diff options
| author | Mohammad Akhlaghi <mohammad@akhlaghi.org> | 2022-05-09 13:32:47 +0200 |
|---|---|---|
| committer | Mohammad Akhlaghi <mohammad@akhlaghi.org> | 2022-05-09 23:52:29 +0200 |
| commit | 9fdeebaacd06d57c479cd69e9937c4bfe5d0a286 (patch) | |
| tree | 012e6194ad6e25a81a9c99b4d0bd0852bc9a12af /reproduce/software/make | |
| parent | 480184b3da399fab11b50e67f01d2efa6bea0e3e (diff) | |
| parent | f51b5e2e500dd6450a5a3425e85df78245fc5c5c (diff) | |
Imported recent updates in Maneage, conflicts fixed
Until now, Maneage had undergone some updates.
With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.
In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).
Diffstat (limited to 'reproduce/software/make')
| -rw-r--r-- | reproduce/software/make/README.md | 2 | ||||
| -rw-r--r-- | reproduce/software/make/atlas-multiple.mk | 4 | ||||
| -rw-r--r-- | reproduce/software/make/atlas-single.mk | 4 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 788 | ||||
| -rw-r--r-- | reproduce/software/make/build-rules.mk | 73 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 881 | ||||
| -rw-r--r-- | reproduce/software/make/python.mk | 313 | ||||
| -rw-r--r-- | reproduce/software/make/r-cran.mk | 487 | ||||
| -rw-r--r-- | reproduce/software/make/xorg.mk | 33 |
9 files changed, 1607 insertions, 978 deletions
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 fb378b8..5967a1d 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 @@ -59,7 +60,7 @@ ibidir = $(BDIR)/software/installed/version-info/proglib # Ultimate Makefile target. GNU Nano (a simple and very light-weight text # editor) is installed by default, it is recommended to have it in the # 'basic.mk', so Maneaged projects can be edited on any system (even when -# there is no command-line text editor is available). +# there is no command-line text editor available). targets-proglib = low-level-links \ gcc-$(gcc-version) \ nano-$(nano-version) @@ -90,17 +91,20 @@ export CPPFLAGS := -I$(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 "" > $@ @@ -395,75 +398,76 @@ $(ibidir)/patchelf-$(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.$$so ]; then + unalias ls || true # avoid decorated 'ls' commands with extra characters sov=$$(ls -l $(ildir)/libncursesw* \ | awk '/^-/{print $$NF}' \ - | sed -e's|'$(ildir)/libncursesw.'||') + | sed -e "s;$(ildir)/libncursesw\.;;") cd "$(ildir)" for lib in ncurses ncurses++ form panel menu; do @@ -488,7 +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, \ @@ -496,12 +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. # @@ -509,11 +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); \ @@ -529,18 +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; @@ -553,22 +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)" > $@ @@ -584,9 +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) @@ -595,7 +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=$$(echo $(perl-version) \ | sed -e's/\./ /g' \ @@ -605,7 +607,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) | awk '{printf("%d.%d", $$1, $$2)}') cd $(ddir) rm -rf perl-$(perl-version) - tar xf $(tdir)/$$tarball + tar -xf $(tdir)/$$tarball cd perl-$(perl-version) ./Configure -des \ -Dusethreads \ @@ -615,7 +617,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version) -Dprivlib=$(idir)/share/perl$$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 \ @@ -641,17 +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 @@ -664,32 +666,33 @@ $(ibidir)/coreutils-$(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 instprogs=$$(ls junkinst/$(ibdir)) for f in $$instprogs; do $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/$$f @@ -697,12 +700,34 @@ $(ibidir)/coreutils-$(coreutils-version): \ echo "PatchELF applied to all programs." fi - # Come back up to the unpacking directory, delete the source - # directory and write the final target. +# Come back up to the unpacking directory, delete the source +# directory and write the final target. cd .. rm -rf coreutils-$(coreutils-version) echo "GNU Coreutils $(coreutils-version)" > $@ +# Podlators +# +# POD is short for "Plain Old Documentation", that is the format used in +# Perl's documentation. Podlators provies two executables pod2man and +# pod2text convert this into the roff format (used in man pages) or pod2 It +# is used by some software like OpenSSL to create their man pages. +$(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version) + tarball=podlators-$(podlators-version).tar.lz + $(call import-source, $(podlators-url), $(podlators-checksum)) + cd $(ddir) + rm -rf podlators-$(podlators-version) + tar -xf $(tdir)/$$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 @@ -710,26 +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" @@ -743,28 +768,19 @@ $(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \ --with-zlib-include=$(idir)/include, \ -j$(numthreads), , ./config ) - # Manually insert RPATH inside the OpenSSL library. +# 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)/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 # ----------- @@ -773,13 +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), , \ @@ -809,8 +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. @@ -823,12 +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), , \ @@ -861,13 +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) @@ -875,7 +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)" > $@ @@ -885,19 +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 @@ -908,31 +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) @@ -946,8 +962,8 @@ $(ibidir)/gettext-$(gettext-version): \ $(ibidir)/libunistring-$(libunistring-version) tarball=gettext-$(gettext-version).tar.lz $(call import-source, $(gettext-url), $(gettext-checksum)) - $(call gbuild, gettext-$(gettext-version), static,, \ - V=1 -j$(numthreads)) + $(call gbuild, gettext-$(gettext-version), static, \ + --without-emacs, V=1 -j$(numthreads)) echo "GNU gettext $(gettext-version)" > $@ $(ibidir)/git-$(git-version): \ @@ -955,7 +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 @@ -979,7 +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 @@ -988,9 +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)) @@ -998,162 +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 @@ -1163,7 +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)" > $@ @@ -1171,7 +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 @@ -1181,14 +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 "" > $@ @@ -1200,7 +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 "" > $@ @@ -1223,33 +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) @@ -1261,20 +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) @@ -1282,11 +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. @@ -1295,7 +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. @@ -1322,45 +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) @@ -1373,52 +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 $$odir/gcc-$(gcc-version) $(ddir)/gcc-$(gcc-version) fi cd gcc-$(gcc-version) + +# Set the build directory for the processing. mkdir build cd build - # Configure, build and install GCC, if any of three steps fails, - # the error message will be printed. +# Configure, build and install GCC, if any of three steps fails, +# the error message will be printed. if ! ../configure SHELL=$(ibdir)/bash \ --prefix=$(idir) \ --with-mpc=$(idir) \ @@ -1437,26 +1341,25 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) --enable-languages=c,c++,fortran,objc,obj-c++ \ --disable-nls \ --disable-libada \ - --disable-multilib \ - --disable-multiarch; then error_message; fi + --disable-multilib; then error_message; fi if ! make SHELL=$(ibdir)/bash -j$(numthreads); then error_message; fi if ! make SHELL=$(ibdir)/bash install; then error_message; fi - # We need to manually fix the RPATH inside GCC's libraries, the - # programs built by GCC already have RPATH. +# We need to manually fix the RPATH inside GCC's libraries, the +# programs built by GCC already have RPATH. tempname=$$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) $$tempname @@ -1470,8 +1373,8 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) done fi - # Come back up to the un-packing directory and delete the GCC - # source directory. +# Come back up to the un-packing directory and delete the GCC +# source directory. cd ../.. rm -rf gcc-$(gcc-version) cd $$current_dir @@ -1480,11 +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 @@ -1503,18 +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) |