17ade1fc37402179f52e1f2b9c7b7d3a1a9590fea13046eb0c5193b4796289431cd99388eac01e8e59de77db45d2c9675d4f05ef8cf3ba6382c3dd31
-libxext-checksum = 09146397d95f80c04701be1cc0a9c580ab5a085842ac31d17dfb6d4c2e42b4253b89cba695e54444e520be359883a76ffd02f42484c9e2ba2c33a5a40c29df4a
-libice-checksum = 2f1ef2c32c833c71894a08fa7e7ed53f301f6c7bd22485d71c12884d8e8b36b99f362ec886349dcc84d08edc81c8b2cea035320831d64974edeba021b433c468
-libsm-checksum = 74c42e27029db78475e62025b4711dbac5e22d2f8e8a24be98a1c31b03c0fc4afe859928f851800ea0b76854f12147900dc4f27bbfd3d8ea45daaaf24b70a903
-libxt-checksum = 06248508b6fe5dfba8ceb4518475f656162351d78136eeb5d65086d680dabe9aca7bba3c94347f9c13ef03f82dab3ac19d0952ee610bc8c51c14cee7cf65f0b1
-libpthread-stubs-checksum = 5293c847f5d0c47a6956dd85b6630866f717e51e1e9c48fa10f70aa1e8268adc778eaf92504989c5df58c0dcde656f036248993b0ea5f79d4303012bfeff3c72
+xcb-proto-checksum = 385ea15eac6326b73849f1dae790619760f473f4c5471a3ccf990b01350931395e988cd83f632c94fe987eec74198f59835b8140686774710462e0019f90c168
+libxcb-checksum = c69c7e5d6c172aa0bd65d6f3ad25d9a8388194cf2281ee9c9e02baf73c351752b7c287fd04f8ee3429d5b55358806c81565046796263212379593db4e32c4287
+fontconfig-checksum = 12dfddb3b37d71555764fe97dcb439496f3fc0e6d34e4536a92eda1069cc78ceb1dda5b2c0b247f779a093a6c75c56afcac6f0cd099d897c2ce30740a9fbb183
+xtrans-checksum = 1c2fdd7cb906f012f7db5d42466734f89608bf3376b6bf4b115c2efbf71c4247587cc218ccfcfaa6d50f0cf336865d10fc604515b25bc6e95917db8acb7e3000
+libx11-checksum = 740cc5364d49cee8fd86f3dc0f43d7b358c94989717ea8991addea9b2307df6e5b2ae1f8f7aa3571f7294b8760c7aca7be9fdf5b477dec55da14e915dccafd7c
+libxext-checksum = 58f4e87f200bfde2b9a2cd85c1c39d5462b702e12274ffa5fae5bd3a08b3dfab1290b399c31224c86627d927106e4dbfcdec6152c11b169834442008228796d4
+libice-checksum = 9e3488abaff115ac919e5df85479044579802b38a10597425e13466c22c149ef56a8adba77e2adbbcccb8d2e72e23976313f4af3dcee66128b768c971c513932
+libsm-checksum = b9eec391f0438e85e32cf771afbb35bf215119ec31d9e31be40c1b653f2c3e894c2d19add0d6ff69e944d1230f681275e8abad86a8912ec37c1c41e0f1ce4d00
+libxt-checksum = 9ec0f95ae073360ea7a80ffca2dcd998c991363b79696550c4f88edf2c9cbf740caca23929660b77fffca4ca292465a101398e9e891cd00db85f8eceaa78cde0
+libpthread-stubs-checksum = a99695c007e17d81879d5c113652c5e1edab2d63aac9b2984c4f334d85e2cebc1d0b4e8134d6196ed8eea4d4da41972fca27bb8a0c76c2946460f785233a2c03
# Python packages
# ---------------
#
# Similar to optional programs and libraries above.
#
-# IMPORTANT: If you intend to change the version of any of the Python
-# modules/libraries below, please fix the hash strings of the respective
-# URL in `reproduce/software/make/python.mk'.
+# The sha512sum hash strings for the Python modules/libraries below should
+# correspond to the version numbers in
+# 'reproduce/software/conf/version.conf'. If you update the version and are
+# confident that the new version is safe to use, then you can update the
+# hash here.
asn1crypto-checksum = 44d442a6ddfa971e31e24712fe084368356deb5e1c4c3b3e813e0910931860215bc1c4f9eb2c4bd4fdef607c324086c096e9357068646efd28c97f2d4f85c62f
asteval-checksum = 4d64900b2f7dfdd098d6c8c102f9d9fd46f9ec265a54330e7d94479ba41f0ee0698855658e18b8b32b9c255159eb9a085af5f0306eb6508663d3fea7d2e00b4a
-astropy-checksum = c32e874d208f312f894643ab5b3d71dc37630e544da0ceb5ee998d752f9a055d32f6e4319f2cb6928637aaf8573bac58d2882bd636b6a89f5501e3ac7e5ab681
+astropy-checksum = 52b7feae68308445014665e3fc80201ca82955916fbe4d065dbb1a439885befb4f669932cec6fd7d359094138fab0ca188162efab764c4591d53896cdb335426
astroquery-checksum = 43846791d8469a26cf6bb8819db58b830cfe50a34bc0091c2e843dd7dc78b1317530855d432a3a567a9f6a6f4d2682382a32edc91ea01716246b99b3625ec521
-beautifulsoup4-checksum = 7aa77bc6008bbcbbbe91b0a850007ab237d2832b63a787fbd94b7cbf47d4276b185e0c61c134df73221406458edff2b75b6b8c2b53b543aa3bb1b0e2202dac5a
+beautifulsoup4-checksum = bf8fd3e54da63a506f294f0e5f1201fd46bf2edcc2db23e99eda995313b8a8d24db3cd2d1903853c539a9320bfb9eb4b29e311772bfddc0d125f0b4aec71e384
+beniget-checksum = 32a19d77323a0a21544ce7fbbb71cc5f4c66949dba280d81deb36f38364544d9fdfb3d24fc48a1ff6d251fb22c24357e81dd7fa4a7e6c11d8b931723e150a182
certifi-checksum = 6a6bf1ff98caefcdbf78a8c83e11e155368bacdd806f0ae0c6afa8f513667df6598e594b3584de61acdca3d6049f4a776937f2aa8672b602bd6db7b737f6074e
-cffi-checksum = af4fe47cf5d6f1126222898365cfa21e9f11d0e71b87d869014dbb37af30dca9ddf50c989030d0f610f50e8099e8dfd08a688d8c3629abbcc4f0294f5f91b817
+cffi-checksum = 50e2b8215ddedfa8f1d569680cc0023cf061c2c52b7b86b6b26ced56e5107b362aaf6dc10a77b9dbbbfca2e5611f7cfb42c59501f9ab7da29fb3ad3ccf418cb4
chardet-checksum = 61a03b23447a2bfe52ceed4dd1b9afdb5784da1933a623776883ee9f297e341f633e27f0ce0230bd5fdc5fdb5382105ab42736a74a417ddeb9f83af57455dba5
corner-checksum = ebd625ab1e4591b4c21d25ec706c35d37f560b727e1e0d6a79948c4a112ee6f21d3ca30162901a27715074e1345f3bdee1a0345c63e5fec24113e495fb094127
-cryptography-checksum = f14319e24d9dca52e74548cada5b78a6235f089ef875dbff4799e862f94da8b087f1b6e03e84dcef9fc7d7693c4a349c5f0cd54b8535806da777420ce8757d39
-cycler-checksum = b7d2ba19861ffaf4dea0444bfe68b5a6264a022d7b3f02c9ff5e5859e3901de12a90f8dc7469e995e09c418515b3df55dbf05a0cfe5368d40790a2c878a74819
-cython-checksum = 6216e63996e83b887cdcee6cd912d42e7da853640336b9190f5115d687848a902ee5a8edd6bfaef645c066b89e17dcd80ca1387688eb80a527ec23a0a4636e8f
+cryptography-checksum = 051b5007512521638981a8e975c7bbcb688b1a1c384babc81ba105c7bc2a7e776a8bf46af5939627528b2b57d99aaacf215a041018c47f6d3ae6d7a0e8eafccf
+cycler-checksum = bfd1b625c785b48f9795c4ef701ce1c8fdebaa0e82530b904ed7f481f644178834a1cbcdc6a2732bd5fa3a39f7bb543ce51b710a3e4101a6ecee89a6ff270ebc
+cython-checksum = 1db604326d0cbeb7b113bd163056ba1d4e3685aa66081911a836604dcb7f3654fedc91f4686a9e6514eed1f6cc8873b2d30ffbe6663844ce5bd04dbe5c120844
eigency-checksum = 1e7cdfc43071da5edba30a0d32cd655442b516f15c166b049a195d151dec8c20a2177ad69bed3bba4788a668fa25a4c551ef4990717ff98d5b2f407bffb214c8
emcee-checksum = dd60aace8879525fd3fe42b747d82170b24b2ed21f538f9186ba96b9d04c084812e3303f5d2e04119dabd2f9d3286d510b4d4a5324c71dd24b1c7e5f0a9a0ac6
entrypoints-checksum = aa1274362d3a4b00266103319ca51aa266605b4999c89a9d0673eb61bfae9e646cb0ec6b86c95544493f6fe048385a2c7641d64adca8f45815546fb1e663c858
-esutil-checksum = c1cf8e7912b16dc675fdc7195ecc2bbffcd156c1257b2df45afdf09cc487c49f2e18a66cd5520ab30c77e60abb8ca802e327075bdd0f23eb634cc4f5a7e974f3
+esutil-checksum = 7f1f22b0a05855819e3bd9bc2eee14942c2f536fb99f4af03575eb41d3d3fd1d2e6091ad076bfab4d51a8f30e213b607af35ed00d063fb2895b58f7a57cde5ae
+extension-helpers-checksum = ea62d537d0f76af9f975ad577d3a679e027fe0dd21f8a125ccb34bff1e4cfb69ecc15c8bceb406744033e91827fc8b78477e30e8f3cc45396bb6ed8102159b08
flake8-checksum = a25076bb7f978ca23af0f2016b30bf5fe4680371b4c0939361a6f8c496f3c846cf98ecadee35fc2dedd588116c8cd982529972dd2411ab139621912b69132a1e
future-checksum = c70565a660cf87c5e7e994bae0d4eb0b2b8b607ecb5ce65521c027bf0a39ce5699f0578413bd3c7edd5d01aeb1617de48dcea098a9e9021d8487a73007573030
-galsim-checksum = 11ecbfb9628cf85a4c25024c6f3a34bbdadf522f64e4e93e6428b545c65a48906a05eb7774d0faaacf52a48dddfd599bfc7cc7252ca854a18c3930f116533a3c
+galsim-checksum = d7e354778de87cf5c8964a7f252025eeeabc04ef2fb673c35adc536b449442aca261e2bd96befaaa872065376ac79cbe23d1ee7d034bcab5916f74b98112b8b8
+gast-checksum = 8311f48788daf060bee54ad8986eae054c2a426adcf97f1503cde37c4da2827cd0f664188e51f5c2f932a0a4ded78166a8466465595a640106060c8b6c7072a5
h5py-checksum = c49b04f7dcddf03f36d4f063d79ecbe544e0b1daee432d4a76cfa83dac3a1f2cb144f40a74fb85ea17cb5b778f57f709969ea5d1a2afc5bdd5aecbc9d732898d
healpy-checksum = installed-with-healpix
html5lib-checksum = 35939b4450893864da04e735ee5e0addacf1dd34bae6a6909c76572abf6bfded446a78a713dfde91c1485ba45867d7abeb6a45cf0545c16ea968707be7de5dd2
idna-checksum = 8ca5cfe6350c51250bafdac7c6e4ddd54c4a5d6bf7acbcef896760a759868c8e9df1fdf550121d8512fa3eb316dcf031ec6058e03b4f66eadee21b63e2187d33
jeepney-checksum = 43083994a7c6af84a5a68d3ff8f6dc4d9129ce9fa55517838fb62d9f62bb78bdf52067649d0b95d08d689b7d7475cb9b2a956662e265a776ad42dcf4ccc0ab63
+jinja2-checksum = db19498dbc9bd6419b474fbb465ce8c689b96f72d33ed1a31cee3c42e2c545dfd0fd5bfca610075e2e126fbdd27300a73efd76fb7ea449727ed61a6127806dcd
keyring-checksum = 3863f2cd89131d7e927e55691b4eb4b7c2599af189525293d0948aef5215efbbbd74d45db3cd4885ba5b18a79f0fa0b0edc3783a020a6702f6a6fb7ed86b2cf2
-kiwisolver-checksum = 80ed3d7429a2ed4944aa09766bebac2709a3a0e0a184ff414f04bf3c7ec3034ea7d0f70dff319922b870dedaf13d64fc87eff86a82e720ec93a2510885ad738d
+kiwisolver-checksum = d5aec6da0a5038f969227eb6320bf6ccdae2668b5730fe3e94ea1be5a2e64d121516abea16764c4659e05d821d044e76d97054385c0bc62780c3b0cd82468aed
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+
+# R-CRAN packages
+# ---------------
+#
+# Similar to optional programs and libraries above.
+#
+# The sha512sum hash strings for the R modules/libraries below should
+# correspond to the version numbers in
+# 'reproduce/software/conf/versions.conf'. If you update the version and are
+# confident that the new version is safe to use, then you can update the
+# hash here.
+r-cran-cli-checksum = 29782b4cb00a94536c871276835a5f762f3deca8355c35b9366434cd2873604ea20f2746ef624eb4e6ec1514cb9079e8c101e50ace85fb1336f3befcf77be244
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+r-cran-digest-checksum = 44a2978be00b7a90f88f05ad8ec114fb07a8e3816fa263749d44aa61f7706c3f802feaa7b7e9267cce1d0dd5c49e7f7ae3ccd9f968a7025aeef16181f7c0d70f
+r-cran-ellipsis-checksum = b82fab404c3e1bb9df2f7ee5ae6e62b237c15c661a417adabbd86f984a2128970e0ad5581e9a8b7541b9f9b07418de469398e6bc06775bd4a3c8bc1472947f62
+r-cran-fansi-checksum = 50a7a8e597b89b49fa33fa93861a906c38508a42980072027a5f2746f047b82333074248e5c7724faf4559eb6a4cdfe7a8ccfd2dc5b637a8f3d5a8584afdbc75
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+r-cran-glue-checksum = 5e679884f45a00a011e284f59370cabc2d470515351324ba2748b06ec780d65b6f64901eb5589713e9b122b103e58cd040eb342c88d7d4a3734a6e23064552d1
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+r-cran-gtable-checksum = e3cc4328bbb42a59ff1b315f0b030a9fe240bc6b6844f460835c25497179c3a5d9ea10fa2af1aec4b7384e78a564eb99eb4c51067f98a57ef919f2e11f6fbafe
+r-cran-isoband-checksum = 253d0b768492b64d5c32ab20f3b896cfe206305b8a53b31055813bc6957069eb76ea94a403b931fdada06ab33ee91f7105ef080fcd88af0c05860865950d99d1
+r-cran-labeling-checksum = 0ba0cb33863f79868ec6f2289f29ddc742cc620b7ed85364099448d39d71a51cce45028097100aeeaf8a8a7e4ad0982b459ef20a15faed9c5c7db79e9f9b01fe
+r-cran-lifecycle-checksum = 1ac7aafb41925d19abfd78f454d1acd5102a72ee7017840f14cf54d035cf3999d5b6dc2979b00214358e3c26dfac3407c8b525b434e8882c123a92a132bb07df
+r-cran-magrittr-checksum = b0bca6000602b90c996efc3681799a8a965a5bb90eb5e3436b7a26be15e5a219ef6300f4086f0b6efda734272775688a8ca77a4094eda429926a9179125b87c7
+r-cran-MASS-checksum = 0d22ff69cff1414bf52d11aefd75b442c9c8fecb343fe3733c7b28a6b881f3c87ac8b6e4b0d76709c36e612523ef386d207d403c2292881c083e03d21b3709ec
+r-cran-mgcv-checksum = 83df262152d9ee5081b3d16711b5cae3860f7dd879f97db014b987edd6b110b11219bac0e07f8ca04169181291aea76399d465b9bf0e96a1b6aaf83692fdf5bc
+r-cran-munsell-checksum = 59536096c637d84b80f097bf400bcbb9fcb7ddf6267ce6b026e3c7b3cbcf548caef118439a1928dd8833359a18b14e49f38fe90ea7919c28c215b3b297c036a3
+r-cran-pillar-checksum = dd2bc53539ec6838cb8d5bb5ddf30cff9c43c5de0f8d148374d5a394385429a06243db48e7cf6bdb463bad7a130fb47b172ceaac8d04ca3205b4c4210ab672ff
+r-cran-pkgconfig-checksum = 0b636d9b1233a00974ac93eb2a1e0ad6b552fa043bfe9743ec74ef884c1d01a73c372586516abca8772a836c50dcd9eed4d10c50f6883fc68ba2494e79872aaf
+r-cran-R6-checksum = 5986510ff19c1e0129bb0b88d72020d30255e26d6da9a40c123b7b0c42c3e121188c8de34b79ad5eb0e0390eb4d59f2b7f0224b58679459bec0c4d677dec6ea9
+r-cran-RColorBrewer-checksum = 62aae85a0cf349a58ff51922886f71e2a9dc7b9548b061390f3b370f240bcec72340b3ebc03077a0374ce18ccf16121247e0500eca875ef2ab2f755c809e8f28
+r-cran-rlang-checksum = 8dc647e59dc767471345f9cfda7b77316215b0bf5a96e28f63e216d80f239ba9ed260b90926d175080e256d645f9a1b621d7602bfe27c32d0151758753b6cac8
+r-cran-scales-checksum = a1c693f993010613a33b9a165d5f853ad5f4fbbd790deae2bd5b19adc6ea0adbf27962e0f56807297ec56a71a6a5f57e3aa0ef78c266e74dc600da34c24d16e8
+r-cran-tibble-checksum = 4a4953b9083064ba10e240e304617f0b2c65039eb188f56761cfac228e99186054b543aef045607b63e5ebf9da2d20255f0ae724fd974c497507706d21a92864
+r-cran-utf8-checksum = 51b98a3fd07dd82fba249ff78f6e8b1318592151be49f1fe98c061051dca4d4506f7c7c8f1ebccadab4312cef7e01f700b39f4d5a6ba0b7227acd27e028f515d
+r-cran-vctrs-checksum = 23cde893f027f876f37b704a5074fafbbc376b85a053ccdc2862a3e6dc0b68ae2ac3511e2c61ad7a0a0d55524d3f3b724f39a4eeaf1a855ace62634ddea04b4f
+r-cran-viridisLite-checksum = f59a771b4cdca74df641c936812a008bdec99578cd1c82ee8f3119087dbdc72e307b2f3093df971ee7166c010a246fb5ef6c05cec4e51f7cfe721f3343e0fd6a
+r-cran-withr-checksum = 97877fa1ec21244285366818ad51dbe9c5086b377c1217d4ffc250a1f83cd142cc28d35f9aac0527f26bb2e3f0b399537b386a27de2fe546c301029f59614f65
diff --git a/reproduce/software/config/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg
index 3a3171e..09c1627 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice and
@@ -18,7 +18,7 @@
# IMPORTANT NOTE
# --------------
#
-# The `ALL' grouping does't apply to ATLAS!!!!!
+# The 'ALL' grouping does't apply to ATLAS!!!!!
[ALL]
library_dirs = @LIBDIR@
diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf
index 8db0ce1..64de818 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) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 f1454c0..4dfb407 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 Boud Roukema <boud@cosmo.torun.pl>
-# Copyright (C) 2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2022 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2021-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 2cca87a..ff3dad0 100644
--- a/reproduce/software/config/texlive-packages.conf
+++ b/reproduce/software/config/texlive-packages.conf
@@ -1,10 +1,10 @@
# Necessary packages to install in TeX Live.
#
# If any extra TeX package is necessary to build your paper, just add its
-# name to this variable (you can check in `ctan.org' to find the official
+# name to this variable (you can check in 'ctan.org' to find the official
# name).
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice and
@@ -12,13 +12,15 @@
# warranty.
-# Note on `tex' and `fancyhdr': These two packages are installed along with
+# 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
+# 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
+ mweights fancyvrb
diff --git a/reproduce/software/config/texlive.conf b/reproduce/software/config/texlive.conf
index 94a4c89..950dd4f 100644
--- a/reproduce/software/config/texlive.conf
+++ b/reproduce/software/config/texlive.conf
@@ -2,7 +2,7 @@
#
# installdir: Install directory
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 a311524..7177411 100644
--- a/reproduce/software/config/urls.conf
+++ b/reproduce/software/config/urls.conf
@@ -3,8 +3,8 @@
# If un-commented the URLs of this file will be used. Otherwise default
# servers (primarily on 'zenodo.org') will be checked for the tarball.
#
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2020-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 Raul Infante-Sainz <infantesainz@gmail.com>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice and
@@ -19,15 +19,15 @@
# -------------------------------------------------------------
#bash-url = http://akhlaghi.org/src
#binutils-url = http://ftp.gnu.org/gnu/binutils
-#bzip2-url = http://akhlaghi.org/maneage-software
+#bzip2-url = https://sourceware.org/pub/bzip2
#cert-url = http://akhlaghi.org/maneage-software
#coreutils-url = http://ftp.gnu.org/gnu/coreutils
#curl-url = https://curl.haxx.se/download
-#dash-url = http://akhlaghi.org/maneage-software
+#dash-url = http://gondor.apana.org.au/~herbert/dash/files
#diffutils-url = http://ftp.gnu.org/gnu/diffutils
#file-url = ftp://ftp.astron.com/pub/file
#findutils-url = http://ftp.gnu.org/gnu/findutils
-#flock-url = http://akhlaghi.org/src
+#flock-url = https://github.com/discoteq/flock/releases
#gawk-url = http://ftp.gnu.org/gnu/gawk
#gcc-url = http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version)
#gettext-url = https://ftp.gnu.org/gnu/gettext
@@ -36,8 +36,7 @@
#grep-url = http://ftp.gnu.org/gnu/grep
#gzip-url = http://akhlaghi.org/src
#isl-url = ftp://gcc.gnu.org/pub/gcc/infrastructure
-less-url = http://www.greenwoodsoftware.com/less/
-#libbsd-url = http://libbsd.freedesktop.org/releases
+#less-url = http://www.greenwoodsoftware.com/less/
#libiconv-url = https://ftp.gnu.org/pub/gnu/libiconv
#libtool-url = http://ftp.gnu.org/gnu/libtool
#libunistring-url = http://ftp.gnu.org/gnu/libunistring
@@ -45,15 +44,15 @@ less-url = http://www.greenwoodsoftware.com/less/
#lzip-url = http://akhlaghi.org/src
#m4-url = http://akhlaghi.org/maneage-software
#make-url = http://akhlaghi.org/src
-#metastore-url = http://akhlaghi.org/maneage-software
#mpc-url = http://ftp.gnu.org/gnu/mpc
#mpfr-url = http://www.mpfr.org/mpfr-current
#nano-url = https://www.nano-editor.org/dist/v$(word 1, $(subst ., ,$(nano-version)))
#ncurses-url = http://ftp.gnu.org/gnu/ncurses
#openssl-url = http://www.openssl.org/source
-#patchelf-url = http://nixos.org/releases/patchelf/patchelf-$(patchelf-version)
+#patchelf-url = https://github.com/NixOS/patchelf/releases/download/$(patchelf-version)
#perl-url = $(shell echo https://www.cpan.org/src/$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}'))
#pkgconfig-url = http://pkg-config.freedesktop.org/releases
+#podlators-url = https://www.eyrie.org/~eagle/software/podlators/
#readline-url = http://ftp.gnu.org/gnu/readline
#sed-url = http://ftp.gnu.org/gnu/sed
#tar-url = http://ftp.gnu.org/gnu/tar
@@ -73,30 +72,31 @@ less-url = http://www.greenwoodsoftware.com/less/
# ------------------------------------------
#
# These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/TARGETS.conf' will be built as
+# 'reproduce/software/config/TARGETS.conf' will be built as
# part of a project. To specify a software there, just remove the
-# `-url' suffix from the list below.
+# '-url' suffix from the list below.
+
#apachelog4cxx-url = http://akhlaghi.org/maneage-software
-#apr-url = https://www-us.apache.org/dist/apr
-#apr-util-url = https://www-us.apache.org/dist/apr
+#apr-url = https://archive.apache.org/dist/apr/
+#apr-util-url = https://archive.apache.org/dist/apr/
#astrometrynet-url = http://astrometry.net/downloads
#atlas-url = https://sourceforge.net/projects/math-atlas/files/Stable/$(atlas-version)/atlas$(atlas-version).tar.bz2/download
#autoconf-url = http://akhlaghi.org/maneage-software
#automake-url = http://ftp.gnu.org/gnu/automake
#bison-url = http://ftp.gnu.org/gnu/bison
-#boost-url = $(shell vstr=$$(echo $(boost-version) | sed -e's/\./_/g'); echo https://dl.bintray.com/boostorg/release/$(boost-version)/source)
+#boost-url = https://www.boost.org/users/download/
#cairo-url = https://www.cairographics.org/releases
#cdsclient-url = http://cdsarc.u-strasbg.fr/ftp/pub/sw
#cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c
#cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv)
-#eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz
+#eigen-url = https://eigen.tuxfamily.org
#emacs-url = http://ftp.gnu.org/gnu/emacs
-#expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz)
-#fftw-url = ftp://ftp.fftw.org/pub/fftw
+#expat-url = https://github.com/libexpat/libexpat/releases
+#fftw-url = https://fftw.org
#flex-url = https://github.com/westes/flex/files/981163
#freetype-url = https://download.savannah.gnu.org/releases/freetype
#gdb-url = http://ftp.gnu.org/gnu/gdb
-#ghostscript-url = $(shell v=$$(echo $(ghostscript-version) | sed -e's/\.//'); echo https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs$$v)
+#ghostscript-url = https://www.ghostscript.com/releases/gsdnld.html
#gnuastro-url = http://ftp.gnu.org/gnu/gnuastro
#gperf-url = http://ftp.gnu.org/pub/gnu/gperf
#gs-fonts-gnu-url = https://downloads.sourceforge.net/gs-fonts
@@ -105,28 +105,33 @@ less-url = http://www.greenwoodsoftware.com/less/
#hdf5-url = $(shell majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src)
#healpix-url = http://akhlaghi.org/maneage-software
#help2man-url = http://ftp.gnu.org/gnu/help2man
-#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/
-#imagemagick-url = http://akhlaghi.org/maneage-software
+#libpaper-url = http://ftp.debian.org/debian/pool/main/libp/libpaper/
+#icu-url = https://github.com/unicode-org/icu/releases
+#imagemagick-url = https://download.imagemagick.org/ImageMagick/download
#imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit
#lapack-url = http://www.netlib.org/lapack
-#libffi-url = ftp://sourceware.org/pub/libffi
+#libbsd-url = http://libbsd.freedesktop.org/releases
+#libffi-url = https://sourceware.org/libffi/
#libgit2-url = http://akhlaghi.org/src
#libidn-url = https://ftp.gnu.org/gnu/libidn
#libjpeg-url = http://ijg.org/files
+#libmd-url = https://archive.hadrons.org/software/libmd/
#libnsl-url = http://akhlaghi.org/maneage-software
+#libpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/
#libpng-url = https://download.sourceforge.net/libpng
#libtiff-url = https://download.osgeo.org/libtiff
#libtirpc-url = https://downloads.sourceforge.net/libtirpc
+#metastore-url = http://akhlaghi.org/maneage-software
#minizip-url =
#missfits-url = https://www.astromatic.net/download/missfits
-#netpbm-url = http://akhlaghi.org/maneage-software
+#netpbm-url = https://sourceforge.net/projects/netpbm/files/super_stable/
#openblas-url = https://github.com/xianyi/OpenBLAS/archive
#openmpi-url = $(shell majorver=$$(echo $(openmpi-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://download.open-mpi.org/release/open-mpi/v$$majorver)
#openssh-url = https://artfiles.org/openbsd/OpenSSH/portable
#patch-url = http://ftp.gnu.org/gnu/patch
#pixman-url = https://www.cairographics.org/releases
-#python-url = http://akhlaghi.org/src
-#R-url = $(shell majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}'); echo https://cran.r-project.org/src/base/R-$$majver)
+#python-url = https://www.python.org/downloads/
+#r-cran-url = $(shell majver=$$(echo $(r-cran-version) | sed -e's/\./ /g' | awk '{print $$1}'); echo https://cran.r-project.org/src/base/R-$$majver)
#rpcsvc-proto-url = https://github.com/thkukuk/rpcsvc-proto/releases/download
#scamp-url = http://akhlaghi.org/maneage-software
#scons-url = https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download
@@ -149,8 +154,10 @@ less-url = http://www.greenwoodsoftware.com/less/
#libxau-url = https://www.x.org/pub/individual/lib
#libxdmcp-url = https://www.x.org/pub/individual/lib
#libxext-url = https://www.x.org/pub/individual/lib
+#libice-url = https://www.x.org/archive/individual/lib/
#util-macros-url = https://www.x.org/pub/individual/util
#xcb-proto-url = https://xorg.freedesktop.org/archive/individual/proto
+#libxcb-url = https://xcb.freedesktop.org/dist/
#xorgproto-url = https://xorg.freedesktop.org/archive/individual/proto
#xtrans-url = https://www.x.org/pub/individual/lib
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 102ebbd..575cdd6 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -1,7 +1,7 @@
# Versions of the various dependencies
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice and
@@ -15,47 +15,47 @@
# Basic/low-level programs and libraires (installed in any case)
# --------------------------------------------------------------
#
-# CLASS:BASIC (important identifier, don't modify this line)
-bash-version = 5.0.18
-binutils-version = 2.35
-coreutils-version = 8.32
-curl-version = 7.71.1
-dash-version = 0.5.10.2
-diffutils-version = 3.7
-file-version = 5.39
-findutils-version = 4.7.0
-flock-version = 0.2.3
+# CLASS:BASIC (important identifier for 'awk'; don't modify this line)
+bash-version = 5.1.8
+binutils-version = 2.37
+coreutils-version = 9.0
+curl-version = 7.79.1
+dash-version = 0.5.11.5
+diffutils-version = 3.8
+file-version = 5.41
+findutils-version = 4.8.0
+flock-version = 0.4.0
gawk-version = 5.1.0
-gcc-version = 10.2.0
+gcc-version = 11.2.0
gettext-version = 0.21
-git-version = 2.28.0
-gmp-version = 6.2.0
-grep-version = 3.4
-gzip-version = 1.10
+git-version = 2.34.0
+gmp-version = 6.2.1
+grep-version = 3.7
+gzip-version = 1.11
isl-version = 0.18
-less-version = 563
-libbsd-version = 0.10.0
+less-version = 590
libiconv-version = 1.16
libtool-version = 2.4.6
-libunistring-version = 0.9.10
-libxml2-version = 2.9.9
-lzip-version = 1.22-rc2
-m4-version = 1.4.18-patched
+libunistring-version = 1.0
+libxml2-version = 2.9.12
+lzip-version = 1.22
+m4-version = 1.4.19
make-version = 4.3
-metastore-version = 1.1.2-23-fa9170b
-mpc-version = 1.1.0
-mpfr-version = 4.0.2
-nano-version = 5.2
-ncurses-version = 6.2
-patchelf-version = 0.10
-perl-version = 5.32.0
+mpc-version = 1.2.1
+mpfr-version = 4.1.0
+nano-version = 6.0
+ncurses-version = 6.3
+openssl-version = 3.0.0
+patchelf-version = 0.13
+perl-version = 5.34.0
pkgconfig-version = 0.29.2
-readline-version = 8.0
+podlators-version = 4.14
+readline-version = 8.1.1
sed-version = 4.8
-tar-version = 1.32
-texinfo-version = 6.7
+tar-version = 1.34
+texinfo-version = 6.8
unzip-version = 6.0
-wget-version = 1.20.3
+wget-version = 1.21.2
which-version = 2.21
xz-version = 5.2.5
zip-version = 3.0
@@ -67,7 +67,16 @@ zlib-version = 1.2.11
# When updating the version of these programs/libraries, please look into
# the build rule first: In one way or another, the version string becomes
# necessary during their build and must be accounted for.
-bzip2-version = 1.0.6
+bzip2-version = 1.0.8
+
+# PEM Certificate File
+# --------------------
+#
+# This file should be shipped with operating systems and can be found in
+# '/etc/ssl/cert.pem' (which may be a symbolic link to its actual
+# location). The current version was taken from an up-to-date ArchLinux at
+# the date that is also equal to the version.
+certpem-version = 2021-10-15
@@ -77,108 +86,103 @@ bzip2-version = 1.0.6
# ------------------------------------------
#
# These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/TARGETS.conf' will be built as
+# 'reproduce/software/config/TARGETS.conf' will be built as
# part of a project. To specify a software there, just remove the
-# `-version' suffix from the list below.
+# '-version' suffix from the list below.
#
-# CLASS:HIGHLEVEL (important identifier, don't modify this line.)
-apachelog4cxx-version = 0.10.0-603-014954db
+# CLASS:HIGHLEVEL (important identifier for 'awk'; don't modify this line)
+apachelog4cxx-version = 0.12.1
apr-version = 1.7.0
apr-util-version = 1.6.1
-astrometrynet-version = 0.80
+astrometrynet-version = 0.85
atlas-version = 3.10.3
-autoconf-version = 2.69.200-babc
-automake-version = 1.16.2
-bison-version = 3.7
-boost-version = 1.73.0
+autoconf-version = 2.71
+automake-version = 1.16.5
+bison-version = 3.8.2
+boost-version = 1.77.0
cairo-version = 1.16.0
cdsclient-version = 3.84
-cfitsio-version = 3.48
-cmake-version = 3.18.1
-eigen-version = 3.3.7
-emacs-version = 27.1
-expat-version = 2.2.9
-fftw-version = 3.3.8
-flex-version = 2.6.4-91-ga631f5d
-freetype-version = 2.10.2
-gdb-version = 9.2
-ghostscript-version = 9.52
+cfitsio-version = 4.0.0
+cmake-version = 3.21.4
+eigen-version = 3.4.0
+emacs-version = 27.2
+expat-version = 2.4.1
+fftw-version = 3.3.10
+flex-version = 2.6.4
+freetype-version = 2.11.0
+gdb-version = 11.1
+ghostscript-version = 9.55.0
ghostscript-fonts-gnu-version = 6.0
ghostscript-fonts-std-version = 8.11
-gnuastro-version = 0.12
+gnuastro-version = 0.16.1-e0f1
gperf-version = 3.1
-gsl-version = 2.6
-healpix-version = 3.50
-help2man-version = 1.47.11
-imagemagick-version = 7.0.8-67
+gsl-version = 2.7
+help2man-version = 1.48.5
+icu-version = 70.1
+imagemagick-version = 7.1.0-13
imfit-version = 1.6.1
-libffi-version = 3.2.1
-libidn-version = 1.36
-libjpeg-version = v9b
+libbsd-version = 0.11.3
+libffi-version = 3.4.2
+libidn-version = 1.38
+libjpeg-version = 9d
+libmd-version = 1.0.4
libnsl-version = 1.2.0-4a062cf
libpaper-version = 1.1.28
libpng-version = 1.6.37
-libtiff-version = 4.0.10
+libtiff-version = 4.3.0
libtirpc-version = 1.2.6
+metastore-version = 1.1.2-23-fa9170b
missfits-version = 2.8.0
-openblas-version = 0.3.10
-openmpi-version = 4.0.4
+openblas-version = 0.3.18
+openmpi-version = 4.1.1
openssh-version = 8.0p1
patch-version = 2.7.6
pcre-version = 8.44
-pixman-version = 0.38.0
-python-version = 3.8.5
-R-version = 4.0.2
+pixman-version = 0.40.0
+python-version = 3.10.0
+r-cran-version = 4.1.2
rpcsvc-proto-version = 1.4
scamp-version = 2.6.7
scons-version = 3.0.5
sextractor-version = 2.25.0
swarp-version = 2.38.0
-swig-version = 3.0.12
+swig-version = 4.0.2
tides-version = 2.0
-util-linux-version = 2.35
+util-linux-version = 2.37.2
+valgrind-version = 3.18.1
vim-version = 8.2
-xlsxio-version = 0.2.21
yaml-version = 0.2.5
# Xorg packages
-util-macros-version = 1.19.2
-xorgproto-version = 2020.1
+util-macros-version = 1.19.3
+xorgproto-version = 2021.5
libxau-version = 1.0.9
libxdmcp-version = 1.1.3
-xcb-proto-version = 1.14
+xcb-proto-version = 1.14.1
libxcb-version = 1.14
-fontconfig-version = 2.13.1
+fontconfig-version = 2.13.94
xtrans-version = 1.4.0
-libx11-version = 1.6.9
+libx11-version = 1.7.2
libxext-version = 1.3.4
libice-version = 1.0.10
libsm-version = 1.2.3
-libxt-version = 1.2.0
+libxt-version = 1.2.1
libpthread-stubs-version = 0.4
# Version-dependent build
# -----------------------
lapack-version = 3.8.0
-libgit2-version = 1.0.1
-wcslib-version = 7.3
+libgit2-version = 1.3.0
+wcslib-version = 7.7
# Netpbm's questions in the configure steps maybe change with different or
# new versions.
-netpbm-version = 10.86.99
+netpbm-version = 10.73.38
-# Minizip is installed with the same `zlib' tarball, and they have the same
+# Minizip is installed with the same 'zlib' tarball, and they have the same
# version.
minizip-version = $(zlib-version)
-# From version 1.2 OpenSSL may not need a manual addition, as described in
-# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't
-# cause problems, put it back in the list of "Basic/low-level" tools.
-openssl-version = 1.1.1a
-
-# Version 3.15.0 needs two patches, please check if they are necessary on
-# any future release.
-valgrind-version = 3.15.0
# Be careful with updateing hdf5 because h5py 2.10.0 doesn't work with
# version 1.12.0.
@@ -187,6 +191,7 @@ hdf5-version = 1.10.5
+
# Python packages
# ---------------
#
@@ -194,65 +199,151 @@ hdf5-version = 1.10.5
#
# IMPORTANT: If you intend to change the version of any of the Python
# modules/libraries below, please fix the hash strings of the respective
-# URL in `reproduce/software/make/python.mk'.
+# URL in 'reproduce/software/make/python.mk'.
#
-# CLASS:PYTHON (important identifier, don't modify this line.)
+# CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line)
asn1crypto-version = 0.24.0
asteval-version = 0.9.16
-astropy-version = 4.0
-astroquery-version = 0.4
-beautifulsoup4-version = 4.7.1
+astropy-version = 5.0
+beautifulsoup4-version = 4.10.0
+beniget-version = 0.4.1
certifi-version = 2018.11.29
-cffi-version = 1.12.2
+cffi-version = 1.15.0
chardet-version = 3.0.4
corner-version = 2.0.1
-cryptography-version = 2.6.1
-cycler-version = 0.10.0
-cython-version = 0.29.21
+cycler-version = 0.11.0
+cython-version = 0.29.24
eigency-version = 1.77
emcee-version = 3.0.1
entrypoints-version = 0.3
-esutil-version = 0.6.4
+esutil-version = 0.6.9
+extension-helpers-version = 0.1
flake8-version = 3.7.8
future-version = 0.18.1
-galsim-version = 2.2.1
+galsim-version = 2.3.3
+gast-version = 0.5.3
h5py-version = 2.10.0
html5lib-version = 1.0.1
idna-version = 2.8
jeepney-version = 0.4
-keyring-version = 18.0.0
+jinja2-version = 3.0.3
kiwisolver-version = 1.0.1
lmfit-version = 0.9.14
lsstdesccoord-version = 1.2.0
+markupsafe-version = 2.0.1
matplotlib-version = 3.3.0
-mpi4py-version = 3.0.3
+mpi4py-version = 3.1.3
mpmath-version = 1.1.0
-numpy-version = 1.19.1
+numpy-version = 1.21.3
+packaging-version = 21.3
pexpect-version = 4.7.0
+pillow-version = 8.4.0
pip-version = 19.0.2
+ply-version = 3.11
pycodestyle-version = 2.5.0
pycparser-version = 2.19
+pyerfa-version = 2.0.0.1
pyflakes-version = 2.1.1
pybind11-version = 2.5.0
-pyparsing-version = 2.3.1
+pyparsing-version = 3.0.4
pypkgconfig-version = 1.5.1
python-dateutil-version = 2.8.0
+pythran-version = 0.11.0
pyyaml-version = 5.1
requests-version = 2.21.0
-scipy-version = 1.5.2
-secretstorage-version = 3.1.1
-setuptools-version = 41.6.0
+scipy-version = 1.7.3
+setuptools-version = 58.3.0
setuptools_scm-version = 3.3.3
sip_tpv-version = 1.1
-six-version = 1.12.0
+six-version = 1.16.0
soupsieve-version = 1.8
sympy-version = 1.4
-uncertainties-version = 3.1.2
+uncertainties-version = 3.1.6
urllib3-version = 1.24.1
webencodings-version = 0.5.1
+wheel-version = 0.37.0
+# CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line)
# Special Python modules:
#
# Healpy: When any Python module is requested, healpix will also build its
# Python module Healpy.
-healpy-version = xxxxx
+#
+# Bug: Healpix 3.50 doesn't yet support Python 3.10, so we are commenting
+# it here. When future versions fix the problem, we'll un-comment it again.
+#healpy-version = xxxxx
+
+
+
+
+
+# Problematic software that are currently ignored:
+
+# Healpix 3.80 has different installation scheme that is not yet
+# implemented here, and unfortunately healpix 3.50 has conflicts with
+# CFITSIO's new version macro and Python 3.10. So for now, we are ignoring
+# it.
+#healpix-version = 3.50
+
+# XLSX I/O (until version 0.2.29) crashes during compilation with GCC
+# 11.1.0, so we are temporarily commenting it.
+#xlsxio-version = 0.2.21
+
+# Setuptools-rust crash (https://savannah.nongnu.org/bugs/index.php?61731),
+# so it and its dependencies are being ignored: 'cryptography', and thus
+# 'secretstorage' and thus 'keyring' and thus 'astroquery'.
+#setuptools-rust-version = 1.1.2
+#cryptography-version = 36.0.1
+#secretstorage-version = 3.1.1
+#keyring-version = 18.0.0
+#astroquery-version = 0.4
+
+
+
+
+
+# R-CRAN (i.e. 'R') packages
+# ------------------
+#
+# Similar to optional programs and libraries above.
+#
+# Notation: The R package and variables associated with it are by default
+# called 'R-CRAN' (or 'r-cran') in Maneage, because searching on a single
+# letter string 'R' is extremely inefficient.
+#
+# IMPORTANT: If you intend to change the version of any of the R-CRAN
+# modules/libraries below, please fix the hash strings of the respective
+# packages in 'reproduce/software/conf/checksums.conf'.
+#
+# CLASS:R-CRAN-START (important identifier for 'awk'; don't modify this line)
+r-cran-cli-version = 2.5.0
+r-cran-colorspace-version = 2.0-1
+r-cran-cowplot-version = 1.1.1
+r-cran-crayon-version = 1.4.1
+r-cran-digest-version = 0.6.27
+r-cran-ellipsis-version = 0.3.2
+r-cran-fansi-version = 0.5.0
+r-cran-farver-version = 2.1.0
+r-cran-ggplot2-version = 3.3.4
+r-cran-glue-version = 1.4.2
+r-cran-gridExtra-version = 2.3
+r-cran-gtable-version = 0.3.0
+r-cran-isoband-version = 0.2.4
+r-cran-labeling-version = 0.4.2
+r-cran-lifecycle-version = 1.0.0
+r-cran-magrittr-version = 2.0.1
+r-cran-MASS-version = 7.3-54
+r-cran-mgcv-version = 1.8-36
+r-cran-munsell-version = 0.5.0
+r-cran-pillar-version = 1.6.1
+r-cran-pkgconfig-version = 2.0.3
+r-cran-R6-version = 2.5.0
+r-cran-RColorBrewer-version = 1.1-2
+r-cran-rlang-version = 0.4.11
+r-cran-scales-version = 1.1.1
+r-cran-tibble-version = 3.1.2
+r-cran-utf8-version = 1.2.1
+r-cran-vctrs-version = 0.3.8
+r-cran-viridisLite-version = 0.4.0
+r-cran-withr-version = 2.4.2
+# CLASS:R-CRAN-END (important identifier for 'awk'; don't modify this line)
diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md
index 8d12d7a..76ab5c1 100644
--- a/reproduce/software/make/README.md
+++ b/reproduce/software/make/README.md
@@ -1,7 +1,7 @@
Software building instructions
------------------------------
-Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
+Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
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 e782578..b92fbfc 100644
--- a/reproduce/software/make/atlas-multiple.mk
+++ b/reproduce/software/make/atlas-multiple.mk
@@ -3,12 +3,12 @@
# ------------------------------------------------------------------------
# !!!!! IMPORTANT NOTES !!!!!
#
-# This Makefile will be run during the initial `./project configure'
+# This Makefile will be run during the initial './project configure'
# script. It is not included into the reproduction pipe after that.
#
# ------------------------------------------------------------------------
#
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 0934b66..720bad6 100644
--- a/reproduce/software/make/atlas-single.mk
+++ b/reproduce/software/make/atlas-single.mk
@@ -3,12 +3,12 @@
# ------------------------------------------------------------------------
# !!!!! IMPORTANT NOTES !!!!!
#
-# This Makefile will be run during the initial `./project configure'
+# This Makefile will be run during the initial './project configure'
# script. It is not included into the reproduction pipe after that.
#
# ------------------------------------------------------------------------
#
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 6910593..1c96b3f 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -4,7 +4,7 @@
# ------------------------------------------------------------------------
# !!!!! IMPORTANT NOTES !!!!!
#
-# This Makefile will be run by the initial `./project configure' script. It
+# This Makefile will be run by the initial './project configure' script. It
# is not included into the project afterwards.
#
# This Makefile builds low-level and basic tools that are necessary in any
@@ -21,8 +21,9 @@
#
# ------------------------------------------------------------------------
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
#
# 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
@@ -90,17 +91,20 @@ export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) \
-Wno-nullability-completeness
export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
+# Disable built-in rules (which are not needed here!)
+.SUFFIXES:
+
# This is the "basic" tools where we are relying on the host operating
# system, but are slowly populating our basic software envirnoment. To run
-# (system or template) programs, `LD_LIBRARY_PATH' is necessary, so here,
+# (system or template) programs, 'LD_LIBRARY_PATH' is necessary, so here,
# we'll first tell the programs to look into any possible pre-defined
-# `LD_LIBRARY_PATH', then we'll add our own newly installed libraries. We
+# '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 `::'.
+# removing a starting or trailing ':' and any occurance of '::'.
export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \
| sed -e's/::/:/g' -e's/^://' -e's/:$$//')
-# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
+# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
# ultimately redundant. But on some systems, even having a single value
# causes crashs (see bug #56682). So we'll just give it no value at all.
export DYLD_LIBRARY_PATH :=
@@ -150,10 +154,10 @@ backupservers = $(filter-out $(topbackupserver),$(backupservers_all))
#
# About ccache: ccache acts like a wrapper over the C compiler and is made
# to avoid/speed-up compiling of identical files in a system (it is
-# commonly used on large servers). It actually makes `gcc' or `g++' a
+# commonly used on large servers). It actually makes 'gcc' or 'g++' a
# symbolic link to itself so it can control them internally. So, for our
# purpose here, it is very annoying and can cause many complications. We
-# thus remove any part of PATH of that has `ccache' in it before making
+# thus remove any part of PATH of that has 'ccache' in it before making
# symbolic links to the programs we are not building ourselves.
#
# The double quotations after the starting 'export PATH' are necessary in
@@ -172,9 +176,9 @@ makelink = origpath="$$PATH"; \
| tr '\n' :)"; \
if type $(1) > /dev/null 2> /dev/null; then \
if [ x$(3) = x ]; then \
- ln -sf "$$(realpath $$(which $(1)))" $(ibdir)/$(1); \
+ ln -sf "$$(realpath $$(command -v $(1)))" $(ibdir)/$(1); \
else \
- ln -sf "$$(realpath $$(which $(1)))" $(ibdir)/$(3); \
+ ln -sf "$$(realpath $$(command -v $(1)))" $(ibdir)/$(3); \
fi; \
else \
if [ "x$(strip $(2))" = xmandatory ]; then \
@@ -189,11 +193,11 @@ $(ibdir) $(ildir):; mkdir $@
$(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
| $(ibdir) $(ildir)
- # Hardware specific
+# Hardware specific
$(call makelink,lp) # For printing, necessary for R.
$(call makelink,lpr) # For printing, necessary for R.
- # Mac OS specific
+# Mac OS specific
$(call makelink,mig)
$(call makelink,xcrun)
$(call makelink,sysctl)
@@ -201,14 +205,14 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
$(call makelink,dsymutil)
$(call makelink,install_name_tool)
- # On Mac OS, libtool is different compared to GNU Libtool. The
- # libtool we'll build in the high-level dependencies has the
- # executable name `glibtool'.
+# On Mac OS, libtool is different compared to GNU Libtool. The
+# libtool we'll build in the high-level dependencies has the
+# executable name 'glibtool'.
$(call makelink,libtool)
- # Necessary libraries:
- # Libdl (for dynamic loading libraries at runtime)
- # POSIX Threads library for multi-threaded programs.
+# Necessary libraries:
+# Libdl (for dynamic loading libraries at runtime)
+# POSIX Threads library for multi-threaded programs.
for l in dl pthread; do
if [ -f /usr/lib/lib$$l.a ]; then
for f in /usr/lib/lib$$l.*; do
@@ -218,8 +222,8 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
fi
done
- # We want this to be empty (so it doesn't interefere with the other
- # files in `ibidir'.
+# We want this to be empty (so it doesn't interefere with the other
+# files in 'ibidir'.
touch $@
@@ -249,26 +253,26 @@ $(ibidir)/gzip-$(gzip-version): | $(ibdir) $(ildir) $(lockdir)
echo "GNU Gzip $(gzip-version)" > $@
$(ibidir)/xz-$(xz-version): $(ibidir)/gzip-$(gzip-version)
- tarball=xz-$(xz-version).tar.gz
+ tarball=xz-$(xz-version).tar.lz
$(call import-source, $(xz-url), $(xz-checksum))
$(call gbuild, xz-$(xz-version), static)
echo "XZ Utils $(xz-version)" > $@
$(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
- # Download the tarball.
- tarball=bzip2-$(bzip2-version).tar.gz
+# Download the tarball.
+ tarball=bzip2-$(bzip2-version).tar.lz
$(call import-source, $(bzip2-url), $(bzip2-checksum))
- # Bzip2 doesn't have a `./configure' script, and its Makefile
- # doesn't build a shared library. So we can't use the `gbuild'
- # function here and we need to take some extra steps (inspired
- # from the GNU/Linux from Scratch (LFS) guide for Bzip2):
- # 1) The `sed' call is for relative installed symbolic links.
- # 2) The special Makefile-libbz2_so builds shared libraries.
- #
- # NOTE: the major version number appears in the final symbolic
- # link.
+# Bzip2 doesn't have a './configure' script, and its Makefile doesn't
+# build a shared library. So we can't use the 'gbuild' function here
+# and we need to take some extra steps (inspired from the GNU/Linux
+# from Scratch (LFS) guide for Bzip2):
+#
+# 1) The 'sed' call is for relative installed symbolic links.
+# 2) The special Makefile-libbz2_so builds shared libraries.
+#
+# NOTE: the major version number appears in the final symbolic link.
tdir=bzip2-$(bzip2-version)
if [ $(static_build) = yes ]; then
makecommand="make LDFLAGS=-static"
@@ -283,7 +287,7 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
fi
cd $(ddir)
rm -rf $$tdir
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd $$tdir
sed -e 's@\(ln -s -f \)$$(PREFIX)/bin/@\1@' Makefile \
> Makefile.sed
@@ -296,14 +300,13 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
cd ..
rm -rf $$tdir
cd $(ildir)
- ln -fs libbz2.so.1.0 libbz2.so
+ ln -fs libbz2.so.$(bzip2-version) libbz2.so
echo "Bzip2 $(bzip2-version)" > $@
$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
- tarball=unzip-$(unzip-version).tar.gz
- v=$$(echo $(unzip-version) | sed -e's/\.//')
+ tarball=unzip-$(unzip-version).tar.lz
$(call import-source, $(unzip-url), $(unzip-checksum))
- $(call gbuild, unzip$$v, static,, \
+ $(call gbuild, unzip-$(unzip-version), static,, \
-f unix/Makefile generic \
CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
-f unix/Makefile generic \
@@ -311,10 +314,9 @@ $(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
echo "Unzip $(unzip-version)" > $@
$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
- tarball=zip-$(zip-version).tar.gz
- v=$$(echo $(zip-version) | sed -e's/\.//')
+ tarball=zip-$(zip-version).tar.lz
$(call import-source, $(zip-url), $(zip-checksum))
- $(call gbuild, zip$$v, static,, \
+ $(call gbuild, zip-$(zip-version), static,, \
-f unix/Makefile generic \
CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
-f unix/Makefile generic \
@@ -324,10 +326,10 @@ $(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
# Some programs (like Wget and CMake) that use zlib need it to be dynamic
# so they use our custom build. So we won't force a static-only build.
#
-# Note for a static-only build: Zlib's `./configure' doesn't use Autoconf's
-# configure script, it just accepts a direct `--static' option.
+# Note for a static-only build: Zlib's './configure' doesn't use Autoconf's
+# configure script, it just accepts a direct '--static' option.
$(ibidir)/zlib-$(zlib-version): $(ibidir)/gzip-$(gzip-version)
- tarball=zlib-$(zlib-version).tar.gz
+ tarball=zlib-$(zlib-version).tar.lz
$(call import-source, $(zlib-url), $(zlib-checksum))
$(call gbuild, zlib-$(zlib-version))
echo "Zlib $(zlib-version)" > $@
@@ -344,11 +346,12 @@ $(ibidir)/tar-$(tar-version): \
$(ibidir)/zlib-$(zlib-version) \
$(ibidir)/bzip2-$(bzip2-version) \
$(ibidir)/unzip-$(unzip-version)
- # Since all later programs depend on Tar, the configuration will be
- # stuck here, only making Tar. So its more efficient to built it on
- # multiple threads (when the user's Make doesn't pass down the
- # number of threads).
- tarball=tar-$(tar-version).tar.gz
+
+# Since all later programs depend on Tar, the configuration will hit
+# a bottleneck here: only making Tar. So its more efficient to built
+# it on multiple threads (even when the user's Make doesn't pass down
+# the number of threads).
+ tarball=tar-$(tar-version).tar.lz
$(call import-source, $(tar-url), $(tar-checksum))
$(call gbuild, tar-$(tar-version), , , -j$(numthreads) V=1)
echo "GNU Tar $(tar-version)" > $@
@@ -370,7 +373,7 @@ $(ibidir)/tar-$(tar-version): \
# a prerequisite (and forgetting in others causing bugs), we'll put it as a
# dependancy of 'tar'.
$(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version)
- tarball=patchelf-$(patchelf-version).tar.gz
+ tarball=patchelf-$(patchelf-version).tar.lz
$(call import-source, $(patchelf-url), $(patchelf-checksum))
if [ x$(on_mac_os) = xyes ]; then
echo "" > $@
@@ -395,69 +398,69 @@ $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version)
# basic dependencies.
#
# Unfortunately Make needs dynamic linking in two instances: when loading
-# objects (dynamically linked libraries), or when using the `getpwnam'
+# objects (dynamically linked libraries), or when using the 'getpwnam'
# function (for tilde expansion). The first can be disabled with
-# `--disable-load', but unfortunately I don't know any way to fix the
+# '--disable-load', but unfortunately I don't know any way to fix the
# second. So, we'll have to build it dynamically for now.
$(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version)
- tarball=ncurses-$(ncurses-version).tar.gz
+ tarball=ncurses-$(ncurses-version).tar.lz
$(call import-source, $(ncurses-url), $(ncurses-checksum))
- # Delete the library that will be installed (so we can make sure
- # the build process completed afterwards and reset the links).
+# Delete the library that will be installed (so we can make sure the
+# build process completed afterwards and reset the links).
rm -f $(ildir)/libncursesw*
- # Delete the (possibly existing) low-level programs that depend on
- # `readline', and thus `ncurses'. Since these programs are actually
- # used during the building of `ncurses', we need to delete them so
- # the build process doesn't use the project's Bash and AWK, but the
- # host's.
+# Delete the (possibly existing) low-level programs that depend on
+# 'readline', and thus 'ncurses'. Since these programs are actually
+# used during the building of 'ncurses', we need to delete them so
+# the build process doesn't use the project's Bash and AWK, but the
+# host's.
rm -f $(ibdir)/bash* $(ibdir)/awk* $(ibdir)/gawk*
- # Standard build process.
+# Standard build process.
$(call gbuild, ncurses-$(ncurses-version), static, \
--with-shared --enable-rpath --without-normal \
--without-debug --with-cxx-binding \
--with-cxx-shared --enable-widec --enable-pc-files \
--with-pkg-config=$(ildir)/pkgconfig, -j$(numthreads))
- # Unfortunately there are many problems with `ncurses' using
- # "normal" (or 8-bit) characters. The standard way that will work
- # is to build it with wide character mode as you see above in the
- # configuration (or the `w' prefix you see below). Also, most
- # programs (and in particular Bash and AWK), first look for other
- # (mostly obsolete) libraries like tinfo, which define the same
- # symbols. The links below address both situations: we need to fool
- # higher-level packages to find this library even if they aren't
- # explicitly mentioning its name correctly (as a value to `-l' at
- # link time in their configure scripts).
- #
- # This part is taken from the Arch GNU/Linux build script[1], then
- # extended to Mac thanks to Homebrew's script [2].
- #
- # [1] https://git.archlinux.org/svntogit/packages.git/tree/trunk/PKGBUILD?h=packages/ncurses
- # [2] https://github.com/Homebrew/homebrew-core/blob/master/Formula/ncurses.rb
- #
- # Since we can't have comments, in the connected script, here is a
- # summary:
- #
- # 1. We find the actual suffix of the library, from the file that
- # is not a symbolic link (starting with `-' in the output of
- # `ls -l').
- #
- # 2. We make symbolic links to all the "ncurses", "ncurses++",
- # "form", "panel" and "menu" libraries to point to their
- # "wide" (character) library.
- #
- # 3. We make symbolic links to the "tic" and "tinfo" libraries to
- # point to the same `libncursesw' library.
- #
- # 4. Some programs link with "curses" (not "ncurses", notice the
- # starting "n"), so we'll also make links for these to point
- # to the `libncursesw' library.
- #
- # 5. A link is made to also be able to include files from the
- # `ncurses' headers.
+# Unfortunately there are many problems with 'ncurses' using "normal"
+# (or 8-bit) characters. The standard way that will work is to build
+# it with wide character mode as you see above in the configuration
+# (or the 'w' prefix you see below). Also, most programs (and in
+# particular Bash and AWK), first look for other (mostly obsolete)
+# libraries like tinfo, which define the same symbols. The links
+# below address both situations: we need to fool higher-level
+# packages to find this library even if they aren't explicitly
+# mentioning its name correctly (as a value to '-l' at link time in
+# their configure scripts).
+#
+# This part is taken from the Arch GNU/Linux build script[1], then
+# extended to Mac thanks to Homebrew's script [2].
+#
+# [1] https://git.archlinux.org/svntogit/packages.git/tree/trunk/PKGBUILD?h=packages/ncurses
+# [2] https://github.com/Homebrew/homebrew-core/blob/master/Formula/ncurses.rb
+#
+# Since we can't have comments, in the connected script, here is a
+# summary:
+#
+# 1. We find the actual suffix of the library, from the file that
+# is not a symbolic link (starting with '-' in the output of 'ls
+# -l').
+#
+# 2. We make symbolic links to all the "ncurses", "ncurses++",
+# "form", "panel" and "menu" libraries to point to their "wide"
+# (character) library.
+#
+# 3. We make symbolic links to the "tic" and "tinfo" libraries to
+# point to the same 'libncursesw' library.
+#
+# 4. Some programs link with "curses" (not "ncurses", notice the
+# starting "n"), so we'll also make links for these to point to
+# the 'libncursesw' library.
+#
+# 5. A link is made to also be able to include files from the
+# 'ncurses' headers.
if [ x$(on_mac_os) = xyes ]; then so="dylib"; else so="so"; fi
if [ -f $(ildir)/libncursesw.$$so ]; then
@@ -489,7 +492,7 @@ $(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version)
$(ibidir)/readline-$(readline-version): \
$(ibidir)/ncurses-$(ncurses-version)
- tarball=readline-$(readline-version).tar.gz
+ tarball=readline-$(readline-version).tar.lz
$(call import-source, $(readline-url), $(readline-checksum))
$(call gbuild, readline-$(readline-version), static, \
--with-curses --disable-install-examples, \
@@ -497,12 +500,12 @@ $(ibidir)/readline-$(readline-version): \
echo "GNU Readline $(readline-version)" > $@
-# IMPORTANT: Even though we have enabled `rpath', Bash doesn't write the
+# IMPORTANT: Even though we have enabled 'rpath', Bash doesn't write the
# absolute adddress of the libraries it depends on! Therefore, if we
-# configure Bash with `--with-installed-readline' (so the installed version
+# configure Bash with '--with-installed-readline' (so the installed version
# of Readline, that we build below as a prerequisite or AWK, is used) and
-# you run `ldd $(ibdir)/bash' on the resulting binary, it will say that it
-# is linking with the system's `readline'. But if you run that same command
+# you run 'ldd $(ibdir)/bash' on the resulting binary, it will say that it
+# is linking with the system's 'readline'. But if you run that same command
# within a rule in this project, you'll see that it is indeed linking with
# our own built readline.
#
@@ -510,11 +513,11 @@ $(ibidir)/readline-$(readline-version): \
# released as patches. Therefore we'll need to make our own fully-working
# and updated tarball to build the proper version of Bash. You download and
# apply them to the original tarball and make a new one with the following
-# series of commands (just replace `NUMBER' with the total number of
+# series of commands (just replace 'NUMBER' with the total number of
# patches that you want to apply).
#
# $ number=NUMBER
-# $ tar xf bash-5.0.tar.gz
+# $ tar -xf bash-5.0.tar.gz
# $ cd bash-5.0
# $ for i in $(seq 1 $number); do \
# pname=bash50-$(printf "%03d" $i); \
@@ -530,18 +533,18 @@ $(ibidir)/bash-$(bash-version): \
$(ibidir)/gettext-$(gettext-version) \
$(ibidir)/readline-$(readline-version)
- # Download the tarball.
+# Download the tarball.
tarball=bash-$(bash-version).tar.lz
$(call import-source, $(bash-url), $(bash-checksum))
- # Delete the (possibly) existing Bash executable in the project,
- # let it use the default shell of the host.
+# Delete the (possibly) existing Bash executable in the project,
+# let it use the default shell of the host.
rm -f $(ibdir)/bash
- # Bash has many `--enable' features which are already enabled by
- # default. As described in the manual, they are mainly useful when
- # you disable them all with `--enable-minimal-config' and enable a
- # subset using the `--enable' options.
+# Bash has many '--enable' features which are already enabled by
+# default. As described in the manual, they are mainly useful when
+# you disable them all with '--enable-minimal-config' and enable a
+# subset using the '--enable' options.
if [ "x$(static_build)" = xyes ]; then stopt="--enable-static-link"
else stopt=""
fi;
@@ -554,22 +557,20 @@ $(ibidir)/bash-$(bash-version): \
--with-curses=yes, \
-j$(numthreads))
- # Atleast on GNU/Linux systems, Bash doesn't include RPATH by
- # default. So, we have to manually include it, currently we are
- # only doing this on GNU/Linux systems (using the `patchelf'
- # program).
+# Atleast on GNU/Linux systems, Bash doesn't include RPATH by
+# default. So, we have to manually include it, currently we are only
+# doing this on GNU/Linux systems (using the 'patchelf' program).
if [ -f $(ibdir)/patchelf ]; then
$(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/bash;
fi
- # To be generic, some systems use the `sh' command to call the
- # shell. By convention, `sh' is just a symbolic link to the
- # preferred shell executable. So we'll define `$(ibdir)/sh' as a
- # symbolic link to the Bash that we just built and installed.
- #
- # Just to be sure that the installation step above went well,
- # before making the link, we'll see if the file actually exists
- # there.
+# To be generic, some systems use the 'sh' command to call the
+# shell. By convention, 'sh' is just a symbolic link to the preferred
+# shell executable. So we'll define '$(ibdir)/sh' as a symbolic link
+# to the Bash that we just built and installed.
+#
+# Just to be sure that the installation step above went well, before
+# making the link, we'll see if the file actually exists there.
ln -fs $(ibdir)/bash $(ibdir)/sh
echo "GNU Bash $(bash-version)" > $@
@@ -585,9 +586,9 @@ $(ibidir)/bash-$(bash-version): \
# Level 4: Most other programs
# ----------------------------
-# In Perl, The `-shared' flag will cause problems while building on macOS,
+# In Perl, The '-shared' flag will cause problems while building on macOS,
# so we'll only use this configuration option when we are GNU/Linux
-# systems. However, since the whole option must be used (which includes `='
+# systems. However, since the whole option must be used (which includes '='
# and empty space), its easier to define the variable as a Make variable
# outside the recipe, not as a shell variable inside it.
ifeq ($(on_mac_os),yes)
@@ -596,7 +597,7 @@ else
perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS"
endif
$(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
- tarball=perl-$(perl-version).tar.gz
+ tarball=perl-$(perl-version).tar.lz
$(call import-source, $(perl-url), $(perl-checksum))
major_version=$$(echo $(perl-version) \
| sed -e's/\./ /g' \
@@ -606,7 +607,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
| awk '{printf("%d.%d", $$1, $$2)}')
cd $(ddir)
rm -rf perl-$(perl-version)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd perl-$(perl-version)
./Configure -des \
-Dusethreads \
@@ -616,7 +617,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
-Dprivlib=$(idir)/share/perl$$major_version/core_perl \
-Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \
-Dsitelib=$(idir)/share/perl$$major_version/site_perl \
- -Dsitearch=$(idir)/lib/perl$$major_version/$$basever/site_perl \
+ -Dsitearch=$(idir)/lib/perl$$major_version/$$base_version/site_perl \
-Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \
-Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \
-Dscriptdir=$(idir)/bin/core_perl \
@@ -642,17 +643,17 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
# Coreutils
# ---------
#
-# For some reason, Coreutils doesn't include `rpath' in its installed
+# For some reason, Coreutils doesn't include 'rpath' in its installed
# executables (even though it says that by default its included and that
-# even when calling `--enable-rpath=yes'). So we have to manually add
-# `rpath' to Coreutils' executables after the standard build is
+# even when calling '--enable-rpath=yes'). So we have to manually add
+# 'rpath' to Coreutils' executables after the standard build is
# complete.
#
# One problem is that Coreutils installs many very basic executables which
# might be in used by other programs. So we must make sure that when
# Coreutils is being built, no other program is being built in
# parallel. The solution to the many executables it installs is to make a
-# fake installation (with `DESTDIR'), and get a list of the contents of the
+# fake installation (with 'DESTDIR'), and get a list of the contents of the
# directory to find the names.
#
# The echo after the PatchELF loop is to avoid a crash if the last
@@ -665,30 +666,30 @@ $(ibidir)/coreutils-$(coreutils-version): \
$(ibidir)/perl-$(perl-version) \
$(ibidir)/openssl-$(openssl-version)
- # Import, unpack and enter the source directory.
- tarball=coreutils-$(coreutils-version).tar.xz
+# Import, unpack and enter the source directory.
+ tarball=coreutils-$(coreutils-version).tar.lz
$(call import-source, $(coreutils-url), $(coreutils-checksum))
cd $(ddir)
rm -rf coreutils-$(coreutils-version)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$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).
+# 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|\#\! $(ibdir)/bash|' \
configure > configure-tmp
mv configure-tmp configure
chmod +x configure
- # Configure, build and install Coreutils.
+# Configure, build and install Coreutils.
./configure --prefix=$(idir) SHELL=$(ibdir)/bash \
LDFLAGS="$(LDFLAGS)" CPPFLAGS="$(CPPFLAGS)" \
--disable-silent-rules --with-openssl=yes
make SHELL=$(ibdir)/bash -j$(numthreads)
make SHELL=$(ibdir)/bash install
- # Fix RPATH if necessary.
+# Fix RPATH if necessary.
if [ -f $(ibdir)/patchelf ]; then
make SHELL=$(ibdir)/bash install DESTDIR=junkinst
unalias ls || true # avoid decorated 'ls' commands with extra characters
@@ -699,12 +700,34 @@ $(ibidir)/coreutils-$(coreutils-version): \
echo "PatchELF applied to all programs."
fi
- # Come back up to the unpacking directory, delete the source
- # directory and write the final target.
+# Come back up to the unpacking directory, delete the source
+# directory and write the final target.
cd ..
rm -rf coreutils-$(coreutils-version)
echo "GNU Coreutils $(coreutils-version)" > $@
+# Podlators
+#
+# POD is short for "Plain Old Documentation", that is the format used in
+# Perl's documentation. Podlators provies two executables pod2man and
+# pod2text convert this into the roff format (used in man pages) or pod2 It
+# is used by some software like OpenSSL to create their man pages.
+$(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version)
+ tarball=podlators-$(podlators-version).tar.lz
+ $(call import-source, $(podlators-url), $(podlators-checksum))
+ cd $(ddir)
+ rm -rf podlators-$(podlators-version)
+ tar -xf $(tdir)/$$tarball
+ cd podlators-$(podlators-version)
+ perl Makefile.PL
+ make
+ make install
+ ln -sf $(ibdir)/site_perl/pod2man $(ibdir)/pod2man
+ ln -sf $(ibdir)/site_perl/pod2text $(ibdir)/pod2text
+ cd ..
+ rm -rf podlators-$(podlators-version)
+ echo "podlators $(podlators-version)" > $@
+
# OpenSSL
#
# Until we find a nice and generic way to create an updated CA file in the
@@ -712,26 +735,26 @@ $(ibidir)/coreutils-$(coreutils-version): \
# along with the other tarballs.
$(idir)/etc:; mkdir $@
$(idir)/etc/ssl: | $(idir)/etc; mkdir $@
-$(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \
+$(ibidir)/openssl-$(openssl-version): $(ibidir)/podlators-$(podlators-version) \
| $(idir)/etc/ssl
- # First download the certificates and copy them into the
- # installation directory.
- tarball=cert.pem
+# First download the certificates and copy them into the
+# installation directory.
+ tarball=cert.pem-$(certpem-version)
$(call import-source, $(cert-url), $(cert-checksum))
- cp $(tdir)/cert.pem $(idir)/etc/ssl/cert.pem
+ cp $(tdir)/cert.pem-$(certpem-version) $(idir)/etc/ssl/cert.pem
- # Now download the OpenSSL tarball.
- tarball=openssl-$(openssl-version).tar.gz
+# Now download the OpenSSL tarball.
+ tarball=openssl-$(openssl-version).tar.lz
$(call import-source, $(openssl-url), $(openssl-checksum))
- # According to OpenSSL's Wiki (link bellow), it can't automatically
- # detect Mac OS's structure. It will need some help. So we'll use
- # the `on_mac_os' Make variable that we defined in the configure
- # script and help it with some extra configuration options and an
- # environment variable.
- #
- # https://wiki.openssl.org/index.php/Compilation_and_Installation
+# According to OpenSSL's Wiki (link bellow), it can't automatically
+# detect Mac OS's structure. It will need some help. So we'll use the
+# 'on_mac_os' Make variable that we defined in the configure script
+# and help it with some extra configuration options and an
+# environment variable.
+#
+# https://wiki.openssl.org/index.php/Compilation_and_Installation
if [ x$(on_mac_os) = xyes ]; then
export KERNEL_BITS=64
copt="shared no-ssl2 no-ssl3 enable-ec_nistp_64_gcc_128"
@@ -745,29 +768,19 @@ $(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \
--with-zlib-include=$(idir)/include, \
-j$(numthreads), , ./config )
- # Manually insert RPATH inside the two created libraries.
+# Manually insert RPATH inside the two created libraries.
if [ -f $(ibdir)/patchelf ]; then
patchelf --set-rpath $(ildir) $(ildir)/libssl.so
patchelf --set-rpath $(ildir) $(ildir)/libcrypto.so
fi
- # Bug 58263 (https://savannah.nongnu.org/bugs/?58263): In OpenSSL
- # Version 1.1.1a (also checked in 1.1.1g), `openssl/ec.h' fails to
- # include `openssl/openconf.h' on some OSs. The SED hack below
- # inserts a hardwired element of `openssl/openconf.h' that is
- # needed to include sections of code `f` that are deprecated in
- # 1.2.0, but not yet in 1.1.1. This problem may be solved in
- # version 1.2.x, so please check again in that bug.
- mv -v $(idir)/include/openssl/ec.h $(idir)/include/openssl/ec.h.orig
- sed -e 's,\(# include .openssl/opensslconf\.h.\),\1\n#ifndef DEPRECATEDIN_1_2_0\n#define DEPRECATEDIN_1_2_0(f) f;\n#endif\n,' \
- $(idir)/include/openssl/ec.h.orig > $(idir)/include/openssl/ec.h
-
- # Build the final target.
+# Build the final target.
echo "OpenSSL $(openssl-version)" > $@
+
# Downloaders
# -----------
@@ -776,13 +789,13 @@ $(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \
# cURL can optionally link with many different network-related libraries on
# the host system that we are not yet building in the template. Many of
# these are not relevant to most science projects, so we are explicitly
-# using `--without-XXX' or `--disable-XXX' so cURL doesn't link with
+# using '--without-XXX' or '--disable-XXX' so cURL doesn't link with
# them. Note that if it does link with them, the configuration will crash
# when the library is updated/changed by the host, and the whole purpose of
# this project is avoid dependency on the host as much as possible.
$(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
- tarball=curl-$(curl-version).tar.gz
+ tarball=curl-$(curl-version).tar.lz
$(call import-source, $(curl-url), $(curl-checksum))
$(call gbuild, curl-$(curl-version), , \
@@ -812,8 +825,8 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
# GNU Wget
#
# Note that on some systems (for example GNU/Linux) Wget needs to explicity
-# link with `libdl', but on others (for example Mac OS) it doesn't. We
-# check this at configure time and define the `needs_ldl' variable.
+# link with 'libdl', but on others (for example Mac OS) it doesn't. We
+# check this at configure time and define the 'needs_ldl' variable.
#
# Also note that since Wget needs to load outside libraries dynamically, it
# gives a segmentation fault when built statically.
@@ -826,12 +839,12 @@ $(ibidir)/wget-$(wget-version): \
$(ibidir)/libiconv-$(libiconv-version) \
$(ibidir)/coreutils-$(coreutils-version)
- # Download the tarball.
+# Download the tarball.
tarball=wget-$(wget-version).tar.lz
$(call import-source, $(wget-url), $(wget-checksum))
- # We need to explicitly disable `libiconv', because of the
- # `pkg-config' and `libiconv' problem.
+# We need to explicitly disable 'libiconv', because of the
+# 'pkg-config' and 'libiconv' problem.
libs="-pthread"
if [ x$(needs_ldl) = xyes ]; then libs="$$libs -ldl"; fi
$(call gbuild, wget-$(wget-version), , \
@@ -864,13 +877,13 @@ $(ibidir)/wget-$(wget-version): \
# there is no access to the system's PATH.
$(ibidir)/diffutils-$(diffutils-version): \
$(ibidir)/coreutils-$(coreutils-version)
- tarball=diffutils-$(diffutils-version).tar.xz
+ tarball=diffutils-$(diffutils-version).tar.lz
$(call import-source, $(diffutils-url), $(diffutils-checksum))
$(call gbuild, diffutils-$(diffutils-version), static,,V=1)
echo "GNU Diffutils $(diffutils-version)" > $@
$(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version)
- tarball=file-$(file-version).tar.gz
+ tarball=file-$(file-version).tar.lz
$(call import-source, $(file-url), $(file-checksum))
$(call gbuild, file-$(file-version), static, \
--disable-libseccomp, V=1)
@@ -878,7 +891,7 @@ $(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version)
$(ibidir)/findutils-$(findutils-version): \
$(ibidir)/coreutils-$(coreutils-version)
- tarball=findutils-$(findutils-version).tar.xz
+ tarball=findutils-$(findutils-version).tar.lz
$(call import-source, $(findutils-url), $(findutils-checksum))
$(call gbuild, findutils-$(findutils-version), static,,V=1)
echo "GNU Findutils $(findutils-version)" > $@
@@ -888,19 +901,19 @@ $(ibidir)/gawk-$(gawk-version): \
$(ibidir)/mpfr-$(mpfr-version) \
$(ibidir)/coreutils-$(coreutils-version)
- # Download the tarball.
+# Download the tarball.
tarball=gawk-$(gawk-version).tar.lz
$(call import-source, $(gawk-url), $(gawk-checksum))
- # AWK doesn't include RPATH by default, so we'll have to manually
- # include it using the `patchelf' program (which was a dependency
- # of Bash). Just note that AWK produces two executables (for
- # example `gawk-4.2.1' and `gawk') and a symbolic link `awk' to one
- # of those executables.
+# AWK doesn't include RPATH by default, so we'll have to manually
+# include it using the 'patchelf' program (which was a dependency of
+# Bash). Just note that AWK produces two executables (for example
+# 'gawk-4.2.1' and 'gawk') and a symbolic link 'awk' to one of those
+# executables.
$(call gbuild, gawk-$(gawk-version), static, \
--with-readline=$(idir))
- # Correct the RPATH on systems that have installed patchelf.
+# Correct the RPATH on systems that have installed patchelf.
if [ -f $(ibdir)/patchelf ]; then
if [ -f $(ibdir)/gawk ]; then
$(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/gawk
@@ -911,31 +924,31 @@ $(ibidir)/gawk-$(gawk-version): \
fi
fi
- # Build final target.
+# Build final target.
echo "GNU AWK $(gawk-version)" > $@
$(ibidir)/libiconv-$(libiconv-version): \
$(ibidir)/pkg-config-$(pkgconfig-version)
- tarball=libiconv-$(libiconv-version).tar.gz
+ tarball=libiconv-$(libiconv-version).tar.lz
$(call import-source, $(libiconv-url), $(libiconv-checksum))
$(call gbuild, libiconv-$(libiconv-version), static)
echo "GNU libiconv $(libiconv-version)" > $@
$(ibidir)/libunistring-$(libunistring-version): \
$(ibidir)/libiconv-$(libiconv-version)
- tarball=libunistring-$(libunistring-version).tar.xz
+ tarball=libunistring-$(libunistring-version).tar.lz
$(call import-source, $(libunistring-url), $(libunistring-checksum))
$(call gbuild, libunistring-$(libunistring-version), static,, \
-j$(numthreads))
echo "GNU libunistring $(libunistring-version)" > $@
$(ibidir)/libxml2-$(libxml2-version): $(ibidir)/patchelf-$(patchelf-version)
- # The libxml2 tarball also contains Python bindings which are built
- # and installed to a system directory by default. If you don't need
- # the Python bindings, the easiest solution is to compile without
- # Python support: `./configure --without-python'. If you really need
- # the Python bindings, use `--with-python-install-dir=DIR' instead.
- tarball=libxml2-$(libxml2-version).tar.gz
+# The libxml2 tarball also contains Python bindings which are built
+# and installed to a system directory by default. If you don't need
+# the Python bindings, the easiest solution is to compile without
+# Python support: './configure --without-python'. If you really need
+# the Python bindings, use '--with-python-install-dir=DIR' instead.
+ tarball=libxml2-$(libxml2-version).tar.lz
$(call import-source, $(libxml2-url), $(libxml2-checksum))
$(call gbuild, libxml2-$(libxml2-version), static, \
--without-python, V=1)
@@ -958,7 +971,7 @@ $(ibidir)/git-$(git-version): \
$(ibidir)/curl-$(curl-version) \
$(ibidir)/gettext-$(gettext-version) \
$(ibidir)/libiconv-$(libiconv-version)
- tarball=git-$(git-version).tar.xz
+ tarball=git-$(git-version).tar.lz
if [ x$(on_mac_os) = xyes ]; then
export LDFLAGS="$$LDFLAGS -lcharset"
fi
@@ -982,7 +995,7 @@ $(ibidir)/gmp-$(gmp-version): \
# and generally to view large files easily when the project is built in a
# container with a minimal OS.
$(ibidir)/less-$(less-version): $(ibidir)/ncurses-$(ncurses-version)
- tarball=less-$(less-version).tar.gz
+ tarball=less-$(less-version).tar.lz
$(call import-source, $(less-url), $(less-checksum))
$(call gbuild, less-$(less-version), static,,-j$(numthreads))
if [ -f $(ibdir)/patchelf ]; then
@@ -991,9 +1004,9 @@ $(ibidir)/less-$(less-version): $(ibidir)/ncurses-$(ncurses-version)
echo "Less $(less-version)" > $@
# On Mac OS, libtool does different things, so to avoid confusion, we'll
-# prefix GNU's libtool executables with `glibtool'.
+# prefix GNU's libtool executables with 'glibtool'.
$(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version)
- tarball=libtool-$(libtool-version).tar.xz
+ tarball=libtool-$(libtool-version).tar.lz
$(call import-source, $(libtool-url), $(libtool-checksum))
$(call gbuild, libtool-$(libtool-version), static, \
--program-prefix=g, V=1 -j$(numthreads))
@@ -1001,162 +1014,44 @@ $(ibidir)/libtool-$(libtool-version): $(ibidir)/m4-$(m4-version)
echo "GNU Libtool $(libtool-version)" > $@
$(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version)
- tarball=grep-$(grep-version).tar.xz
+ tarball=grep-$(grep-version).tar.lz
$(call import-source, $(grep-url), $(grep-checksum))
$(call gbuild, grep-$(grep-version), static,,V=1)
echo "GNU Grep $(grep-version)" > $@
-$(ibidir)/libbsd-$(libbsd-version): $(ibidir)/coreutils-$(coreutils-version)
- tarball=libbsd-$(libbsd-version).tar.xz
- $(call import-source, $(libbsd-url), $(libbsd-checksum))
- if [ x$(on_mac_os) = xyes ]; then
- echo "" > $@
- else
- $(call gbuild, libbsd-$(libbsd-version), static,,V=1)
- echo "Libbsd $(libbsd-version)" > $@
- fi
-
-# We need to apply a patch to the M4 source to be used properly on macOS.
-# The patch [1] was inspired by Homebrew's build instructions [1].
-#
-# [1] https://raw.githubusercontent.com/macports/macports-ports/edf0ee1e2cf/devel/m4/files/secure_snprintf.patch
-# [2] https://github.com/Homebrew/homebrew-core/blob/master/Formula/m4.rb
-#
# 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.
$(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version)
- tarball=m4-$(m4-version).tar.gz
+ tarball=m4-$(m4-version).tar.lz
$(call import-source, $(m4-url), $(m4-checksum))
- cd $(ddir)
- unpackdir=m4-$(m4-version)
- rm -rf $$unpackdir
- tar xf $(tdir)/$$tarball
- mv m4-* $$unpackdir
- cd $$unpackdir
- if [ x$(on_mac_os) = xyes ]; then
- sed 's|if !(((__GLIBC__ > 2|if !defined(__APPLE__) \&\& !(((__GLIBC__ > 2|' \
- lib/vasnprintf.c > lib/vasnprintf_edited.c
- mv lib/vasnprintf_edited.c lib/vasnprintf.c
- fi
- ./configure --prefix=$(idir) LDFLAGS="$(LDFLAGS)" \
- CPPFLAGS="$(CPPFLAGS)"
- make V=1 -j$(numthreads)
- make V=1 install
- cd ..
- rm -rf $$unpackdir
+ $(call gbuild, m4-$(m4-version), static,,V=1)
echo "GNU M4 $(m4-version)" > $@
-# Metastore is used (through a Git hook) to restore the source modification
-# dates of files after a Git checkout. Another Git hook saves all file
-# metadata just before a commit (to allow restoration after a
-# checkout). Since this project is managed in Makefiles, file modification
-# dates are critical to not having to redo the whole analysis after
-# checking out between branches.
-#
-# Note that we aren't using the standard version of Metastore, but a fork
-# of it that is maintained in this repository:
-# https://gitlab.com/makhlaghi/metastore-fork
-#
-# Note that the prerequisites `coreutils', `gawk' and `sed' are not
-# metastore oficial dependencies, but they are necessaries to run our steps
-# before and after the installation.
-#
-# Libbsd is not necessary on macOS systems, because macOS is already a
-# BSD-based distribution. But on GNU/Linux systems, it is necessary.
-$(ibidir)/metastore-$(metastore-version): \
- $(ibidir)/sed-$(sed-version) \
- $(ibidir)/git-$(git-version) \
- $(ibidir)/gawk-$(gawk-version) \
- $(ibidir)/libbsd-$(libbsd-version) \
- $(ibidir)/coreutils-$(coreutils-version)
-
- # Download the tarball.
- tarball=metastore-$(metastore-version).tar.gz
- $(call import-source, $(metastore-url), $(metastore-checksum))
-
- # Metastore doesn't have any `./configure' script. So we'll just
- # call `pwd' as a place-holder for the `./configure' command.
- #
- # File attributes are also not available on some systems, since the
- # main purpose here is modification dates (and not attributes),
- # we'll also set the `NO_XATTR' flag.
- #
- # After installing Metastore, write the relevant hooks into this
- # system's Git hooks, while setting the system-specific
- # directories/files.
- #
- # Note that the metastore -O and -G options used in this template
- # are currently only available in a fork of `metastore' hosted at:
- # https://github.com/mohammad-akhlaghi/metastore
- #
- # Checking for presence of `.git'. When the project source is
- # downloaded from a non-Git source (for example from arXiv), there
- # is no `.git' directory to work with. So until we find a better
- # solution, avoid the step to to add the Git hooks.
- current_dir=$$(pwd); \
- $(call gbuild, metastore-$(metastore-version), static,, \
- NO_XATTR=1 V=1,,pwd,PREFIX=$(idir))
-
- # Correct RPATH when necessary.
- if [ -f $(ibdir)/patchelf ]; then
- $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/metastore
- fi
-
- # If this project is being built in a directory version controlled
- # by Git, copy the hooks into the Git configuation.
- if [ -f $(ibdir)/metastore ]; then
- if [ -d .git ]; then
- user=$$(whoami)
- group=$$(groups | awk '{print $$1}')
- cd $$current_dir
- for f in pre-commit post-checkout; do
- sed -e's|@USER[@]|'$$user'|g' \
- -e's|@GROUP[@]|'$$group'|g' \
- -e's|@BINDIR[@]|$(ibdir)|g' \
- -e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \
- reproduce/software/shell/git-$$f > .git/hooks/$$f
- chmod +x .git/hooks/$$f
- done
- fi
- echo "Metastore (forked) $(metastore-version)" > $@
- else
- echo; echo; echo
- echo "*****************"
- echo "metastore couldn't be installed!"
- echo
- echo "Its used for preserving timestamps on Git commits."
- echo "Its useful for development, not simple running of "
- echo "the project. So we won't stop the configuration "
- echo "because it wasn't built."
- echo "*****************"
- echo "" > $@
- fi
-
$(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version)
- tarball=mpfr-$(mpfr-version).tar.xz
+ tarball=mpfr-$(mpfr-version).tar.lz
$(call import-source, $(mpfr-url), $(mpfr-checksum))
$(call gbuild, mpfr-$(mpfr-version), static, , , make check)
echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@
$(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version)
- # Download the tarball.
- tarball=pkg-config-$(pkgconfig-version).tar.gz
+# Download the tarball.
+ tarball=pkg-config-$(pkgconfig-version).tar.lz
$(call import-source, $(pkgconfig-url), $(pkgconfig-checksum))
- # An existing `libiconv' can cause a conflict with `pkg-config',
- # this is why `libiconv' depends on `pkg-config'. On a clean build,
- # `pkg-config' is built first. But when we don't have a clean build
- # (and `libiconv' exists) there will be a problem. So before
- # re-building `pkg-config', we'll remove any installation of
- # `libiconv'.
+# An existing 'libiconv' can cause a conflict with 'pkg-config', this
+# is why 'libiconv' depends on 'pkg-config'. On a clean build,
+# 'pkg-config' is built first. But when we don't have a clean build
+# (and 'libiconv' exists) there will be a problem. So before
+# re-building 'pkg-config', we'll remove any installation of
+# 'libiconv'.
rm -f $(ildir)/libiconv* $(idir)/include/iconv.h
- # Some Mac OS systems may have a version of the GNU C Compiler
- # (GCC) installed that doesn't support some necessary features of
- # building Glib (as part of pkg-config). So to be safe, for Mac
- # systems, we'll make sure it will use LLVM's Clang.
+# Some Mac OS systems may have a version of the GNU C Compiler (GCC)
+# installed that doesn't support some necessary features of building
+# Glib (as part of pkg-config). So to be safe, for Mac systems, we'll
+# make sure it will use LLVM's Clang.
if [ x$(on_mac_os) = xyes ]; then export compiler="CC=clang"
else export compiler=""
fi
@@ -1166,7 +1061,7 @@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version
echo "pkg-config $(pkgconfig-version)" > $@
$(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version)
- tarball=sed-$(sed-version).tar.xz
+ tarball=sed-$(sed-version).tar.lz
$(call import-source, $(sed-url), $(sed-checksum))
$(call gbuild, sed-$(sed-version), static,,V=1)
echo "GNU Sed $(sed-version)" > $@
@@ -1174,7 +1069,7 @@ $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version)
$(ibidir)/texinfo-$(texinfo-version): \
$(ibidir)/perl-$(perl-version) \
$(ibidir)/gettext-$(gettext-version)
- tarball=texinfo-$(texinfo-version).tar.xz
+ tarball=texinfo-$(texinfo-version).tar.lz
$(call import-source, $(texinfo-url), $(texinfo-checksum))
$(call gbuild, texinfo-$(texinfo-version), static)
if [ -f $(ibdir)/patchelf ]; then
@@ -1184,14 +1079,14 @@ $(ibidir)/texinfo-$(texinfo-version): \
echo "GNU Texinfo $(texinfo-version)" > $@
$(ibidir)/which-$(which-version): $(ibidir)/coreutils-$(coreutils-version)
- tarball=which-$(which-version).tar.gz
+ tarball=which-$(which-version).tar.lz
$(call import-source, $(which-url), $(which-checksum))
$(call gbuild, which-$(which-version), static)
echo "GNU Which $(which-version)" > $@
# GNU ISL is necessary to build GCC.
$(ibidir)/isl-$(isl-version): $(ibidir)/gmp-$(gmp-version)
- tarball=isl-$(isl-version).tar.bz2
+ tarball=isl-$(isl-version).tar.lz
$(call import-source, $(isl-url), $(isl-checksum))
if [ $(host_cc) = 1 ]; then
echo "" > $@
@@ -1203,7 +1098,7 @@ $(ibidir)/isl-$(isl-version): $(ibidir)/gmp-$(gmp-version)
# GNU MPC is necessary to build GCC.
$(ibidir)/mpc-$(mpc-version): $(ibidir)/mpfr-$(mpfr-version)
- tarball=mpc-$(mpc-version).tar.gz
+ tarball=mpc-$(mpc-version).tar.lz
$(call import-source, $(mpc-url), $(mpc-checksum))
if [ $(host_cc) = 1 ]; then
echo "" > $@
@@ -1226,33 +1121,34 @@ $(ibidir)/mpc-$(mpc-version): $(ibidir)/mpfr-$(mpfr-version)
# -----------------------
#
# The installation of Binutils can cause problems during the build of other
-# programs (http://savannah.nongnu.org/bugs/?56294), but its necessary for
+# programs since it provides the linker that is used to build them
+# (http://savannah.nongnu.org/bugs/?56294). However, it is necessary for
# GCC. Therefore, we'll set all other basic programs as Binutils
-# prerequisite and GCC (the final basic target) ultimately just depends on
-# Binutils.
+# prerequisites, so GCC (the almost-final basic target) ultimately just
+# depends on Binutils.
$(ibidir)/binutils-$(binutils-version): \
- $(ibidir)/sed-$(sed-version) \
+ $(ibidir)/git-$(git-version) \
$(ibidir)/isl-$(isl-version) \
$(ibidir)/mpc-$(mpc-version) \
- $(ibidir)/wget-$(wget-version) \
- $(ibidir)/grep-$(grep-version) \
+ $(ibidir)/sed-$(sed-version) \
$(ibidir)/file-$(file-version) \
$(ibidir)/gawk-$(gawk-version) \
+ $(ibidir)/grep-$(grep-version) \
+ $(ibidir)/wget-$(wget-version) \
$(ibidir)/which-$(which-version) \
- $(ibidir)/texinfo-$(texinfo-version) \
$(ibidir)/libtool-$(libtool-version) \
- $(ibidir)/metastore-$(metastore-version) \
- $(ibidir)/findutils-$(findutils-version) \
+ $(ibidir)/texinfo-$(texinfo-version) \
+ $(ibidir)/coreutils-$(coreutils-version) \
$(ibidir)/diffutils-$(diffutils-version) \
- $(ibidir)/coreutils-$(coreutils-version)
+ $(ibidir)/findutils-$(findutils-version)
- # Download the tarball.
+# Download the tarball.
tarball=binutils-$(binutils-version).tar.lz
$(call import-source, $(binutils-url), $(binutils-checksum))
- # Binutils' assembler (`as') and linker (`ld') will conflict with
- # other compilers. So if we don't build our own compiler, we'll use
- # the host opertating system's equivalents by just making links.
+# Binutils' assembler ('as') and linker ('ld') will conflict with
+# other compilers. So if we don't build our own compiler, we'll use
+# the host opertating system's equivalents by just making links.
if [ x$(on_mac_os) = xyes ]; then
$(call makelink,as)
$(call makelink,ar)
@@ -1264,20 +1160,20 @@ $(ibidir)/binutils-$(binutils-version): \
echo "" > $@
else
- # Build binutils with the standard 'gbuild' function.
+# Build binutils with the standard 'gbuild' function.
$(call gbuild, binutils-$(binutils-version), static, \
--with-lib-path=$(sys_library_path), \
-j$(numthreads) )
- # The `ld' linker of Binutils needs several `*crt*.o' files from
- # the host's GNU C Library to run. On some systems these object
- # files aren't installed in standard places. We defined
- # `LIBRARY_PATH' and that fixed the problem for many
- # systems. However, some software (for example ImageMagick)
- # over-write `LIBRARY_PATH', therefore there is no other way than
- # to put a link to these necessary files in our local build
- # directory. IMPORTANT NOTE: later, when we build the GNU C
- # Library in the project, we should remove this step.
+# The 'ld' linker of Binutils needs several '*crt*.o' files from
+# the host's GNU C Library to run. On some systems these object
+# files aren't installed in standard places. We defined
+# 'LIBRARY_PATH' and that fixed the problem for many
+# systems. However, some software (for example ImageMagick)
+# over-write 'LIBRARY_PATH', therefore there is no other way than
+# to put a link to these necessary files in our local build
+# directory. IMPORTANT NOTE: later, when we build the GNU C Library
+# in the project, we should remove this step.
if ! [ x"$(sys_library_path)" = x ]; then
for f in $(sys_library_path)/*crt*.o; do
b=$$($(ibdir)/basename $$f)
@@ -1285,11 +1181,11 @@ $(ibidir)/binutils-$(binutils-version): \
done
fi
- # Write the final target.
+# Write the final target.
echo "GNU Binutils $(binutils-version)" > $@
fi
-# We are having issues with `libiberty' (part of GCC) on Mac. So for now,
+# We are having issues with 'libiberty' (part of GCC) on Mac. So for now,
# GCC won't be built there. Since almost no natural science paper's
# processing depends so strongly on the compiler used, for now, this isn't
# a bad assumption, but we are indeed searching for a solution.
@@ -1298,7 +1194,7 @@ $(ibidir)/binutils-$(binutils-version): \
# environment. So, we'll build GCC after building all the basic tools that
# are often used in a configure and build scripts of GCC components.
#
-# Objective C and Objective C++ is necessary for installing `matplotlib'.
+# Objective C and Objective C++ is necessary for installing 'matplotlib'.
#
# We are currently having problems installing GCC on macOS, so for the time
# being, if the project is being run on a macOS, we'll just set a link.
@@ -1325,45 +1221,41 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
echo; exit 1
}
- # Download the tarball.
- tarball=gcc-$(gcc-version).tar.xz
+# Download the tarball.
+ tarball=gcc-$(gcc-version).tar.lz
$(call import-source, $(gcc-url), $(gcc-checksum))
- # To avoid any previous build in '.local/bin' causing problems in
- # this build/links of this GCC, we'll first delete all the possibly
- # built/existing compilers in this project. Note that GCC also
- # installs several executables like this 'x86_64-pc-linux-gnu-gcc',
- # 'x86_64-pc-linux-gnu-gcc-ar' or 'x86_64-pc-linux-gnu-g++'.
+# To avoid any previous build in '.local/bin' causing problems in
+# this build/links of this GCC, we'll first delete all the possibly
+# built/existing compilers in this project. Note that GCC also
+# installs several executables like this 'x86_64-pc-linux-gnu-gcc',
+# 'x86_64-pc-linux-gnu-gcc-ar' or 'x86_64-pc-linux-gnu-g++'.
rm -f $(ibdir)/*g++ $(ibdir)/cpp $(ibdir)/gfortran
rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc*
rm -f $(ibdir)/*gcc* $(ibdir)/gcov* $(ibdir)/cc $(ibdir)/c++
rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*
- # GCC builds is own libraries in '$(idir)/lib64'. But all other
- # libraries are in '$(idir)/lib'. Since this project is only for a
- # single architecture, we can trick GCC into building its libraries
- # in '$(idir)/lib' by defining the '$(idir)/lib64' as a symbolic
- # link to '$(idir)/lib'.
+# Build (or set links) to GCC.
if [ $(host_cc) = 1 ]; then
- # Put links to the host's tools in '.local/bin'. Note that some
- # macOS systems have both a native clang *and* a GNU C Compiler
- # (note that this is different from the "normal" macOS situation
- # where 'gcc' actually points to clang, here we mean when 'gcc'
- # is actually the GNU C Compiler).
- #
- # In such cases, the GCC isn't complete and using it will cause
- # problems when building high-level tools (for example openBLAS,
- # rpcsvc-proto, CMake, xlsxio, Python or Matplotlib among
- # others). To avoid such situations macOSs are configured like
- # this: we'll simply set 'gcc' to point to 'clang' and won't set
- # 'gcc' to point to the system's 'gcc'.
- #
- # Also, note that LLVM's clang doesn't have a C Pre-Processor. So
- # we will only put a link to the host's 'cpp' if the system is
- # not macOS. On macOS systems that have a real GCC installed,
- # having GNU CPP in the project build directory is known to cause
- # problems with 'libX11'.
+# Put links to the host's tools in '.local/bin'. Note that some
+# macOS systems have both a native clang *and* a GNU C Compiler
+# (note that this is different from the "normal" macOS situation
+# where 'gcc' actually points to clang, here we mean when 'gcc' is
+# actually the GNU C Compiler).
+#
+# In such cases, the GCC isn't complete and using it will cause
+# problems when building high-level tools (for example openBLAS,
+# rpcsvc-proto, CMake, xlsxio, Python or Matplotlib among
+# others). To avoid such situations macOSs are configured like
+# this: we'll simply set 'gcc' to point to 'clang' and won't set
+# 'gcc' to point to the system's 'gcc'.
+#
+# Also, note that LLVM's clang doesn't have a C Pre-Processor. So
+# we will only put a link to the host's 'cpp' if the system is not
+# macOS. On macOS systems that have a real GCC installed, having
+# GNU CPP in the project build directory is known to cause problems
+# with 'libX11'.
$(call makelink,gfortran)
if [ x$(on_mac_os) = xyes ]; then
$(call makelink,clang)
@@ -1376,59 +1268,61 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
$(call makelink,g++)
fi
- # We also want to have the two 'cc' and 'c++' in the build
- # directory that point to the selected compiler. With the checks
- # above, 'gcc' and 'g++' will point to the proper compiler, so
- # we'll use them to define 'cc' and 'c++'.
+# We also want to have the two 'cc' and 'c++' in the build
+# directory that point to the selected compiler. With the checks
+# above, 'gcc' and 'g++' will point to the proper compiler, so
+# we'll use them to define 'cc' and 'c++'.
$(call makelink,gcc,,cc)
$(call makelink,g++,,c++)
- # Get the first line of the compiler's '--version' output and put
- # that into the target (so we know want compiler was used).
+# Get the first line of the compiler's '--version' output and put
+# that into the target (so we know want compiler was used).
ccinfo=$$(gcc --version | awk 'NR==1')
echo "C compiler (""$$ccinfo"")" > $@
else
- # Mark the current directory.
+# Mark the current directory.
current_dir=$$(pwd)
- # We don't want '.local/lib' and '.local/lib64' to be separate.
- ln -fs $(ildir) $(idir)/lib64
-
- # By default we'll build GCC in the RAM to avoid building so many
- # files and possibly harming the hard-drive or SSD. But if the
- # RAM doesn't have enough space, we can't use it.
+# By default 'ddir' (where GCC is decompressed and built) is in the
+# RAM (on systems that support '/dev/shm'). This is done to avoid
+# building so many small/temporary files and possibly harming the
+# hard-drive or SSD. But if the RAM doesn't have enough space, we
+# should use the hard-drive or SSD. During its build GCC's build
+# directory will become about 7GB (multiple of 1024 bytes, for GCC
+# 11.2.0). So at this step, we are making sure we have more than
+# 7.5GiB (multiple of 1000 bytes, which corresponds to 7.32GB)
+# before GCC starts to build. Note that the 4th column of 'df' is
+# the "available" space at the time of running, not the full
+# space. So the background RAM that the OS will be using during
+# Maneage is accounted for. Also consider that GCC is built alone
+# (no other Maneage software is built at the same time as GCC).
in_ram=$$(df $(ddir) \
- | awk 'NR==2{print ($$4>10000000) ? "yes" : "no"}'); \
+ | awk 'NR==2{print ($$4>7500000) ? "yes" : "no"}'); \
if [ $$in_ram = "yes" ]; then odir=$(ddir)
else
- odir=$(BDIR)/software/build-tmp-gcc
+ odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space
if [ -d $$odir ]; then rm -rf $$odir; fi
mkdir $$odir
fi
- # Go into the proper directory, unpack GCC and prepare the
- # 'build' directory inside it for all the built files.
+# Go into the proper directory, unpack GCC and prepare the 'build'
+# directory inside it for all the built files.
cd $$odir
rm -rf gcc-$(gcc-version)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
if [ $$odir != $(ddir) ]; then
ln -s $$odir/gcc-$(gcc-version) $(ddir)/gcc-$(gcc-version)
fi
cd gcc-$(gcc-version)
- # Handle bug https://savannah.nongnu.org/bugs/index.php?61240 in
- # which gcc preferentially uses a system-level 'unwind' library
- # rather than using its own one.
- ln -sf ../../libgcc/unwind-generic.h libstdc++-v3/libsupc++/unwind.h
- ln -sf ../libgcc/unwind-generic.h libitm/unwind.h
-
+# Set the build directory for the processing.
mkdir build
cd build
- # Configure, build and install GCC, if any of three steps fails,
- # the error message will be printed.
+# Configure, build and install GCC, if any of three steps fails,
+# the error message will be printed.
if ! ../configure SHELL=$(ibdir)/bash \
--prefix=$(idir) \
--with-mpc=$(idir) \
@@ -1447,26 +1341,25 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
--enable-languages=c,c++,fortran,objc,obj-c++ \
--disable-nls \
--disable-libada \
- --disable-multilib \
- --disable-multiarch; then error_message; fi
+ --disable-multilib; then error_message; fi
if ! make SHELL=$(ibdir)/bash -j$(numthreads); then error_message; fi
if ! make SHELL=$(ibdir)/bash install; then error_message; fi
- # We need to manually fix the RPATH inside GCC's libraries, the
- # programs built by GCC already have RPATH.
+# We need to manually fix the RPATH inside GCC's libraries, the
+# programs built by GCC already have RPATH.
tempname=$$odir/gcc-$(gcc-version)/build/rpath-temp-copy
if [ -f $(ibdir)/patchelf ]; then
- # Go over all the installed GCC libraries (its executables are
- # fine!).
+# Go over all the installed GCC libraries (its executables are
+# fine!).
for f in $$(find $(idir)/libexec/gcc -type f) $(ildir)/libstdc++*; do
- # Make sure this is a static library, copy it to a temporary
- # name (to avoid any possible usage of the file while it is
- # being corrected), and add RPATH inside of it and put the
- # corrected file back in its place. In the case of the
- # standard C++ library, we also need to manually insert a
- # linking to libiconv.
+# Make sure this is a static library, copy it to a temporary
+# name (to avoid any possible usage of the file while it is
+# being corrected), and add RPATH inside of it and put the
+# corrected file back in its place. In the case of the standard
+# C++ library, we also need to manually insert a linking to
+# libiconv.
if file $$f | grep -q "dynamically linked"; then
cp $$f $$tempname
patchelf --set-rpath $(ildir) $$tempname
@@ -1480,8 +1373,8 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
done
fi
- # Come back up to the un-packing directory and delete the GCC
- # source directory.
+# Come back up to the un-packing directory and delete the GCC
+# source directory.
cd ../..
rm -rf gcc-$(gcc-version)
cd $$current_dir
@@ -1490,11 +1383,11 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
rm $(ddir)/gcc-$(gcc-version);
fi
- # Set 'cc' to point to 'gcc'.
+# Set 'cc' to point to 'gcc'.
ln -sf $(ibdir)/gcc $(ibdir)/cc
ln -sf $(ibdir)/g++ $(ibdir)/c++
- # Write the final target.
+# Write the final target.
echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@
fi
@@ -1513,18 +1406,19 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
# If the project is built in a minimal environment, there is no text
# editor, making it hard to work on the project. By default a minimal
# (relatively user-friendly: GNU Nano) text editor will thus also be built
-# at the end of the "basic" tools. More advanced editors are available as
-# optional high-level programs. GNU Nano is a very light-weight and small
-# command-line text editor (around 3.5 Mb after installation!).
+# at the end of the "basic" tools. More advanced editors (for example Emacs
+# and Vim) are available as optional high-level programs. GNU Nano is a
+# very light-weight and small command-line text editor (around 3.5 Mb after
+# installation!).
#
# The editor is a top-level target in the basic tools (given to
# 'targets-proglib' above). Hence nothing depends on it, and it just
# depends on GCC. This is done because some projects may choose to not have
-# nano (and use their own optional high-level text editor). To do this,
-# they just have to manually remove 'nano' from 'targets-proglib' above and
+# nano (and use their own optional high-level text editor). To do this, you
+# can just have to manually remove 'nano' from 'targets-proglib' above and
# add their optional text editor in 'TARGETS.conf'.
$(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version)
- tarball=nano-$(nano-version).tar.xz
+ tarball=nano-$(nano-version).tar.lz
$(call import-source, $(nano-url), $(nano-checksum))
$(call gbuild, nano-$(nano-version), static)
echo "GNU Nano $(nano-version)" > $@
diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
index 66c77bc..c25dfb1 100644
--- a/reproduce/software/make/build-rules.mk
+++ b/reproduce/software/make/build-rules.mk
@@ -3,7 +3,7 @@
# imported into 'basic.mk' and 'high-level.mk'. They should be activated
# with Make's 'Call' function.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# This Makefile is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -29,8 +29,13 @@
# its checksum and if it is correct, remove the extra suffix.
#
# Arguments:
-# 1: The optional URL to use for this tarball.
-# 2: The expeced checksum of the tarball.
+# 1: The optional base URL (directory) to use for this tarball.
+# 2: The expected checksum of the tarball.
+# 3: The upstream name of the tarball file, if not automatically derived
+# from the version number.
+# 4: [Optional]: Alternative upstream base URL (directory) for the
+# tarball, to be used in preference to user or Maneage backup
+# servers.
#
# Necessary shell variables
# 'tarball': This is the name of the actual tarball file without a
@@ -56,7 +61,14 @@ import-source = final=$(tdir)/$$tarball; \
tarballurl=$(topbackupserver)/$$tarball; \
else \
bservers="$(backupservers_all)"; \
- tarballurl=$$url/$$tarball; \
+ if [ "x$(strip $(3))" = "x" ]; then \
+ tarballurl=$$url/$$tarball; \
+ else \
+ tarballurl=$$url/$(strip $(3)); \
+ fi; \
+ fi; \
+ if [ x"$(4)" != x ]; then \
+ bservers="$(strip $(4)) $$bservers"; \
fi; \
if [ -f $(ibdir)/wget ]; then \
downloader="wget --no-use-server-timestamps -O"; \
@@ -89,6 +101,48 @@ import-source = final=$(tdir)/$$tarball; \
+# Double-check an already downloaded R source
+# -------------------------------------------
+#
+# It is probably too late to protect the system if you have already
+# installed an insecure or wrong R package. However, it's still useful
+# to check that the source package is the one that you think it is.
+#
+# Calculate the checksum and exit with a non-zero error code if
+# there's a mismatch, after informing the user.
+#
+# Arguments:
+# 1: The expected checksum of the tarball.
+#
+# Necessary shell variables
+# 'tarball': This is the name of the actual tarball file without a
+# directory.
+double-check-R-source = final=$(tdir)/R-project/$$tarball; \
+ exp_checksum="$(strip $(1))"; \
+ if [ x"$$exp_checksum" = x"NO-CHECK-SUM" ]; then \
+ result=0; \
+ else \
+ if type sha512sum > /dev/null 2>/dev/null; then \
+ checksum=$$(sha512sum "$$final" | awk '{print $$1}'); \
+ if [ x"$$checksum" = x"$$exp_checksum" ]; then \
+ result=0; \
+ else \
+ echo "ERROR: Non-matching checksum: $$final"; \
+ echo "Checksum should be: $$exp_checksum"; \
+ echo "Checksum is: $$checksum"; \
+ result=1; \
+ exit 1; \
+ fi; \
+ else \
+ echo "ERROR: sha512sum is unavailable."; \
+ exit 1; \
+ fi; \
+ fi
+
+
+
+
+
# Unpack a tarball
# ----------------
#
@@ -106,7 +160,7 @@ uncompress = csuffix=$$(echo $$utarball \
intarrm=0; \
intar=$$utarball; \
fi; \
- if tar xf $$intar; then \
+ if tar -xf $$intar; then \
if [ x$$intarrm = x1 ]; then rm $$intar; fi; \
else \
echo; echo "Tar error"; exit 1; \
@@ -166,10 +220,13 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
else shellop="SHELL=/bin/sh"; \
fi; \
\
+ if [ x$$gbuild_prefix = x ]; then prefixdir="$(idir)"; \
+ else prefixdir="$$gbuild_prefix"; fi; \
+ \
if [ -f "$$confscript" ]; then \
if [ x"$(strip $(1))" = x"zlib-$(zlib-version)" ]; then \
- configop="--prefix=$(idir)"; \
- else configop="$$shellop --prefix=$(idir)"; \
+ configop="--prefix=$$prefixdir"; \
+ else configop="$$shellop --prefix=$$prefixdir"; \
fi; \
fi; \
\
@@ -190,7 +247,7 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(2)" = xstatic ]; then \
make "$$shellop" install $(7); \
cd ..; \
fi; \
- rm -rf $(1)
+ rm -rf $(1);
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 6ea782c..34c829b 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -3,7 +3,7 @@
# ------------------------------------------------------------------------
# !!!!! IMPORTANT NOTES !!!!!
#
-# This Makefile will be run by the initial `./project configure' script. It
+# This Makefile will be run by the initial './project configure' script. It
# is not included into the project afterwards.
#
# This Makefile builds the high-level (optional) software in Maneage that
@@ -12,8 +12,8 @@
#
# ------------------------------------------------------------------------
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
#
# This Makefile is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
@@ -60,6 +60,9 @@ patchdir = "$(shell pwd)"/reproduce/software/patches
itidir = $(BDIR)/software/installed/version-info/tex
ictdir = $(BDIR)/software/installed/version-info/cite
ipydir = $(BDIR)/software/installed/version-info/python
+ircrandir = $(BDIR)/software/installed/version-info/r-cran
+ilibrcrandir = $(BDIR)/software/installed/lib/R/library
+
# Targets to build.
ifeq ($(strip $(all_highlevel)),1)
@@ -75,7 +78,7 @@ ifeq ($(strip $(all_highlevel)),1)
# included here because there is no explicit target for them: they will
# be built as part of the other package.
targets-proglib := $(filter-out minizip-% lapack-% ghostscript-fonts-%, \
- $(shell awk '/^# CLASS:PYTHON/{good=0} \
+ $(shell awk '/^# CLASS:(PYTHON|R-CRAN)/{good=0} \
good==1 && !/^#/ && $$1 ~ /-version$$/ { \
printf("%s %s ", $$1, $$3)} \
/^# CLASS:HIGHLEVEL/{good=1}' \
@@ -85,14 +88,25 @@ ifeq ($(strip $(all_highlevel)),1)
# List all existing Python packages.
targets-python := $(shell \
- awk '/^# CLASS:PYTHON/{good=1} \
- good==1 && !/^#/ && $$1 ~ /-version$$/ {printf("%s %s ",$$1,$$3)}' \
- reproduce/software/config/versions.conf | sed 's/version //g')
+ awk '/^# CLASS:PYTHON-START/{good=1} good; \
+ /^# CLASS:PYTHON-END/{good=0}' \
+ reproduce/software/config/versions.conf \
+ | awk '!/^#/' \
+ | sed 's/-version = /-/g')
+
+ # List all existing R-CRAN packages.
+ targets-r-cran := $(shell \
+ awk '/^# CLASS:R-CRAN-START/{good=1} good; \
+ /^# CLASS:R-CRAN-END/{good=0}' \
+ reproduce/software/config/versions.conf \
+ | awk '!/^#/' \
+ | sed 's/-version = /-/g')
else
- # Append the version of each software to its name. We are using a Make
+ # Append the version of each software package to its name. We are using a Make
# feature where a variable name is defined with another variable.
targets-python := $(foreach p,$(top-level-python),$(p)-$($(p)-version))
+ targets-r-cran := $(foreach p,$(top-level-r-cran),$(p)-$($(p)-version))
targets-proglib := $(foreach p,$(top-level-programs),$(p)-$($(p)-version))
endif
@@ -100,6 +114,7 @@ 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
# Define the shell environment
@@ -112,14 +127,18 @@ all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \
#
# To investigate:
#
-# 1) Set SHELL to `$(ibdir)/env - NAME=VALUE $(ibdir)/bash' and set all
-# the parameters defined bellow as `NAME=VALUE' statements before
+# 1) Set SHELL to '$(ibdir)/env - NAME=VALUE $(ibdir)/bash' and set all
+# the parameters defined bellow as 'NAME=VALUE' statements before
# calling Bash. This will enable us to completely ignore the user's
# native environment.
#
-# 2) Add `--noprofile --norc' to `.SHELLFLAGS' so doesn't load the
+# 2) Add '--noprofile --norc' to '.SHELLFLAGS' so doesn't load the
# user's environment.
#
+# 3) Add the '-u' flag so that an error occurs if an environment
+# variable is empty; this reduces the chance of catastrophic
+# file removal with 'rm -fr ../../$${FORGOT_TO_DEFINE_THIS}'.
+#
# Shell settings similar to 'basic.mk':
.ONESHELL:
export PATH := $(ibdir)
@@ -131,6 +150,9 @@ export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
export CPPFLAGS := -I$(idir)/include -Wno-nullability-completeness
export PKG_CONFIG_PATH := $(ildir)/pkgconfig:$(idir)/share/pkgconfig
+# Disable built-in rules (which are not needed here!)
+.SUFFIXES:
+
# Settings specific to this Makefile.
export CC := $(ibdir)/gcc
export CXX := $(ibdir)/g++
@@ -147,16 +169,16 @@ export C_INCLUDE_PATH := $(iidir)
export CPLUS_INCLUDE_PATH := $(iidir)
endif
-# Recipe startup script, see `reproduce/software/shell/bashrc.sh'.
+# Recipe startup script, see 'reproduce/software/shell/bashrc.sh'.
export PROJECT_STATUS := configure_highlevel
export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
# Until we build our own C library, without this, our GCC won't be able to
# compile anything! Note that on most systems (in particular
-# non-Debian-based), `sys_cpath' will be empty.
+# non-Debian-based), 'sys_cpath' will be empty.
export CPATH := $(sys_cpath)
-# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
+# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
# ultimately redundant. But on some systems, even having a single value
# causes crashs (see bug #56682). So we'll just give it no value at all.
export DYLD_LIBRARY_PATH :=
@@ -164,8 +186,8 @@ export DYLD_LIBRARY_PATH :=
# On Debian-based OSs, the basic C libraries are in a target-specific
# location, not in standard places. Until we merge the building of the C
# library, it is thus necessary to include this location here. On systems
-# that don't need it, `sys_library_path' is just empty. This is necessary
-# for `ld'.
+# that don't need it, 'sys_library_path' is just empty. This is necessary
+# for 'ld'.
#
# If this variable is not defined, it will be interpretted as the current
# directory. In this case, when the program source has a 'specs' directory,
@@ -179,12 +201,18 @@ endif
# Building flags:
#
# C++ flags: when we build GCC, the C++ standard library needs to link with
-# libiconv. So it is necessary to generically include `-liconv' for all C++
+# libiconv. So it is necessary to generically include '-liconv' for all C++
# builds.
ifeq ($(host_cc),0)
export CXXFLAGS := -liconv
endif
+# Custom installation prefix for software that can cause conflicts with
+# others, to avoid crowding the to Maneage installed software directory,
+# we'll put them all in a 'custom' directory.
+idircustom = $(idir)/custom
+$(idircustom):; mkdir $@
+
# Servers to use as backup. Maneage already has some fixed servers that can
# be used to download software tarballs. They are in a configuation
# file. But we give precedence to the "user" backup servers.
@@ -211,6 +239,8 @@ backupservers = $(filter-out $(topbackupserver),$(backupservers_all))
# Import rules to build specialized software
include reproduce/software/make/xorg.mk
include reproduce/software/make/python.mk
+include reproduce/software/make/r-cran.mk
+
@@ -226,61 +256,27 @@ include reproduce/software/make/python.mk
#
# We would prefer to build static libraries, but some compilers like LLVM
# don't have static capabilities, so they'll only build dynamic/shared
-# libraries. Therefore, we can't use the easy `.a' suffix for static
+# libraries. Therefore, we can't use the easy '.a' suffix for static
# libraries as targets and there are different conventions for shared
# library names.
-
-# Until version 0.11.0 is released, we are using the version corresponding
-# to commit 014954db (603 commits after version 0.10.0, most recent when
-# first importing log4cxx into this project).
-#
-# Note that after cloning the project, the following changes are necessary
-# in `configure.ac'.
-# - Update the final name of the tarball and its version (from `git
-# - describe') by modifying the `AC_INIT' line:
-# AC_INIT([apachelog4cxx], [0.10.0-603-014954db])
-# - Because of the long file names in the project, some files will not be
-# packaged by default, so pass the `tar-ustar' option to Automake (the
-# `AM_INIT_AUTOMAKE' line of `configure.ac':
-# AM_INIT_AUTOMAKE([foreign subdir-objects -Wall tar-ustar])
-#
-# You can then simply bootstrap the project and make the distribution
-# tarball like this:
-# ./autogen.sh && ./configure && make -j8 && make dist-lzip
-#
-# Unfortunately we have to re-run the `autogen.sh' script on the tarball to
-# build it because it will complain about the version of libtool, so until
-# the version 0.11.0 of log4cxx, we'll have to run `autogen.sh' on the
-# unpacked source also.
$(ibidir)/apachelog4cxx-$(apachelog4cxx-version): \
+ $(ibidir)/cmake-$(cmake-version) \
$(ibidir)/expat-$(expat-version) \
$(ibidir)/apr-util-$(apr-util-version) \
$(ibidir)/automake-$(automake-version)
- tarball=apachelog4cxx-$(apachelog4cxx-version).tar.lz
+ tarball=apache-log4cxx-$(apachelog4cxx-version).tar.lz
$(call import-source, $(apachelog4cxx-url), $(apachelog4cxx-checksum))
- pdir=apachelog4cxx-$(apachelog4cxx-version)
- rm -rf $(ddir)/$$pdir
- topdir=$(pwd)
- cd $(ddir)
- tar xf $(tdir)/$$tarball
- cd $$pdir
- ./autogen.sh
- ./configure SHELL=$(ibdir)/bash --prefix=$(idir)
- make -j$(numthreads) SHELL=$(ibdir)/bash
- make install
- cd ..
- rm -rf $$pdir
- cd $$topdir
+ $(call cbuild, apache-log4cxx-$(apachelog4cxx-version), static)
echo "Apache log4cxx $(apachelog4cxx-version)" > $@
$(ibidir)/apr-$(apr-version):
- tarball=apr-$(apr-version).tar.gz
+ tarball=apr-$(apr-version).tar.lz
$(call import-source, $(apr-url), $(apr-checksum))
$(call gbuild, apr-$(apr-version), ,--disable-static)
echo "Apache Portable Runtime $(apr-version)" > $@
$(ibidir)/apr-util-$(apr-util-version): $(ibidir)/apr-$(apr-version)
- tarball=apr-util-$(apr-util-version).tar.gz
+ tarball=apr-util-$(apr-util-version).tar.lz
$(call import-source, $(apr-util-url), $(apr-util-checksum))
$(call gbuild, apr-util-$(apr-util-version), , \
--disable-static \
@@ -291,20 +287,19 @@ $(ibidir)/apr-util-$(apr-util-version): $(ibidir)/apr-$(apr-version)
$(ibidir)/atlas-$(atlas-version):
- tarball=lapack-$(lapack-version).tar.gz
+ tarball=lapack-$(lapack-version).tar.lz
$(call import-source, $(lapack-url), $(lapack-checksum))
- tarball=atlas-$(atlas-version).tar.bz2
+ tarball=atlas-$(atlas-version).tar.lz
$(call import-source, $(atlas-url), $(atlas-checksum))
- # Get the operating system specific features (how to get
- # CPU frequency and the library suffixes). To make the steps
- # more readable, the different library version suffixes are
- # named with a single character: `s' for no version in the
- # name, `m' for the major version suffix, and `f' for the
- # full version suffix.
- # GCC in Mac OS doesn't work. To work around this issue, on Mac
- # systems we force ATLAS to use `clang' instead of `gcc'.
+# Get the operating system specific features (how to get CPU
+# frequency and the library suffixes). To make the steps more
+# readable, the different library version suffixes are named with a
+# single character: 's' for no version in the name, 'm' for the major
+# version suffix, and 'f' for the full version suffix. GCC in Mac OS
+# doesn't work. To work around this issue, on Mac systems we force
+# ATLAS to use 'clang' instead of 'gcc'.
if [ x$(on_mac_os) = xyes ]; then
s=dylib
m=3.dylib
@@ -321,8 +316,8 @@ $(ibidir)/atlas-$(atlas-version):
| sed "s/.*: \([0-9.]*\).*/\1/")
fi
- # See if the shared libraries should be build for a single CPU
- # thread or multiple threads.
+# See if the shared libraries should be build for a single CPU thread
+# or multiple threads.
N=$$(nproc)
srcdir=$$(pwd)/reproduce/software/make
if [ $$N = 1 ]; then
@@ -331,25 +326,25 @@ $(ibidir)/atlas-$(atlas-version):
sharedmk=$$srcdir/atlas-multiple.mk
fi
- # The linking step here doesn't recognize the `-Wl' in the
- # `rpath_command'.
+# The linking step here doesn't recognize the '-Wl' in the
+# 'rpath_command'.
export LDFLAGS=-L$(ildir)
cd $(ddir)
- tar xf $(tdir)/atlas-$(atlas-version).tar.bz2
+ tar -xf $(tdir)/atlas-$(atlas-version).tar.lz
cd ATLAS
rm -rf build
mkdir build
cd build
../configure -b 64 -D c -DPentiumCPS=$$core \
- --with-netlib-lapack-tarfile=$(tdir)/lapack-$(lapack-version).tar.gz \
+ --with-netlib-lapack-tarfile=$(tdir)/lapack-$(lapack-version).tar.lz \
--cripple-atlas-performance \
-Fa alg -fPIC --shared $$clangflag \
--prefix=$(idir)
- # Static build.
+# Static build.
make
- # Currently the shared libraries have problems on macOS.
+# Currently the shared libraries have problems on macOS.
if [ "x$(on_mac_os)" != xyes ]; then
cd lib
make -f $$sharedmk
@@ -362,21 +357,21 @@ $(ibidir)/atlas-$(atlas-version):
ln -fs $(ildir)/liblapack.$$f $(ildir)/liblapack.$$m
fi
- # Install the libraries.
+# Install the libraries.
make install
- # We need to check the existance of `libptlapack.a', but we can't
- # do this in the `&&' steps above (it will conflict). So we'll do
- # the check after seeing if `libtatlas.so' is installed, then we'll
- # finalize the build (delete the untarred directory).
+# We need to check the existance of 'libptlapack.a', but we can't do
+# this in the '&&' steps above (it will conflict). So we'll do the
+# check after seeing if 'libtatlas.so' is installed, then we'll
+# finalize the build (delete the untarred directory).
if [ "x$(on_mac_os)" != xyes ]; then \
[ -e lib/libptlapack.a ] && cp lib/libptlapack.a $(ildir); \
cd $(ddir); \
rm -rf ATLAS; \
fi
- # We'll check the full installation with the static library (not
- # currently building shared library on Mac.
+# We'll check the full installation with the static library (not
+# currently building shared library on Mac.
if [ -f $(ildir)/libatlas.a ]; then \
echo "ATLAS $(atlas-version)" > $@; \
fi
@@ -391,7 +386,7 @@ $(ibidir)/boost-$(boost-version): \
rm -rf $(ddir)/$$unpackdir
topdir=$(pwd)
cd $(ddir)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd $$unpackdir
./bootstrap.sh --prefix=$(idir) --with-libraries=all \
--with-python=python3
@@ -404,15 +399,15 @@ $(ibidir)/boost-$(boost-version): \
$(ibidir)/cfitsio-$(cfitsio-version):
- # Download the tarball
- tarball=cfitsio-$(cfitsio-version).tar.gz
+# Download the tarball
+ tarball=cfitsio-$(cfitsio-version).tar.lz
$(call import-source, $(cfitsio-url), $(cfitsio-checksum))
- # CFITSIO hard-codes '@rpath' inside the shared library on
- # Mac systems. So we need to change it to our library
- # installation path. It doesn't affect GNU/Linux, so we'll
- # just do it in any case to keep things clean.
- topdir=$(pwd); cd $(ddir); tar xf $(tdir)/$$tarball
+# CFITSIO hard-codes '@rpath' inside the shared library on Mac
+# systems. So we need to change it to our library installation
+# path. It doesn't affect GNU/Linux, so we'll just do it in any case
+# to keep things clean.
+ topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball
customtar=cfitsio-$(cfitsio-version)-custom.tar.gz
cd cfitsio-$(cfitsio-version)
sed configure -e's|@rpath|$(ildir)|g' > configure_tmp
@@ -422,9 +417,9 @@ $(ibidir)/cfitsio-$(cfitsio-version):
tar cf $$customtar cfitsio-$(cfitsio-version)
cd $$topdir
- # Continue the standard build on the customized tarball. Note that
- # with the installation of CFITSIO, `fpack' and `funpack' are not
- # installed by default. Because of that, they are added explicity.
+# Continue the standard build on the customized tarball. Note that
+# with the installation of CFITSIO, 'fpack' and 'funpack' are not
+# installed by default. Because of that, they are added explicity.
export gbuild_tar=$(ddir)/$$customtar
$(call gbuild, cfitsio-$(cfitsio-version), , \
--enable-sse2 --enable-reentrant \
@@ -437,24 +432,25 @@ $(ibidir)/cairo-$(cairo-version): \
$(ibidir)/pixman-$(pixman-version) \
$(ibidir)/libpng-$(libpng-version) \
$(ibidir)/freetype-$(freetype-version)
- tarball=cairo-$(cairo-version).tar.xz
+ tarball=cairo-$(cairo-version).tar.lz
$(call import-source, $(cairo-url), $(cairo-checksum))
$(call gbuild, cairo-$(cairo-version), static, \
--with-x=yes, -j$(numthreads) V=1)
echo "Cairo $(cairo-version)" > $@
# Eigen is just headers! So it doesn't need to be compiled. Once unpacked
-# it has a checksum after `eigen-eigen', so we'll just use a `*' to choose
+# it has a checksum after 'eigen-eigen', so we'll just use a '*' to choose
# the unpacked directory.
$(ibidir)/eigen-$(eigen-version):
- tarball=eigen-$(eigen-version).tar.gz
+ tarball=eigen-$(eigen-version).tar.lz
$(call import-source, $(eigen-url), $(eigen-checksum))
rm -rf $(ddir)/eigen-eigen-*
- topdir=$(pwd); cd $(ddir); tar xf $(tdir)/$$tarball
- cd eigen-eigen-*
- cp -r Eigen $(iidir)/eigen3
+ topdir=$(pwd); cd $(ddir); tar -xf $(tdir)/$$tarball
+ cd eigen-$(eigen-version)
+ if ! [ -d $(iidir)/eigen3 ]; then mkdir $(iidir)/eigen3; fi
+ cp -r Eigen/* $(iidir)/eigen3/
cd $$topdir
- rm -rf $(ddir)/eigen-eigen-*
+ rm -rf $(ddir)/eigen-$(eigen-version)
echo "Eigen $(eigen-version)" > $@
# GNU Emacs is an advanced text editor (among many other things!), so it
@@ -468,7 +464,7 @@ $(ibidir)/eigen-$(eigen-version):
# except the core Emacs functionality (using '--without-all') and we are
# also disabling all graphic user interface features (using '--without-x').
$(ibidir)/emacs-$(emacs-version):
- tarball=emacs-$(emacs-version).tar.xz
+ tarball=emacs-$(emacs-version).tar.lz
$(call import-source, $(emacs-url), $(emacs-checksum))
$(call gbuild, emacs-$(emacs-version), static, \
--without-all --without-x \
@@ -483,15 +479,28 @@ $(ibidir)/expat-$(expat-version):
echo "Expat $(expat-version)" > $@
$(ibidir)/fftw-$(fftw-version):
- # Prepare the source tarball.
- tarball=fftw-$(fftw-version).tar.gz
+
+# Prepare the source tarball.
+ tarball=fftw-$(fftw-version).tar.lz
$(call import-source, $(fftw-url), $(fftw-checksum))
- # FFTW's single and double precission libraries must be built
- # independently: for the the single-precision library, we need to
- # add the `--enable-float' option. We will build this first, then
- # the default double-precision library.
- confop="--enable-shared --enable-threads --enable-avx --enable-sse2"
+# FFTW's single and double precision libraries must be built
+# independently: for the the single-precision library, we need to add
+# the '--enable-float' option. We will build this first, then the
+# default double-precision library.
+#
+# There are Intel-specific optimizations that can be enabled by
+# adding the following two options to 'confop'
+#
+# --enable-avx --enable-sse2
+#
+# However, they cause crashs on non-Intel processors (has been
+# confirmed in ARM's aarch64). So in the generic scenario they are
+# removed. Checking how these optimizations affect the numeric
+# accuracy of the result (and thus optionally adding them for
+# Intel-based processors) should be studied before they are
+# optionally added for Intel-based CPUs (and ignored for others).
+ confop="--enable-shared --enable-threads"
$(call gbuild, fftw-$(fftw-version), static, \
$$confop --enable-float)
$(call gbuild, fftw-$(fftw-version), static, \
@@ -500,19 +509,19 @@ $(ibidir)/fftw-$(fftw-version):
echo "FFTW $(fftw-version) \citep{fftw}" > $@
$(ibidir)/freetype-$(freetype-version): $(ibidir)/libpng-$(libpng-version)
- tarball=freetype-$(freetype-version).tar.gz
+ tarball=freetype-$(freetype-version).tar.lz
$(call import-source, $(freetype-url), $(freetype-checksum))
$(call gbuild, freetype-$(freetype-version), static)
echo "FreeType $(freetype-version)" > $@
$(ibidir)/gperf-$(gperf-version):
- tarball=gperf-$(gperf-version).tar.gz
+ tarball=gperf-$(gperf-version).tar.lz
$(call import-source, $(gperf-url), $(gperf-checksum))
$(call gbuild, gperf-$(gperf-version), static)
echo "GNU gperf $(gperf-version)" > $@
$(ibidir)/gsl-$(gsl-version):
- tarball=gsl-$(gsl-version).tar.gz
+ tarball=gsl-$(gsl-version).tar.lz
$(call import-source, $(gsl-url), $(gsl-checksum))
$(call gbuild, gsl-$(gsl-version), static)
echo "GNU Scientific Library $(gsl-version)" > $@
@@ -531,14 +540,14 @@ $(ibidir)/hdf5-$(hdf5-version): $(ibidir)/openmpi-$(openmpi-version)
# HEALPix includes the source of its C, C++, Python (and several other
# languages) libraries within one tarball. We will include the Python
# installation only when any other Python module is requested (in
-# `TARGETS.conf').
+# 'TARGETS.conf').
#
-# Note that the default `./configure' script is an interactive script which
-# is hard to automate. So we need to go into the `autotools' directory of
-# the `C' and `cxx' directories and configure the GNU Build System (with
-# `autoreconf', which uses `autoconf' and `automake') to easily build the
+# Note that the default './configure' script is an interactive script which
+# is hard to automate. So we need to go into the 'autotools' directory of
+# the 'C' and 'cxx' directories and configure the GNU Build System (with
+# 'autoreconf', which uses 'autoconf' and 'automake') to easily build the
# HEALPix C/C++ libraries in batch mode.
-ifeq ($(strip $(top-level-python)),)
+ifeq ($(strip $(targets-python)),)
healpix-python-dep =
else
healpix-python-dep = $(ipydir)/matplotlib-$(matplotlib-version) \
@@ -548,7 +557,7 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
$(ibidir)/cfitsio-$(cfitsio-version) \
$(ibidir)/autoconf-$(autoconf-version) \
$(ibidir)/automake-$(automake-version)
- tarball=healpix-$(healpix-version).tar.gz
+ tarball=healpix-$(healpix-version).tar.lz
$(call import-source, $(healpix-url), $(healpix-checksum))
if [ x"$(healpix-python-dep)" = x ]; then
pycommand1="echo no-healpy-because-no-other-python"
@@ -559,7 +568,7 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
fi
rm -rf $(ddir)/Healpix_$(healpix-version)
topdir=$(pwd); cd $(ddir);
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd Healpix_$(healpix-version)/src/C/autotools/
autoreconf --install
./configure --prefix=$(idir)
@@ -568,6 +577,13 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
cd ../../cxx/autotools/
autoreconf --install
./configure --prefix=$(idir)
+
+# With CFITSIO 4.0, the 'CFITSIO_VERSION' macro has three
+# components. But this version of Healpix doesn't yet account for
+# this.
+ sed -i -e's/CFITSIO_VERSION/fitsversion/' cxxsupport/fitshandle.cc
+
+# Continue with the building.
make V=1 -j$(numthreads) SHELL=$(ibdir)/bash
make install
cd ../../healpy
@@ -578,19 +594,52 @@ $(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
cp $(dtexdir)/healpix.tex $(ictdir)/
echo "HEALPix $(healpix-version) \citep{healpix}" > $@
+$(ibidir)/libbsd-$(libbsd-version): $(ibidir)/libmd-$(libmd-version)
+ tarball=libbsd-$(libbsd-version).tar.lz
+ $(call import-source, $(libbsd-url), $(libbsd-checksum))
+ if [ x$(on_mac_os) = xyes ]; then
+ echo "" > $@
+ else
+ export LDFLAGS="-L$(idirlibmd)/lib $$LDFLAGS"
+ export CPPFLAGS="-I$(idirlibmd)/include $$CPPFLAGS"
+ $(call gbuild, libbsd-$(libbsd-version), static,,V=1)
+ echo "Libbsd $(libbsd-version)" > $@
+ fi
+
$(ibidir)/libidn-$(libidn-version):
- tarball=libidn-$(libidn-version).tar.gz
+ tarball=libidn-$(libidn-version).tar.lz
$(call import-source, $(libidn-url), $(libidn-checksum))
$(call gbuild, libidn-$(libidn-version), static, \
--disable-doc, -j$(numthreads) V=1)
echo "Libidn $(libidn-version)" > $@
$(ibidir)/libjpeg-$(libjpeg-version):
- tarball=jpegsrc.$(libjpeg-version).tar.gz
+ tarball=libjpeg-$(libjpeg-version).tar.lz
$(call import-source, $(libjpeg-url), $(libjpeg-checksum))
- $(call gbuild, jpeg-9b, static,,V=1)
+ $(call gbuild, libjpeg-$(libjpeg-version), static,,V=1)
echo "Libjpeg $(libjpeg-version)" > $@
+# libmd is a set of "message digest" functions that are available in in the
+# C library of BSD-based systems, but not others (like GNU-based
+# systems). It includes hash functions like MD5 and SHAs.
+#
+# Libmd is being installed in a non-standard location because its headers
+# (like 'md5.h') will conflict with similarly named headers by the system
+# during the building of Binutils later! So any program that needs libmd's
+# headers or libraries (like 'libbsd'), should add this special location to
+# its CPPFLAGS and LDFLAGS.
+idirlibmd=$(idircustom)/libmd
+$(ibidir)/libmd-$(libmd-version): | $(idircustom)
+ tarball=libmd-$(libmd-version).tar.lz
+ $(call import-source, $(libmd-url), $(libmd-checksum))
+ if [ x$(on_mac_os) = xyes ]; then
+ echo "" > $@
+ else
+ export gbuild_prefix=$(idirlibmd)
+ $(call gbuild, libmd-$(libmd-version), static,,V=1)
+ echo "Libmd $(libmd-version)" > $@
+ fi
+
$(ibidir)/libnsl-$(libnsl-version): \
$(ibidir)/libtirpc-$(libtirpc-version) \
$(ibidir)/rpcsvc-proto-$(rpcsvc-proto-version)
@@ -603,11 +652,11 @@ $(ibidir)/libnsl-$(libnsl-version): \
$(ibidir)/libpaper-$(libpaper-version): \
$(ibidir)/automake-$(automake-version)
- # Download the tarball.
- tarball=libpaper-$(libpaper-version).tar.gz
+# Download the tarball.
+ tarball=libpaper-$(libpaper-version).tar.lz
$(call import-source, $(libpaper-url), $(libpaper-checksum))
- # Unpack, build the configure system, build and install.
+# Unpack, build the configure system, build and install.
cd $(ddir)
tar -xf $(tdir)/$$tarball
unpackdir=libpaper-$(libpaper-version)
@@ -620,10 +669,10 @@ $(ibidir)/libpaper-$(libpaper-version): \
cd ..
rm -rf $$unpackdir
- # Post-processing: according to Linux From Scratch, libpaper
- # expects that packages will install files into this directory and
- # 'paperconfig' is a script which will invoke 'run-parts' if
- # '/etc/libpaper.d' exists
+# Post-processing: according to Linux From Scratch, libpaper expects
+# that packages will install files into this directory and
+# 'paperconfig' is a script which will invoke 'run-parts' if
+# '/etc/libpaper.d' exists
mkdir -vp $(idir)/etc/libpaper.d
sed -e's|MANEAGESHELL|$(SHELL)|' $(shsrcdir)/run-parts.in \
> $(ibdir)/run-parts
@@ -631,15 +680,19 @@ $(ibidir)/libpaper-$(libpaper-version): \
echo "Libpaper $(libpaper-version)" > $@
$(ibidir)/libpng-$(libpng-version):
- tarball=libpng-$(libpng-version).tar.xz
+
+# The option '-DPNG_ARM_NEON_OPT=0' prevents an arm64 'neon' library
+# from being required at compile time.
+ tarball=libpng-$(libpng-version).tar.lz
$(call import-source, $(libpng-url), $(libpng-checksum))
- $(call gbuild, libpng-$(libpng-version), static)
+ $(call gbuild, libpng-$(libpng-version), static, \
+ CFLAGS="-DPNG_ARM_NEON_OPT=0")
echo "Libpng $(libpng-version)" > $@
$(ibidir)/libtiff-$(libtiff-version): $(ibidir)/libjpeg-$(libjpeg-version)
- tarball=tiff-$(libtiff-version).tar.gz
+ tarball=libtiff-$(libtiff-version).tar.lz
$(call import-source, $(libtiff-url), $(libtiff-checksum))
- $(call gbuild, tiff-$(libtiff-version), static, \
+ $(call gbuild, libtiff-$(libtiff-version), static, \
--disable-jbig \
--disable-webp \
--disable-zstd)
@@ -652,12 +705,90 @@ $(ibidir)/libtirpc-$(libtirpc-version):
--disable-gssapi, V=1)
echo "libtirpc $(libtirpc-version)" > $@
+# Metastore is used (through a Git hook) to restore the source modification
+# dates of files after a Git checkout. Another Git hook saves all file
+# metadata just before a commit (to allow restoration after a
+# checkout). Since this project is managed in Makefiles, file modification
+# dates are critical to not having to redo the whole analysis after
+# checking out between branches.
+#
+# Note that we aren't using the standard version of Metastore, but a fork
+# of it that is maintained in this repository:
+# https://gitlab.com/makhlaghi/metastore-fork
+#
+# Libbsd is not necessary on macOS systems, because macOS is already a
+# BSD-based distribution. But on GNU/Linux systems, it is necessary.
+$(ibidir)/metastore-$(metastore-version): \
+ $(ibidir)/libbsd-$(libbsd-version)
+
+# Download the tarball.
+ tarball=metastore-$(metastore-version).tar.lz
+ $(call import-source, $(metastore-url), $(metastore-checksum))
+
+# Metastore doesn't have any './configure' script. So we'll just call
+# 'pwd' as a place-holder for the './configure' command.
+#
+# File attributes are also not available on some systems, since the
+# main purpose here is modification dates (and not attributes), we'll
+# also set the 'NO_XATTR' flag.
+#
+# After installing Metastore, write the relevant hooks into this
+# system's Git hooks, while setting the system-specific
+# directories/files.
+#
+# Note that the metastore -O and -G options used in this template are
+# currently only available in a fork of 'metastore' hosted at:
+# https://github.com/mohammad-akhlaghi/metastore
+#
+# Checking for presence of '.git'. When the project source is
+# downloaded from a non-Git source (for example from arXiv), there is
+# no '.git' directory to work with. So until we find a better
+# solution, avoid the step to to add the Git hooks.
+ current_dir=$$(pwd); \
+ $(call gbuild, metastore-$(metastore-version), static,, \
+ NO_XATTR=1 V=1,,pwd,PREFIX=$(idir))
+
+# Correct RPATH when necessary.
+ if [ -f $(ibdir)/patchelf ]; then
+ $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/metastore
+ fi
+
+# If this project is being built in a directory version controlled
+# by Git, copy the hooks into the Git configuation.
+ if [ -f $(ibdir)/metastore ]; then
+ if [ -d .git ]; then
+ user=$$(whoami)
+ group=$$(groups | awk '{print $$1}')
+ cd $$current_dir
+ for f in pre-commit post-checkout; do
+ sed -e's|@USER[@]|'$$user'|g' \
+ -e's|@GROUP[@]|'$$group'|g' \
+ -e's|@BINDIR[@]|$(ibdir)|g' \
+ -e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \
+ reproduce/software/shell/git-$$f > .git/hooks/$$f
+ chmod +x .git/hooks/$$f
+ done
+ fi
+ echo "Metastore (forked) $(metastore-version)" > $@
+ else
+ echo; echo; echo
+ echo "*****************"
+ echo "metastore couldn't be installed!"
+ echo
+ echo "Its used for preserving timestamps on Git commits."
+ echo "Its useful for development, not simple running of "
+ echo "the project. So we won't stop the configuration "
+ echo "because it wasn't built."
+ echo "*****************"
+ echo "" > $@
+ fi
+
$(ibidir)/openblas-$(openblas-version):
- tarball=OpenBLAS-$(openblas-version).tar.gz
+ tarball=OpenBLAS-$(openblas-version).tar.lz
$(call import-source, $(openblas-url), $(openblas-checksum))
if [ x$(on_mac_os) = xyes ]; then export CC=clang; fi
cd $(ddir)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd OpenBLAS-$(openblas-version)
make -j$(numthreads)
make PREFIX=$(idir) install
@@ -666,7 +797,7 @@ $(ibidir)/openblas-$(openblas-version):
echo "OpenBLAS $(openblas-version)" > $@
$(ibidir)/openmpi-$(openmpi-version):
- tarball=openmpi-$(openmpi-version).tar.gz
+ tarball=openmpi-$(openmpi-version).tar.lz
$(call import-source, $(openmpi-url), $(openmpi-checksum))
$(call gbuild, openmpi-$(openmpi-version), static, \
--with-pmix=internal \
@@ -692,22 +823,22 @@ $(ibidir)/openssh-$(openssh-version):
echo "OpenSSH $(openssh-version)" > $@
$(ibidir)/pixman-$(pixman-version):
- tarball=pixman-$(pixman-version).tar.gz
+ tarball=pixman-$(pixman-version).tar.lz
$(call import-source, $(pixman-url), $(pixman-checksum))
$(call gbuild, pixman-$(pixman-version), static, , \
-j$(numthreads) V=1)
echo "Pixman $(pixman-version)" > $@
$(ibidir)/rpcsvc-proto-$(rpcsvc-proto-version):
- # 'libintl' is installed as part of GNU Gettext in
- # 'basic.mk'. rpcsvc-proto needs to link with it on macOS.
+# 'libintl' is installed as part of GNU Gettext in
+# 'basic.mk'. rpcsvc-proto needs to link with it on macOS.
if [ x$(on_mac_os) = xyes ]; then
export CC=clang
export CXX=clang++
export LDFLAGS="-lintl $$LDFLAGS"
fi
- # Download the tarball and build rpcsvc-proto.
+# Download the tarball and build rpcsvc-proto.
tarball=rpcsvc-proto-$(rpcsvc-proto-version).tar.xz
$(call import-source, $(rpcsvc-proto-url), $(rpcsvc-proto-checksum))
$(call gbuild, rpcsvc-proto-$(rpcsvc-proto-version), static)
@@ -721,35 +852,10 @@ $(ibidir)/tides-$(tides-version):
cp $(dtexdir)/tides.tex $(ictdir)/
echo "TIDES $(tides-version) \citep{tides}" > $@
-$(ibidir)/valgrind-$(valgrind-version): \
- $(ibidir)/patch-$(patch-version) \
- $(ibidir)/autoconf-$(autoconf-version) \
- $(ibidir)/automake-$(automake-version)
- # Import the tarball
- tarball=valgrind-$(valgrind-version).tar.bz2
+$(ibidir)/valgrind-$(valgrind-version):
+ tarball=valgrind-$(valgrind-version).tar.lz
$(call import-source, $(valgrind-url), $(valgrind-checksum))
-
- # For valgrind-3.15.0, see
- # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329 for a
- # report on an MPI-related compile bug and the two patches
- # below. These two patches and `automake` should allow valgrind to
- # compile with gcc-9.2.0.
- cd $(ddir)
- tar -xf $(tdir)/$$tarball
- valgrinddir=valgrind-$(valgrind-version)
- cd $${valgrinddir}
- printf "valgrindir=$${valgrinddir} ; pwd = %s .\n" $$($(ibdir)/pwd)
- if [ "x$(valgrind-version)" = "x3.15.0" ]; then
- patch --verbose -p1 < $(patchdir)/valgrind-3.15.0-mpi-fix1.patch
- patch --verbose -p1 < $(patchdir)/valgrind-3.15.0-mpi-fix2.patch
- fi
- autoreconf
- ./configure --prefix=$(idir)
- make -j$(numthreads)
- if ! make check -j$(numthreads); then
- echo; echo "Valgrind's 'make check' failed!"; echo
- fi
- make install
+ $(call gbuild, valgrind-$(valgrind-version), static)
echo "Valgrind $(valgrind-version)" > $@
$(ibidir)/yaml-$(yaml-version):
@@ -773,47 +879,48 @@ $(ibidir)/yaml-$(yaml-version):
# manually.
#
# For example, Libgit2 page recommends doing a static build, especially for
-# Mac systems (with `-DBUILD_SHARED_LIBS=OFF'): "It’s highly recommended
+# Mac systems (with '-DBUILD_SHARED_LIBS=OFF'): "It’s highly recommended
# that you build libgit2 as a static library for Xcode projects. This
# simplifies distribution significantly, as the resolution of dynamic
# libraries at runtime can be extremely problematic.". This is a major
# problem we have been having so far with Mac systems:
# https://libgit2.org/docs/guides/build-and-link
-# On macOS system, `libgit2' complains about not finding `_iconv*'
-# functions! But apparently `libgit2' has its own implementation of libiconv
+# On macOS system, 'libgit2' complains about not finding '_iconv*'
+# functions! But apparently 'libgit2' has its own implementation of libiconv
# that it uses if it can't find libiconv on macOS. So, to fix this problem
-# it is necessary to use the option `-DUSE_ICONV=OFF` in the configure step.
+# it is necessary to use the option '-DUSE_ICONV=OFF' in the configure step.
$(ibidir)/libgit2-$(libgit2-version): $(ibidir)/cmake-$(cmake-version)
- tarball=libgit2-$(libgit2-version).tar.gz
+ tarball=libgit2-$(libgit2-version).tar.lz
$(call import-source, $(libgit2-url), $(libgit2-checksum))
$(call cbuild, libgit2-$(libgit2-version), static, \
-DUSE_SSH=OFF -DBUILD_CLAR=OFF \
-DTHREADSAFE=ON -DUSE_ICONV=OFF )
if [ x$(on_mac_os) = xyes ]; then
- install_name_tool -id $(ildir)/libgit2.1.0.dylib \
- $(ildir)/libgit2.1.0.dylib
+ install_name_tool -id $(ildir)/libgit2.1.3.dylib \
+ $(ildir)/libgit2.1.3.dylib
fi
echo "Libgit2 $(libgit2-version)" > $@
$(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
- # Import the tarball.
- tarball=wcslib-$(wcslib-version).tar.bz2
+
+# Import the tarball.
+ tarball=wcslib-$(wcslib-version).tar.lz
$(call import-source, $(wcslib-url), $(wcslib-checksum))
- # If Fortran isn't present, don't build WCSLIB with it.
+# If Fortran isn't present, don't build WCSLIB with it.
if type gfortran &> /dev/null; then fortranopt="";
else fortranopt="--disable-fortran"
fi
- # Build WCSLIB.
+# Build WCSLIB.
$(call gbuild, wcslib-$(wcslib-version), , \
LIBS="-pthread -lcurl -lm" \
--with-cfitsiolib=$(ildir) \
--with-cfitsioinc=$(idir)/include \
--without-pgplot $$fortranopt)
if [ x$(on_mac_os) = xyes ]; then
- install_name_tool -id $(ildir)/libwcs.7.3.dylib \
- $(ildir)/libwcs.7.3.dylib
+ install_name_tool -id $(ildir)/libwcs.7.7.dylib \
+ $(ildir)/libwcs.7.7.dylib
fi
echo "WCSLIB $(wcslib-version)" > $@
@@ -843,17 +950,17 @@ $(ibidir)/astrometrynet-$(astrometrynet-version): \
$(ibidir)/cfitsio-$(cfitsio-version) \
$(ibidir)/libjpeg-$(libjpeg-version)
- # Import the tarball
- tarball=astrometry.net-$(astrometrynet-version).tar.gz
+# Import the tarball
+ tarball=astrometry.net-$(astrometrynet-version).tar.lz
$(call import-source, $(astrometrynet-url), $(astrometrynet-checksum))
- # We are modifying the Makefile in two steps because on Mac OS
- # system we do not have `/proc/cpuinfo' nor `free'. Since this is
- # only for the `report.txt', this changes do not causes problems in
- # running `astrometrynet'
+# We are modifying the Makefile in two steps because on Mac OS system
+# we do not have '/proc/cpuinfo' nor 'free'. Since this is only for
+# the 'report.txt', this changes do not causes problems in running
+# 'astrometrynet'
cd $(ddir)
rm -rf astrometry.net-$(astrometrynet-version)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd astrometry.net-$(astrometrynet-version)
sed -e 's|cat /proc/cpuinfo|echo "Ignoring CPU info"|' \
-e 's|-free|echo "Ignoring RAM info"|' Makefile > Makefile.tmp
@@ -874,7 +981,7 @@ $(ibidir)/autoconf-$(autoconf-version):
echo "GNU Autoconf $(autoconf-version)" > $@
$(ibidir)/automake-$(automake-version): $(ibidir)/autoconf-$(autoconf-version)
- tarball=automake-$(automake-version).tar.gz
+ tarball=automake-$(automake-version).tar.lz
$(call import-source, $(automake-url), $(automake-checksum))
$(call gbuild, automake-$(automake-version), static, ,V=1)
echo "GNU Automake $(automake-version)" > $@
@@ -886,17 +993,18 @@ $(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version)
echo "GNU Bison $(bison-version)" > $@
# cdsclient is a set of software written in c to interact with astronomical
-# database servers. It is a dependency of `scamp' to be able to download
+# database servers. It is a dependency of 'scamp' to be able to download
# reference catalogues.
-# NOTE: we do not use a convencional `gbuild' installation because the
+#
+# NOTE: we do not use a convencional 'gbuild' installation because the
# programs are scripts and we need to touch them before installing.
# Otherwise this software will be re-built each time the configure step is
# invoked.
$(ibidir)/cdsclient-$(cdsclient-version):
- tarball=cdsclient-$(cdsclient-version).tar.gz
+ tarball=cdsclient-$(cdsclient-version).tar.lz
$(call import-source, $(cdsclient-url), $(cdsclient-checksum))
cd $(ddir)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd cdsclient-$(cdsclient-version)
touch *
./configure --prefix=$(idir)
@@ -906,25 +1014,27 @@ $(ibidir)/cdsclient-$(cdsclient-version):
rm -rf cdsclient-$(cdsclient-version)
echo "cdsclient $(cdsclient-version)" > $@
-# CMake can be built with its custom `./bootstrap' script.
-$(ibidir)/cmake-$(cmake-version): $(ibidir)/curl-$(curl-version)
- # Import the tarball
- tarball=cmake-$(cmake-version).tar.gz
+# CMake can be built with its custom './bootstrap' script and has no
+# dependencies beyond the basic Maneage software.
+$(ibidir)/cmake-$(cmake-version):
+
+# Import the tarball
+ tarball=cmake-$(cmake-version).tar.lz
$(call import-source, $(cmake-url), $(cmake-checksum))
- # After searching in `bootstrap', I couldn't find `LIBS', only
- # `LDFLAGS'. So the extra libraries are being added to `LDFLAGS',
- # not `LIBS'.
- #
- # On Mac systems, the build complains about `clang' specific
- # features, so we can't use our own GCC build here.
+# After searching in 'bootstrap', I couldn't find 'LIBS', only
+# 'LDFLAGS'. So the extra libraries are being added to 'LDFLAGS', not
+# 'LIBS'.
+#
+# On Mac systems, the build complains about 'clang' specific
+# features, so we can't use our own GCC build here.
if [ x$(on_mac_os) = xyes ]; then
export CC=clang
export CXX=clang++
fi
cd $(ddir)
rm -rf cmake-$(cmake-version)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd cmake-$(cmake-version)
./bootstrap --prefix=$(idir) --system-curl --system-zlib \
--system-bzip2 --system-liblzma --no-qt-gui \
@@ -942,7 +1052,7 @@ $(ibidir)/flex-$(flex-version): $(ibidir)/bison-$(bison-version)
echo "Flex $(flex-version)" > $@
$(ibidir)/gdb-$(gdb-version): $(ibidir)/python-$(python-version)
- tarball=gdb-$(gdb-version).tar.gz
+ tarball=gdb-$(gdb-version).tar.lz
export configure_in_different_directory=1;
$(call import-source, $(gdb-url), $(gdb-checksum))
$(call gbuild, gdb-$(gdb-version),,,V=1 -j$(numthreads))
@@ -956,49 +1066,51 @@ $(ibidir)/ghostscript-$(ghostscript-version): \
$(ibidir)/libtiff-$(libtiff-version) \
$(ibidir)/libpaper-$(libpaper-version)
- # Download the standard collection of Ghostscript fonts.
- tarball=ghostscript-fonts-std-$(ghostscript-fonts-std-version).tar.gz
+# Download the standard collection of Ghostscript fonts.
+ tarball=ghostscript-fonts-std-$(ghostscript-fonts-std-version).tar.lz
$(call import-source, $(ghostscript-fonts-std-url), \
$(ghostscript-fonts-std-checksum))
- # Download the extra GNU fonts for Ghostscript.
- tarball=ghostscript-fonts-gnu-$(ghostscript-fonts-gnu-version).tar.gz
+# Download the extra GNU fonts for Ghostscript.
+ tarball=ghostscript-fonts-gnu-$(ghostscript-fonts-gnu-version).tar.lz
$(call import-source, $(ghostscript-fonts-gnu-url), \
$(ghostscript-fonts-gnu-checksum))
- # Download the tarball
- tarball=ghostscript-$(ghostscript-version).tar.gz
+# Download the tarball
+ tarball=ghostscript-$(ghostscript-version).tar.lz
$(call import-source, $(ghostscript-url), $(ghostscript-checksum))
- # Unpack it and configure Ghostscript.
+# Unpack it and configure Ghostscript. The option
+# '-DPNG_ARM_NEON_OPT=0' prevents an arm64 'neon' library from being
+# required at compile time.
cd $(ddir)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd ghostscript-$(ghostscript-version)
./configure --prefix=$(idir) \
--disable-cups \
--enable-dynamic \
- --with-system-libtiff \
- --disable-compile-inits
+ --disable-compile-inits \
+ CFLAGS="-DPNG_ARM_NEON_OPT=0"
- # Build and install the program and the shared libraries.
+# Build and install the program and the shared libraries.
make V=1 -j$(numthreads)
make so V=1 -j$(numthreads)
make install
make soinstall
- # Install headers and set PostScript (PS) headers to point there.
+# Install headers and set PostScript (PS) headers to point there.
install -v -m644 base/*.h $(iidir)/ghostscript
ln -sfvn $(iidir)/ghostscript $(iidir)/ps
- # Install the fonts.
- tar -xvf $(tdir)/ghostscript-fonts-std-$(ghostscript-fonts-std-version).tar.gz \
+# Install the fonts.
+ tar -xvf $(tdir)/ghostscript-fonts-std-$(ghostscript-fonts-std-version).tar.lz \
-C $(idir)/share/ghostscript
- tar -xvf $(tdir)/ghostscript-fonts-gnu-$(ghostscript-fonts-gnu-version).tar.gz \
+ tar -xvf $(tdir)/ghostscript-fonts-gnu-$(ghostscript-fonts-gnu-version).tar.lz \
-C $(idir)/share/ghostscript
fc-cache -v $(idir)/share/ghostscript/fonts/
echo; echo "Ghostscript fonts added to Fontconfig."; echo;
- # Clean up and write the output target.
+# Clean up and write the output target.
cd ..
rm -rf ghostscript-$(ghostscript-version)
echo "GPL Ghostscript $(ghostscript-version)" > $@
@@ -1018,48 +1130,74 @@ $(ibidir)/gnuastro-$(gnuastro-version): \
echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
$(ibidir)/help2man-$(help2man-version):
- tarball=help2man-$(help2man-version).tar.xz
+ tarball=help2man-$(help2man-version).tar.lz
$(call import-source, $(help2man-url), $(help2man-checksum))
$(call gbuild, help2man-$(help2man-version), static, ,V=1)
echo "Help2man $(Help2man-version)" > $@
+$(ibidir)/icu-$(icu-version): $(ibidir)/python-$(python-version)
+
+# First, we need to remove any possibly existing ICU installation
+# because it can cause conflicts during a new configuration
+# (especially if a new version is to replace the old one).
+ for i in data i18n io test tu uc; do
+ rm -fv $(ildir)/libicu$$i.*;
+ done
+
+# Prepare the tarball, unpack, build and install ICU (some
+# customizations are necessary, so we're not using 'gbuild').
+ tarball=icu-$(icu-version).tar.lz
+ $(call import-source, $(icu-url), $(icu-checksum))
+ cd $(ddir)
+ tar -xf $(tdir)/$$tarball
+ unpackdir=icu-$(icu-version)
+ cd $$unpackdir/icu4c/source
+ ./configure --enable-static --prefix=$(idir)
+ make -j$(numthreads) V=1
+ make install
+ cd $(ddir)
+ rm -rf $$unpackdir
+ echo "ICU $(icu-version)" > $@
+
$(ibidir)/imagemagick-$(imagemagick-version): \
$(ibidir)/zlib-$(zlib-version) \
$(ibidir)/libjpeg-$(libjpeg-version) \
$(ibidir)/libtiff-$(libtiff-version)
- tarball=imagemagick-$(imagemagick-version).tar.xz
+ tarball=ImageMagick-$(imagemagick-version).tar.lz
$(call import-source, $(imagemagick-url), $(imagemagick-checksum))
$(call gbuild, ImageMagick-$(imagemagick-version), static, \
--without-x --disable-openmp, V=1 -j$(numthreads))
echo "ImageMagick $(imagemagick-version)" > $@
-# `imfit' doesn't use the traditional `configure' and `make' to install
-# itself. Instead of that, it uses `scons'. As a consequence, the
+# 'imfit' doesn't use the traditional 'configure' and 'make' to install
+# itself. Instead of that, it uses 'scons'. As a consequence, the
# installation is manually done by decompressing the tarball, and running
-# `scons' with the necessary flags. Despite of that, it is necessary to
+# 'scons' with the necessary flags. Despite of that, it is necessary to
# replace the default searching paths in this script by our installation
-# paths. This is done with `sed', replacing each ocurrence of `/usr/local'
-# by `$(idir)'. After that, each compiled program (`imfit', `imfit-mcmc'
-# and `makeimage') is copied into the installation directory and an `rpath'
+# paths. This is done with 'sed', replacing each ocurrence of '/usr/local'
+# by '$(idir)'. After that, each compiled program ('imfit', 'imfit-mcmc'
+# and 'makeimage') is copied into the installation directory and an 'rpath'
# is added.
$(ibidir)/imfit-$(imfit-version): \
$(ibidir)/gsl-$(gsl-version) \
$(ibidir)/fftw-$(fftw-version) \
$(ibidir)/scons-$(scons-version) \
$(ibidir)/cfitsio-$(cfitsio-version)
+
+# Prepare the source.
tarball=imfit-$(imfit-version).tar.gz
$(call import-source, $(imfit-url), $(imfit-checksum))
- # If the C library is in a non-standard location.
+# If the C library is in a non-standard location.
if ! [ x$(SYS_CPATH) = x ]; then
headerpath="--header-path=$(SYS_CPATH)"
fi
- # Unpack and build imfit and its accompanying programs.
+# Unpack and build imfit and its accompanying programs.
cd $(ddir)
unpackdir=imfit-$(imfit-version)
rm -rf $$unpackdir
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd $$unpackdir
sed -i 's|/usr/local|$(idir)|g' SConstruct
sed -i 's|/usr/include|$(idir)/include|g' SConstruct
@@ -1086,6 +1224,8 @@ $(ibidir)/imfit-$(imfit-version): \
done
fi
cp $(dtexdir)/imfit.tex $(ictdir)/
+ cd ..
+ rm -rf $$unpackdir
echo "Imfit $(imfit-version) \citep{imfit2015}" > $@
# Minizip 1.x is actually distributed within zlib. It doesn't have its own
@@ -1098,13 +1238,13 @@ $(ibidir)/imfit-$(imfit-version): \
# About deleting the final crypt.h file after installation, see
# https://bugzilla.redhat.com/show_bug.cgi?id=1424609
$(ibidir)/minizip-$(minizip-version): $(ibidir)/automake-$(automake-version)
- tarball=zlib-$(zlib-version).tar.gz
- $(call import-source, $(minizip-url), $(minizip-checksum))
+ tarball=zlib-$(zlib-version).tar.lz
+ $(call import-source, $(zlib-url), $(zlib-checksum))
cd $(ddir)
unpackdir=minizip-$(minizip-version)
rm -rf $$unpackdir
mkdir $$unpackdir
- tar xf $(tdir)/$$tarball -C$$unpackdir --strip-components=1
+ tar -xf $(tdir)/$$tarball -C$$unpackdir --strip-components=1
cd $$unpackdir
./configure --prefix=$(idir)
make
@@ -1140,16 +1280,18 @@ $(ibidir)/missfits-$(missfits-version):
# Netpbm is a prerequisite of Astrometry-net, it contains a lot of programs.
# This program has a crazy dialogue installation which is override using the
-# printf statment. Each `\n' is a new question that the installation process
+# printf statment. Each '\n' is a new question that the installation process
# ask to the user. We give all answers with a pipe to the scripts (configure
# and install). The questions are different depending on the system (tested
# on GNU/Linux and Mac OS).
$(ibidir)/netpbm-$(netpbm-version): \
+ $(ibidir)/flex-$(flex-version) \
$(ibidir)/libpng-$(libpng-version) \
+ $(ibidir)/libx11-$(libx11-version) \
$(ibidir)/libjpeg-$(libjpeg-version) \
$(ibidir)/libtiff-$(libtiff-version) \
$(ibidir)/libxml2-$(libxml2-version)
- tarball=netpbm-$(netpbm-version).tar.gz
+ tarball=netpbm-$(netpbm-version).tar.lz
$(call import-source, $(netpbm-url), $(netpbm-checksum))
if [ x$(on_mac_os) = xyes ]; then
answers='\n\n$(ildir)\n\n\n\n\n\n$(ildir)/include\n\n$(ildir)/include\n\n$(ildir)/include\nnone\n\n'
@@ -1159,7 +1301,7 @@ $(ibidir)/netpbm-$(netpbm-version): \
cd $(ddir)
unpackdir=netpbm-$(netpbm-version)
rm -rf $$unpackdir
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd $$unpackdir
printf "$$answers" | ./configure
make
@@ -1189,60 +1331,15 @@ $(ibidir)/pcre-$(pcre-version):
, V=1 -j$(numthreads))
echo "Perl Compatible Regular Expressions $(pcre-version)" > $@
-# Comment on building R without GUI support ('--without-tcltlk')
-#
-# Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support
-# in some software. But they are not yet natively built within Maneage,
-# primarily because we have higher-priority work right now (if anyone is
-# interested, they can ofcourse contribute!). GUI tools in general aren't
-# high on our priority list right now because they are generally good for
-# human interaction (which is contrary to the reproducible philosophy:
-# there will always be human-error and frustration, for example in GUI
-# tools the best level of reproducibility is statements like this: "move
-# your mouse to button XXX, then click on menu YYY and etc"). A robust
-# reproducible solution must be done automatically.
-#
-# If someone wants to use R's GUI functionalities while investigating for
-# their analysis, they can do the GUI part on their host OS
-# implementation. Later, they can bring the finalized source into Maneage
-# to be automatically run in Maneage. This will also be the recommended way
-# to deal with GUI tools later when we do install them within Maneage.
-$(ibidir)/R-$(R-version): \
- $(ibidir)/pcre-$(pcre-version) \
- $(ibidir)/cairo-$(cairo-version) \
- $(ibidir)/libpng-$(libpng-version) \
- $(ibidir)/libjpeg-$(libjpeg-version) \
- $(ibidir)/libtiff-$(libtiff-version) \
- $(ibidir)/libpaper-$(libpaper-version)
- tarball=R-$(R-version).tar.gz
- $(call import-source, $(R-url), $(R-checksum))
- cd $(ddir)
- tar xf $(tdir)/$$tarball
- cd R-$(R-version)
-
- # We need to manually remove the lines with '~autodetect~', they
- # cause the configure script to crash in version 4.0.2. They are
- # used in relation to Java, and we don't use Java anyway.
- sed -i -e '/\~autodetect\~/ s/^/#/g' configure
- export R_SHELL=$(SHELL)
- ./configure --prefix=$(idir) \
- --without-x \
- --with-pcre1 \
- --disable-java \
- --with-readline \
- --without-tcltk \
- --disable-openmp
- make -j$(numthreads)
- make install
- cd ..
- rm -rf R-$(R-version)
- echo "R $(R-version)" > $@
+# 2022-01-01 The rules for building R - identified as r-cran to avoid the
+# difficulties in searching text for a one-letter string - were shifted to
+# 'r-cran.mk'.
# SCAMP documentation says ATLAS is a mandatory prerequisite for using
# SCAMP. We have ATLAS into the project but there are some problems with the
# libraries that are not yet solved. However, we tried to install it with
# the option --enable-openblas and it worked (same issue happened with
-# `sextractor'.
+# 'sextractor'.
$(ibidir)/scamp-$(scamp-version): \
$(ibidir)/fftw-$(fftw-version) \
$(ibidir)/openblas-$(openblas-version) \
@@ -1250,7 +1347,7 @@ $(ibidir)/scamp-$(scamp-version): \
tarball=scamp-$(scamp-version).tar.lz
$(call import-source, $(scamp-url), $(scamp-checksum))
- # See comment above 'missfits' for '-fcommon'.
+# See comment above 'missfits' for '-fcommon'.
$(call gbuild, scamp-$(scamp-version), static, \
CFLAGS="-fcommon" \
--enable-threads \
@@ -1263,17 +1360,19 @@ $(ibidir)/scamp-$(scamp-version): \
cp $(dtexdir)/scamp.tex $(ictdir)/
echo "SCAMP $(scamp-version) \citep{scamp}" > $@
-# Since `scons' doesn't use the traditional GNU installation with
-# `configure' and `make' it is installed manually using `python'.
+# Since 'scons' doesn't use the traditional GNU installation with
+# 'configure' and 'make' it is installed manually using 'python'.
$(ibidir)/scons-$(scons-version): $(ibidir)/python-$(python-version)
tarball=scons-$(scons-version).tar.gz
$(call import-source, $(scons-url), $(scons-checksum))
cd $(ddir)
unpackdir=scons-$(scons-version)
rm -rf $$unpackdir
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd $$unpackdir
python setup.py install
+ cd ..
+ rm -rf $$unpackdir
echo "SCons $(scons-version)" > $@
# Sextractor crashes complaining about not linking with some ATLAS
@@ -1289,7 +1388,7 @@ $(ibidir)/sextractor-$(sextractor-version): \
tarball=sextractor-$(sextractor-version).tar.lz
$(call import-source, $(sextractor-url), $(sextractor-checksum))
- # See comment above 'missfits' for '-fcommon'.
+# See comment above 'missfits' for '-fcommon'.
$(call gbuild, sextractor-$(sextractor-version), static, \
CFLAGS="-fcommon" \
--enable-threads \
@@ -1304,7 +1403,7 @@ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version)
tarball=swarp-$(swarp-version).tar.gz
$(call import-source, $(swarp-url), $(swarp-checksum))
- # See comment above 'missfits' for '-fcommon'.
+# See comment above 'missfits' for '-fcommon'.
$(call gbuild, swarp-$(swarp-version), static, \
CFLAGS="-fcommon" \
--enable-threads)
@@ -1312,10 +1411,11 @@ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version)
echo "SWarp $(swarp-version) \citep{swarp}" > $@
$(ibidir)/swig-$(swig-version):
- # Option --without-pcre was a suggestion once the configure step
- # was tried and it failed. It was not recommended but it works!
- # pcr is a dependency of swig
- tarball=swig-$(swig-version).tar.gz
+
+# Option --without-pcre was a suggestion once the configure step was
+# tried and it failed. It was not recommended but it works! pcr is a
+# dependency of swig
+ tarball=swig-$(swig-version).tar.lz
$(call import-source, $(swig-url), $(swig-checksum))
$(call gbuild, swig-$(swig-version), static, \
--without-pcre --without-tcl)
@@ -1345,19 +1445,19 @@ $(ibidir)/swig-$(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-$(util-linux-version):
+$(ibidir)/util-linux-$(util-linux-version): | $(idircustom)
- # Import the source.
- tarball=util-linux-$(util-linux-version).tar.xz
+# Import the source.
+ tarball=util-linux-$(util-linux-version).tar.lz
$(call import-source, $(util-linux-url), $(util-linux-checksum))
- # Unpack the source and set it to install in a special directory
- # (as explained above). As shown below, later, we'll put a symbolic
- # link of all the necessary binaries in the main '$(idir)/bin'.
+# Unpack the source and set it to install in a special directory (as
+# explained above). As shown below, later, we'll put a symbolic link
+# of all the necessary binaries in the main '$(idir)/bin'.
cd $(ddir)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
cd util-linux-$(util-linux-version)
- ./configure --prefix=$(idir)/util-linux \
+ ./configure --prefix=$(idircustom)/util-linux \
--disable-dependency-tracking \
--disable-silent-rules \
--without-systemd \
@@ -1368,21 +1468,21 @@ $(ibidir)/util-linux-$(util-linux-version):
--disable-wall \
--disable-su
- # Build and install it.
+# Build and install it.
make V=1 -j$(numthreads)
make install
- # Put a symbolic link to installed programs in main installation
- # directory. If 'sbin' exists in the main installation directory,
- # put util-linux's 'sbin/' directory there too.
- ln -sf $(idir)/util-linux/bin/* $(ibdir)/
+# Put a symbolic link to installed programs in main installation
+# directory. If 'sbin' exists in the main installation directory, put
+# util-linux's 'sbin/' directory there too.
+ ln -sf $(idircustom)/util-linux/bin/* $(ibdir)/
if [ -d $(idir)/sbin ]; then
- ln -sf $(idir)/util-linux/sbin/* $(idir)/sbin
+ ln -sf $(idircustom)/util-linux/sbin/* $(idir)/sbin
else
- ln -sf $(idir)/util-linux/sbin/* $(idir)/bin
+ ln -sf $(idircustom)/util-linux/sbin/* $(idir)/bin
fi
- # Clean up and write the main target.
+# Clean up and write the main target.
cd ../
rm -rf util-linux-$(util-linux-version)
echo "util-Linux $(util-linux-version)" > $@
@@ -1428,7 +1528,7 @@ $(ibidir)/vim-$(vim-version):
tarball=vim-$(vim-version).tar.bz2
$(call import-source, $(vim-url), $(vim-checksum))
cd $(ddir)
- tar xf $(tdir)/$$tarball
+ tar -xf $(tdir)/$$tarball
n=$$(echo $(vim-version) | sed -e's|\.||')
cd $(ddir)/vim$$n
./configure --prefix=$(idir) \
@@ -1455,7 +1555,7 @@ $(ibidir)/vim-$(vim-version):
# hard to track for Make (as a target). Also, TeX in general is optional
# for the project (the processing is the main target, not the generation of
# the final PDF). So we'll make a simple ASCII file called
-# `texlive-ready-tlmgr' and use its contents to mark if we can use it or
+# 'texlive-ready-tlmgr' and use its contents to mark if we can use it or
# not.
#
# TeX Live mirror
@@ -1463,8 +1563,8 @@ $(ibidir)/vim-$(vim-version):
#
# The automatic mirror finding fails sometimes. So we'll manually set it to
# use a fixed mirror. I first tried the LaTeX root webpage
-# (`ftp.dante.de'), however, it is far too slow (when I tested it). The
-# `rit.edu' server seems to be a good alternative (given the importance of
+# ('ftp.dante.de'), however, it is far too slow (when I tested it). The
+# 'rit.edu' server seems to be a good alternative (given the importance of
# NY on the internet infrastructure).
texlive-url=http://mirrors.rit.edu/CTAN/systems/texlive/tlnet
$(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
@@ -1472,81 +1572,81 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
tarball=install-tl-unx.tar.gz
$(call import-source, $(texlive-url), NO-CHECK-SUM)
- # Unpack, enter the directory, and install based on the given
- # configuration (prerequisite of this rule).
+# Unpack, enter the directory, and install based on the given
+# configuration (prerequisite of this rule).
@topdir=$$(pwd)
cd $(ddir)
rm -rf install-tl-*
- tar xf $(tdir)/install-tl-unx.tar.gz
+ tar -xf $(tdir)/install-tl-unx.tar.gz
cd install-tl-*
sed -e's|@installdir[@]|$(idir)|g' \
"$$topdir"/reproduce/software/config/texlive.conf \
> texlive.conf
- # 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 messages will be saved into `log.txt' and if it
- # fails, 'log.txt' will be checked to see if the error is due to
- # the different version of the current tarball and the TeXLive
- # server or something else.
- #
- # The problem with versions is this: each installer tarball (that
- # is downloaded and a user may backup) is for a specific version of
- # TeXLive (specified by year, usually around April). So if a user
- # has an old tarball, but the CTAN server has been updated, the
- # script will fail with a message like this:
- #
- # =============================================================
- # ./install-tl: The TeX Live versions of the local installation
- # and the repository being accessed are not compatible:
- # local: 2019
- # repository: 2020
- # Perhaps you need to use a different CTAN mirror?
- # (For more, see the output of install-tl --help, especially the
- # -repository option. Online via https://tug.org/texlive/doc.)
- # =============================================================
- #
- # To address this problem, when this happens, we simply download a
- # the most recent tarball, and if it succeeds, we will build
- # TeXLive using that. The old tarball will be preserved, but will
- # have an '-OLD' suffix after it.
+# 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
+# messages will be saved into 'log.txt' and if it fails, 'log.txt'
+# will be checked to see if the error is due to the different version
+# of the current tarball and the TeXLive server or something else.
+#
+# The problem with versions is this: each installer tarball (that is
+# downloaded and a user may backup) is for a specific version of
+# TeXLive (specified by year, usually around April). So if a user has
+# an old tarball, but the CTAN server has been updated, the script
+# will fail with a message like this:
+#
+# =============================================================
+# ./install-tl: The TeX Live versions of the local installation
+# and the repository being accessed are not compatible:
+# local: 2019
+# repository: 2020
+# Perhaps you need to use a different CTAN mirror?
+# (For more, see the output of install-tl --help, especially the
+# -repository option. Online via https://tug.org/texlive/doc.)
+# =============================================================
+#
+# To address this problem, when this happens, we simply download a
+# the most recent tarball, and if it succeeds, we will build TeXLive
+# using that. The old tarball will be preserved, but will have an
+# '-OLD' suffix after it.
if ./install-tl --profile=texlive.conf -repository \
$(texlive-url) 2> log.txt; then
- # Put a symbolic link of the TeX Live executables in `ibdir' to
- # avoid all the complexities of its sub-directories and additions
- # to PATH.
+# Put a symbolic link of the TeX Live executables in 'ibdir' to
+# avoid all the complexities of its sub-directories and additions
+# to PATH.
ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/
- # Register that the build was successful.
+# Register that the build was successful.
echo "TeX Live is ready." > $@
- # The build failed!
+# The build failed!
else
- # Print on the command line the error messages during the
- # installation.
+# Print on the command line the error messages during the
+# installation.
cat log.txt
- # Look for words `repository:' and `local:' in `log.txt' and make
- # sure that two lines are returned. Note that we need to check
- # for two lines because one of them may exist, but another may
- # not (in this case, its not a version conflict scenario).
+# Look for words 'repository:' and 'local:' in 'log.txt' and make
+# sure that two lines are returned. Note that we need to check for
+# two lines because one of them may exist, but another may not (in
+# this case, its not a version conflict scenario).
version_check=$$(grep -w 'repository:\|local:' log.txt | wc -l)
- # If these words exists and two lines are found, there is a
- # conflict with the main TeXLive version in the tarball and on
- # the server. So it is necessary to move the old tarball and
- # download the new one to install it.
+# If these words exists and two lines are found, there is a
+# conflict with the main TeXLive version in the tarball and on the
+# server. So it is necessary to move the old tarball and download
+# the new one to install it.
if [ x"$$version_check" = x2 ]; then
- # Go back to the top project directory, don't remove the
- # tarball, just rename it.
+
+# Go back to the top project directory, don't remove the tarball,
+# just rename it.
cd $$topdir
mv $(tdir)/install-tl-unx.tar.gz $(tdir)/install-tl-unx-OLD.tar.gz
- # Download using the script specially defined for this job. If
- # the download of new tarball success, install it (same lines
- # than above). If not, record the fail into the target.
+# Download using the script specially defined for this job. If
+# the download of new tarball success, install it (same lines
+# than above). If not, record the fail into the target.
url=http://mirror.ctan.org/systems/texlive/tlnet
tarballurl=$$url/install-tl-unx.tar.gz
touch $(lockdir)/download
@@ -1556,7 +1656,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
"$(backupservers)"; then
cd $(ddir)
rm -rf install-tl-*
- tar xf $(tdir)/install-tl-unx.tar.gz
+ tar -xf $(tdir)/install-tl-unx.tar.gz
cd install-tl-*
sed -e's|@installdir[@]|$(idir)|g' \
$$topdir/reproduce/software/config/texlive.conf \
@@ -1576,7 +1676,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
fi
fi
- # Clean up
+# Clean up
cd ..
rm -rf install-tl-*
@@ -1590,49 +1690,50 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
#
# Note that Biber needs to link with libraries like libnsl. However, we
# don't currently build biber from source. So we can't choose the library
-# version. But we have the source and build instructions for the `nsl'
+# version. But we have the source and build instructions for the 'nsl'
# library. When we later build biber from source, we can easily use them.
$(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
$(itidir)/texlive-ready-tlmgr
- # To work with TeX live installation, we'll need the internet.
+# To work with TeX live installation, we'll need the internet.
@res=$$(cat $(itidir)/texlive-ready-tlmgr)
if [ x"$$res" = x"NOT!" ]; then
echo "" > $@
else
- # To update itself, tlmgr needs a backup directory.
+
+# To update itself, tlmgr needs a backup directory.
backupdir=$(idir)/texlive/backups
mkdir -p $$backupdir
- # Before checking LaTeX packages, update tlmgr itself.
+# Before checking LaTeX packages, update tlmgr itself.
tlmgr option backupdir $$backupdir
tlmgr -repository $(texlive-url) update --self
- # Install all the extra necessary packages. If LaTeX complains
- # about not finding a command/file/what-ever/XXXXXX, simply run
- # the following command to find which package its in, then add it
- # to the `texlive-packages' variable of the first prerequisite.
- #
- # ./.local/bin/tlmgr info XXXXXX
- #
- # We are putting a notice, because if there is no internet,
- # `tlmgr' just hangs waiting.
+# Install all the extra necessary packages. If LaTeX complains
+# about not finding a command/file/what-ever/XXXXXX, simply run the
+# following command to find which package its in, then add it to
+# the 'texlive-packages' variable of the first prerequisite.
+#
+# ./.local/bin/tlmgr info XXXXXX
+#
+# We are putting a notice, because if there is no internet, 'tlmgr'
+# just hangs waiting.
tlmgr install $(texlive-packages)
- # Make a symbolic link of all the TeX Live executables in the bin
- # directory so we don't have to modify `PATH'.
+# Make a symbolic link of all the TeX Live executables in the bin
+# directory so we don't have to modify 'PATH'.
ln -fs $(idir)/texlive/maneage/bin/*/* $(ibdir)/
- # Get all the necessary versions.
+# Get all the necessary versions.
texlive=$$(pdflatex --version \
| awk 'NR==1' \
| sed 's/.*(\(.*\))/\1/' \
| awk '{print $$NF}');
- # Package names and versions. Note that all TeXLive packages
- # don't have a version unfortunately! So we need to also read the
- # `revision' and `cat-date' elements and print them incase
- # version isn't available.
+# Package names and versions. Note that all TeXLive packages
+# don't have a version unfortunately! So we need to also read the
+# 'revision' and 'cat-date' elements and print them incase
+# version isn't available.
tlmgr info $(texlive-packages) --only-installed | awk \
'$$1=="package:" { \
if(name!=0) \
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 18c68de..6766744 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -4,7 +4,7 @@
# !!!!! IMPORTANT NOTES !!!!!
#
# This Makefile will be loaded into 'high-level.mk', which is called by the
-# `./project configure' script. It is not included into the project
+# './project configure' script. It is not included into the project
# afterwards.
#
# This Makefile contains instructions to build all the Python-related
@@ -12,8 +12,8 @@
#
# ------------------------------------------------------------------------
#
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -35,7 +35,7 @@
# Python enviroment
# -----------------
#
-# The main Python environment variable is `PYTHONPATH'. However, so far we
+# The main Python environment variable is 'PYTHONPATH'. However, so far we
# have found several other Python-related environment variables on some
# systems which might interfere. To be safe, we are removing all their
# values.
@@ -62,19 +62,20 @@ python-major-version = $(shell echo $(python-version) | awk 'BEGIN{FS="."} \
# While this Makefile is for Python programs, in some cases, we need
# certain programs (like Python itself), or libraries for the modules.
$(ibidir)/libffi-$(libffi-version):
- # Prepare the source.
- tarball=libffi-$(libffi-version).tar.gz
+
+# Prepare the source.
+ tarball=libffi-$(libffi-version).tar.lz
$(call import-source, $(libffi-url), $(libffi-checksum))
- # Build libffi.
+# Build libffi.
$(call gbuild, libffi-$(libffi-version), , \
CFLAGS="-DNO_JAVA_RAW_API=1")
- # On some Fedora systems, libffi installs in `lib64', not
- # `lib'. This will cause problems when building setuptools
- # later. To fix this problem, we'll first check if this has indeed
- # happened (it exists under `lib64', but not under `lib'). If so,
- # we'll put a copy of the installed libffi libraries in `lib'.
+# On some Fedora systems, libffi installs in 'lib64', not 'lib'. This
+# will cause problems when building setuptools later. To fix this
+# problem, we'll first check if this has indeed happened (it exists
+# under 'lib64', but not under 'lib'). If so, we'll put a copy of the
+# installed libffi libraries in 'lib'.
if [ -f $(idir)/lib64/libffi.a ] && ! [ -f $(idir)/lib/libffi.a ]; then
cp $(idir)/lib64/libffi* $(ildir)/
fi
@@ -82,17 +83,17 @@ $(ibidir)/libffi-$(libffi-version):
$(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
- # Download the source.
- tarball=python-$(python-version).tar.gz
+# Download the source.
+ tarball=python-$(python-version).tar.lz
$(call import-source, $(python-url), $(python-checksum))
- # On Mac systems, the build complains about `clang' specific
- # features, so we can't use our own GCC build here.
+# On Mac systems, the build complains about 'clang' specific
+# features, so we can't use our own GCC build here.
if [ x$(on_mac_os) = xyes ]; then
export CC=clang
export CXX=clang++
fi
- $(call gbuild, Python-$(python-version),, \
+ $(call gbuild, python-$(python-version),, \
--without-ensurepip \
--with-system-ffi \
--enable-shared, -j$(numthreads))
@@ -110,10 +111,10 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
# Non-PiP Python module installation
# ----------------------------------
#
-# To build Python packages with direct access to a `setup.py' (if no direct
-# access to `setup.py' is needed, pip can be used). Note that the
+# To build Python packages with direct access to a 'setup.py' (if no direct
+# access to 'setup.py' is needed, pip can be used). Note that the
# software's packaged source code is the first prerequisite that is in the
-# `tdir' directory.
+# 'tdir' directory.
#
# Arguments of this function are the numbers
# 1) Unpack command
@@ -122,8 +123,8 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
# 4) Official software name (for paper).
#
# Hooks:
-# pyhook_before: optional steps before running `python setup.py build'
-# pyhook_after: optional steps after running `python setup.py install'
+# pyhook_before: optional steps before running 'python setup.py build'
+# pyhook_after: optional steps after running 'python setup.py install'
pybuild = cd $(ddir); rm -rf $(2); \
if ! $(1) $(tdir)/$$tarball; then \
echo; echo "Tar error"; exit 1; \
@@ -153,13 +154,13 @@ pybuild = cd $(ddir); rm -rf $(2); \
$(ipydir)/asn1crypto-$(asn1crypto-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=asn1crypto-$(asn1crypto-version).tar.gz
$(call import-source, $(asn1crypto-url), $(asn1crypto-checksum))
- $(call pybuild, tar xf, asn1crypto-$(asn1crypto-version), , \
+ $(call pybuild, tar -xf, asn1crypto-$(asn1crypto-version), , \
Asn1crypto $(asn1crypto-version))
$(ipydir)/asteval-$(asteval-version): $(ipydir)/numpy-$(numpy-version)
tarball=asteval-$(asteval-version).tar.gz
$(call import-source, $(asteval-url), $(asteval-checksum))
- $(call pybuild, tar xf, asteval-$(asteval-version), , \
+ $(call pybuild, tar -xf, asteval-$(asteval-version), , \
ASTEVAL $(asteval-version))
$(ipydir)/astroquery-$(astroquery-version): \
@@ -168,7 +169,7 @@ $(ipydir)/astroquery-$(astroquery-version): \
$(ipydir)/requests-$(requests-version)
tarball=astroquery-$(astroquery-version).tar.gz
$(call import-source, $(astroquery-url), $(astroquery-checksum))
- $(call pybuild, tar xf, astroquery-$(astroquery-version), , \
+ $(call pybuild, tar -xf, astroquery-$(astroquery-version), , \
Astroquery $(astroquery-version))
$(ipydir)/astropy-$(astropy-version): \
@@ -177,87 +178,84 @@ $(ipydir)/astropy-$(astropy-version): \
$(ipydir)/scipy-$(scipy-version) \
$(ipydir)/numpy-$(numpy-version) \
$(ipydir)/pyyaml-$(pyyaml-version) \
+ $(ipydir)/jinja2-$(jinja2-version) \
+ $(ipydir)/pyerfa-$(pyerfa-version) \
$(ipydir)/html5lib-$(html5lib-version) \
- $(ipydir)/beautifulsoup4-$(beautifulsoup4-version)
-
- # Download the source.
- tarball=astropy-$(astropy-version).tar.gz
+ $(ipydir)/beautifulsoup4-$(beautifulsoup4-version) \
+ $(ipydir)/extension-helpers-$(extension-helpers-version)
+ tarball=astropy-$(astropy-version).tar.lz
$(call import-source, $(astropy-url), $(astropy-checksum))
-
- # Currently, when the Expat library is already built in a project
- # (for example as a dependency of another program), Astropy's
- # internal building of Expat will conflict with the project's. So
- # we have added Expat as a dependency of Astropy (so it is always
- # built before it, and we tell Astropy to use the project's
- # libexpat.
- pyhook_before () {
- echo "" >> setup.cfg
- echo "[build]" >> setup.cfg
- echo "use_system_expat=1" >> setup.cfg
- }
- $(call pybuild, tar xf, astropy-$(astropy-version))
+ $(call pybuild, tar -xf, astropy-$(astropy-version))
cp $(dtexdir)/astropy.tex $(ictdir)/
echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@
$(ipydir)/beautifulsoup4-$(beautifulsoup4-version): \
$(ipydir)/soupsieve-$(soupsieve-version)
- tarball=beautifulsoup4-$(beautifulsoup4-version).tar.gz
+ tarball=beautifulsoup4-$(beautifulsoup4-version).tar.lz
$(call import-source, $(beautifulsoup4-url), $(beautifulsoup4-checksum))
- $(call pybuild, tar xf, beautifulsoup4-$(beautifulsoup4-version), , \
+ $(call pybuild, tar -xf, beautifulsoup4-$(beautifulsoup4-version), , \
BeautifulSoup $(beautifulsoup4-version))
+$(ipydir)/beniget-$(beniget-version): $(ipydir)/setuptools-$(setuptools-version)
+ tarball=beniget-$(beniget-version).tar.lz
+ $(call import-source, $(beniget-url), $(beniget-checksum))
+ $(call pybuild, tar -xf, beniget-$(beniget-version), , \
+ Beniget $(beniget-version))
+
$(ipydir)/certifi-$(certifi-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=certifi-$(certifi-version).tar.gz
$(call import-source, $(certifi-url), $(certifi-checksum))
- $(call pybuild, tar xf, certifi-$(certifi-version), , \
+ $(call pybuild, tar -xf, certifi-$(certifi-version), , \
Certifi $(certifi-version))
$(ipydir)/cffi-$(cffi-version): \
$(ibidir)/libffi-$(libffi-version) \
$(ipydir)/pycparser-$(pycparser-version)
- tarball=cffi-$(cffi-version).tar.gz
+ tarball=cffi-$(cffi-version).tar.lz
$(call import-source, $(cffi-url), $(cffi-checksum))
- $(call pybuild, tar xf, cffi-$(cffi-version), ,cffi $(cffi-version))
+ $(call pybuild, tar -xf, cffi-$(cffi-version), ,cffi $(cffi-version))
$(ipydir)/chardet-$(chardet-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=chardet-$(chardet-version).tar.gz
$(call import-source, $(chardet-url), $(chardet-checksum))
- $(call pybuild, tar xf, chardet-$(chardet-version), , \
+ $(call pybuild, tar -xf, chardet-$(chardet-version), , \
Chardet $(chardet-version))
$(ipydir)/corner-$(corner-version): $(ipydir)/matplotlib-$(matplotlib-version)
tarball=corner-$(corner-version).tar.gz
$(call import-source, $(corner-url), $(corner-checksum))
- $(call pybuild, tar xf, corner-$(corner-version), , \
+ $(call pybuild, tar -xf, corner-$(corner-version), , \
Corner $(corner-version))
cp $(dtexdir)/corner.tex $(ictdir)/
echo "Corner $(corner-version) \citep{corner}" > $@
$(ipydir)/cryptography-$(cryptography-version): \
$(ipydir)/cffi-$(cffi-version) \
- $(ipydir)/asn1crypto-$(asn1crypto-version)
- tarball=cryptography-$(cryptography-version).tar.gz
+ $(ipydir)/asn1crypto-$(asn1crypto-version) \
+ $(ipydir)/setuptools-rust-$(setuptools-rust-version)
+ tarball=cryptography-$(cryptography-version).tar.lz
$(call import-source, $(cryptography-url), $(cryptography-checksum))
- $(call pybuild, tar xf, cryptography-$(cryptography-version), , \
+ $(call pybuild, tar -xf, cryptography-$(cryptography-version), , \
Cryptography $(cryptography-version))
$(ipydir)/cycler-$(cycler-version): $(ipydir)/six-$(six-version)
- tarball=cycler-$(cycler-version).tar.gz
+ tarball=cycler-$(cycler-version).tar.lz
$(call import-source, $(cycler-url), $(cycler-checksum))
- $(call pybuild, tar xf, cycler-$(cycler-version), , \
+ $(call pybuild, tar -xf, cycler-$(cycler-version), , \
Cycler $(cycler-version))
$(ipydir)/cython-$(cython-version): $(ipydir)/setuptools-$(setuptools-version)
- tarball=cython-$(cython-version).tar.gz
+ tarball=Cython-$(cython-version).tar.lz
$(call import-source, $(cython-url), $(cython-checksum))
- $(call pybuild, tar xf, Cython-$(cython-version))
+ $(call pybuild, tar -xf, Cython-$(cython-version))
cp $(dtexdir)/cython.tex $(ictdir)/
echo "Cython $(cython-version) \citep{cython2011}" > $@
$(ipydir)/esutil-$(esutil-version): $(ipydir)/numpy-$(numpy-version)
- tarball=esutil-$(esutil-version).tar.gz
+ export CFLAGS="-std=c++14 $$CFLAGS"
+ tarball=esutil-$(esutil-version).tar.lz
$(call import-source, $(esutil-url), $(esutil-checksum))
- $(call pybuild, tar xf, esutil-$(esutil-version), , \
+ $(call pybuild, tar -xf, esutil-$(esutil-version), , \
esutil $(esutil-version))
$(ipydir)/eigency-$(eigency-version): \
@@ -266,7 +264,7 @@ $(ipydir)/eigency-$(eigency-version): \
$(ipydir)/cython-$(cython-version)
tarball=eigency-$(eigency-version).tar.gz
$(call import-source, $(eigency-url), $(eigency-checksum))
- $(call pybuild, tar xf, eigency-$(eigency-version), , \
+ $(call pybuild, tar -xf, eigency-$(eigency-version), , \
eigency $(eigency-version))
$(ipydir)/emcee-$(emcee-version): \
@@ -274,28 +272,35 @@ $(ipydir)/emcee-$(emcee-version): \
$(ipydir)/setuptools_scm-$(setuptools_scm-version)
tarball=emcee-$(emcee-version).tar.gz
$(call import-source, $(emcee-url), $(emcee-checksum))
- $(call pybuild, tar xf, emcee-$(emcee-version), , \
+ $(call pybuild, tar -xf, emcee-$(emcee-version), , \
emcee $(emcee-version))
$(ipydir)/entrypoints-$(entrypoints-version): \
$(ipydir)/setuptools-$(setuptools-version)
tarball=entrypoints-$(entrypoints-version).tar.gz
$(call import-source, $(entrypoints-url), $(entrypoints-checksum))
- $(call pybuild, tar xf, entrypoints-$(entrypoints-version), , \
+ $(call pybuild, tar -xf, entrypoints-$(entrypoints-version), , \
EntryPoints $(entrypoints-version))
+$(ipydir)/extension-helpers-$(extension-helpers-version): \
+ $(ipydir)/setuptools-$(setuptools-version)
+ tarball=extension-helpers-$(extension-helpers-version).tar.lz
+ $(call import-source, $(extension-helpers-url), $(extension-helpers-checksum))
+ $(call pybuild, tar -xf, extension-helpers-$(extension-helpers-version), , \
+ Extension-Helpers $(extension-helpers-version))
+
$(ipydir)/flake8-$(flake8-version): \
$(ipydir)/pyflakes-$(pyflakes-version) \
$(ipydir)/pycodestyle-$(pycodestyle-version)
tarball=flake8-$(flake8-version).tar.gz
$(call import-source, $(flake8-url), $(flake8-checksum))
- $(call pybuild, tar xf, flake8-$(flake8-version), , \
+ $(call pybuild, tar -xf, flake8-$(flake8-version), , \
Flake8 $(flake8-version))
$(ipydir)/future-$(future-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=future-$(future-version).tar.gz
$(call import-source, $(future-url), $(future-checksum))
- $(call pybuild, tar xf, future-$(future-version), , \
+ $(call pybuild, tar -xf, future-$(future-version), , \
Future $(future-version))
$(ipydir)/galsim-$(galsim-version): \
@@ -304,12 +309,18 @@ $(ipydir)/galsim-$(galsim-version): \
$(ipydir)/eigency-$(eigency-version) \
$(ipydir)/pybind11-$(pybind11-version) \
$(ipydir)/lsstdesccoord-$(lsstdesccoord-version)
- tarball=galsim-$(galsim-version).tar.gz
+ tarball=galsim-$(galsim-version).tar.lz
$(call import-source, $(galsim-url), $(galsim-checksum))
- $(call pybuild, tar xf, GalSim-$(galsim-version))
+ $(call pybuild, tar -xf, galsim-$(galsim-version))
cp $(dtexdir)/galsim.tex $(ictdir)/
echo "Galsim $(galsim-version) \citep{galsim}" > $@
+$(ipydir)/gast-$(gast-version): $(ipydir)/setuptools-$(setuptools-version)
+ tarball=gast-$(gast-version).tar.lz
+ $(call import-source, $(gast-url), $(gast-checksum))
+ $(call pybuild, tar -xf, gast-$(gast-version), , \
+ Gast $(gast-version))
+
$(ipydir)/h5py-$(h5py-version): \
$(ipydir)/six-$(six-version) \
$(ibidir)/hdf5-$(hdf5-version) \
@@ -321,15 +332,15 @@ $(ipydir)/h5py-$(h5py-version): \
export HDF5_DIR=$(ildir)
tarball=h5py-$(h5py-version).tar.gz
$(call import-source, $(h5py-url), $(h5py-checksum))
- $(call pybuild, tar xf, h5py-$(h5py-version), , \
+ $(call pybuild, tar -xf, h5py-$(h5py-version), , \
h5py $(h5py-version))
-# `healpy' is actually installed as part of the HEALPix package. It will be
+# 'healpy' is actually installed as part of the HEALPix package. It will be
# installed with its C/C++ libraries if any other Python library is
-# requested with HEALPix. So actually calling for `healpix' (when `healpix'
+# requested with HEALPix. So actually calling for 'healpix' (when 'healpix'
# is requested) is not necessary. But some users might not know about this
-# and just ask for `healpy'. To avoid confusion in such cases, we'll just
-# set `healpy' to be dependent on `healpix' and not download any tarball
+# and just ask for 'healpy'. To avoid confusion in such cases, we'll just
+# set 'healpy' to be dependent on 'healpix' and not download any tarball
# for it, or write anything in the final target.
$(ipydir)/healpy-$(healpy-version): $(ibidir)/healpix-$(healpix-version)
touch $@
@@ -339,34 +350,40 @@ $(ipydir)/html5lib-$(html5lib-version): \
$(ipydir)/webencodings-$(webencodings-version)
tarball=html5lib-$(html5lib-version).tar.gz
$(call import-source, $(html5lib-url), $(html5lib-checksum))
- $(call pybuild, tar xf, html5lib-$(html5lib-version), , \
+ $(call pybuild, tar -xf, html5lib-$(html5lib-version), , \
HTML5lib $(html5lib-version))
$(ipydir)/idna-$(idna-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=idna-$(idna-version).tar.gz
$(call import-source, $(idna-url), $(idna-checksum))
- $(call pybuild, tar xf, idna-$(idna-version), , \
+ $(call pybuild, tar -xf, idna-$(idna-version), , \
idna $(idna-version))
$(ipydir)/jeepney-$(jeepney-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=jeepney-$(jeepney-version).tar.gz
$(call import-source, $(jeepney-url), $(jeepney-checksum))
- $(call pybuild, tar xf, jeepney-$(jeepney-version), , \
+ $(call pybuild, tar -xf, jeepney-$(jeepney-version), , \
Jeepney $(jeepney-version))
+$(ipydir)/jinja2-$(jinja2-version): $(ipydir)/markupsafe-$(markupsafe-version)
+ tarball=jinja2-$(jinja2-version).tar.lz
+ $(call import-source, $(jinja2-url), $(jinja2-checksum))
+ $(call pybuild, tar -xf, jinja2-$(jinja2-version), , \
+ Jinja2 $(jinja2-version))
+
$(ipydir)/keyring-$(keyring-version): \
$(ipydir)/entrypoints-$(entrypoints-version) \
$(ipydir)/secretstorage-$(secretstorage-version) \
$(ipydir)/setuptools_scm-$(setuptools_scm-version)
tarball=keyring-$(keyring-version).tar.gz
$(call import-source, $(keyring-url), $(keyring-checksum))
- $(call pybuild, tar xf, keyring-$(keyring-version), , \
+ $(call pybuild, tar -xf, keyring-$(keyring-version), , \
Keyring $(keyring-version))
$(ipydir)/kiwisolver-$(kiwisolver-version): $(ipydir)/setuptools-$(setuptools-version)
- tarball=kiwisolver-$(kiwisolver-version).tar.gz
+ tarball=kiwisolver-$(kiwisolver-version).tar.lz
$(call import-source, $(kiwisolver-url), $(kiwisolver-checksum))
- $(call pybuild, tar xf, kiwisolver-$(kiwisolver-version), , \
+ $(call pybuild, tar -xf, kiwisolver-$(kiwisolver-version), , \
Kiwisolver $(kiwisolver-version))
$(ipydir)/lmfit-$(lmfit-version): \
@@ -379,20 +396,28 @@ $(ipydir)/lmfit-$(lmfit-version): \
$(ipydir)/uncertainties-$(uncertainties-version)
tarball=lmfit-$(lmfit-version).tar.gz
$(call import-source, $(lmfit-url), $(lmfit-checksum))
- $(call pybuild, tar xf, lmfit-$(lmfit-version), , \
+ $(call pybuild, tar -xf, lmfit-$(lmfit-version), , \
LMFIT $(lmfit-version))
$(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \
- $(ipydir)/setuptools-$(setuptools-version)
+ $(ipydir)/cython-$(cython-version)
tarball=lsstdesccoord-$(lsstdesccoord-version).tar.gz
$(call import-source, $(lsstdesccoord-url), $(lsstdesccoord-checksum))
- $(call pybuild, tar xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \
+ $(call pybuild, tar -xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \
LSSTDESC.Coord $(lsstdesccoord-version))
+$(ipydir)/markupsafe-$(markupsafe-version): \
+ $(ipydir)/setuptools-$(setuptools-version)
+ tarball=markupsafe-$(markupsafe-version).tar.lz
+ $(call import-source, $(markupsafe-url), $(markupsafe-checksum))
+ $(call pybuild, tar -xf, markupsafe-$(markupsafe-version), , \
+ MarkupSafe $(markupsafe-version))
+
$(ipydir)/matplotlib-$(matplotlib-version): \
$(itidir)/texlive \
$(ipydir)/numpy-$(numpy-version) \
$(ipydir)/cycler-$(cycler-version) \
+ $(ipydir)/pillow-$(pillow-version) \
$(ibidir)/freetype-$(freetype-version) \
$(ipydir)/pyparsing-$(pyparsing-version) \
$(ipydir)/kiwisolver-$(kiwisolver-version) \
@@ -400,33 +425,33 @@ $(ipydir)/matplotlib-$(matplotlib-version): \
$(ibidir)/imagemagick-$(imagemagick-version) \
$(ipydir)/python-dateutil-$(python-dateutil-version)
- # Download the source.
- tarball=matplotlib-$(matplotlib-version).tar.gz
+# Prepare the source.
+ tarball=matplotlib-$(matplotlib-version).tar.lz
$(call import-source, $(matplotlib-url), $(matplotlib-checksum))
- # On Mac systems, the build complains about `clang' specific
- # features, so we can't use our own GCC build here.
+# On Mac systems, the build complains about 'clang' specific
+# features, so we can't use our own GCC build here.
if [ x$(on_mac_os) = xyes ]; then
export CC=clang
export CXX=clang++
fi
- $(call pybuild, tar xf, matplotlib-$(matplotlib-version))
+ $(call pybuild, tar -xf, matplotlib-$(matplotlib-version))
cp $(dtexdir)/matplotlib.tex $(ictdir)/
echo "Matplotlib $(matplotlib-version) \citep{matplotlib2007}" > $@
$(ipydir)/mpi4py-$(mpi4py-version): \
$(ibidir)/openmpi-$(openmpi-version) \
$(ipydir)/setuptools-$(setuptools-version)
- tarball=mpi4py-$(mpi4py-version).tar.gz
+ tarball=mpi4py-$(mpi4py-version).tar.lz
$(call import-source, $(mpi4py-url), $(mpi4py-checksum))
- $(call pybuild, tar xf, mpi4py-$(mpi4py-version))
+ $(call pybuild, tar -xf, mpi4py-$(mpi4py-version))
cp $(dtexdir)/mpi4py.tex $(ictdir)/
echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
$(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=mpmath-$(mpmath-version).tar.gz
$(call import-source, $(mpmath-url), $(mpmath-checksum))
- $(call pybuild, tar xf, mpmath-$(mpmath-version), , \
+ $(call pybuild, tar -xf, mpmath-$(mpmath-version), , \
mpmath $(mpmath-version))
$(ipydir)/numpy-$(numpy-version): \
@@ -434,7 +459,7 @@ $(ipydir)/numpy-$(numpy-version): \
$(ipydir)/cython-$(cython-version) \
$(ibidir)/openblas-$(openblas-version) \
$(ipydir)/setuptools-$(setuptools-version)
- tarball=numpy-$(numpy-version).zip
+ tarball=numpy-$(numpy-version).tar.lz
$(call import-source, $(numpy-url), $(numpy-checksum))
if [ x$(on_mac_os) = xyes ]; then
export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"
@@ -443,28 +468,48 @@ $(ipydir)/numpy-$(numpy-version): \
fi
export CFLAGS="--std=c99 $$CFLAGS"
conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
- $(call pybuild, unzip, numpy-$(numpy-version),$$conf, \
+ $(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \
Numpy $(numpy-version))
cp $(dtexdir)/numpy.tex $(ictdir)/
echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
+$(ipydir)/packaging-$(packaging-version): \
+ $(ipydir)/pyparsing-$(pyparsing-version)
+ tarball=packaging-$(packaging-version).tar.lz
+ $(call import-source, $(packaging-url), $(packaging-checksum))
+ $(call pybuild, tar -xf, packaging-$(packaging-version), , \
+ Packaging $(packaging-version))
+
$(ipydir)/pexpect-$(pexpect-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=pexpect-$(pexpect-version).tar.gz
$(call import-source, $(pexpect-url), $(pexpect-checksum))
- $(call pybuild, tar xf, pexpect-$(pexpect-version), , \
+ $(call pybuild, tar -xf, pexpect-$(pexpect-version), , \
Pexpect $(pexpect-version))
+$(ipydir)/pillow-$(pillow-version): $(ibidir)/libjpeg-$(libjpeg-version) \
+ $(ipydir)/setuptools-$(setuptools-version)
+ tarball=Pillow-$(pillow-version).tar.lz
+ $(call import-source, $(pillow-url), $(pillow-checksum))
+ $(call pybuild, tar -xf, Pillow-$(pillow-version), , \
+ Pillow $(pillow-version))
+
$(ipydir)/pip-$(pip-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=pip-$(pip-version).tar.gz
$(call import-source, $(pip-url), $(pip-checksum))
- $(call pybuild, tar xf, pip-$(pip-version), , \
+ $(call pybuild, tar -xf, pip-$(pip-version), , \
PiP $(pip-version))
+$(ipydir)/ply-$(ply-version): $(ipydir)/setuptools-$(setuptools-version)
+ tarball=ply-$(ply-version).tar.lz
+ $(call import-source, $(ply-url), $(ply-checksum))
+ $(call pybuild, tar -xf, ply-$(ply-version), , \
+ ply $(ply-version))
+
$(ipydir)/pycodestyle-$(pycodestyle-version): \
$(ipydir)/setuptools-$(setuptools-version)
tarball=pycodestyle-$(pycodestyle-version).tar.gz
$(call import-source, $(pycodestyle-url), $(pycodestyle-checksum))
- $(call pybuild, tar xf, pycodestyle-$(pycodestyle-version), , \
+ $(call pybuild, tar -xf, pycodestyle-$(pycodestyle-version), , \
pycodestyle $(pycodestyle-version))
$(ipydir)/pybind11-$(pybind11-version): \
@@ -476,31 +521,40 @@ $(ipydir)/pybind11-$(pybind11-version): \
pyhook_after() {
cp -r include/pybind11 $(iidir)/python$(python-major-version)m/
}
- $(call pybuild, tar xf, pybind11-$(pybind11-version), , \
+ $(call pybuild, tar -xf, pybind11-$(pybind11-version), , \
pybind11 $(pybind11-version))
$(ipydir)/pycparser-$(pycparser-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=pycparser-$(pycparser-version).tar.gz
$(call import-source, $(pycparser-url), $(pycparser-checksum))
- $(call pybuild, tar xf, pycparser-$(pycparser-version), , \
+ $(call pybuild, tar -xf, pycparser-$(pycparser-version), , \
pycparser $(pycparser-version))
+$(ipydir)/pyerfa-$(pyerfa-version): \
+ $(ipydir)/numpy-$(numpy-version) \
+ $(ipydir)/packaging-$(packaging-version)
+ tarball=pyerfa-$(pyerfa-version).tar.lz
+ $(call import-source, $(pyerfa-url), $(pyerfa-checksum))
+ $(call pybuild, tar -xf, pyerfa-$(pyerfa-version), , \
+ PyERFA $(pyerfa-version))
+
$(ipydir)/pyflakes-$(pyflakes-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=pyflakes-$(pyflakes-version).tar.gz
$(call import-source, $(pyflakes-url), $(pyflakes-checksum))
- $(call pybuild, tar xf, pyflakes-$(pyflakes-version), , \
+ $(call pybuild, tar -xf, pyflakes-$(pyflakes-version), , \
pyflakes $(pyflakes-version))
-$(ipydir)/pyparsing-$(pyparsing-version): $(ipydir)/setuptools-$(setuptools-version)
- tarball=pyparsing-$(pyparsing-version).tar.gz
+$(ipydir)/pyparsing-$(pyparsing-version): \
+ $(ipydir)/setuptools-$(setuptools-version)
+ tarball=pyparsing-$(pyparsing-version).tar.lz
$(call import-source, $(pyparsing-url), $(pyparsing-checksum))
- $(call pybuild, tar xf, pyparsing-$(pyparsing-version), , \
+ $(call pybuild, tar -xf, pyparsing-$(pyparsing-version), , \
PyParsing $(pyparsing-version))
$(ipydir)/pypkgconfig-$(pypkgconfig-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=pkgconfig-$(pypkgconfig-version).tar.gz
$(call import-source, $(pypkgconfig-url), $(pypkgconfig-checksum))
- $(call pybuild, tar xf, pkgconfig-$(pypkgconfig-version), ,
+ $(call pybuild, tar -xf, pkgconfig-$(pypkgconfig-version), ,
pkgconfig $(pypkgconfig-version))
$(ipydir)/python-dateutil-$(python-dateutil-version): \
@@ -508,15 +562,26 @@ $(ipydir)/python-dateutil-$(python-dateutil-version): \
$(ipydir)/setuptools_scm-$(setuptools_scm-version)
tarball=python-dateutil-$(python-dateutil-version).tar.gz
$(call import-source, $(python-dateutil-url), $(python-dateutil-checksum))
- $(call pybuild, tar xf, python-dateutil-$(python-dateutil-version), , \
+ $(call pybuild, tar -xf, python-dateutil-$(python-dateutil-version), , \
python-dateutil $(python-dateutil-version))
+$(ipydir)/pythran-$(pythran-version): \
+ $(ipydir)/ply-$(ply-version) \
+ $(ipydir)/gast-$(gast-version) \
+ $(ibidir)/boost-$(boost-version) \
+ $(ipydir)/beniget-$(beniget-version) \
+ $(ipydir)/setuptools_scm-$(setuptools_scm-version)
+ tarball=pythran-$(pythran-version).tar.lz
+ $(call import-source, $(pythran-url), $(pythran-checksum))
+ $(call pybuild, tar -xf, pythran-$(pythran-version), , \
+ pythran $(pythran-version))
+
$(ipydir)/pyyaml-$(pyyaml-version): \
$(ibidir)/yaml-$(yaml-version) \
$(ipydir)/cython-$(cython-version)
tarball=pyyaml-$(pyyaml-version).tar.gz
$(call import-source, $(pyyaml-url), $(pyyaml-checksum))
- $(call pybuild, tar xf, PyYAML-$(pyyaml-version), , \
+ $(call pybuild, tar -xf, PyYAML-$(pyyaml-version), , \
PyYAML $(pyyaml-version))
$(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
@@ -526,13 +591,14 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
$(ipydir)/urllib3-$(urllib3-version)
tarball=requests-$(requests-version).tar.gz
$(call import-source, $(requests-url), $(requests-checksum))
- $(call pybuild, tar xf, requests-$(requests-version), , \
+ $(call pybuild, tar -xf, requests-$(requests-version), , \
Requests $(requests-version))
$(ipydir)/scipy-$(scipy-version): \
$(ipydir)/numpy-$(numpy-version) \
+ $(ipydir)/pythran-$(pythran-version) \
$(ipydir)/pybind11-$(pybind11-version)
- tarball=scipy-$(scipy-version).tar.gz
+ tarball=scipy-$(scipy-version).tar.lz
$(call import-source, $(scipy-url), $(scipy-checksum))
if [ x$(on_mac_os) = xyes ]; then
export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"
@@ -540,7 +606,7 @@ $(ipydir)/scipy-$(scipy-version): \
export LDFLAGS="$(LDFLAGS) -shared"
fi
conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
- $(call pybuild, tar xf, scipy-$(scipy-version),$$conf)
+ $(call pybuild, tar -xf, scipy-$(scipy-version),$$conf)
cp $(dtexdir)/scipy.tex $(ictdir)/
echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@
@@ -549,68 +615,81 @@ $(ipydir)/secretstorage-$(secretstorage-version): \
$(ipydir)/cryptography-$(cryptography-version)
tarball=secretstorage-$(secretstorage-version).tar.gz
$(call import-source, $(secretstorage-url), $(secretstorage-checksum))
- $(call pybuild, tar xf, SecretStorage-$(secretstorage-version), , \
+ $(call pybuild, tar -xf, SecretStorage-$(secretstorage-version), , \
SecretStorage $(secretstorage-version))
$(ipydir)/setuptools-$(setuptools-version): \
$(ibidir)/unzip-$(unzip-version) \
$(ibidir)/python-$(python-version)
- tarball=setuptools-$(setuptools-version).zip
+ tarball=setuptools-$(setuptools-version).tar.lz
$(call import-source, $(setuptools-url), $(setuptools-checksum))
- $(call pybuild, unzip, setuptools-$(setuptools-version), , \
+ $(call pybuild, tar -xf, setuptools-$(setuptools-version), , \
Setuptools $(setuptools-version))
$(ipydir)/setuptools_scm-$(setuptools_scm-version): \
$(ipydir)/setuptools-$(setuptools-version)
tarball=setuptools_scm-$(setuptools_scm-version).tar.gz
$(call import-source, $(setuptools_scm-url), $(setuptools_scm-checksum))
- $(call pybuild, tar xf, setuptools_scm-$(setuptools_scm-version), , \
+ $(call pybuild, tar -xf, setuptools_scm-$(setuptools_scm-version), , \
Setuptools-scm $(setuptools_scm-version))
+$(ipydir)/setuptools-rust-$(setuptools-rust-version): \
+ $(ipydir)/setuptools-$(setuptools-version)
+ tarball=setuptools-rust-$(setuptools-rust-version).tar.lz
+ $(call import-source, $(setuptools-rust-url), $(setuptools-rust-checksum))
+ $(call pybuild, tar -xf, setuptools-rust-$(setuptools-rust-version), , \
+ Setuptools-scm $(setuptools-rust-version))
+
$(ipydir)/sip_tpv-$(sip_tpv-version): \
$(ipydir)/sympy-$(sympy-version) \
$(ipydir)/astropy-$(astropy-version)
tarball=sip_tpv-$(sip_tpv-version).tar.gz
$(call import-source, $(sip_tpv-url), $(sip_tpv-checksum))
- $(call pybuild, tar xf, sip_tpv-$(sip_tpv-version), ,)
+ $(call pybuild, tar -xf, sip_tpv-$(sip_tpv-version), ,)
cp $(dtexdir)/sip_tpv.tex $(ictdir)/
echo "sip_tpv $(sip_tpv-version) \citep{sip-tpv}" > $@
$(ipydir)/six-$(six-version): $(ipydir)/setuptools-$(setuptools-version)
- tarball=six-$(six-version).tar.gz
+ tarball=six-$(six-version).tar.lz
$(call import-source, $(six-url), $(six-checksum))
- $(call pybuild, tar xf, six-$(six-version), , \
+ $(call pybuild, tar -xf, six-$(six-version), , \
Six $(six-version))
$(ipydir)/soupsieve-$(soupsieve-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=soupsieve-$(soupsieve-version).tar.gz
$(call import-source, $(soupsieve-url), $(soupsieve-checksum))
- $(call pybuild, tar xf, soupsieve-$(soupsieve-version), , \
+ $(call pybuild, tar -xf, soupsieve-$(soupsieve-version), , \
SoupSieve $(soupsieve-version))
$(ipydir)/sympy-$(sympy-version): $(ipydir)/mpmath-$(mpmath-version)
tarball=sympy-$(sympy-version).tar.gz
$(call import-source, $(sympy-url), $(sympy-checksum))
- $(call pybuild, tar xf, sympy-$(sympy-version), ,)
+ $(call pybuild, tar -xf, sympy-$(sympy-version), ,)
cp $(dtexdir)/sympy.tex $(ictdir)/
echo "SymPy $(sympy-version) \citep{sympy}" > $@
$(ipydir)/uncertainties-$(uncertainties-version): $(ipydir)/numpy-$(numpy-version)
- tarball=uncertainties-$(uncertainties-version).tar.gz
+ tarball=uncertainties-$(uncertainties-version).tar.lz
$(call import-source, $(uncertainties-url), $(uncertainties-checksum))
- $(call pybuild, tar xf, uncertainties-$(uncertainties-version), , \
+ $(call pybuild, tar -xf, uncertainties-$(uncertainties-version), , \
uncertainties $(uncertainties-version))
$(ipydir)/urllib3-$(urllib3-version): $(ipydir)/setuptools-$(setuptools-version)
tarball=urllib3-$(urllib3-version).tar.gz
$(call import-source, $(urllib3-url), $(urllib3-checksum))
- $(call pybuild, tar xf, urllib3-$(urllib3-version), , \
+ $(call pybuild, tar -xf, urllib3-$(urllib3-version), , \
Urllib3 $(urllib3-version))
$(ipydir)/webencodings-$(webencodings-version): \
$(ipydir)/setuptools-$(setuptools-version)
tarball=webencodings-$(webencodings-version).tar.gz
$(call import-source, $(webencodings-url), $(webencodings-checksum))
- $(call pybuild, tar xf, webencodings-$(webencodings-version), , \
+ $(call pybuild, tar -xf, webencodings-$(webencodings-version), , \
Webencodings $(webencodings-version))
+
+$(ipydir)/wheel-$(wheel-version): $(ipydir)/setuptools-$(setuptools-version)
+ tarball=wheel-$(wheel-version).tar.lz
+ $(call import-source, $(wheel-url), $(wheel-checksum))
+ $(call pybuild, tar -xf, wheel-$(wheel-version), , \
+ Wheel $(wheel-version))
diff --git a/reproduce/software/make/r-cran.mk b/reproduce/software/make/r-cran.mk
new file mode 100644
index 0000000..617b8de
--- /dev/null
+++ b/reproduce/software/make/r-cran.mk
@@ -0,0 +1,487 @@
+# Build the project's R (here called R-CRAN) dependencies.
+#
+# ------------------------------------------------------------------------
+# !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be loaded into 'high-level.mk', which is called by the
+# './project configure' script. It is not included into the project
+# afterwards.
+#
+# This Makefile contains instructions to build all the R-CRAN-related
+# software within the project.
+#
+# ------------------------------------------------------------------------
+#
+# Copyright (C) 2022 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# 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
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This Makefile 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 Makefile. If not, see <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# BUGS/IMPROVEMENTS
+# -----------------
+#
+# As of 2021-06-20, the R system is still very new and has not yet
+# been tested on non-Debian-derived systems. Please provide bug
+# reports ( https://savannah.nongnu.org/task/?15772 ) or propose fixes
+# as git pull requests on a public git server (e.g. on a fork of
+# https://codeberg.org/boud/maneage_dev ).
+
+
+
+
+
+# R-CRAN enviroment
+# -----------------
+#
+# It may be necessary to override host-level R-related environment
+# variables that interfere with the Maneage-installed R system.
+# systems which might interfere.
+
+# Ideas for which environment variables might create problems
+# and might need to be set to be empty here:
+#
+# https://stat.ethz.ch/R-manual/R-devel/library/base/html/EnvVar.html
+
+# These first variables should be set automatically when R starts:
+#export R_HOME := $(idir)/lib/R
+#export R_INCLUDE_DIR := $(idir)/lib/R/include
+
+
+
+
+
+# R-CRAN-specific installation directories.
+r-cran-major-version = $(shell echo $(r-cran-version) \
+ | awk 'BEGIN{FS="."} \
+ {printf "%d.%d\n", $$1, $$2}')
+
+
+
+
+
+# R-CRAN-specific build rules for 'make'
+# ======================================
+
+# Double-check an already downloaded R source
+# -------------------------------------------
+#
+# Check that the tarball with the version in
+# 'reproduce/software/conf/versions.conf' has the sha512sum (checksum)
+# stated 'reproduce/software/conf/checksums.conf'. This does not do any
+# security checks; it only checks that the source file package is the one
+# that is expected the last time that someone updated these two files for
+# the R package of interest.
+#
+# Calculate the checksum and exit with a non-zero error code if there's a
+# mismatch, after informing the user.
+#
+# Arguments:
+# 1: The expected checksum of the tarball.
+#
+# Necessary shell variables
+# 'tarball': This is the name of the actual tarball file without a
+# directory.
+double-check-R-source = final=$(tdir)/$$tarball; \
+ exp_checksum="$(strip $(1))"; \
+ if [ x"$$exp_checksum" = x"NO-CHECK-SUM" ]; then \
+ result=0; \
+ else \
+ if type sha512sum > /dev/null 2>/dev/null; then \
+ checksum=$$(sha512sum "$$final" | awk '{print $$1}'); \
+ if [ x"$$checksum" = x"$$exp_checksum" ]; then \
+ result=0; \
+ else \
+ echo "ERROR: Non-matching checksum: $$final"; \
+ echo "Checksum should be: $$exp_checksum"; \
+ echo "Checksum is: $$checksum"; \
+ result=1; \
+ exit 1; \
+ fi; \
+ else \
+ echo "ERROR: sha512sum is unavailable."; \
+ exit 1; \
+ fi; \
+ fi
+
+# Default 'make' build rules for an CRAN package
+# -----------------------------------------------
+#
+# The default 'install.packages' function of R only recognizes 'tar.gz'
+# tarballs. But Maneage uses '.tar.lz' format for its archival. So to be
+# agnostic to the compression algorithm, we will be using 'tar' externally
+# (before entering R), then give the un-compressed directory to
+# 'install.packages'.
+#
+# Parameters:
+# 1. package name (without 'r-cran', without the version string)
+# 2. version string
+# 3. checksum of the package
+r_cran_build = \
+ pkg=$(strip $(1)); \
+ version=$(strip $(2)); \
+ checksum=$(strip $(3)); \
+ $(call import-source, \
+ https://cran.r-project.org/src/contrib, \
+ $$checksum, \
+ $$tarball, \
+ https://cran.r-project.org/src/contrib/00Archive/$$pkg); \
+ cd "$(ddir)"; \
+ tar -xf $(tdir)/$$tarball; \
+ unpackdir=$$pkg-$$version; \
+ (printf "install.packages(c(\"$(ddir)/$$unpackdir\"),"; \
+ printf 'lib="$(ilibrcrandir)",'; \
+ printf 'repos=NULL,'; \
+ printf 'type="source")\n'; \
+ printf 'quit()\n'; \
+ printf 'n\n') | R --no-save; \
+ rm -rf $$unpackdir; \
+ if [ $$pkg = r-pkgconfig ]; then iname=pkgconfig; \
+ else iname=$$pkg; fi; \
+ if [ -e "$(ilibrcrandir)"/$$iname/Meta/nsInfo.rds ]; then \
+ $(call double-check-R-source, $$checksum) \
+ && echo "$$pkg $$version" > $@; \
+ else \
+ printf "r-cran-$$pkg failed: Meta/nsInfo.rds missing.\n"; \
+ exit 1; \
+ fi
+
+
+
+
+
+# Necessary programs and libraries
+# --------------------------------
+#
+# While this Makefile is for R programs, in some cases, we need certain
+# programs (like R itself), or libraries for the modules. Comment on
+# building R without GUI support ('--without-tcltlk')
+#
+# Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support
+# in some software. But they are not yet natively built within Maneage,
+# primarily because we have higher-priority work right now (if anyone is
+# interested, they can ofcourse contribute!). GUI tools in general aren't
+# high on our priority list right now because they are generally good for
+# human interaction (which is contrary to the reproducible philosophy:
+# there will always be human-error and frustration, for example in GUI
+# tools the best level of reproducibility is statements like this: "move
+# your mouse to button XXX, then click on menu YYY and etc"). A robust
+# reproducible solution must be done automatically.
+#
+# If someone wants to use R's GUI functionalities while investigating for
+# their analysis, they can do the GUI part on their host OS
+# implementation. Later, they can bring the finalized source into Maneage
+# to be automatically run in Maneage. This will also be the recommended way
+# to deal with GUI tools later when we do install them within Maneage.
+$(ibidir)/r-cran-$(r-cran-version): \
+ $(itidir)/texlive \
+ $(ibidir)/icu-$(icu-version) \
+ $(ibidir)/pcre-$(pcre-version) \
+ $(ibidir)/cairo-$(cairo-version) \
+ $(ibidir)/libpng-$(libpng-version) \
+ $(ibidir)/libjpeg-$(libjpeg-version) \
+ $(ibidir)/libtiff-$(libtiff-version) \
+ $(ibidir)/libpaper-$(libpaper-version)
+
+# Prepare the tarball, unpack it and enter the directory.
+ tarball=R-$(r-cran-version).tar.lz
+ $(call import-source, $(r-cran-url), $(r-cran-checksum))
+ cd $(ddir)
+ tar -xf $(tdir)/$$tarball
+ unpackdir=R-$(r-cran-version)
+ cd $$unpackdir
+
+# We need to manually remove the lines with '~autodetect~', they
+# cause the configure script to crash in version 4.0.2. They are used
+# in relation to Java, and we don't use Java anyway.
+ sed -i -e '/\~autodetect\~/ s/^/#/g' configure
+ export R_SHELL=$(SHELL)
+ ./configure --prefix=$(idir) \
+ --without-x \
+ --with-pcre1 \
+ --disable-java \
+ --with-readline \
+ --without-tcltk \
+ --disable-openmp
+ make -j$(numthreads)
+ make install
+ cd ..
+ rm -rf R-$(r-cran-version)
+ cp -p $(dtexdir)/r-cran.tex $(ictdir)/
+ echo "R $(r-cran-version) \citep{RIhakaGentleman1996}" > $@
+
+
+
+
+
+# Non-Maneage'd tarballs
+# ----------------------
+#
+# CRAN tarballs differ in two aspects from Maneage'd tarballs:
+# - CRAN uses '.tar.gz', while Maneage uses 'tar.lz'.
+# - CRAN uses 'name_version', while Maneage uses 'name-version'.
+#
+# So if you add a new R package, or update the version of an existing one
+# (that is not yet in Maneage's archive), you need to use the CRAN naming
+# format for the 'tarball' variable.
+
+
+
+
+
+# R-CRAN modules
+# ---------------
+#
+# The rules for downloading, compiling and installing any R-CRAN modules
+# that are needed should be provided here. Each target (before the colon)
+# is first shown with its dependence on prerequisites (which are listed
+# after the colon. The default macro 'r_cran_build' will install the
+# package without checking on dependencies.
+
+$(ircrandir)/r-cran-cli-$(r-cran-cli-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-glue-$(r-cran-glue-version)
+ tarball=cli-$(r-cran-cli-version).tar.lz
+ $(call r_cran_build, cli, $(r-cran-cli-version), \
+ $(r-cran-cli-checksum))
+
+$(ircrandir)/r-cran-colorspace-$(r-cran-colorspace-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=colorspace-$(r-cran-colorspace-version).tar.lz
+ $(call r_cran_build, colorspace, $(r-cran-colorspace-version), \
+ $(r-cran-colorspace-checksum))
+
+$(ircrandir)/r-cran-cowplot-$(r-cran-cowplot-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+ $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) \
+ $(ircrandir)/r-cran-scales-$(r-cran-scales-version) \
+ $(ircrandir)/r-cran-ggplot2-$(r-cran-ggplot2-version)
+ tarball=cowplot-$(r-cran-cowplot-version).tar.lz
+ $(call r_cran_build, cowplot, $(r-cran-cowplot-version), \
+ $(r-cran-cowplot-checksum))
+
+$(ircrandir)/r-cran-crayon-$(r-cran-crayon-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=crayon-$(r-cran-crayon-version).tar.lz
+ $(call r_cran_build, crayon, $(r-cran-crayon-version), \
+ $(r-cran-crayon-checksum))
+
+$(ircrandir)/r-cran-digest-$(r-cran-digest-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=digest-$(r-cran-digest-version).tar.lz
+ $(call r_cran_build, digest, $(r-cran-digest-version), \
+ $(r-cran-digest-checksum))
+
+$(ircrandir)/r-cran-farver-$(r-cran-farver-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=farver-$(r-cran-farver-version).tar.lz
+ $(call r_cran_build, farver, $(r-cran-farver-version), \
+ $(r-cran-farver-checksum))
+
+$(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version)
+ tarball=ellipsis-$(r-cran-ellipsis-version).tar.lz
+ $(call r_cran_build, ellipsis, $(r-cran-ellipsis-version), \
+ $(r-cran-ellipsis-checksum))
+
+$(ircrandir)/r-cran-fansi-$(r-cran-fansi-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=fansi-$(r-cran-fansi-version).tar.lz
+ $(call r_cran_build, fansi, $(r-cran-fansi-version), \
+ $(r-cran-fansi-checksum))
+
+$(ircrandir)/r-cran-ggplot2-$(r-cran-ggplot2-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+ $(ircrandir)/r-cran-mgcv-$(r-cran-mgcv-version) \
+ $(ircrandir)/r-cran-MASS-$(r-cran-MASS-version) \
+ $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+ $(ircrandir)/r-cran-withr-$(r-cran-withr-version) \
+ $(ircrandir)/r-cran-digest-$(r-cran-digest-version) \
+ $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version) \
+ $(ircrandir)/r-cran-scales-$(r-cran-scales-version) \
+ $(ircrandir)/r-cran-tibble-$(r-cran-tibble-version) \
+ $(ircrandir)/r-cran-isoband-$(r-cran-isoband-version)
+ tarball=ggplot2-$(r-cran-ggplot2-version).tar.lz
+ $(call r_cran_build, ggplot2, $(r-cran-ggplot2-version), \
+ $(r-cran-ggplot2-checksum))
+
+$(ircrandir)/r-cran-glue-$(r-cran-glue-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=glue-$(r-cran-glue-version).tar.lz
+ $(call r_cran_build, glue, $(r-cran-glue-version), \
+ $(r-cran-glue-checksum))
+
+$(ircrandir)/r-cran-gridExtra-$(r-cran-gridExtra-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-gtable-$(r-cran-gtable-version)
+ tarball=gridExtra-$(r-cran-gridExtra-version).tar.lz
+ $(call r_cran_build, gridExtra, $(r-cran-gridExtra-version), \
+ $(r-cran-gridExtra-checksum))
+
+$(ircrandir)/r-cran-gtable-$(r-cran-gtable-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=gtable-$(r-cran-gtable-version).tar.lz
+ $(call r_cran_build, gtable, $(r-cran-gtable-version), \
+ $(r-cran-gtable-checksum))
+
+$(ircrandir)/r-cran-isoband-$(r-cran-isoband-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=isoband-$(r-cran-isoband-version).tar.lz
+ $(call r_cran_build, isoband, $(r-cran-isoband-version), \
+ $(r-cran-isoband-checksum))
+
+$(ircrandir)/r-cran-labeling-$(r-cran-labeling-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=labeling-$(r-cran-labeling-version).tar.lz
+ $(call r_cran_build, labeling, $(r-cran-labeling-version), \
+ $(r-cran-labeling-checksum))
+
+$(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+ $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version)
+ tarball=lifecycle-$(r-cran-lifecycle-version).tar.lz
+ $(call r_cran_build, lifecycle, $(r-cran-lifecycle-version), \
+ $(r-cran-lifecycle-checksum))
+
+$(ircrandir)/r-cran-magrittr-$(r-cran-magrittr-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=magrittr-$(r-cran-magrittr-version).tar.lz
+ $(call r_cran_build, magrittr, $(r-cran-magrittr-version), \
+ $(r-cran-magrittr-checksum))
+
+$(ircrandir)/r-cran-MASS-$(r-cran-MASS-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=MASS-$(r-cran-MASS-version).tar.lz
+ $(call r_cran_build, MASS, $(r-cran-MASS-version), \
+ $(r-cran-MASS-checksum))
+
+# The base R-2.0.4 install includes nlme and Matrix.
+# https://cran.r-project.org/web/packages/mgcv/index.html
+$(ircrandir)/r-cran-mgcv-$(r-cran-mgcv-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=mgcv-$(r-cran-mgcv-version).tar.lz
+ $(call r_cran_build, mgcv, $(r-cran-mgcv-version), \
+ $(r-cran-mgcv-checksum))
+
+$(ircrandir)/r-cran-munsell-$(r-cran-munsell-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-colorspace-$(r-cran-colorspace-version)
+ tarball=munsell-$(r-cran-munsell-version).tar.lz
+ $(call r_cran_build, munsell, $(r-cran-munsell-version), \
+ $(r-cran-munsell-checksum))
+
+#TODO: https://cran.r-project.org/web/packages/pillar/index.html
+$(ircrandir)/r-cran-pillar-$(r-cran-pillar-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-cli-$(r-cran-cli-version) \
+ $(ircrandir)/r-cran-utf8-$(r-cran-utf8-version) \
+ $(ircrandir)/r-cran-fansi-$(r-cran-fansi-version) \
+ $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+ $(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version) \
+ $(ircrandir)/r-cran-crayon-$(r-cran-crayon-version) \
+ $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) \
+ $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version)
+ tarball=pillar-$(r-cran-pillar-version).tar.lz
+ $(call r_cran_build, pillar, $(r-cran-pillar-version), \
+ $(r-cran-pillar-checksum))
+
+# Since we have other software packages with the name 'pkgconfig', to avoid
+# confusion with those tarballs, we have put a 'r-' prefix in the tarball
+# name. If you want to use the CRAN tarball, please correct the name
+# accordingly (as described in the comment above this group of rules).
+$(ircrandir)/r-cran-pkgconfig-$(r-cran-pkgconfig-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=r-pkgconfig-$(r-cran-pkgconfig-version).tar.lz
+ $(call r_cran_build, r-pkgconfig, $(r-cran-pkgconfig-version), \
+ $(r-cran-pkgconfig-checksum))
+
+$(ircrandir)/r-cran-RColorBrewer-$(r-cran-RColorBrewer-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=RColorBrewer-$(r-cran-RColorBrewer-version).tar.lz
+ $(call r_cran_build, RColorBrewer, $(r-cran-RColorBrewer-version), \
+ $(r-cran-RColorBrewer-checksum))
+
+$(ircrandir)/r-cran-R6-$(r-cran-R6-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=R6-$(r-cran-R6-version).tar.lz
+ $(call r_cran_build, R6, $(r-cran-R6-version), $(r-cran-R6-checksum))
+
+$(ircrandir)/r-cran-rlang-$(r-cran-rlang-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=rlang-$(r-cran-rlang-version).tar.lz
+ $(call r_cran_build, rlang, $(r-cran-rlang-version), \
+ $(r-cran-rlang-checksum))
+
+# https://cran.r-project.org/web/packages/scales/index.html
+$(ircrandir)/r-cran-scales-$(r-cran-scales-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-R6-$(r-cran-R6-version) \
+ $(ircrandir)/r-cran-farver-$(r-cran-farver-version) \
+ $(ircrandir)/r-cran-munsell-$(r-cran-munsell-version) \
+ $(ircrandir)/r-cran-labeling-$(r-cran-labeling-version) \
+ $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) \
+ $(ircrandir)/r-cran-viridisLite-$(r-cran-viridisLite-version) \
+ $(ircrandir)/r-cran-RColorBrewer-$(r-cran-RColorBrewer-version)
+ tarball=scales-$(r-cran-scales-version).tar.lz
+ $(call r_cran_build, scales, $(r-cran-scales-version), \
+ $(r-cran-scales-checksum))
+
+#https://cran.r-project.org/web/packages/tibble/index.html
+$(ircrandir)/r-cran-tibble-$(r-cran-tibble-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-fansi-$(r-cran-fansi-version) \
+ $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+ $(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version) \
+ $(ircrandir)/r-cran-pillar-$(r-cran-pillar-version) \
+ $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version) \
+ $(ircrandir)/r-cran-magrittr-$(r-cran-magrittr-version) \
+ $(ircrandir)/r-cran-lifecycle-$(r-cran-lifecycle-version) \
+ $(ircrandir)/r-cran-pkgconfig-$(r-cran-pkgconfig-version)
+ tarball=tibble-$(r-cran-tibble-version).tar.lz
+ $(call r_cran_build, tibble, $(r-cran-tibble-version), \
+ $(r-cran-tibble-checksum))
+
+$(ircrandir)/r-cran-utf8-$(r-cran-utf8-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=utf8-$(r-cran-utf8-version).tar.lz
+ $(call r_cran_build, utf8, $(r-cran-utf8-version), \
+ $(r-cran-utf8-checksum))
+
+$(ircrandir)/r-cran-vctrs-$(r-cran-vctrs-version): \
+ $(ibidir)/r-cran-$(r-cran-version) \
+ $(ircrandir)/r-cran-glue-$(r-cran-glue-version) \
+ $(ircrandir)/r-cran-rlang-$(r-cran-rlang-version) \
+ $(ircrandir)/r-cran-ellipsis-$(r-cran-ellipsis-version)
+ tarball=vctrs-$(r-cran-vctrs-version).tar.lz
+ $(call r_cran_build, vctrs, $(r-cran-vctrs-version), \
+ $(r-cran-vctrs-checksum))
+
+$(ircrandir)/r-cran-viridisLite-$(r-cran-viridisLite-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=viridisLite-$(r-cran-viridisLite-version).tar.lz
+ $(call r_cran_build, viridisLite, $(r-cran-viridisLite-version), \
+ $(r-cran-viridisLite-checksum))
+
+$(ircrandir)/r-cran-withr-$(r-cran-withr-version): \
+ $(ibidir)/r-cran-$(r-cran-version)
+ tarball=withr-$(r-cran-withr-version).tar.lz
+ $(call r_cran_build, withr, $(r-cran-withr-version), \
+ $(r-cran-withr-checksum))
diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk
index 3178cb4..6e62595 100644
--- a/reproduce/software/make/xorg.mk
+++ b/reproduce/software/make/xorg.mk
@@ -4,7 +4,7 @@
# !!!!! IMPORTANT NOTES !!!!!
#
# This Makefile will be loaded into 'high-level.mk', which is called by the
-# `./project configure' script. It is not included into the project
+# './project configure' script. It is not included into the project
# afterwards.
#
# This Makefile contains instructions to build all the Xorg-related
@@ -14,8 +14,8 @@
#
# ------------------------------------------------------------------------
#
-# Copyright (C) 2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2021-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com>
#
# 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
@@ -57,7 +57,7 @@ $(idir)/etc/profile.d/xorg.sh: | $(idir)/etc/profile.d
$(ibidir)/util-macros-$(util-macros-version): \
$(idir)/etc/profile.d/xorg.sh \
$(ibidir)/automake-$(automake-version)
- tarball=util-macros-$(util-macros-version).tar.bz2
+ tarball=util-macros-$(util-macros-version).tar.lz
$(call import-source, $(util-macros-url), $(util-macros-checksum))
$(call gbuild, util-macros-$(util-macros-version),,$(XORG_CONFIG),V=1)
echo "util-macros (Xorg) $(util-macros-version)" > $@
@@ -65,14 +65,14 @@ $(ibidir)/util-macros-$(util-macros-version): \
# Necessaary headers to define the Xorg protocols.
$(ibidir)/xorgproto-$(xorgproto-version): \
$(ibidir)/util-macros-$(util-macros-version)
- tarball=xorgproto-$(xorgproto-version).tar.bz2
+ tarball=xorgproto-$(xorgproto-version).tar.lz
$(call import-source, $(xorg-proto-url), $(xorgproto-checksum))
$(call gbuild, xorgproto-$(xorgproto-version),,$(XORG_CONFIG),V=1)
echo "xorgproto $(xorgproto-version)" > $@
# Necessaary headers to define the Xorg protocols.
$(ibidir)/libxau-$(libxau-version): $(ibidir)/xorgproto-$(xorgproto-version)
- tarball=libXau-$(libxau-version).tar.bz2
+ tarball=libXau-$(libxau-version).tar.lz
$(call import-source, $(libaxu-url), $(libxau-checksum))
$(call gbuild, libXau-$(libxau-version),,$(XORG_CONFIG), V=1)
echo "libXau (Xorg) $(libxau-version)" > $@
@@ -88,7 +88,7 @@ $(ibidir)/libxdmcp-$(libxdmcp-version): $(ibidir)/libxau-$(libxau-version)
$(ibidir)/xcb-proto-$(xcb-proto-version): \
$(ibidir)/python-$(python-version) \
$(ibidir)/libxml2-$(libxml2-version)
- tarball=xcb-proto-$(xcb-proto-version).tar.xz
+ tarball=xcb-proto-$(xcb-proto-version).tar.lz
$(call import-source, $(xcb-proto-url), $(xcb-proto-checksum))
$(call gbuild, xcb-proto-$(xcb-proto-version),,$(XORG_CONFIG), V=1)
echo "XCB-proto (Xorg) $(xcb-proto-version)" > $@
@@ -98,7 +98,7 @@ $(ibidir)/libxcb-$(libxcb-version): \
$(ibidir)/libxdmcp-$(libxdmcp-version) \
$(ibidir)/xcb-proto-$(xcb-proto-version) \
$(ibidir)/libpthread-stubs-$(libpthread-stubs-version)
- tarball=libxcb-$(libxcb-version).tar.xz
+ tarball=libxcb-$(libxcb-version).tar.lz
$(call import-source, $(libxcb-url), $(libxcb-checksum))
$(call gbuild, libxcb-$(libxcb-version),, \
$(XORG_CONFIG) --without-doxygen, \
@@ -107,7 +107,7 @@ $(ibidir)/libxcb-$(libxcb-version): \
$(ibidir)/libpthread-stubs-$(libpthread-stubs-version): \
$(ibidir)/automake-$(automake-version)
- tarball=libpthread-stubs-$(libpthread-stubs-version).tar.gz
+ tarball=libpthread-stubs-$(libpthread-stubs-version).tar.lz
$(call import-source, $(libpthread-stubs-url), $(libpthread-stubs-checksum))
$(call gbuild, libpthread-stubs-$(libpthread-stubs-version),, V=1)
echo "libpthread-stubs (Xorg) $(libpthread-stubs-version)" > $@
@@ -116,11 +116,12 @@ $(ibidir)/libpthread-stubs-$(libpthread-stubs-version): \
$(ibidir)/fontconfig-$(fontconfig-version): \
$(ibidir)/gperf-$(gperf-version) \
$(ibidir)/expat-$(expat-version) \
+ $(ibidir)/python-$(python-version) \
$(ibidir)/libxml2-$(libxml2-version) \
$(ibidir)/freetype-$(freetype-version) \
$(ibidir)/util-linux-$(util-linux-version)
# Import the source.
- tarball=fontconfig-$(fontconfig-version).tar.bz2
+ tarball=fontconfig-$(fontconfig-version).tar.lz
$(call import-source, $(fontconfig-url), $(fontconfig-checksum))
# Add the extra environment variables for using 'libuuid' of
@@ -139,27 +140,27 @@ $(ibidir)/fontconfig-$(fontconfig-version): \
$(ibidir)/xtrans-$(xtrans-version): \
$(ibidir)/libxcb-$(libxcb-version) \
$(ibidir)/fontconfig-$(fontconfig-version)
- tarball=xtrans-$(xtrans-version).tar.bz2
+ tarball=xtrans-$(xtrans-version).tar.lz
$(call import-source, $(xtrans-url), $(xtrans-checksum))
$(call gbuild, xtrans-$(xtrans-version),,$(XORG_CONFIG), V=1)
echo "xtrans (Xorg) $(xtrans-version)" > $@
$(ibidir)/libx11-$(libx11-version): $(ibidir)/xtrans-$(xtrans-version)
- tarball=libX11-$(libx11-version).tar.bz2
+ tarball=libX11-$(libx11-version).tar.lz
$(call import-source, $(libx11-url), $(libx11-checksum))
$(call gbuild, libX11-$(libx11-version),,$(XORG_CONFIG), \
-j$(numthreads) V=1)
echo "X11 library $(libx11-version)" > $@
$(ibidir)/libxext-$(libxext-version): $(ibidir)/libx11-$(libx11-version)
- tarball=libXext-$(libxext-version).tar.bz2
+ tarball=libXext-$(libxext-version).tar.lz
$(call import-source, $(libxext-url), $(libxext-checksum))
$(call gbuild, libXext-$(libxext-version),,$(XORG_CONFIG), \
-j$(numthreads) V=1)
echo "libXext $(libxext-version)" > $@
$(ibidir)/libice-$(libice-version): $(ibidir)/libxext-$(libxext-version)
- tarball=libICE-$(libice-version).tar.bz2
+ tarball=libICE-$(libice-version).tar.lz
$(call import-source, $(libice-url), $(libice-checksum))
$(call gbuild, libICE-$(libice-version),, \
$(XORG_CONFIG) ICE_LIBS=-lpthread, \
@@ -167,14 +168,14 @@ $(ibidir)/libice-$(libice-version): $(ibidir)/libxext-$(libxext-version)
echo "libICE $(libice-version)" > $@
$(ibidir)/libsm-$(libsm-version): $(ibidir)/libice-$(libice-version)
- tarball=libSM-$(libsm-version).tar.bz2
+ tarball=libSM-$(libsm-version).tar.lz
$(call import-source, $(libsm-url), $(libsm-checksum))
$(call gbuild, libSM-$(libsm-version),, \
$(XORG_CONFIG), -j$(numthreads) V=1)
echo "libSM $(libsm-version)" > $@
$(ibidir)/libxt-$(libxt-version): $(ibidir)/libsm-$(libsm-version)
- tarball=libXt-$(libxt-version).tar.bz2
+ tarball=libXt-$(libxt-version).tar.lz
$(call import-source, $(libxt-url), $(libxt-checksum))
$(call gbuild, libXt-$(libxt-version),, \
$(XORG_CONFIG), -j$(numthreads) V=1)
diff --git a/reproduce/software/patches/README.md b/reproduce/software/patches/README.md
new file mode 100644
index 0000000..804d7ec
--- /dev/null
+++ b/reproduce/software/patches/README.md
@@ -0,0 +1,6 @@
+Patches to apply to software source
+===================================
+
+This directory is for keeping patches that may be necessary for some
+versions of some software. So it may be empty in some instances (when no
+software in that commit needs a patch).
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
deleted file mode 100644
index 94dcab5..0000000
--- a/reproduce/software/patches/valgrind-3.15.0-mpi-fix1.patch
+++ /dev/null
@@ -1,37 +0,0 @@
----
- mpi/libmpiwrap.c | 12 +++++++++++-
- 1 file changed, 11 insertions(+), 1 deletion(-)
- Patch by Samuel Thibault:
- https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=10
- and hacked further by Boud Roukema 2020-05-10.
---- a/mpi/libmpiwrap.c
-+++ b/mpi/libmpiwrap.c
-@@ -278,8 +278,12 @@ static void showTy ( FILE* f, MPI_Dataty
- else if (ty == MPI_LONG_INT) fprintf(f,"LONG_INT");
- else if (ty == MPI_SHORT_INT) fprintf(f,"SHORT_INT");
- else if (ty == MPI_2INT) fprintf(f,"2INT");
-+# if defined(MPI_UB_ENABLED_IN_MPI1)
- else if (ty == MPI_UB) fprintf(f,"UB");
-+# endif
-+# if defined(MPI_LB_ENABLED_IN_MPI1)
- else if (ty == MPI_LB) fprintf(f,"LB");
-+# endif
- # if defined(MPI_WCHAR)
- else if (ty == MPI_WCHAR) fprintf(f,"WCHAR");
- # endif
-@@ -733,8 +737,14 @@ void walk_type ( void(*f)(void*,long), c
- f(base + offsetof(Ty,loc), sizeof(int));
- return;
- }
-- if (ty == MPI_LB || ty == MPI_UB)
-+#if defined(MPI_LB_ENABLED_IN_MPI1)
-+ if (ty == MPI_LB)
-+ return; /* have zero size, so nothing needs to be done */
-+#endif
-+#if defined(MPI_UB_ENABLED_IN_MPI1)
-+ if (ty == MPI_UB)
- return; /* have zero size, so nothing needs to be done */
-+#endif
- goto unhandled;
- /*NOTREACHED*/
- }
diff --git a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch b/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
deleted file mode 100644
index 12b50a2..0000000
--- a/reproduce/software/patches/valgrind-3.15.0-mpi-fix2.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Index: valgrind-3.15.0/mpi/Makefile.am
-===================================================================
- Patch by Samuel Thibault:
- https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946329;msg=22
---- valgrind-3.15.0.orig/mpi/Makefile.am
-+++ valgrind-3.15.0/mpi/Makefile.am
-@@ -42,14 +42,14 @@ libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@
- libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
- libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_CFLAGS = \
- $(CFLAGS_MPI) $(MPI_FLAG_M3264_PRI) -Wno-deprecated-declarations
--libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDFLAGS = $(LDFLAGS_MPI)
-+libmpiwrap_@VGCONF_ARCH_PRI@_@VGCONF_OS@_so_LDADD = $(LDFLAGS_MPI)
- endif
- if BUILD_MPIWRAP_SEC
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_SOURCES = libmpiwrap.c
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CPPFLAGS = -I$(top_srcdir)/include
- libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_CFLAGS = \
- $(CFLAGS_MPI) $(MPI_FLAG_M3264_SEC) -Wno-deprecated-declarations
--libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDFLAGS = $(LDFLAGS_MPI)
-+libmpiwrap_@VGCONF_ARCH_SEC@_@VGCONF_OS@_so_LDADD = $(LDFLAGS_MPI)
- endif
-
- #----------------------------------------------------------------------------
diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh
index 23845d6..6bb871b 100755
--- a/reproduce/software/shell/bashrc.sh
+++ b/reproduce/software/shell/bashrc.sh
@@ -3,10 +3,10 @@
# To have better control over the environment of each analysis step (Make
# recipe), besides having environment variables (directly included from
# Make), it may also be useful to have a Bash startup file (this file). All
-# of the Makefiles set this file as the `BASH_ENV' environment variable, so
+# of the Makefiles set this file as the 'BASH_ENV' environment variable, so
# it is loaded into all the Make recipes within the project.
#
-# The special `PROJECT_STATUS' environment variable is defined in every
+# The special 'PROJECT_STATUS' environment variable is defined in every
# top-level Makefile of the project. It defines the the state of the Make
# that is calling this script. It can have three values:
#
@@ -29,7 +29,7 @@
# versions.
#
#
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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 0f7278f..07381e6 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -2,8 +2,9 @@
#
# Necessary preparations/configurations for the reproducible project.
#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
#
# 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
@@ -112,7 +113,7 @@ absolute_dir ()
# Check file permission handling (POSIX-compatibility)
# ----------------------------------------------------
#
-# Check if a `given' directory handles permissions as expected.
+# Check if a 'given' directory handles permissions as expected.
#
# This is to prevent a known bug in the NTFS filesystem that prevents
# proper installation of Perl, and probably some other packages. This
@@ -120,15 +121,15 @@ absolute_dir ()
# file, and examines whether the given directory handles the file
# permissions as expected.
#
-# Returns `0' if everything is fine, and `255' otherwise. Choosing `0' is
-# to mimic the `$ echo $?' behavior, while choosing `255' is to prevent
+# Returns '0' if everything is fine, and '255' otherwise. Choosing '0' is
+# to mimic the '$ echo $?' behavior, while choosing '255' is to prevent
# misunderstanding 0 and 1 as true and false.
#
# ===== CAUTION! ===== #
#
-# Since there is a `set -e' before running this function, the whole script
-# stops and exits IF the `check_permission' (or any other function) returns
-# anything OTHER than `0'! So, only use this function as a test. Here's a
+# Since there is a 'set -e' before running this function, the whole script
+# stops and exits IF the 'check_permission' (or any other function) returns
+# anything OTHER than '0'! So, only use this function as a test. Here's a
# minimal example:
#
# if $(check_permission $some_directory) ; then
@@ -136,7 +137,7 @@ absolute_dir ()
# fi ;
check_permission ()
{
- # Make a `junk' file, activate its executable flag and record its
+ # Make a 'junk' file, activate its executable flag and record its
# permissions generally.
local junkfile="$1"/check_permission_tmp_file
rm -f "$junkfile"
@@ -309,7 +310,9 @@ fi
# system. Here, it is checked that this is the case, and if not, warn the user
# about not having Xcode already installed.
if [ x$on_mac_os = xyes ]; then
- xcode=$(which xcodebuild)
+
+ # 'which' isn't in POSIX, so we are using 'command -v' instead.
+ xcode=$(command -v xcodebuild)
if [ x$xcode != x ]; then
xcode_version=$(xcodebuild -version | grep Xcode)
echo " "
@@ -475,8 +478,8 @@ fi
# See if we need the dynamic-linker (-ldl)
# ----------------------------------------
#
-# Some programs (like Wget) need dynamic loading (using `libdl'). On
-# GNU/Linux systems, we'll need the `-ldl' flag to link such programs. But
+# Some programs (like Wget) need dynamic loading (using 'libdl'). On
+# GNU/Linux systems, we'll need the '-ldl' flag to link such programs. But
# Mac OS doesn't need any explicit linking. So we'll check here to see if
# it is present (thus necessary) or not.
cat > $testsource <<EOF
@@ -508,7 +511,7 @@ fi
# programs will go and find their necessary libraries on the host system.
#
# Another good advantage of shared libraries is that we can actually use
-# the shared library tool of the system (`ldd' with GNU C Library) and see
+# the shared library tool of the system ('ldd' with GNU C Library) and see
# exactly where each linked library comes from. But in static building,
# unless you follow the build closely, its not easy to see if the source of
# the library came from the system or our build.
@@ -545,7 +548,7 @@ fi
#
# On some systems (in particular Debian-based OSs), the static C library
# and necessary headers in a non-standard place, and we can't build GCC. So
-# we need to find them first. The `sys/cdefs.h' header is also in a
+# we need to find them first. The 'sys/cdefs.h' header is also in a
# similarly different location.
sys_cpath=""
sys_library_path=""
@@ -576,7 +579,7 @@ fi
# See if a link-able static C library exists
# ------------------------------------------
#
-# A static C library and the `sys/cdefs.h' header are necessary for
+# A static C library and the 'sys/cdefs.h' header are necessary for
# building GCC.
if [ x"$host_cc" = x0 ]; then
echo; echo; echo "Checking if static C library is available...";
@@ -752,9 +755,9 @@ EOF
# What to do with possibly existing configuration file
# ----------------------------------------------------
#
-# `LOCAL.conf' is the top-most local configuration for the project. If it
+# 'LOCAL.conf' is the top-most local configuration for the project. If it
# already exists when this script is run, we'll make a copy of it as backup
-# (for example the user might have ran `./project configure' by mistake).
+# (for example the user might have ran './project configure' by mistake).
printnotice=yes
rewritepconfig=yes
if [ -f $pconf ]; then
@@ -807,16 +810,18 @@ fi
# need to check the host's available tool for downloading at this step.
if [ $rewritepconfig = yes ]; then
if type wget > /dev/null 2>/dev/null; then
- name=$(which wget)
+
+ # 'which' isn't in POSIX, so we are using 'command -v' instead.
+ name=$(command -v wget)
# By default Wget keeps the remote file's timestamp, so we'll have
# to disable it manually.
downloader="$name --no-use-server-timestamps -O";
elif type curl > /dev/null 2>/dev/null; then
- name=$(which curl)
+ name=$(command -v curl)
# - cURL doesn't keep the remote file's timestamp by default.
- # - With the `-L' option, we tell cURL to follow redirects.
+ # - With the '-L' option, we tell cURL to follow redirects.
downloader="$name -L -o"
else
cat <<EOF
@@ -913,7 +918,7 @@ EOF
# If it was newly created, it will be empty, so delete it.
if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi
- # Inform the user that this is not acceptable and reset `bdir'.
+ # Inform the user that this is not acceptable and reset 'bdir'.
bdir=
echo " ** The build-directory cannot be under the source-directory."
fi
@@ -960,7 +965,7 @@ EOF
fi
# If the build directory was good, the loop will stop, if not,
- # reset `build_dir' to blank, so it continues asking for another
+ # reset 'build_dir' to blank, so it continues asking for another
# directory and let the user know that they must select a new
# directory.
if [ x"$bdir" = x ]; then
@@ -1118,7 +1123,7 @@ else
if [ x"$downloader" = x ]; then novalue="$novalue"DOWNLOADER; fi
if [ x"$novalue" != x ]; then verr=1; err=1; fi
- # Make sure `bdir' is an absolute path and it exists.
+ # Make sure 'bdir' is an absolute path and it exists.
berr=0
ierr=0
bdir="$(absolute_dir "$inbdir")"
@@ -1202,6 +1207,10 @@ if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi
ipydir="$verdir"/python
if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi
+# R module versions and citation.
+ircrandir="$verdir"/r-cran
+if ! [ -d "$ircrandir" ]; then mkdir "$ircrandir"; fi
+
# Used software BibTeX entries.
ictdir="$verdir"/cite
if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
@@ -1210,6 +1219,15 @@ if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
itidir="$verdir"/tex
if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi
+# Some software install their libraries in '$(idir)/lib64'. But all other
+# libraries are in '$(idir)/lib'. Since Maneage's build is only for a
+# single architecture, we can set the '$(idir)/lib64' as a symbolic link to
+# '$(idir)/lib' so all the libraries are always available in the same
+# place.
+instlibdir="$instdir"/lib
+if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi
+ln -fs "$instlibdir" "$instdir"/lib64
+
@@ -1312,38 +1330,69 @@ if [ x"$shmdir" != x ]; then
# Set the Maneage-specific directory within the shared
# memory. We'll use the names of the two parent directories to the
- # current/running directory, separated by a `-' instead of
- # `/'. We'll then appended that with the user's name (in case
+ # current/running directory, separated by a '-' instead of
+ # '/'. We'll then appended that with the user's name (in case
# multiple users may be working on similar project names).
#
- # Maybe later, we can use something like `mktemp' to add random
+ # Maybe later, we can use something like 'mktemp' to add random
# characters to this name and make it unique to every run (even for
# a single user).
dirname=$(pwd | sed -e's/\// /g' \
| awk '{l=NF-1; printf("%s-%s", $l, $NF)}')
tbshmdir="$shmdir"/"$dirname"-$(whoami)
- if ! [ -d "$tbshmdir" ]; then mkdir "$tbshmdir"; fi
+
+ # Try to make the directory if it does not yet exist. A failed
+ # directory creation will be tested for a few lines later, when
+ # testing for the existence and executability of a test file.
+ if ! [ -d "$tbshmdir" ]; then (mkdir "$tbshmdir" || true); fi
# Some systems may protect '/dev/shm' against the right to execute
# programs by ordinary users. We thus need to check that the device
# allows execution within this directory by this user.
shmexecfile="$tbshmdir"/shm-execution-check.sh
rm -f $shmexecfile # We also don't want any existing flags.
- cat > "$shmexecfile" <<EOF
+
+ # Create the file to be executed, but do not fail fatally if it
+ # cannot be created. We will check a few lines later if the file
+ # really exists.
+ (cat > "$shmexecfile" <<EOF || true)
#!/bin/sh
-printf "This file successfully executed.\n"
+echo "This file successfully executed."
EOF
- # Make the file executable and see if it runs. If not, set
- # 'tbshmdir' to an empty string so it is not used in later steps.
- # In any case, delete the temporary file afterwards.
- chmod u+x "$shmexecfile"
- if ! "$shmexecfile" &> /dev/null; then tbshmdir=""; fi
- rm "$shmexecfile"
+
+ # If the file was successfully created, then make the file
+ # executable and see if it runs. If not, set 'tbshmdir' to an empty
+ # string so it is not used in later steps. In any case, delete the
+ # temporary file afterwards.
+ #
+ # We aren't adding '&> /dev/null' after the execution command
+ # because it can produce false failures randomly on some systems.
+ if [ -e "$shmexecfile" ]; then
+
+ # Add the executable flag.
+ chmod +x "$shmexecfile"
+
+ # The following line tries to execute the file.
+ if "$shmexecfile"; then
+ # Successful execution. The colon is a "no-op" (no
+ # operation) shell command.
+ :
+ else
+ tbshmdir=""
+ fi
+ rm "$shmexecfile"
+ else
+ tbshmdir=""
+ fi
fi
else
tbshmdir=""
fi
+
+
+
+
# If a shared memory directory was created, set the software building
# directory to be a symbolic link to it. Otherwise, just build the
# temporary build directory under the project's build directory.
@@ -1426,7 +1475,7 @@ fi
# See if the linker accepts -Wl,-rpath-link
# -----------------------------------------
#
-# `-rpath-link' is used to write the information of the linked shared
+# '-rpath-link' is used to write the information of the linked shared
# library into the shared object (library or program). But some versions of
# LLVM's linker don't accept it an can cause problems.
#
@@ -1459,13 +1508,13 @@ rm -rf $compilertestdir
-# Paths needed by the host compiler (only for `basic.mk')
+# Paths needed by the host compiler (only for 'basic.mk')
# -------------------------------------------------------
#
# At the end of the basic build, we need to build GCC. But GCC will build
# in multiple phases, making its own simple compiler in order to build
# itself completely. The intermediate/simple compiler doesn't recognize
-# some system specific locations like `/usr/lib/ARCHITECTURE' that some
+# some system specific locations like '/usr/lib/ARCHITECTURE' that some
# operating systems use. We thus need to tell the intermediate compiler
# where its necessary libraries and headers are.
if [ x"$sys_library_path" != x ]; then
@@ -1502,7 +1551,7 @@ 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 option '--debug' is used.
zenodourl=""
user_backup_urls=""
zenodocheck=.build/software/zenodo-check.html
@@ -1535,6 +1584,7 @@ user_backup_urls="$user_backup_urls $zenodourl"
# (compression program), GNU Make (that 'basic.mk' is written in), Dash
# (minimal Bash-like shell) and Flock (to lock files and enable serial
# download).
+export on_mac_os
./reproduce/software/shell/pre-make-build.sh \
"$bdir" "$ddir" "$downloader" "$user_backup_urls"
@@ -1672,7 +1722,7 @@ fi
# software.
prepare_name_version ()
{
- # First see if the (possible) `*' in the input arguments corresponds to
+ # First see if the (possible) '*' in the input arguments corresponds to
# anything. Note that some of the given directories may be empty (no
# software installed).
hasfiles=0
@@ -1773,9 +1823,9 @@ hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')"
# ---------------------------------
#
# By the time the script reaches here the temporary software build
-# directory should be empty, so just delete it. Note `tmpblddir' may be a
+# directory should be empty, so just delete it. Note 'tmpblddir' may be a
# symbolic link to shared memory. So, to work in any scenario, first delete
-# the contents of the directory (if it has any), then delete `tmpblddir'.
+# the contents of the directory (if it has any), then delete 'tmpblddir'.
.local/bin/rm -rf $tmpblddir/* $tmpblddir
diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout
index 7a90108..d49504d 100755
--- a/reproduce/software/shell/git-post-checkout
+++ b/reproduce/software/shell/git-post-checkout
@@ -1,14 +1,14 @@
#!@BINDIR@/bash
#
# The example hook script to store the metadata information of version
-# controlled files (with each commit) using the `metastore' program.
+# controlled files (with each commit) using the 'metastore' program.
#
# Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
-# This script is taken from the `examples/hooks/pre-commit' file of the
-# `metastore' package (installed within the project, with an MIT license
-# for copyright). We have just changed the name of the `MSFILE' and also
+# This script is taken from the 'examples/hooks/pre-commit' file of the
+# 'metastore' package (installed within the project, with an MIT license
+# for copyright). We have just changed the name of the 'MSFILE' and also
# set special characters for the installation location of meta-store so our
# own installation is found by Git.
#
diff --git a/reproduce/software/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit
index 85d3474..10ad710 100755
--- a/reproduce/software/shell/git-pre-commit
+++ b/reproduce/software/shell/git-pre-commit
@@ -1,10 +1,10 @@
#!@BINDIR@/bash
#
# The example hook script to store the metadata information of version
-# controlled files (with each commit) using the `metastore' program.
+# controlled files (with each commit) using the 'metastore' program.
#
# Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# WARNING:
#
@@ -17,9 +17,9 @@
# git reset HEAD -- .metadata
# git checkout HEAD -- .metadata
#
-# This script is taken from the `examples/hooks/pre-commit' file of the
-# `metastore' package (installed within the project, with an MIT license
-# for copyright). Here, the name of the `MSFILE' and also set special
+# This script is taken from the 'examples/hooks/pre-commit' file of the
+# 'metastore' package (installed within the project, with an MIT license
+# for copyright). Here, the name of the 'MSFILE' and also set special
# characters for the installation location of meta-store so our own
# installation is found by Git.
#
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index a033963..e7de93d 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) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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
@@ -185,6 +185,19 @@ build_program() {
# All others accept the configure script.
./configure --prefix="$instdir" $configoptions
+ # In Flock 0.4.0 there is a crash that can be fixed by simply
+ # replacing '%1u' with '%ld' on GNU/Linux and '%d' on macOS. This
+ # has been reported to flock maintainers:
+ # https://github.com/discoteq/flock/issues/33
+ if [ x$progname = xflock ]; then
+ case $on_mac_os in
+ yes) sed -e's/\%1u/\%d/' src/flock.c > src/flock-new.c;;
+ no) sed -e's/\%1u/\%ld/' src/flock.c > src/flock-new.c;;
+ *) echo "pre-make-build.sh: '$on_mac_os' unrecognized value for on_mac_os";;
+ esac
+ mv src/flock-new.c src/flock.c
+ fi
+
# To build GNU Make, we don't want to assume the existance of a
# Make program, so we use its 'build.sh' script and its own built
# 'make' program to install itself.
@@ -192,7 +205,7 @@ build_program() {
/bin/sh build.sh
./make install
else
- make
+ make V=1
make install
fi
fi
@@ -235,13 +248,20 @@ build_program
# '--disable-dependency-tracking' configure-time option is necessary so
# Make doesn't check for an existing 'make' implementation (recall that we
# aren't assuming any 'make' on the host).
+#
+# If GNU Guile is already present on the host system, Make will try to link
+# with it, and this will cause dependency problems later. So we have
+# distabled Guile. If a project needs the Guile extensions of Make, we need
+# to add a build rule for Guile in Maneage, with a special Guile-enabled
+# 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"
url=$(awk '/^'$progname'-url/{print $3}' $urlfile)
version=$(awk '/^'$progname'-version/{print $3}' $versionsfile)
tarball=$progname-$version.tar.lz
download_tarball
-build_program --disable-dependency-tracking
+build_program "--disable-dependency-tracking --without-guile"
@@ -274,11 +294,11 @@ fi
# -----
#
# Flock (or file-lock) is necessary to serialize operations when
-# necessary. GNU/Linux machines have it as part of their `util-linux'
+# necessary. GNU/Linux machines have it as part of their 'util-linux'
# programs. But to be consistent in non-GNU/Linux systems, we will be using
# our own build.
#
-# The reason that `flock' is built here is that generally the building of
+# The reason that 'flock' is built here is that generally the building of
# software is done in parallel, but we need it to serialize the download
# process of the software tarballs to avoid network complications when too
# many simultaneous download commands are called.
diff --git a/reproduce/software/shell/run-parts.in b/reproduce/software/shell/run-parts.in
index 7e649b1..a6db9e0 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) 2021 Authors mentioned above.
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2022 Authors mentioned above.
+# Copyright (C) 2020-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# 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