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-rw-r--r--reproduce/software/make/basic.mk229
1 files changed, 179 insertions, 50 deletions
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index d90d945..99e81d2 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -21,9 +21,9 @@
#
# ------------------------------------------------------------------------
#
-# 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>
+# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022-2023 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
@@ -55,6 +55,7 @@ ddir = $(BDIR)/software/build-tmp
idir = $(BDIR)/software/installed
ibdir = $(BDIR)/software/installed/bin
ildir = $(BDIR)/software/installed/lib
+iidir = $(BDIR)/software/installed/include
ibidir = $(BDIR)/software/installed/version-info/proglib
# Ultimate Makefile target. GNU Nano (a simple and very light-weight text
@@ -87,13 +88,18 @@ export SHELL := $(ibdir)/dash
export PATH := $(ibdir):$(PATH)
export PKG_CONFIG_PATH := $(ildir)/pkgconfig
export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
-export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) \
- -Wno-nullability-completeness
export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
# Disable built-in rules (which are not needed here!)
.SUFFIXES:
+# See description of '-Wno-nullability-completeness' in
+# 'reproduce/software/shell/configure.sh'.
+ifeq ($(on_mac_os),yes)
+ noccwarnings=-Wno-nullability-completeness
+endif
+export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings)
+
# 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,
@@ -202,6 +208,7 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
$(call makelink,xcrun)
$(call makelink,sysctl)
$(call makelink,sw_vers)
+ $(call makelink,codesign)
$(call makelink,dsymutil)
$(call makelink,install_name_tool)
@@ -222,6 +229,10 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
fi
done
+# Useful tools: 'ldd' (list libraries linked by binary on GNU
+# systems)
+ $(call makelink,ldd)
+
# We want this to be empty (so it doesn't interefere with the other
# files in 'ibidir'.
touch $@
@@ -252,10 +263,46 @@ $(ibidir)/gzip-$(gzip-version): | $(ibdir) $(ildir) $(lockdir)
$(call gbuild, gzip-$(gzip-version), static, , V=1)
echo "GNU Gzip $(gzip-version)" > $@
+# 2022-07-14 B Roukema
+#
+# xz-5.2.5 fails on (at least) CentOS 7 (Redhat) systems while trying
+# to compile 'cmake' in Maneage - this is Maneage bug 62700 [1].
+#
+# The fix appears to be just a few lines, although it's not clear
+# how robust or long-term it is. Since we don't yet have 'patch' in
+# 'basic.mk', this file has to be copied into place rather than patched.
+
+# xz-5.2.5_src_liblzma_liblzma.map is a patched
+# version of xz-5.2.5/src/liblzma/liblzma.map based on discussion at
+# [1] + [2] + the patch file [3].
+#
+# [1] https://savannah.nongnu.org/bugs/index.php?62700
+# [2] https://github.com/easybuilders/easybuild-easyconfigs/issues/14991
+# [3] https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/bcebb3320ffb63f9804ca8d4d64d1822ec7c9792/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch
$(ibidir)/xz-$(xz-version): $(ibidir)/gzip-$(gzip-version)
+
+# Prepare the tarball.
tarball=xz-$(xz-version).tar.lz
$(call import-source, $(xz-url), $(xz-checksum))
- $(call gbuild, xz-$(xz-version), static)
+
+# Until the bug mentioned above is fixed, we'll can't use the generic
+# rule.
+# $(call gbuild, xz-$(xz-version), static)
+
+# Configure and build with patched file.
+ srcdir=$$(pwd)
+ unpackdir=xz-$(xz-version)
+ patchedfile=xz-5.2.5_src_liblzma_liblzma.map
+ cd $(ddir)
+ rm -rf $$unpackdir
+ tar -x -f $(tdir)/$$tarball
+ cd $$unpackdir
+ cp -pv $$srcdir/reproduce/software/patches/$$patchedfile \
+ src/liblzma/liblzma.map # copy the fixed file into place
+ ./configure --prefix=$(idir)
+ make install
+ cd ..
+ rm -rf $$unpackdir
echo "XZ Utils $(xz-version)" > $@
$(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
@@ -303,26 +350,6 @@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version)
ln -fs libbz2.so.$(bzip2-version) libbz2.so
echo "Bzip2 $(bzip2-version)" > $@
-$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
- tarball=unzip-$(unzip-version).tar.lz
- $(call import-source, $(unzip-url), $(unzip-checksum))
- $(call gbuild, unzip-$(unzip-version), static,, \
- -f unix/Makefile generic \
- CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
- -f unix/Makefile generic \
- BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
- echo "Unzip $(unzip-version)" > $@
-
-$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
- tarball=zip-$(zip-version).tar.lz
- $(call import-source, $(zip-url), $(zip-checksum))
- $(call gbuild, zip-$(zip-version), static,, \
- -f unix/Makefile generic \
- CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
- -f unix/Makefile generic \
- BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
- echo "Zip $(zip-version)" > $@
-
# Some programs (like Wget and CMake) that use zlib need it to be dynamic
# so they use our custom build. So we won't force a static-only build.
#
@@ -341,11 +368,9 @@ $(ibidir)/zlib-$(zlib-version): $(ibidir)/gzip-$(gzip-version)
# software to be built).
$(ibidir)/tar-$(tar-version): \
$(ibidir)/xz-$(xz-version) \
- $(ibidir)/zip-$(zip-version) \
$(ibidir)/gzip-$(gzip-version) \
$(ibidir)/zlib-$(zlib-version) \
- $(ibidir)/bzip2-$(bzip2-version) \
- $(ibidir)/unzip-$(unzip-version)
+ $(ibidir)/bzip2-$(bzip2-version)
# Since all later programs depend on Tar, the configuration will hit
# a bottleneck here: only making Tar. So its more efficient to built
@@ -629,7 +654,7 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
-Dcccdlflags='-fPIC' \
$(perl-conflddlflags) \
-Dldflags="$$LDFLAGS"
- make -j$(numthreads)
+ make -j$(numthreads) V=1
make install
cd ..
rm -rf perl-$(perl-version)
@@ -807,6 +832,8 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
--without-librtmp \
--without-libidn2 \
--without-wolfssl \
+ --without-nghttp2 \
+ --without-nghttp3 \
--without-brotli \
--without-gnutls \
--without-cyassl \
@@ -814,6 +841,7 @@ $(ibidir)/curl-$(curl-version): $(ibidir)/coreutils-$(coreutils-version)
--without-axtls \
--disable-ldaps \
--disable-ldap \
+ --without-zstd \
--without-nss, V=1)
if [ -f $(ibdir)/patchelf ]; then
@@ -875,6 +903,12 @@ $(ibidir)/wget-$(wget-version): \
# process of the higher-level programs and libraries. Note that during the
# building of those higher-level programs (after this Makefile finishes),
# there is no access to the system's PATH.
+$(ibidir)/bison-$(bison-version): $(ibidir)/help2man-$(help2man-version)
+ tarball=bison-$(bison-version).tar.lz
+ $(call import-source, $(bison-url), $(bison-checksum))
+ $(call gbuild, bison-$(bison-version), static, ,V=1 -j$(numthreads))
+ echo "GNU Bison $(bison-version)" > $@
+
$(ibidir)/diffutils-$(diffutils-version): \
$(ibidir)/coreutils-$(coreutils-version)
tarball=diffutils-$(diffutils-version).tar.lz
@@ -928,6 +962,13 @@ $(ibidir)/gawk-$(gawk-version): \
# Build final target.
echo "GNU AWK $(gawk-version)" > $@
+$(ibidir)/help2man-$(help2man-version): \
+ $(ibidir)/coreutils-$(coreutils-version)
+ 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)" > $@
+
$(ibidir)/libiconv-$(libiconv-version): \
$(ibidir)/pkg-config-$(pkgconfig-version)
tarball=libiconv-$(libiconv-version).tar.lz
@@ -998,7 +1039,19 @@ $(ibidir)/gmp-$(gmp-version): \
$(ibidir)/less-$(less-version): $(ibidir)/ncurses-$(ncurses-version)
tarball=less-$(less-version).tar.lz
$(call import-source, $(less-url), $(less-checksum))
- $(call gbuild, less-$(less-version), static,,-j$(numthreads))
+
+# Without the '--with-regex=posix' option, the build will depend on
+# PCRE (perl compatible regular expressions) which are not available
+# on some systems/compilers and can cause a crash. Maneage was
+# successfully built with the POSIX regular expression (regex), and
+# 'less' is generally, an interactive software, not a batch-mode
+# software (it is just added in 'basic.mk' because Git uses it to
+# display things. Again, this is an interactive meta-operation in
+# maneage (operations you only do when you are developing Maneage
+# within Maneage interactively, and will not affect into the actual
+# reproducible analysis!)
+ $(call gbuild, less-$(less-version), static, \
+ --with-regex=posix,-j$(numthreads))
if [ -f $(ibdir)/patchelf ]; then
$(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/less;
fi
@@ -1032,7 +1085,7 @@ $(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version)
$(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version)
tarball=mpfr-$(mpfr-version).tar.lz
$(call import-source, $(mpfr-url), $(mpfr-checksum))
- $(call gbuild, mpfr-$(mpfr-version), static, , , make check)
+ $(call gbuild, mpfr-$(mpfr-version), static)
echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@
$(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version)
@@ -1070,6 +1123,17 @@ $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version)
$(ibidir)/texinfo-$(texinfo-version): \
$(ibidir)/perl-$(perl-version) \
$(ibidir)/gettext-$(gettext-version)
+
+# Setting for the XS sub-package. "This is because in theory, the XS
+# module could be built with a different compiler to the rest of the
+# project, needing completely different flags" (part of [1])
+#
+# [1] https://lists.gnu.org/archive/html/bug-texinfo/2022-08/msg00068.html
+ export PERL="$(ibdir)/perl"
+ export PERL_EXT_LDFLAGS="-L$(ildir)"
+ export PERL_EXT_CPPFLAGS="-I$(iidir)"
+
+# Basic build commands.
tarball=texinfo-$(texinfo-version).tar.lz
$(call import-source, $(texinfo-url), $(texinfo-checksum))
$(call gbuild, texinfo-$(texinfo-version), static)
@@ -1136,6 +1200,7 @@ $(ibidir)/binutils-$(binutils-version): \
$(ibidir)/gawk-$(gawk-version) \
$(ibidir)/grep-$(grep-version) \
$(ibidir)/wget-$(wget-version) \
+ $(ibidir)/bison-$(bison-version) \
$(ibidir)/which-$(which-version) \
$(ibidir)/libtool-$(libtool-version) \
$(ibidir)/texinfo-$(texinfo-version) \
@@ -1164,7 +1229,7 @@ $(ibidir)/binutils-$(binutils-version): \
# Build binutils with the standard 'gbuild' function.
$(call gbuild, binutils-$(binutils-version), static, \
--with-lib-path=$(sys_library_path), \
- -j$(numthreads) )
+ -j$(numthreads) V=1)
# The 'ld' linker of Binutils needs several '*crt*.o' files from
# the host's GNU C Library to run. On some systems these object
@@ -1287,20 +1352,35 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
current_dir=$$(pwd)
# By default 'ddir' (where GCC is decompressed and built) is in the
-# RAM (on systems that support '/dev/shm'). This is done to avoid
-# building so many small/temporary files and possibly harming the
-# hard-drive or SSD. But if the RAM doesn't have enough space, we
-# should use the hard-drive or SSD. During its build GCC's build
-# directory will become about 7GB (multiple of 1024 bytes, for GCC
-# 11.2.0). So at this step, we are making sure we have more than
-# 7.5GiB (multiple of 1000 bytes, which corresponds to 7.32GB)
-# before GCC starts to build. Note that the 4th column of 'df' is
-# the "available" space at the time of running, not the full
-# space. So the background RAM that the OS will be using during
-# Maneage is accounted for. Also consider that GCC is built alone
-# (no other Maneage software is built at the same time as GCC).
- in_ram=$$(df $(ddir) \
- | awk 'NR==2{print ($$4>7500000) ? "yes" : "no"}'); \
+# RAM (on systems that support a '/dev/shm' RAM disk). This is done
+# to avoid building so many small/temporary files and possibly
+# harming the hard-drive or SSD. But if the RAM doesn't have enough
+# space, we should use the hard-drive or SSD. During its build,
+# GCC's build directory will become about 7GiB (in units of 1024^3
+# bytes, for GCC 12.1.0, which corresponds to 7.5GB, in units of
+# 1000^3 bytes). So at this step, we make sure that we have more
+# than 12GiB before GCC starts to build. See the figure in the link
+# below for GCC's RAM consumption as a function of time:
+#
+# https://savannah.nongnu.org/task/?16244#comment12
+#
+# For POSIX portability and longevity (default sizes might change),
+# we use the '-P' option, and we use the environment variable
+# POSIXLY_CORRECT=1, so the 'block size' is 512 bytes. We'll also
+# allow for about ~0.5 GB at the start.
+#
+# So we need 8 GiB * 1024^3 (B/GiB) / 512 blocks/B = 16777216
+# blocks, in blocks of 512 bytes.
+#
+# The 4th column of 'df' is the "available" space at the time of
+# running, not the full space. So the 'RAM disk' that the OS
+# will be using as "pretend" disk space (e.g. using 'tmpfs'; this
+# is physically RAM, but appears as if it is disk space)
+# during this stage of Maneage is accounted for. GCC is built
+# alone - no other Maneage software is built at the same time as
+# GCC - so this amount of RAM should be enough.
+ in_ram=$$(POSIXLY_CORRECT=1 df -P $(ddir) \
+ | awk 'NR==2{print ($$4>16777216) ? "yes" : "no"}'); \
if [ $$in_ram = "yes" ]; then odir=$(ddir)
else
odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space
@@ -1308,9 +1388,11 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
mkdir $$odir
fi
-# Go into the proper directory, unpack GCC and prepare the 'build'
-# directory inside it for all the built files.
+# Go into the directory to uncompress GCC.
cd $$odir
+
+# Unpack GCC and prepare the 'build' directory inside it for all
+# the built files.
rm -rf gcc-$(gcc-version)
tar -xf $(tdir)/$$tarball
if [ $$odir != $(ddir) ]; then
@@ -1318,6 +1400,34 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
fi
cd gcc-$(gcc-version)
+# Unfortunately binutils installs headers like 'ansidecl.h' that
+# have been seen to conflict with GCC's internal versions of those
+# headers. For example in the 'ansidecl.h' of Binutils 2.39, the
+# 'PTR' macro isn't defined, while the same file in GCC 12.1.0 has
+# defined it. Therefore, without this change, GCC will include the
+# file installed from Binutils, not find what it needs and crash!
+# Therefore, with the 'CPPFLAGS' modification below, we tell GCC to
+# first look into its own 'include' directory before anything else.
+ export CPPFLAGS="-I$$(pwd)/include $(CPPFLAGS)"
+
+# In the GNU C Library 2.36 (which is more recent than GCC 12.1.0),
+# the 'linux/mount.h' (loaded by 'linux/fs.h', which is loaded by
+# 'libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp'
+# in GCC) conflicts with 'sys/mount.h' which is directly loaded by
+# the same file! This is a known conflict in glibc 2.36 (see
+# [1]). As described in [1], one solution is the final job done in
+# [2]. We therefore do this process here: 1) Not loading
+# 'linux/fs.h', and adding the necessary macros directly.
+#
+# [1] https://sourceware.org/glibc/wiki/Release/2.36#Usage_of_.3Clinux.2Fmount.h.3E_and_.3Csys.2Fmount.h.3E
+# [2] https://reviews.llvm.org/D129471
+ sed -e's|\#include <linux/fs.h>||' \
+ -e"s|FS_IOC_GETFLAGS;|_IOR('f', 1, long);|" \
+ -e"s|FS_IOC_GETVERSION;|_IOR('v', 1, long);|" \
+ -e"s|FS_IOC_SETFLAGS;|_IOW('f', 2, long);|" \
+ -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \
+ -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
+
# Set the build directory for the processing.
mkdir build
cd build
@@ -1396,6 +1506,25 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
+# Software that need re-compilation (to use our own libraries)
+$(ibidir)/lzip-$(lzip-version): $(ibidir)/gcc-$(gcc-version)
+ tarball=lzip-$(lzip-version).tar
+ unpackdir=lzip-$(lzip-version)
+ cd $(ddir)
+ rm -rf $$unpackdir
+ tar -xf $(tdir)/$$tarball
+ cd $$unpackdir
+ ./configure --build --check --installdir="$(ibdir)"
+ if [ -f $(ibdir)/patchelf ]; then
+ $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/lzip;
+ fi
+ cd ..
+ rm -rf $$unpackdir
+ echo "Lzip $(lzip-version)" > $@
+
+
+
+
@@ -1418,7 +1547,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
# nano (and use their own optional high-level text editor). To do this, you
# can just have to manually remove 'nano' from 'targets-proglib' above and
# add their optional text editor in 'TARGETS.conf'.
-$(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version)
+$(ibidir)/nano-$(nano-version): $(ibidir)/lzip-$(lzip-version)
tarball=nano-$(nano-version).tar.lz
$(call import-source, $(nano-url), $(nano-checksum))
$(call gbuild, nano-$(nano-version), static)