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-rw-r--r--reproduce/software/make/basic.mk37
-rw-r--r--reproduce/software/make/build-rules.mk16
-rw-r--r--reproduce/software/make/high-level.mk1
-rwxr-xr-xreproduce/software/shell/apptainer.sh19
-rwxr-xr-xreproduce/software/shell/configure.sh21
-rwxr-xr-xreproduce/software/shell/prep-source.sh9
6 files changed, 93 insertions, 10 deletions
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 000f62d..b045bb1 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -87,6 +87,7 @@ all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)); @echo > /dev/null
# own build-directory comes first.
.ONESHELL:
.SHELLFLAGS := -e -c
+export LC_ALL := C
export CCACHE_DISABLE := 1
export SHELL := $(ibdir)/dash
export PATH := $(ibdir):$(PATH)
@@ -123,6 +124,7 @@ export LD_LIBRARY_PATH=$(sys_library_sh_path)
endif
export LD_LIBRARY_PATH := $(shell echo $(ildir):$(LD_LIBRARY_PATH) \
| sed -e's/::/:/g' -e's/^://' -e's/:$$//')
+ldpathorig := $(subst $(ildir):,,$(LD_LIBRARY_PATH))
# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
# ultimately redundant. But on some systems, even having a single value
@@ -459,6 +461,21 @@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/tar-$(tar-version)
printf ' glib/configure\n' >> $$confsh
printf 'exec ./configure "$$@"\n' >> $$confsh
chmod +x $$confsh
+
+# For its 'glib' installation within macOS, pkg-config needs a
+# working Python for its build (not affecting its final code), but
+# only searches for '/usr/bin/python'. However, some users may have
+# Python available in another location, so we'll set it externally
+# here to be safe. Note that 'which' is not present on some
+# systems, 'command -v' is more portable).
+ if type python > /dev/null 2> /dev/null; then
+ pypath=$$(command -v python)
+ elif type python3 > /dev/null 2> /dev/null; then
+ pypath=$$(command -v python3)
+ else
+ printf "pkg-config: ERROR: a local Python is necessary"; exit 1
+ fi
+ export PYTHON=$$pypath
fi
# Configuration options:
@@ -479,6 +496,8 @@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/tar-$(tar-version)
+
+
# Level 3 (THIRD MOST BASIC): Bash
# --------------------------------
#
@@ -687,7 +706,6 @@ $(ibidir)/bash-$(bash-version): \
-
# Level 4: Most other programs
# ----------------------------
@@ -940,6 +958,23 @@ $(ibidir)/wget-$(wget-version): \
tarball=wget-$(wget-version).tar.lz
$(call import-source, $(wget-url), $(wget-checksum))
+# Wget needs a working Python for its tests (VERY BAD DESIGN!), this
+# does not affect its final operation. But only searches for
+# '/usr/bin/python'. However, some users may have Python available in
+# another location, so we'll set it externally here to be safe. Note
+# that 'which' is not present on some systems, 'command -v' is more
+# portable).
+ if [ x$(on_mac_os) = xyes ]; then
+ if type python > /dev/null 2> /dev/null; then
+ pypath=$$(command -v python)
+ elif type python3 > /dev/null 2> /dev/null; then
+ pypath=$$(command -v python3)
+ else
+ printf "Wget: ERROR: a local Python is necessary"; exit 1
+ fi
+ export PYTHON=$$pypath
+ fi
+
# We need to explicitly disable 'libiconv', because of the
# 'pkg-config' and 'libiconv' problem.
libs="-pthread"
diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
index 984d0bf..454a255 100644
--- a/reproduce/software/make/build-rules.mk
+++ b/reproduce/software/make/build-rules.mk
@@ -40,6 +40,14 @@
# Necessary shell variables
# 'tarball': This is the name of the actual tarball file without a
# directory.
+#
+# Notes:
+# - The LD_LIBRARY_PATH correction is because we build the dependencies of
+# the downloaders (Wget or cURL) before they are built them selves. In
+# the time between the installation of the downloader dependencies and
+# the downloader, the Gnuastro libraries may cause crashes in the host's
+# downloader since normally, Gnuastro's library has higher precedence in
+# 'LD_LIBRARY_PATH'.
import-source = final=$(tdir)/$$tarball; \
url=$(strip $(1)); \
exp_checksum="$(strip $(2))"; \
@@ -82,8 +90,14 @@ import-source = final=$(tdir)/$$tarball; \
if [ x"$$exp_checksum" = x"NO-CHECK-SUM" ]; then \
mv "$$unchecked" "$$final"; \
else \
- if type sha512sum > /dev/null 2>/dev/null; then \
+ if type sha512sum > /dev/null 2> /dev/null; then \
+ if ! sha512sum --version > /dev/null 2> /dev/null; then \
+ export LD_LIBRARY_PATH=$(ldpathorig); \
+ fi; \
checksum=$$(sha512sum "$$unchecked" | awk '{print $$1}'); \
+ if [ LD_LIBRARY_PATH = $(ldpathorig) ]; then \
+ export LD_LIBRARY_PATH=$(LD_LIBRARY_PATH); \
+ fi; \
if [ x"$$checksum" = x"$$exp_checksum" ]; then \
mv "$$unchecked" "$$final"; \
else \
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 281bd84..0f6f63d 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -166,6 +166,7 @@ export PKG_CONFIG_PATH := $(ildir)/pkgconfig:$(idir)/share/pkgconfig
.SUFFIXES:
# Settings specific to this Makefile.
+export LC_ALL := C
export CC := $(ibdir)/gcc
export CXX := $(ibdir)/g++
export F77 := $(ibdir)/gfortran
diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh
index eb24e9e..2aa3535 100755
--- a/reproduce/software/shell/apptainer.sh
+++ b/reproduce/software/shell/apptainer.sh
@@ -73,7 +73,9 @@ set -e
# Default option values
sif=""
jobs=0
+debug=0
quiet=0
+host_cc=0
source_dir=
build_only=
base_sif=""
@@ -101,6 +103,10 @@ Top-level script to build and run a Maneage'd project within Apptainer.
--base-os=STR Base OS name (default: '$base_os').
--base-sif=STR Base OS apptainer image (a '.sif' file).
+ Configuration options
+ --host-cc Use containers's C compiler, don't build GCC.
+ -d, --debug[=FLAGS] Use -j1 and stop on first crash.
+
Interactive shell
--project-shell Open the project's shell within the container.
--container-shell Open the container shell.
@@ -162,6 +168,12 @@ do
--base-sif) base_sif="$2"; check_v "$1" "$base_sif"; shift;shift;;
--base-sif=*) base_sif="${1#*=}"; check_v "$1" "$base_sif"; shift;;
+ # Configuration options.
+ --host-cc) host_cc=1; shift;;
+ --host-cc=*) on_off_option_error --host-cc;;
+ -d|--debug) debug=1; shift;;
+ -d|--debug=*) on_off_option_error --debug;;
+
# Interactive shell.
--project-shell) project_shell=1; shift;;
--project_shell=*) on_off_option_error --project-shell;;
@@ -329,8 +341,11 @@ EOF
# software tarball directory, they will all be symbolic links that
# aren't valid when the user runs the container (since we only
# mount the software tarballs at build time).
+ confopts=""
intbuild=/home/maneager/build
maneage_def=$build_dir/maneage.def
+ if [ $host_cc = 1 ]; then confopts="--host-cc"; fi
+ if [ $debug = 1 ]; then confopts="$confopts --debug"; fi
cat <<EOF > $maneage_def
Bootstrap: localimage
From: $base_sif
@@ -343,7 +358,7 @@ From: $base_sif
%post
cd /home/maneager/source
- ./project configure --jobs=$jobs --no-pause \\
+ ./project configure --jobs=$jobs --no-pause $confopts \\
--input-dir=/home/maneager/input \\
--build-dir=$intbuild \\
--software-dir=/home/maneager/tarballs-software
@@ -351,7 +366,7 @@ From: $base_sif
%runscript
cd /home/maneager/source
- if ./project configure --build-dir=$intbuild \\
+ if ./project configure --build-dir=$intbuild $confopts \\
--existing-conf --no-pause \\
--offline --quiet; then \\
if [ x"\$maneage_apptainer_stat" = xshell ]; then \\
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index e17c9ad..19c14ac 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -1342,11 +1342,17 @@ elapsed_time_from_prev_step software-dir
# complete the configuration, we may also need to download the source code
# of some necessary software packages (including the downloaders). So we
# need to check the host's available tool for downloading at this step.
+#
+# NOTE: it is important that the name of the programs are not recorded to
+# be absolute (for example 'wget' instead of '/usr/bin/wget'). This is
+# because we build both 'wget' and 'curl' within 'basic.mk'. After they are
+# built, Maneage's built software have higher precedence in 'PATH'. So
+# without an absolute address, our own built software will be used as soon
+# as they are installed/available.
if [ $rewritelconfig = yes ]; then
- if type wget > /dev/null 2>/dev/null; then
- # 'which' isn't in POSIX, so we are using 'command -v' instead.
- name=$(command -v wget)
+ # First look for wget on the host.
+ if type wget > /dev/null 2>/dev/null; then
# See if the host wget has the '--no-use-server-timestamps' option
# (for example wget 1.12 doesn't have it). If not, we'll have to
@@ -1363,13 +1369,16 @@ if [ $rewritelconfig = yes ]; then
# By default Wget keeps the remote file's timestamp, so we'll have
# to disable it manually.
- downloader="$name $wgetts -O";
+ downloader="wget $wgetts -O";
+
+ # In case Wget doesn't exist, try cURL.
elif type curl > /dev/null 2>/dev/null; then
- name=$(command -v curl)
# - cURL doesn't keep the remote file's timestamp by default.
# - With the '-L' option, we tell cURL to follow redirects.
- downloader="$name -L -o"
+ downloader="curl -L -o"
+
+ # Neither Wget or cURL could be found.
else
cat <<EOF
diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh
index 2959255..7f49b5c 100755
--- a/reproduce/software/shell/prep-source.sh
+++ b/reproduce/software/shell/prep-source.sh
@@ -32,6 +32,15 @@ set -e
+
+# Set the locale to C to make sure local language settings do not
+# interefere (especially with the SED command).
+export LC_ALL=C
+
+
+
+
+
# Read the first argument.
bindir="$1"
if [ x"$bindir" = x ]; then
generated by cgit v1.2.1 (git 2.18.0) at 2026-07-21 13:14:47 +0000