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-rw-r--r--reproduce/software/bibtex/missfits.tex18
-rw-r--r--reproduce/software/config/installation/LOCAL.conf.in (renamed from reproduce/software/config/installation/LOCAL.mk.in)1
-rw-r--r--reproduce/software/config/installation/TARGETS.conf (renamed from reproduce/software/config/installation/TARGETS.mk)6
-rw-r--r--reproduce/software/config/installation/checksums.conf (renamed from reproduce/software/config/installation/checksums.mk)11
-rw-r--r--reproduce/software/config/installation/texlive-packages.conf (renamed from reproduce/software/config/installation/texlive.mk)0
-rw-r--r--reproduce/software/config/installation/versions.conf (renamed from reproduce/software/config/installation/versions.mk)11
-rw-r--r--reproduce/software/make/README.md2
-rw-r--r--reproduce/software/make/basic.mk234
-rw-r--r--reproduce/software/make/build-rules.mk4
-rw-r--r--reproduce/software/make/high-level.mk53
-rw-r--r--reproduce/software/make/python.mk12
-rwxr-xr-xreproduce/software/shell/bashrc.sh (renamed from reproduce/software/bash/bashrc.sh)0
-rwxr-xr-xreproduce/software/shell/configure.sh (renamed from reproduce/software/bash/configure.sh)923
-rwxr-xr-xreproduce/software/shell/git-post-checkout (renamed from reproduce/software/bash/git-post-checkout)0
-rwxr-xr-xreproduce/software/shell/git-pre-commit (renamed from reproduce/software/bash/git-pre-commit)0
15 files changed, 701 insertions, 574 deletions
diff --git a/reproduce/software/bibtex/missfits.tex b/reproduce/software/bibtex/missfits.tex
new file mode 100644
index 0000000..85a1645
--- /dev/null
+++ b/reproduce/software/bibtex/missfits.tex
@@ -0,0 +1,18 @@
+%% Copyright (C) 2020 Surena Fatemi <surena.fatemi@ipm.ir>
+%%
+%% Copying and distribution of this file, with or without modification,
+%% are permitted in any medium without royalty provided the copyright
+%% notice and this notice are preserved. This file is offered as-is,
+%% without any warranty.
+
+@ARTICLE{missfits,
+ author = {{Marmo}, C. and {Bertin}, E.},
+ title = "{MissFITS and WeightWatcher: Two Optimised Tools for Managing FITS Data.}",
+ journal = {Astronomical Data Analysis Software and Systems XVII},
+ year = 2008,
+ volume = {394},
+ series = {Astronomical Society of the Pacific Conference Series},
+ pages = {619},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2008ASPC..394..619M},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+} \ No newline at end of file
diff --git a/reproduce/software/config/installation/LOCAL.mk.in b/reproduce/software/config/installation/LOCAL.conf.in
index 1045f72..0579218 100644
--- a/reproduce/software/config/installation/LOCAL.mk.in
+++ b/reproduce/software/config/installation/LOCAL.conf.in
@@ -12,5 +12,6 @@
BDIR = @bdir@
INDIR = @indir@
DEPENDENCIES-DIR = @ddir@
+SYS_CPATH = @sys_cpath@
DOWNLOADER = @downloader@
GROUP-NAME = @groupname@
diff --git a/reproduce/software/config/installation/TARGETS.mk b/reproduce/software/config/installation/TARGETS.conf
index 0352d53..bb402be 100644
--- a/reproduce/software/config/installation/TARGETS.mk
+++ b/reproduce/software/config/installation/TARGETS.conf
@@ -18,17 +18,17 @@
# All software that are currently available for installation can be seen in
# the following file.
#
-# reproduce/software/config/installation/versions.mk
+# reproduce/software/config/installation/versions.conf
#
# Please add any software that you need for your project in the respective
-# part below (using its name in `versions.mk', but without the `-version'
+# part below (using its name in `versions.conf', but without the `-version'
# part). Just note that if a program/library is a dependency of another,
# you don't need to include it here (it will be installed before the
# higher-level software anyway).
#
# Note that many low-level software will be installed before those that are
# installed in this step. They are clearly distinguished from the
-# higher-level (optional) software in `versions.mk'. These low-level
+# higher-level (optional) software in `versions.conf'. These low-level
# software MUST NOT be added here.
diff --git a/reproduce/software/config/installation/checksums.mk b/reproduce/software/config/installation/checksums.conf
index a1a3767..4a5d8aa 100644
--- a/reproduce/software/config/installation/checksums.mk
+++ b/reproduce/software/config/installation/checksums.conf
@@ -43,7 +43,7 @@ libiconv-checksum = 365dac0b34b4255a0066e8033a8b3db4bdb94b9b57a9dca17ebf2d779139
libtool-checksum = a6eef35f3cbccf2c9e2667f44a476ebc80ab888725eb768e91a3a6c33b8c931afc46eb23efaee76c8696d3e4eed74ab1c71157bcb924f38ee912c8a90a6521a4
lzip-checksum= 0349b4c6c0b41e601b7ee381c3254d741397beb3ef9354c08162f346f131f4f48f6613ee0a610cdc6d827530df634f884ecfeee35215b10045a40fee76f8e938
m4-checksum = a92cad4441b3fd7c033837389ca3499494523d364a5fda043d92c517051510f1758b3b837f0477f42d2258a179ab79a4993e5d1694ef2673db6d96d1faff84fe
-make-checksum = 6ebf886a394c61eea53dc0fa277b00cda263861e8e647608e0fce549cd619946981224408ee519bbd71068e9424798d3c5791451f60ff06d766f563142703d32
+make-checksum = 9a1185cc468368f4ec06478b1cfa343bf90b5cd7c92c0536567db0315b0ee909af53ecce3d44cfd93dd137dbca1ed13af5713e8663590c4fdd21ea635d78496b
metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a
mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628
mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88
@@ -71,9 +71,9 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff
# ------------------------------------------
#
# These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/installation/TARGETS.mk' will be built as part
-# of a project. To specify a software there, just remove the `-checksum'
-# suffix from the list below.
+# `reproduce/software/config/installation/TARGETS.conf' will be built as
+# part of a project. To specify a software there, just remove the
+# `-checksum' suffix from the list below.
apachelog4cxx-checksum = aa59ce549c2c5cbeec031361dfce09cdfc3e62ee3bc9ecbc809507b7ec878c14409b98536b7d13c27690809c8e9d5ebafc3589c9fb5e4aecd5cc064943ae7d6b
apr-checksum = daa140c83c7e2c45c3980d9dc81d34fa662bebd050653562c39572d0ddf2eaedb71767c518a59d77f59db9b32e00221ef48b9f72ec3666c4521dd511969f3706
apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536
@@ -111,6 +111,7 @@ libtiff-checksum = d213e5db09fd56b8977b187c5a756f60d6e3e998be172550c2892dbdb4b2a
libtirpc-checksum = 392f391f9fc1bd68d81dc44e4058831a64b32790b5c8c37338b0ab416fad2ae4d16389e632596734dba09780347918cc65c6f134e0c1afd09e81ec250785ed23
libxml2-checksum = cb7784ba4e72e942614e12e4f83f4ceb275f3d738b30e3b5c1f25edf8e9fa6789e854685974eed95b362049dbf6c8e7357e0327d64c681ed390534ac154e6810
minizip-checksum = 56b5443f79d1a0a5f563a563f7b1c27b0b0fc5ba5b37248367b204a89a9373df7d12ea802c678f3f39c987d5f1766003eac3dd31b643773afa4463a3f6406628
+missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795
netpbm-checksum = 064720f8a9d0a502488e1af4daecdbf3936910996507ca6f311073a0ad842346692a148eb1ddf7b717f7b108f60500246cb4b83f4d3665f5fc285a84ae1d63d6
openblas-checksum = 91b3074eb922453bf843158b4281cde65db9e8bbdd7590e75e9e6cdcb486157f7973f2936f327bb3eb4f1702ce0ba51ae6729d8d4baf2d986c50771e8f696df0
openmpi-checksum = 760716974cb6b25ad820184622e1ee7926bc6fda87db6b574f76792bc1ca99522e52195866c14b7cb2df5a4981efdaf9f71d2c5533cc0e8e45c2c4b3b74cbacc
@@ -144,7 +145,7 @@ yaml-checksum = 13d2197135946204323dbfccafa0ac7b3d05437e920545a56f46811fd7319c01
asn1crypto-checksum = 44d442a6ddfa971e31e24712fe084368356deb5e1c4c3b3e813e0910931860215bc1c4f9eb2c4bd4fdef607c324086c096e9357068646efd28c97f2d4f85c62f
asteval-checksum = 4d64900b2f7dfdd098d6c8c102f9d9fd46f9ec265a54330e7d94479ba41f0ee0698855658e18b8b32b9c255159eb9a085af5f0306eb6508663d3fea7d2e00b4a
astropy-checksum = c32e874d208f312f894643ab5b3d71dc37630e544da0ceb5ee998d752f9a055d32f6e4319f2cb6928637aaf8573bac58d2882bd636b6a89f5501e3ac7e5ab681
-astroquery-checksum = 0da57f687ac0aa7611cd97085771d79c99e9ac8c11f0828fcbc7390faf24e1e87d86812020e0ae8be1749f5f2ae9cb3733e5922d38a897a9e212247175c28e52
+astroquery-checksum = 43846791d8469a26cf6bb8819db58b830cfe50a34bc0091c2e843dd7dc78b1317530855d432a3a567a9f6a6f4d2682382a32edc91ea01716246b99b3625ec521
beautifulsoup4-checksum = 7aa77bc6008bbcbbbe91b0a850007ab237d2832b63a787fbd94b7cbf47d4276b185e0c61c134df73221406458edff2b75b6b8c2b53b543aa3bb1b0e2202dac5a
certifi-checksum = 6a6bf1ff98caefcdbf78a8c83e11e155368bacdd806f0ae0c6afa8f513667df6598e594b3584de61acdca3d6049f4a776937f2aa8672b602bd6db7b737f6074e
cffi-checksum = af4fe47cf5d6f1126222898365cfa21e9f11d0e71b87d869014dbb37af30dca9ddf50c989030d0f610f50e8099e8dfd08a688d8c3629abbcc4f0294f5f91b817
diff --git a/reproduce/software/config/installation/texlive.mk b/reproduce/software/config/installation/texlive-packages.conf
index 6760eba..6760eba 100644
--- a/reproduce/software/config/installation/texlive.mk
+++ b/reproduce/software/config/installation/texlive-packages.conf
diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.conf
index 988f668..1b678ad 100644
--- a/reproduce/software/config/installation/versions.mk
+++ b/reproduce/software/config/installation/versions.conf
@@ -41,7 +41,7 @@ libiconv-version = 1.16
libtool-version = 2.4.6
lzip-version= 1.20
m4-version = 1.4.18
-make-version = 4.2.90
+make-version = 4.3
metastore-version = 1.1.2-23-fa9170b
mpc-version = 1.1.0
mpfr-version = 4.0.2
@@ -69,9 +69,9 @@ zlib-version = 1.2.11
# ------------------------------------------
#
# These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/installation/TARGETS.mk' will be built as part
-# of a project. To specify a software there, just remove the `-version'
-# suffix from the list below.
+# `reproduce/software/config/installation/TARGETS.conf' will be built as
+# part of a project. To specify a software there, just remove the
+# `-version' suffix from the list below.
apachelog4cxx-version = 0.10.0-603-014954db
apr-version = 1.7.0
apr-util-version = 1.6.1
@@ -108,6 +108,7 @@ libtiff-version = 4.0.10
libtirpc-version = 1.1.4
libxml2-version = 2.9.9
minizip-version = 2.9.2
+missfits-version = 2.8.0
openblas-version = 0.3.5
openmpi-version = 4.0.1
openssh-version = 8.0p1
@@ -139,7 +140,7 @@ yaml-version = 0.2.2
asn1crypto-version = 0.24.0
asteval-version = 0.9.16
astropy-version = 4.0
-astroquery-version = 0.3.9
+astroquery-version = 0.4
beautifulsoup4-version = 4.7.1
certifi-version = 2018.11.29
cffi-version = 1.12.2
diff --git a/reproduce/software/make/README.md b/reproduce/software/make/README.md
index fc04dfb..d71a3d5 100644
--- a/reproduce/software/make/README.md
+++ b/reproduce/software/make/README.md
@@ -2,7 +2,7 @@ Software building instructions
==============================
This directory contains Makefiles that are called by the high-level
-`reproduce/software/bash/configure.sh` script. The main target for the
+`reproduce/software/shell/configure.sh` script. The main target for the
installation of each software is a simple plain text file that contains the
name of the software and its version (which is put in the paper in the
end). Once built, these plain-text files are all put in the proper
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index e7d00df..212c738 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -34,9 +34,9 @@
# Top level environment
include reproduce/software/make/build-rules.mk
-include reproduce/software/config/installation/LOCAL.mk
-include reproduce/software/config/installation/versions.mk
-include reproduce/software/config/installation/checksums.mk
+include reproduce/software/config/installation/LOCAL.conf
+include reproduce/software/config/installation/versions.conf
+include reproduce/software/config/installation/checksums.conf
lockdir = $(BDIR)/locks
tdir = $(BDIR)/software/tarballs
@@ -48,7 +48,7 @@ ibidir = $(BDIR)/software/installed/version-info/proglib
# We'll need the system's PATH for making links to low-level programs we
# won't be building ourselves.
-syspath := $(PATH)
+syspath := $(PATH)
# As we build more programs, we want to use this project's built programs
# and libraries, not the host's.
@@ -58,7 +58,15 @@ export PKG_CONFIG_PATH := $(ildir)/pkgconfig
export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
export CPPFLAGS := -I$(idir)/include $(CPPFLAGS)
export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
-export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH) \
+
+# 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,
+# 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
+# will also make sure that there is no "current directory" in it (by
+# 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/:$$//')
# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
@@ -66,14 +74,18 @@ export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH) \
# causes crashs (see bug #56682). So we'll just give it no value at all.
export DYLD_LIBRARY_PATH :=
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# Recipe startup script.
export PROJECT_STATUS := configure_basic
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
# Define the top-level basic programs (that don't depend on any other).
top-level-programs = low-level-links gcc
all: $(foreach p, $(top-level-programs), $(ibidir)/$(p))
+# Servers to use as backup, later this should go in a file that is not
+# under version control (the actual server that the tarbal comes from is
+# irrelevant).
+backupservers = http://akhlaghi.org/reproduce-software
@@ -176,7 +188,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
mergenames=0; \
c=$(m4-checksum); \
w=http://akhlaghi.org/reproduce-software/m4-1.4.18-patched.tar.gz; \
- elif [ $$n = make ]; then c=$(make-checksum); w=https://alpha.gnu.org/gnu/make; \
+ elif [ $$n = make ]; then c=$(make-checksum); w=https://ftp.gnu.org/gnu/make; \
elif [ $$n = metastore ]; then c=$(metastore-checksum); w=http://akhlaghi.org/reproduce-software; \
elif [ $$n = mpc ]; then c=$(mpc-checksum); w=http://ftp.gnu.org/gnu/mpc; \
elif [ $$n = mpfr ]; then c=$(mpfr-checksum); w=http://www.mpfr.org/mpfr-current;\
@@ -228,15 +240,19 @@ $(tarballs): $(tdir)/%: | $(lockdir)
\
touch $(lockdir)/download; \
$(downloadwrapper) "$$downloader" $(lockdir)/download \
- $$tarballurl "$@.unchecked"; \
+ $$tarballurl "$@.unchecked" "$(backupservers)"; \
fi; \
\
\
if type sha512sum > /dev/null 2>/dev/null; then \
checksum=$$(sha512sum "$@.unchecked" | awk '{print $$1}'); \
- echo "$*: should be '$$c', is '$$checksum'"; \
- if [ x$$checksum = x$$c ]; then mv "$@.unchecked" "$@"; \
- else echo "ERROR: Non-matching checksum for '$*'."; exit 1; \
+ if [ x"$$checksum" = x"$$c" ]; then \
+ mv "$@.unchecked" "$@"; \
+ else \
+ echo "ERROR: Non-matching checksum for '$*'."; \
+ echo "Checksum should be: $$c"; \
+ echo "Checksum is: $$checksum"; \
+ exit 1; \
fi; \
else mv "$@.unchecked" "$@"; \
fi;
@@ -658,6 +674,66 @@ $(ibidir)/bash: $(ibidir)/readline \
+# The `-shared' flag will cause problems while building Perl on macOS, so
+# we'll only use this configuration option when we are GNU/Linux
+# systems. However, since the whole option must be used (which includes `='
+# and empty space), its easier to define the variable as a Make variable
+# outside the recipe, not as a shell variable inside it.
+ifeq ($(on_mac_os),yes)
+perl-conflddlflags =
+else
+perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS"
+endif
+$(ibidir)/perl: | $(ibidir)/bash \
+ $(tdir)/perl-$(perl-version).tar.gz
+ major_version=$$(echo $(perl-version) \
+ | sed -e's/\./ /g' \
+ | awk '{printf("%d", $$1)}'); \
+ base_version=$$(echo $(perl-version) \
+ | sed -e's/\./ /g' \
+ | awk '{printf("%d.%d", $$1, $$2)}'); \
+ cd $(ddir) \
+ && rm -rf perl-$(perl-version) \
+ && if ! tar xf $(word 1,$(filter $(tdir)/%,$|)); then \
+ echo; echo "Tar error"; exit 1; \
+ fi \
+ && cd perl-$(perl-version) \
+ && sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \
+ -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \
+ Configure > Configure-tmp \
+ && mv -f Configure-tmp Configure \
+ && chmod +x Configure \
+ && ./Configure -des \
+ -Dusethreads \
+ -Duseshrplib \
+ -Dprefix=$(idir) \
+ -Dvendorprefix=$(idir) \
+ -Dprivlib=$(idir)/share/perl$$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/$$basever/site_perl \
+ -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \
+ -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \
+ -Dscriptdir=$(idir)/bin/core_perl \
+ -Dsitescript=$(idir)/bin/site_perl \
+ -Dvendorscript=$(idir)/bin/vendor_perl \
+ -Dinc_version_list=none \
+ -Dman1ext=1perl \
+ -Dman3ext=3perl \
+ -Dcccdlflags='-fPIC' \
+ $(perl-conflddlflags) \
+ -Dldflags="$$LDFLAGS" \
+ && make SHELL=$(ibdir)/bash -j$(numthreads) \
+ && make SHELL=$(ibdir)/bash install \
+ && cd .. \
+ && rm -rf perl-$(perl-version) \
+ && cd $$topdir \
+ && echo "Perl $(perl-version)" > $@
+
+
+
+
+
# Coreutils
# ---------
#
@@ -677,8 +753,10 @@ $(ibidir)/bash: $(ibidir)/readline \
# The echo after the PatchELF loop is to avoid a crash if the last
# file that PatchELF encounters is not usable (and it returns with
# an error).
+#
+# Coreutils uses Perl to create man pages!
$(ibidir)/coreutils: $(ibidir)/openssl \
- | $(ibidir)/bash \
+ | $(ibidir)/perl \
$(tdir)/coreutils-$(coreutils-version).tar.xz
cd $(ddir) \
&& rm -rf coreutils-$(coreutils-version) \
@@ -847,17 +925,17 @@ $(ibidir)/wget: $(ibidir)/libiconv \
# there is no access to the system's PATH.
$(ibidir)/diffutils: | $(ibidir)/coreutils \
$(tdir)/diffutils-$(diffutils-version).tar.xz
- $(call gbuild, diffutils-$(diffutils-version), static, , V=1) \
+ $(call gbuild, diffutils-$(diffutils-version), static,,V=1) \
&& echo "GNU Diffutils $(diffutils-version)" > $@
$(ibidir)/file: | $(ibidir)/coreutils \
$(tdir)/file-$(file-version).tar.gz
- $(call gbuild, file-$(file-version), static) \
+ $(call gbuild, file-$(file-version), static,,V=1) \
&& echo "File $(file-version)" > $@
$(ibidir)/findutils: | $(ibidir)/coreutils \
$(tdir)/findutils-$(findutils-version).tar.xz
- $(call gbuild, findutils-$(findutils-version), static, , V=1) \
+ $(call gbuild, findutils-$(findutils-version), static,,V=1) \
&& echo "GNU Findutils $(findutils-version)" > $@
$(ibidir)/gawk: $(ibidir)/gmp \
@@ -910,13 +988,13 @@ $(ibidir)/gmp: | $(ibidir)/m4 \
$(ibidir)/glibtool: | $(ibidir)/m4 \
$(tdir)/libtool-$(libtool-version).tar.xz
$(call gbuild, libtool-$(libtool-version), static, \
- --program-prefix=g) \
+ --program-prefix=g, V=1) \
&& ln -s $(ibdir)/glibtoolize $(ibdir)/libtoolize \
&& echo "GNU Libtool $(libtool-version)" > $@
$(ibidir)/grep: | $(ibidir)/coreutils \
$(tdir)/grep-$(grep-version).tar.xz
- $(call gbuild, grep-$(grep-version), static) \
+ $(call gbuild, grep-$(grep-version), static,,V=1) \
&& echo "GNU Grep $(grep-version)" > $@
$(ibidir)/libbsd: | $(ibidir)/coreutils \
@@ -927,7 +1005,7 @@ $(ibidir)/libbsd: | $(ibidir)/coreutils \
$(ibidir)/m4: | $(ibidir)/coreutils \
$(ibidir)/texinfo \
$(tdir)/m4-$(m4-version).tar.gz
- $(call gbuild, m4-$(m4-version), static) \
+ $(call gbuild, m4-$(m4-version), static,,V=1) \
&& echo "GNU M4 $(m4-version)" > $@
# Metastore is used (through a Git hook) to restore the source modification
@@ -997,7 +1075,7 @@ $(ibidir)/metastore: $(needlibbsd) \
-e's|@GROUP[@]|'$$group'|g' \
-e's|@BINDIR[@]|$(ibdir)|g' \
-e's|@TOP_PROJECT_DIR[@]|'$$current_dir'|g' \
- reproduce/software/bash/git-$$f > .git/hooks/$$f \
+ reproduce/software/shell/git-$$f > .git/hooks/$$f \
&& chmod +x .git/hooks/$$f; \
done; \
fi \
@@ -1020,63 +1098,6 @@ $(ibidir)/mpfr: $(ibidir)/gmp \
$(call gbuild, mpfr-$(mpfr-version), static, , , make check) \
&& echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@
-# The `-shared' flag will cause problems while building Perl on macOS, so
-# we'll only use this configuration option when we are GNU/Linux
-# systems. However, since the whole option must be used (which includes `='
-# and empty space), its easier to define the variable as a Make variable
-# outside the recipe, not as a shell variable inside it.
-ifeq ($(on_mac_os),yes)
-perl-conflddlflags =
-else
-perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS"
-endif
-$(ibidir)/perl: | $(ibidir)/coreutils \
- $(tdir)/perl-$(perl-version).tar.gz
- major_version=$$(echo $(perl-version) \
- | sed -e's/\./ /g' \
- | awk '{printf("%d", $$1)}'); \
- base_version=$$(echo $(perl-version) \
- | sed -e's/\./ /g' \
- | awk '{printf("%d.%d", $$1, $$2)}'); \
- cd $(ddir) \
- && rm -rf perl-$(perl-version) \
- && if ! tar xf $(word 1,$(filter $(tdir)/%,$|)); then \
- echo; echo "Tar error"; exit 1; \
- fi \
- && cd perl-$(perl-version) \
- && sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \
- -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \
- Configure > Configure-tmp \
- && mv -f Configure-tmp Configure \
- && chmod +x Configure \
- && ./Configure -des \
- -Dusethreads \
- -Duseshrplib \
- -Dprefix=$(idir) \
- -Dvendorprefix=$(idir) \
- -Dprivlib=$(idir)/share/perl$$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/$$basever/site_perl \
- -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \
- -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \
- -Dscriptdir=$(idir)/bin/core_perl \
- -Dsitescript=$(idir)/bin/site_perl \
- -Dvendorscript=$(idir)/bin/vendor_perl \
- -Dinc_version_list=none \
- -Dman1ext=1perl \
- -Dman3ext=3perl \
- -Dcccdlflags='-fPIC' \
- $(perl-conflddlflags) \
- -Dldflags="$$LDFLAGS" \
- && make SHELL=$(ibdir)/bash -j$(numthreads) \
- && make SHELL=$(ibdir)/bash install \
- && cd .. \
- && rm -rf perl-$(perl-version) \
- && cd $$topdir \
- && echo "Perl $(perl-version)" > $@
-
-
$(ibidir)/pkg-config: | $(ibidir)/coreutils \
$(tdir)/pkg-config-$(pkgconfig-version).tar.gz
# An existing `libiconv' can cause a conflict with `pkg-config',
@@ -1101,7 +1122,7 @@ $(ibidir)/pkg-config: | $(ibidir)/coreutils \
$(ibidir)/sed: | $(ibidir)/coreutils \
$(tdir)/sed-$(sed-version).tar.xz
- $(call gbuild, sed-$(sed-version), static) \
+ $(call gbuild, sed-$(sed-version), static,,V=1) \
&& echo "GNU Sed $(sed-version)" > $@
$(ibidir)/texinfo: | $(ibidir)/perl \
@@ -1111,7 +1132,7 @@ $(ibidir)/texinfo: | $(ibidir)/perl \
$(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/info; \
$(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/install-info; \
fi \
- && echo "GNU Texinfo $(sed-version)" > $@
+ && echo "GNU Texinfo $(texinfo-version)" > $@
$(ibidir)/which: | $(ibidir)/coreutils \
$(tdir)/which-$(which-version).tar.gz
@@ -1161,6 +1182,15 @@ endif
# programs (http://savannah.nongnu.org/bugs/?56294). Therefore, we'll set
# all other basic programs as Binutils prerequisite and GCC (the final
# basic target) ultimately just depends on Binutils.
+#
+# The `ld' linker of Binutils needs several `*crt*.o' file 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.
$(ibidir)/binutils: | $(ibidir)/sed \
$(ibidir)/wget \
$(ibidir)/grep \
@@ -1174,6 +1204,7 @@ $(ibidir)/binutils: | $(ibidir)/sed \
$(ibidir)/diffutils \
$(ibidir)/coreutils \
$(gcc-prerequisites)
+
if [ x$(on_mac_os) = xyes ]; then \
$(call makelink,as); \
$(call makelink,ar); \
@@ -1181,9 +1212,17 @@ $(ibidir)/binutils: | $(ibidir)/sed \
$(call makelink,nm); \
$(call makelink,ps); \
$(call makelink,ranlib); \
- echo "" > $@; \
+ echo "" > $@; \
else \
- $(call gbuild, binutils-$(binutils-version), static) \
+ $(call gbuild, binutils-$(binutils-version), static, \
+ --with-lib-path=$(sys_library_path), \
+ -j$(numthreads) ) \
+ && if ! [ x"$(sys_library_path)" = x ]; then \
+ for f in $(sys_library_path)/*crt*.o; do \
+ b=$$($(ibdir)/basename $$f); \
+ ln -s $$f $(ildir)/$$b; \
+ done; \
+ fi \
&& echo "GNU Binutils $(binutils-version)" > $@; \
fi
@@ -1222,15 +1261,27 @@ $(ibidir)/gcc: | $(ibidir)/binutils \
ccinfo=$$(gcc --version | awk 'NR==1'); \
echo "C compiler (""$$ccinfo"")" > $@; \
else \
+ current_dir=$$(pwd); \
rm -f $(ibdir)/gcc* $(ibdir)/g++ $(ibdir)/gfortran $(ibdir)/gcov*;\
rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc*; \
rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*;\
\
ln -fs $(ildir) $(idir)/lib64; \
- \
- cd $(ddir); \
+ \
+ in_ram=$$(df $(ddir) \
+ | awk 'NR==2{print ($$4>10000000) ? "yes" : "no"}'); \
+ if [ $$in_ram = "yes" ]; then odir=$(ddir); \
+ else \
+ odir=$(BDIR)/software/build-tmp-gcc; \
+ if [ -d $$odir ]; then rm -rf $$odir; fi; \
+ mkdir $$odir; \
+ fi; \
+ cd $$odir; \
rm -rf gcc-$(gcc-version); \
- tar xf $(word 1,$(filter $(tdir)/%,$|)) \
+ tar xf $(word 1,$(filter $(tdir)/%,$|)); \
+ if [ $$odir != $(ddir) ]; then \
+ ln -s $$odir/gcc-$(gcc-version) $(ddir)/gcc-$(gcc-version); \
+ fi \
&& cd gcc-$(gcc-version) \
&& mkdir build \
&& cd build \
@@ -1257,15 +1308,24 @@ $(ibidir)/gcc: | $(ibidir)/binutils \
&& make SHELL=$(ibdir)/bash -j$(numthreads) \
&& make SHELL=$(ibdir)/bash install \
&& cd ../.. \
- && rm -rf gcc-$(gcc-version) \
+ && tempname=$$odir/gcc-$(gcc-version)/build/rpath-temp-copy \
&& if [ "x$(on_mac_os)" != xyes ]; then \
patchelf --add-needed $(ildir)/libiconv.so $(ildir)/libstdc++.so; \
for f in $$(find $(idir)/libexec/gcc) $(ildir)/libstdc++*; do \
- if ldd $$f &> /dev/null; then \
- patchelf --set-rpath $(ildir) $$f; \
+ isdynamic=$$(file $$f | grep "dynamically linked"); \
+ if [ x"$$isdynamic" != x ]; then \
+ cp $$f $$tempname; \
+ patchelf --set-rpath $(ildir) $$tempname; \
+ mv $$tempname $$f; echo "corrected"; \
fi; \
done; \
fi \
+ && rm -rf gcc-$(gcc-version) \
+ && cd $$current_dir \
+ && if [ "$$odir" != "$(ddir)" ]; then \
+ rm -rf $$odir; \
+ rm $(ddir)/gcc-$(gcc-version); \
+ fi \
&& ln -sf $(ibdir)/gcc $(ibdir)/cc \
&& echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@; \
fi
diff --git a/reproduce/software/make/build-rules.mk b/reproduce/software/make/build-rules.mk
index cbde70b..f3ca7d2 100644
--- a/reproduce/software/make/build-rules.mk
+++ b/reproduce/software/make/build-rules.mk
@@ -1,7 +1,7 @@
# Generic configurable recipes to build packages with GNU Build system or
# CMake. This is Makefile is not intended to be run directly, it will be
-# imported into `dependencies-basic.mk' and `dependencies.mk'. They should
-# be activated with Make's `Call' function.
+# imported into `basic.mk' and `high-level.mk'. They should be activated
+# with Make's `Call' function.
#
# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index ac46f3a..5f1d2b2 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -28,11 +28,11 @@
# Top level environment
include reproduce/software/make/build-rules.mk
-include reproduce/software/config/installation/LOCAL.mk
-include reproduce/software/config/installation/TARGETS.mk
-include reproduce/software/config/installation/texlive.mk
-include reproduce/software/config/installation/versions.mk
-include reproduce/software/config/installation/checksums.mk
+include reproduce/software/config/installation/LOCAL.conf
+include reproduce/software/config/installation/TARGETS.conf
+include reproduce/software/config/installation/versions.conf
+include reproduce/software/config/installation/checksums.conf
+include reproduce/software/config/installation/texlive-packages.conf
lockdir = $(BDIR)/locks
tdir = $(BDIR)/software/tarballs
@@ -70,8 +70,8 @@ all: $(foreach p, $(top-level-programs), $(ibidir)/$(p)) \
.SHELLFLAGS := --noprofile --norc -ec
export CCACHE_DISABLE := 1
export PATH := $(ibdir)
-export CXX := $(ibdir)/g++
export CC := $(ibdir)/gcc
+export CXX := $(ibdir)/g++
export SHELL := $(ibdir)/bash
export F77 := $(ibdir)/gfortran
export LD_RUN_PATH := $(ildir):$(il64dir)
@@ -79,14 +79,31 @@ export PKG_CONFIG_PATH := $(ildir)/pkgconfig
export LD_LIBRARY_PATH := $(ildir):$(il64dir)
export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
+# 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.
+export CPATH := $(sys_cpath)
+
# 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 :=
-# Recipe startup script, see `reproduce/software/bash/bashrc.sh'.
+# 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'.
+export LIBRARY_PATH := $(sys_library_path)
+
+# Recipe startup script, see `reproduce/software/shell/bashrc.sh'.
export PROJECT_STATUS := configure_highlevel
-export BASH_ENV := $(shell pwd)/reproduce/software/bash/bashrc.sh
+export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
+
+# Servers to use as backup, later this should go in a file that is not
+# under version control (the actual server that the tarbal comes from is
+# irrelevant).
+backupservers = http://akhlaghi.org/reproduce-software
# Building flags:
#
@@ -168,6 +185,7 @@ tarballs = $(foreach t, apachelog4cxx-$(apachelog4cxx-version).tar.lz \
libtirpc-$(libtirpc-version).tar.bz2 \
libxml2-$(libxml2-version).tar.gz \
minizip-$(minizip-version).tar.gz \
+ missfits-$(missfits-version).tar.gz \
netpbm-$(netpbm-version).tar.gz \
openblas-$(openblas-version).tar.gz \
openmpi-$(openmpi-version).tar.gz \
@@ -268,6 +286,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
mergenames=0
c=$(minizip-checksum);
w=https://github.com/nmoinvaz/minizip/archive/$(minizip-version).tar.gz
+ elif [ $$n = missfits ]; then c=$(missfits-checksum); w=https://www.astromatic.net/download/missfits
elif [ $$n = netpbm ]; then c=$(netpbm-checksum); w=http://akhlaghi.org/reproduce-software
elif [ $$n = openblas ]; then
mergenames=0
@@ -325,7 +344,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
touch $(lockdir)/download
downloader="wget --no-use-server-timestamps -O"
$(downloadwrapper) "$$downloader" $(lockdir)/download \
- $$tarballurl "$@.unchecked"
+ $$tarballurl "$@.unchecked" "$(backupservers)"
fi
# Make sure this is the expected tarball. Note that we now have a
@@ -601,7 +620,7 @@ $(ibidir)/hdf5: $(ibidir)/openmpi \
# 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.mk').
+# `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
@@ -647,7 +666,7 @@ $(ibidir)/healpix: $(ibidir)/cfitsio \
&& echo "HEALPix $(healpix-version) \citep{healpix}" > $@
$(ibidir)/libjpeg: | $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
- $(call gbuild, jpeg-9b, static) \
+ $(call gbuild, jpeg-9b, static,,V=1) \
&& echo "Libjpeg $(libjpeg-version)" > $@
$(ibidir)/libnsl: $(ibidir)/libtirpc \
@@ -1017,12 +1036,15 @@ $(ibidir)/imfit: $(ibidir)/gsl \
fi \
&& echo "Imfit $(imfit-version) \citep{imfit2015}" > $@
-
$(ibidir)/minizip: $(ibidir)/cmake \
| $(tdir)/minizip-$(minizip-version).tar.gz
$(call cbuild, minizip-$(minizip-version), static) \
&& echo "minizip $(minizip-version)" > $@
+$(ibidir)/missfits: | $(tdir)/missfits-$(missfits-version).tar.gz
+ $(call gbuild, missfits-$(missfits-version), static) \
+ && cp $(dtexdir)/missfits.tex $(ictdir)/ \
+ && echo "MissFITS $(missfits-version) \citep{missfits}" > $@
# 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
@@ -1135,7 +1157,10 @@ $(ibidir)/xlsxio: $(ibidir)/expat \
| $(tdir)/xlsxio-$(xlsxio-version).tar.gz
export LDFLAGS="-lbz2 -lbsd"; \
$(call cbuild, xlsxio-$(xlsxio-version), static) \
- && echo "XLSX I/O $(xlsxio-version)" > $@
+ && echo "XLSX I/O $(xlsxio-version)" > $
+
+
+
@@ -1216,7 +1241,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co
#else
#forbiber = $(ibidir)/libnsl
#endif
-$(itidir)/texlive: reproduce/software/config/installation/texlive.mk \
+$(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf \
$(itidir)/texlive-ready-tlmgr \
$(forbiber)
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 8c7b6f0..fef1605 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -185,7 +185,7 @@ $(pytarballs): $(tdir)/%:
h=$(pytopurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz
elif [ $$n = asn ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4; c=$(asn1crypto-checksum)
elif [ $$n = asteval ]; then h=50/3f/29b7935c6dc09ee96dc347edc66c57e8ef68d595dd35b763a36a117acc8c; c=$(asteval-checksum)
- elif [ $$n = astroquery ]; then h=61/50/a7a08f9e54d7d9d97e69433cd88231e1ad2901811c9d1ae9ac7ccaef9396; c=$(astroquery-checksum)
+ elif [ $$n = astroquery ]; then h=e2/af/a3cd3b30745832a0e81f5f13327234099aaf5d03b7979ac947a888e68e91; c=$(astroquery-checksum)
elif [ $$n = astropy ]; then h=de/96/7feaca4b9be134128838395a9d924ea0b389ed4381702dcd9d11ae31789f; c=$(astropy-checksum)
elif [ $$n = beautifulsoup ]; then h=80/f2/f6aca7f1b209bb9a7ef069d68813b091c8c3620642b568dac4eb0e507748; c=$(beautifulsoup4-checksum)
elif [ $$n = certifi ]; then h=55/54/3ce77783acba5979ce16674fc98b1920d00b01d337cfaaf5db22543505ed; c=$(certifi-checksum)
@@ -259,7 +259,7 @@ $(pytarballs): $(tdir)/%:
touch $(lockdir)/download
downloader="wget --no-use-server-timestamps -O"
$(downloadwrapper) "$$downloader" $(lockdir)/download \
- $$tarballurl "$@.unchecked"
+ $$tarballurl "$@.unchecked" "$(backupservers)"
fi
# Make sure this is the expected tarball. Note that we now have a
@@ -373,12 +373,9 @@ $(ipydir)/asteval: $(ipydir)/numpy \
$(call pybuild, tar xf, asteval-$(asteval-version), , \
ASTEVAL $(asteval-version))
-$(ipydir)/astroquery: $(ipydir)/numpy \
- $(ipydir)/astropy \
+$(ipydir)/astroquery: $(ipydir)/astropy \
$(ipydir)/keyring \
- $(ipydir)/html5lib \
$(ipydir)/requests \
- $(ipydir)/beautifulsoup4 \
| $(tdir)/astroquery-$(astroquery-version).tar.gz
$(call pybuild, tar xf, astroquery-$(astroquery-version), ,\
Astroquery $(astroquery-version))
@@ -386,6 +383,9 @@ $(ipydir)/astroquery: $(ipydir)/numpy \
$(ipydir)/astropy: $(ipydir)/h5py \
$(ipydir)/scipy \
$(ipydir)/numpy \
+ $(ipydir)/pyyaml \
+ $(ipydir)/html5lib \
+ $(ipydir)/beautifulsoup4 \
| $(tdir)/astropy-$(astropy-version).tar.gz
$(call pybuild, tar xf, astropy-$(astropy-version)) \
&& cp $(dtexdir)/astropy.tex $(ictdir)/ \
diff --git a/reproduce/software/bash/bashrc.sh b/reproduce/software/shell/bashrc.sh
index b2a151f..b2a151f 100755
--- a/reproduce/software/bash/bashrc.sh
+++ b/reproduce/software/shell/bashrc.sh
diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/shell/configure.sh
index f7fa9c8..6e1b5fb 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -1,4 +1,4 @@
-#! /bin/bash
+#! /bin/sh
#
# Necessary preparations/configurations for the reproducible project.
#
@@ -38,11 +38,11 @@ cdir=reproduce/software/config
sbdir=$cdir/installation
-pconf=$sbdir/LOCAL.mk
-ptconf=$sbdir/LOCAL_tmp.mk
-poconf=$sbdir/LOCAL_old.mk
-depverfile=$cdir/installation/versions.mk
-depshafile=$cdir/installation/checksums.mk
+pconf=$sbdir/LOCAL.conf
+ptconf=$sbdir/LOCAL_tmp.conf
+poconf=$sbdir/LOCAL_old.conf
+depverfile=$cdir/installation/versions.conf
+depshafile=$cdir/installation/checksums.conf
# --------- Delete for no Gnuastro ---------
glconf=$cdir/gnuastro/gnuastro-local.conf
# ------------------------------------------
@@ -57,7 +57,8 @@ glconf=$cdir/gnuastro/gnuastro-local.conf
# In case someone opens the files output from the configuration scripts in
# a text editor and wants to edit them, it is important to let them know
# that their changes are not going to be permenant.
-function create_file_with_notice() {
+create_file_with_notice ()
+{
if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1"
then
echo "#" >> "$1"
@@ -81,7 +82,8 @@ function create_file_with_notice() {
#
# Since the build directory will go into a symbolic link, we want it to be
# an absolute address. With this function we can make sure of that.
-function absolute_dir() {
+absolute_dir ()
+{
if stat "$1" 1> /dev/null; then
echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
else
@@ -93,6 +95,415 @@ function absolute_dir() {
+# Check for C/C++ compilers
+# -------------------------
+#
+# To build the software, we'll need some basic tools (the compilers in
+# particular) to be present.
+hascc=0;
+if type cc > /dev/null 2>/dev/null; then
+ if type c++ > /dev/null 2>/dev/null; then export CC=cc; hascc=1; fi
+else
+ if type gcc > /dev/null 2>/dev/null; then
+ if type g++ > /dev/null 2>/dev/null; then export CC=gcc; hascc=1; fi
+ else
+ if type clang > /dev/null 2>/dev/null; then
+ if type clang++ > /dev/null 2>/dev/null; then export CC=clang; hascc=1; fi
+ fi
+ fi
+fi
+if [ $hascc = 0 ]; then
+ cat <<EOF
+______________________________________________________
+!!!!!!! C/C++ Compiler NOT FOUND !!!!!!!
+
+To build the project's software, the host system needs to have basic C and
+C++ compilers. The executables that were checked are 'cc', 'gcc' and
+'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++
+compiler. If you have a relevant compiler that is not checked, please get
+in touch with us (with the form below) so we add it:
+
+ https://savannah.nongnu.org/support/?func=additem&group=reproduce
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ exit 1
+fi
+
+
+
+
+
+# Special directory for compiler testing
+# --------------------------------------
+#
+# This directory will be deleted when the compiler testing is finished.
+compilertestdir=.compiler_test_dir_please_delete
+if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi
+
+
+
+
+
+# Check C compiler
+# ----------------
+gcc_works=0
+testprog=$compilertestdir/test
+testsource=$compilertestdir/test.c
+echo; echo; echo "Checking host C compiler...";
+cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+int main(void){printf("...C compiler works.\n");
+ return EXIT_SUCCESS;}
+EOF
+if $CC $testsource -o$testprog && $testprog; then
+ rm $testsource $testprog
+else
+ rm $testsource
+ cat <<EOF
+
+______________________________________________________
+!!!!!!! C compiler doesn't work !!!!!!!
+
+Host C compiler ('gcc') can't build a simple program.
+
+A working C compiler is necessary for building the project's software.
+Please use the error message above to find a good solution and re-run the
+project configuration.
+
+If you can't find a solution, please send the error message above to the
+link below and we'll try to help
+
+https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+TIP: Once you find the solution, you can use the '-e' option to use
+existing configuration:
+
+ $ ./project configure -e
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+ exit 1
+fi
+
+
+
+
+
+# See if the linker accepts -Wl,-rpath-link
+# -----------------------------------------
+#
+# `-rpath-link' is used to write the information of the linked shared
+# library into the shared object (library or program). But some versions of
+# LLVM's linker don't accept it an can cause problems.
+cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+int main(void) {return EXIT_SUCCESS;}
+EOF
+if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then
+ export rpath_command="-Wl,-rpath-link=$instdir/lib"
+else
+ export rpath_command=""
+fi
+rm -f $testprog $testsource
+
+
+
+
+
+# See if we need the dynamic-linker (-ldl)
+# ----------------------------------------
+#
+# Some programs (like Wget) need dynamic loading (using `libdl'). On
+# GNU/Linux systems, we'll need the `-ldl' flag to link such programs. But
+# Mac OS doesn't need any explicit linking. So we'll check here to see if
+# it is present (thus necessary) or not.
+cat > $testsource <<EOF
+#include <stdio.h>
+#include <dlfcn.h>
+int
+main(void) {
+ void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
+ return 0;
+}
+EOF
+if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then
+ needs_ldl=no;
+else
+ needs_ldl=yes;
+fi
+rm -f $testprog $testsource
+
+
+
+
+
+# See if the C compiler can build static libraries
+# ------------------------------------------------
+
+# We are manually only working with shared libraries: because some
+# high-level programs like Wget and cURL need dynamic linking and if we
+# build the libraries statically, our own builds will be ignored and these
+# programs will go and find their necessary libraries on the host system.
+#
+# Another good advantage of shared libraries is that we can actually use
+# the shared library tool of the system (`ldd' with GNU C Library) and see
+# exactly where each linked library comes from. But in static building,
+# unless you follow the build closely, its not easy to see if the source of
+# the library came from the system or our build.
+static_build=no
+
+
+
+
+
+# If we are on a Mac OS system
+# ----------------------------
+#
+# For the time being, we'll use the existance of `otool' to see if we are
+# on a Mac OS system or not. Some tools (for example OpenSSL) need to know
+# this.
+#
+# On Mac OS, the building of GCC crashes sometimes while building libiberty
+# with CLang's `g++'. Until we find a solution, we'll just use the host's C
+# compiler.
+if type otool > /dev/null 2>/dev/null; then
+ host_cc=1
+ on_mac_os=yes
+ cat <<EOF
+
+______________________________________________________
+!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!
+
+The GNU Compiler Collection (GCC, including compilers for C, C++, Fortran
+and etc) is currently not built on macOS systems for this project. To build
+the project's necessary software on this system, we need to use your
+system's C compiler.
+
+Project's configuration will continue in 5 seconds.
+______________________________________________________
+
+EOF
+ sleep 5
+else
+ host_cc=0
+ on_mac_os=no
+fi
+
+
+
+
+
+# Necessary C library element positions
+# -------------------------------------
+#
+# On some systems (in particular Debian-based OSs), the static C library
+# and necessary headers in a non-standard place, and we can't build GCC. So
+# we need to find them first. The `sys/cdefs.h' header is also in a
+# similarly different location.
+sys_cpath=""
+sys_library_path=""
+if [ x"$$on_mac_os" != xyes ]; then
+
+ # Get the GCC target name of the compiler, when its given, special
+ # C libraries and headers are in a sub-directory of the host.
+ gcctarget=$(gcc -v 2>&1 \
+ | tr ' ' '\n' \
+ | awk '/\-\-target/' \
+ | sed -e's/\-\-target=//')
+ if [ x"$gcctarget" != x ]; then
+ if [ -f /usr/lib/$gcctarget/libc.a ]; then
+ export sys_library_path=/usr/lib/$gcctarget
+ export sys_cpath=/usr/include/$gcctarget
+ fi
+ fi
+
+ # For a check:
+ #echo "sys_library_path: $sys_library_path"
+ #echo "sys_cpath: $sys_cpath"
+fi
+
+
+
+
+
+# See if a link-able static C library exists
+# ------------------------------------------
+#
+# After building GCC, we must use PatchELF to correct its RPATHs. However,
+# PatchELF links internally with `libstdc++'. So a dynamicly linked
+# PatchELF cannot be used to correct the links to `libstdc++' in general
+# (on some systems this causes no problem, but on others it doesn't!).
+#
+# However, to build a Static PatchELF, we need to be able to link with the
+# static C library, which is not always available on some GNU/Linux
+# systems. Therefore we need to check this here. If we can't build a static
+# PatchELF, we won't build any GCC either.
+if [ x"$host_cc" = x0 ]; then
+ echo; echo; echo "Checking if static C library is available...";
+ cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/cdefs.h>
+int main(void){printf("...yes\n");
+ return EXIT_SUCCESS;}
+EOF
+ cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc"
+ if $cc_call && $testprog; then
+ gccwarning=0
+ good_static_libc=1
+ rm $testsource $testprog
+ else
+ echo; echo "Compilation command:"; echo "$cc_call"
+ good_static_libc=0
+ rm $testsource
+ gccwarning=1
+ host_cc=1
+ cat <<EOF
+
+_______________________________________________________
+!!!!!!!!!!!! Warning !!!!!!!!!!!!
+
+The 'sys/cdefs.h' header cannot be included, or a usable static C library
+('libc.a', in any directory) cannot be used with the current settings of
+this system. SEE THE ERROR MESSAGE ABOVE.
+
+Because of this, we can't build GCC. You either 1) don't have them, or 2)
+the default system environment aren't enough to find them.
+
+1) If you don't have them, your operating system provides them as separate
+packages that you must manually install. Please look into your operating
+system documentation or contact someone familiar with it. For example on
+some Redhat-based GNU/Linux distributions, the static C library package can
+be installed with this command:
+
+ $ sudo yum install glibc-static
+
+2) If you have 'libc.a' and 'sys/cdefs.h', but in a non-standard location (for
+example in '/PATH/TO/STATIC/LIBC/libc.a' and
+'/PATH/TO/SYS/CDEFS_H/sys/cdefs.h'), please run the commands below, then
+re-configure the project to fix this problem.
+
+ $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
+ $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS"
+
+_______________________________________________________
+
+EOF
+ fi
+fi
+
+# Print a warning if GCC is not meant to be built.
+if [ x"$gccwarning" = x1 ]; then
+ cat <<EOF
+
+PLEASE SEE THE WARNINGS ABOVE.
+
+Since GCC is pretty low-level, this configuration script will continue in 5
+seconds and use your system's C compiler (it won't build a custom GCC). But
+please consider installing the necessary package(s) to complete your C
+compiler, then re-run './project configure'.
+
+Project's configuration will continue in 5 seconds.
+
+EOF
+ sleep 5
+fi
+
+
+
+
+
+# Fortran compiler
+# ----------------
+#
+# If GCC is ultimately build within the project, the user won't need to
+# have a fortran compiler, we'll build it internally for high-level
+# programs. However, when the host C compiler is to be used, the user needs
+# to have a Fortran compiler available.
+if [ $host_cc = 1 ]; then
+
+ # See if a Fortran compiler exists.
+ hasfc=0;
+ if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
+ if [ $hasfc = 0 ]; then
+ cat <<EOF
+______________________________________________________
+!!!!!!! Fortran Compiler NOT FOUND !!!!!!!
+
+The project won't be building its own GCC (which includes a Fortran
+compiler) on this system. If you need software that need a Fortran
+compiler, it will crash with an error. Fortran is necessary for many
+lower-level scientific programs, hence this warning. Currently we search
+for 'gfortran'. If you have a Fortran compiler that is not checked, please
+get in touch with us (with the form below) so we add it:
+
+ https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+Project's configuration will continue in 5 seconds.
+______________________________________________________
+
+EOF
+ sleep 5
+ else
+
+ # See if the Fortran compiler works
+ testsource=$compilertestdir/test.f
+ echo; echo; echo "Checking host Fortran compiler...";
+ echo " PRINT *, \"... Fortran Compiler works.\"" > $testsource
+ echo " END" >> $testsource
+ if gfortran $testsource -o$testprog && $testprog; then
+ rm $testsource $testprog
+ else
+ rm $testsource
+ cat <<EOF
+
+______________________________________________________
+!!!!!!! Fortran compiler doesn't work !!!!!!!
+
+Host Fortran compiler ('gfortran') can't build a simple program.
+
+A working Fortran compiler is necessary for building some of the project's
+software. Please use the error message above to find a good solution and
+re-run the project configuration.
+
+If you can't find a solution, please send the error message above to the
+link below and we'll try to help
+
+https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+TIP: Once you find the solution, you can use the '-e' option to use
+existing configuration:
+
+ $ ./project configure -e
+
+Project's configuration will continue in 5 seconds.
+______________________________________________________
+
+EOF
+ sleep 5
+ fi
+ fi
+fi
+
+
+
+
+
+# Delete the compiler testing directory
+# -------------------------------------
+#
+# This directory was made above to make sure the necessary compilers can be
+# run.
+rm -rf $compilertestdir
+
+
+
+
+
# Inform the user
# ---------------
#
@@ -117,7 +528,7 @@ EOF
# What to do with possibly existing configuration file
# ----------------------------------------------------
#
-# `LOCAL.mk' is the top-most local configuration for the project. If it
+# `LOCAL.conf' is the top-most local configuration for the project. If it
# already exists when this script is run, we'll make a copy of it as backup
# (for example the user might have ran `./project configure' by mistake).
printnotice=yes
@@ -239,7 +650,7 @@ EOF
bdir=
currentdir=$(pwd)
junkname=pure-junk-974adfkj38
- while [ x$bdir == x ]
+ while [ x$bdir = x ]
do
# Ask the user (if not already set on the command-line).
if [ x"$build_dir" = x ]; then
@@ -264,10 +675,12 @@ EOF
fi
fi
- # Make sure the given directory is not a subdirectory of the
- # source directory.
+ # If its given, make sure it isn't a subdirectory of the source
+ # directory.
if ! [ x"$bdir" = x ]; then
- if [[ $bdir == $currentdir* ]]; then
+ echo "Given build directory: $bdir"
+ if echo "$bdir/" \
+ | grep '^'$currentdir 2> /dev/null > /dev/null; then
# If it was newly created, it will be empty, so delete it.
if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
@@ -299,10 +712,10 @@ if [ x"$input_dir" = x ]; then
else
indir=$input_dir
fi
-mk20name=$(awk '!/^#/ && $1=="MK20DATA" {print $3}' $adir/INPUTS.mk)
-mk20md5=$(awk '!/^#/ && $1=="MK20MD5" {print $3}' $adir/INPUTS.mk)
-mk20size=$(awk '!/^#/ && $1=="MK20SIZE" {print $3}' $adir/INPUTS.mk)
-mk20url=$(awk '!/^#/ && $1=="MK20URL" {print $3}' $adir/INPUTS.mk)
+mk20name=$(awk '!/^#/ && $1=="MK20DATA" {print $3}' $adir/INPUTS.conf)
+mk20md5=$(awk '!/^#/ && $1=="MK20MD5" {print $3}' $adir/INPUTS.conf)
+mk20size=$(awk '!/^#/ && $1=="MK20SIZE" {print $3}' $adir/INPUTS.conf)
+mk20url=$(awk '!/^#/ && $1=="MK20URL" {print $3}' $adir/INPUTS.conf)
if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
cat <<EOF
@@ -387,6 +800,7 @@ if [ $rewritepconfig = yes ]; then
sed -e's|@bdir[@]|'"$bdir"'|' \
-e's|@indir[@]|'"$indir"'|' \
-e's|@ddir[@]|'"$ddir"'|' \
+ -e's|@sys_cpath[@]|'"$sys_cpath"'|' \
-e's|@downloader[@]|'"$downloader"'|' \
-e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
$pconf.in >> $pconf
@@ -630,195 +1044,7 @@ fi
-# Check for C/C++ compilers
-# -------------------------
-#
-# To build the software, we'll need some basic tools (the compilers in
-# particular) to be present.
-hascc=0;
-if type cc > /dev/null 2>/dev/null; then
- if type c++ > /dev/null 2>/dev/null; then hascc=1; fi
-else
- if type gcc > /dev/null 2>/dev/null; then
- if type g++ > /dev/null 2>/dev/null; then hascc=1; fi
- else
- if type clang > /dev/null 2>/dev/null; then
- if type clang++ > /dev/null 2>/dev/null; then hascc=1; fi
- fi
- fi
-fi
-if [ $hascc = 0 ]; then
- cat <<EOF
-______________________________________________________
-!!!!!!! C/C++ Compiler NOT FOUND !!!!!!!
-
-To build the project's software, the host system needs to have basic C and
-C++ compilers. The executables that were checked are 'cc', 'gcc' and
-'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++
-compiler. If you have a relevant compiler that is not checked, please get
-in touch with us (with the form below) so we add it:
-
- https://savannah.nongnu.org/support/?func=additem&group=reproduce
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
-fi
-
-
-
-
-
-# Check C compiler
-# ----------------
-gcc_works=0
-testprog=$tmpblddir/test-c
-testsource=$tmpblddir/test.c
-echo; echo; echo "Checking host C compiler...";
-echo "#include <stdio.h>" > $testsource
-echo "#include <stdlib.h>" >> $testsource
-echo "int main(void){printf(\"...C compiler works.\n\");" >> $testsource
-echo " return EXIT_SUCCESS;}" >> $testsource
-if gcc $testsource -o$testprog && $testprog; then
- rm $testsource $testprog
-else
- rm $testsource
- cat <<EOF
-
-______________________________________________________
-!!!!!!! C compiler doesn't work !!!!!!!
-
-Host C compiler ('gcc') can't build a simple program.
-
-A working C compiler is necessary for building the project's software.
-Please use the error message above to find a good solution and re-run the
-project configuration.
-
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
-
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
-
- $ ./project configure -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
-fi
-
-
-
-
-
-# See if the linker accepts -Wl,-rpath-link
-# -----------------------------------------
-#
-# `-rpath-link' is used to write the information of the linked shared
-# library into the shared object (library or program). But some versions of
-# LLVM's linker don't accept it an can cause problems.
-oprog=$sdir/rpath-test
-cprog=$sdir/rpath-test.c
-echo "#include <stdio.h>" > $cprog
-echo "int main(void) {return 0;}" >> $cprog
-if [ x$CC = x ]; then CC=gcc; fi;
-if $CC $cprog -o$oprog -Wl,-rpath-link &> /dev/null; then
- export rpath_command="-Wl,-rpath-link=$instdir/lib"
-else
- export rpath_command=""
-fi
-rm -f $oprog $cprog
-
-
-
-
-
-# See if we need the dynamic-linker (-ldl)
-# ----------------------------------------
-#
-# Some programs (like Wget) need dynamic loading (using `libdl'). On
-# GNU/Linux systems, we'll need the `-ldl' flag to link such programs. But
-# Mac OS doesn't need any explicit linking. So we'll check here to see if
-# it is present (thus necessary) or not.
-oprog=$sdir/ldl-test
-cprog=$sdir/ldl-test.c
-cat > $cprog <<EOF
-#include <stdio.h>
-#include <dlfcn.h>
-int
-main(void) {
- void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
- return 0;
-}
-EOF
-if gcc $cprog -o$oprog &> /dev/null; then needs_ldl=no; else needs_ldl=yes; fi
-rm -f $oprog $cprog
-
-
-
-
-
-# See if the C compiler can build static libraries
-# ------------------------------------------------
-
-# We are manually only working with shared libraries: because some
-# high-level programs like Wget and cURL need dynamic linking and if we
-# build the libraries statically, our own builds will be ignored and these
-# programs will go and find their necessary libraries on the host system.
-#
-# Another good advantage of shared libraries is that we can actually use
-# the shared library tool of the system (`ldd' with GNU C Library) and see
-# exactly where each linked library comes from. But in static building,
-# unless you follow the build closely, its not easy to see if the source of
-# the library came from the system or our build.
-static_build=no
-
-#oprog=$sdir/static-test
-#cprog=$sdir/static-test.c
-#echo "#include <stdio.h>" > $cprog
-#echo "int main(void) {return 0;}" >> $cprog
-#if [ x$CC = x ]; then CC=gcc; fi;
-#if $CC $cprog -o$oprog -static &> /dev/null; then
-# export static_build="yes"
-#else
-# export static_build="no"
-#fi
-#rm -f $oprog $cprog
-#if [ $printnotice = yes ] && [ $static_build = "no" ]; then
-# cat <<EOF
-#_________________________________________________________________________
-#!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!!
-#
-#Your system's C compiler ('$CC') doesn't support building static
-#libraries. Therefore the dependencies will be built dynamically. This means
-#that they will depend more strongly on changes/updates in the host
-#system. For high-level applications (like most research projects in natural
-#sciences), this shouldn't be a significant problem.
-#
-#But generally, for reproducibility, its better to build static libraries
-#and programs. For more on their difference (and generally an introduction
-#on linking), please see the link below:
-#
-#https://www.gnu.org/software/gnuastro/manual/html_node/Linking.html
-#
-#If you have other compilers on your system, you can select a different
-#compiler by setting the 'CC' environment variable before running
-#'./project configure'.
-#
-#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-#
-#EOF
-# sleep 5
-#fi
-
-
-
-
-
-# inform the user that the build process is starting
+# Inform the user that the build process is starting
# -------------------------------------------------
if [ $printnotice = yes ]; then
tsec=10
@@ -839,12 +1065,13 @@ will be installed in:
**TIP**: you can see which software is being installed at every moment with
the following command. See "Inspecting status" section of
'README-hacking.md' for more. In short, run it while the project is being
-configured (in another terminal, but on this same directory: '`pwd`'):
+configured (in another terminal, but on this same directory: 'pwd'):
- $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done
+ $ ./project --check-config
--------------------------
+Project's configuration will continue in $tsec seconds.
+-------------------------
EOF
sleep $tsec
@@ -854,241 +1081,6 @@ fi
-# If we are on a Mac OS system
-# ----------------------------
-#
-# For the time being, we'll use the existance of `otool' to see if we are
-# on a Mac OS system or not. Some tools (for example OpenSSL) need to know
-# this.
-#
-# On Mac OS, the building of GCC crashes sometimes while building libiberty
-# with CLang's `g++'. Until we find a solution, we'll just use the host's C
-# compiler.
-if type otool > /dev/null 2>/dev/null; then
- host_cc=1
- on_mac_os=yes
-else
- on_mac_os=no
-fi
-
-
-
-
-
-# See if GCC can be built
-# -----------------------
-#
-# On some GNU/Linux distros, the C compiler is broken into `multilib' (for
-# 32-bit and 64-bit support, with their own headers). On these systems,
-# `/usr/include/sys/cdefs.h' and `/usr/lib/libc.a' are not available by
-# default. So GCC will crash with different ugly errors! The only solution
-# is that user manually installs the `multilib' part as root, before
-# running the configure script.
-#
-# Note that `sys/cdefs.h' may be available in other directories (for
-# example `/usr/include/x86_64-linux-gnu/') that are automatically included
-# in an installed GCC. HOWEVER during the build of GCC, all those other
-# directories are ignored. So even if they exist, they are useless.
-gccwarning=0
-if [ $host_cc = 0 ]; then
- if ! [ -f /usr/include/sys/cdefs.h ]; then
- host_cc=1
- gccwarning=1
- cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-This system doesn't have '/usr/include/sys/cdefs.h'. Because of this, the
-project can't build its custom GCC to ensure better reproducibility. We
-strongly recommend installing the proper package (for your operating
-system) that installs this necessary file. For example on some Debian-based
-GNU/Linux distros, you need these two packages: 'gcc-multilib' and
-'g++-multilib'.
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- fi
-
- if [ -f /usr/lib/libc.a ] || [ -f /usr/lib64/libc.a ]; then
- # This is just a place holder
- host_cc=$host_cc
- else
- host_cc=1
- gccwarning=1
- cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-This system doesn't have '/usr/lib/libc.a' or '/usr/lib64/libc.a'. Because
-of this, the project can't build its custom GCC to ensure better
-reproducibility. We recommend installing the proper package (for your
-operating system) that installs this necessary file.
-
-Some possible solutions:
- 1. On some Debian-based GNU/Linux distros, these two packages may fix the
- problem: 'gcc-multilib' and 'g++-multilib'.
- 2. (BE CAREFUL!) If you have '/usr/lib/x86_64-linux-gnu' but don't have
- '/usr/lib64', then running the following command might fix this
- particular problem by making a symbolic link.
- $ sudo ln -s /usr/lib/x86_64-linux-gnu /usr/lib64
- After the configure script is finished, delete the link with 'rm
- /usr/lib64' (you won't need it any more as far as this project is
- concerned).
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- fi
-fi
-
-# See if a link-able static C library exists
-# ------------------------------------------
-#
-# After building GCC, we must use PatchELF to correct its RPATHs. However,
-# PatchELF links internally with `libstdc++'. So a dynamicly linked
-# PatchELF cannot be used to correct the links to `libstdc++' in general
-# (on some systems this causes no problem, but on others it doesn't!).
-#
-# However, to build a Static PatchELF, we need to be able to link with the
-# static C library, which is not always available on some GNU/Linux
-# systems. Therefore we need to check this here. If we can't build a static
-# PatchELF, we won't build any GCC either.
-if [ $host_cc = 0 ]; then
- testprog=$tmpblddir/test-c
- testsource=$tmpblddir/test.c
- echo; echo; echo "Checking if static C library is available...";
- echo "#include <stdio.h>" > $testsource
- echo "#include <stdlib.h>" >> $testsource
- echo "int main(void){printf(\"...yes\");" >> $testsource
- echo " return EXIT_SUCCESS;}" >> $testsource
- if gcc $testsource -o$testprog -static -lc && $testprog; then
- good_static_libc=1
- rm $testsource $testprog
- else
- good_static_libc=0
- rm $testsource
- gccwarning=1
- host_cc=1
- cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-A usable static C library ('libc.a', in any directory) cannot be linked in
-the current settings of this system. Because of this we can't build a
-static PatchELF, hence we can't build GCC.
-
-If you have 'libc.a', but in a non-standard location (for example in
-'/PATH/TO/STATIC/LIBC/libc.a'), please run this command, then re-configure
-the project to fix this problem.
-
-export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- fi
-fi
-
-# Print a warning if GCC is not meant to be built.
-if [ $gccwarning = 1 ]; then
- cat <<EOF
-
-PLEASE SEE THE WARNINGS ABOVE.
-
-Since GCC is pretty low-level, this configuration script will continue in 5
-seconds and use your system's C compiler (it won't build a custom GCC). But
-please consider installing the necessary package(s) to complete your C
-compiler, then re-run './project configure'.
-
-EOF
- sleep 5
-fi
-
-
-
-
-
-# Fortran compiler
-# ----------------
-#
-# If GCC is ultimately build within the project, the user won't need to
-# have a fortran compiler, we'll build it internally for high-level
-# programs. However, when the host C compiler is to be used, the user needs
-# to have a Fortran compiler available.
-if [ $host_cc = 1 ]; then
-
- # See if a Fortran compiler exists.
- hasfc=0;
- if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
- if [ $hasfc = 0 ]; then
- cat <<EOF
-______________________________________________________
-!!!!!!! Fortran Compiler NOT FOUND !!!!!!!
-
-Because the project won't be building its own GCC (which includes a Fortran
-compiler), you need to have a Fortran compiler available. Fortran is
-commonly necessary for many lower-level scientific programs. Currently we
-search for 'gfortran'. If you have a Fortran compiler that is not checked,
-please get in touch with us (with the form below) so we add it:
-
- https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-Note: GCC will not be built because you are either using the '--host-cc'
-option, or you are using an operating system that currently has bugs when
-building GCC.
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
- fi
-
- # See if the Fortran compiler works
- testprog=$tmpblddir/test-f
- testsource=$tmpblddir/test.f
- echo; echo; echo "Checking host Fortran compiler...";
- echo " PRINT *, \"... Fortran Compiler works.\"" > $testsource
- echo " END" >> $testsource
- if gfortran $testsource -o$testprog && $testprog; then
- rm $testsource $testprog
- else
- rm $testsource
- cat <<EOF
-
-______________________________________________________
-!!!!!!! Fortran compiler doesn't work !!!!!!!
-
-Host Fortran compiler ('gfortran') can't build a simple program.
-
-A working Fortran compiler is necessary for building some of the project's
-software. Please use the error message above to find a good solution and
-re-run the project configuration.
-
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
-
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
-
- $ ./project configure -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
- exit 1
- fi
-fi
-
-
-
-
-
# Number of threads for basic builds
# ----------------------------------
#
@@ -1181,6 +1173,32 @@ fi
+# Paths needed by the host compiler (only for `basic.mk')
+# -------------------------------------------------------
+#
+# At the end of the basic build, we need to build GCC. But GCC will build
+# in multiple phases, making its own simple compiler in order to build
+# itself completely. The intermediate/simple compiler doesn't recognize
+# some system specific locations like `/usr/lib/ARCHITECTURE' that some
+# operating systems use. We thus need to tell the intermediate compiler
+# where its necessary libraries and headers are.
+if [ x"$sys_library_path" != x ]; then
+ if [ x"$LIBRARY_PATH" = x ]; then
+ export LIBRARY_PATH="$sys_library_path"
+ else
+ export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path"
+ fi
+ if [ x"$CPATH" = x ]; then
+ export CPATH="$sys_cpath"
+ else
+ export CPATH="$CPATH:$sys_cpath"
+ fi
+fi
+
+
+
+
+
# Build basic software
# --------------------
#
@@ -1188,13 +1206,14 @@ fi
# Bash, Make, or AWK. In this step, we'll install such low-level basic
# tools, but we have to be very portable (and use minimal features in all).
echo; echo "Building necessary software (if necessary)..."
-make -f reproduce/software/make/basic.mk \
+make -k -f reproduce/software/make/basic.mk \
+ sys_library_path=$sys_library_path \
good_static_libc=$good_static_libc \
rpath_command=$rpath_command \
static_build=$static_build \
+ numthreads=$numthreads \
needs_ldl=$needs_ldl \
on_mac_os=$on_mac_os \
- numthreads=$numthreads \
host_cc=$host_cc \
-j$numthreads
@@ -1215,11 +1234,13 @@ else
numthreads=$jobs
fi
.local/bin/env -i HOME=$bdir \
- .local/bin/make -f reproduce/software/make/high-level.mk \
+ .local/bin/make -k -f reproduce/software/make/high-level.mk \
+ sys_library_path=$sys_library_path \
rpath_command=$rpath_command \
static_build=$static_build \
numthreads=$numthreads \
on_mac_os=$on_mac_os \
+ sys_cpath=$sys_cpath \
host_cc=$host_cc \
-j$numthreads
@@ -1279,8 +1300,8 @@ fi
# After everything is installed, we'll put all the names and versions in a
# human-readable paragraph and also prepare the BibTeX citation for the
# software.
-function prepare_name_version() {
-
+prepare_name_version ()
+{
# First see if the (possible) `*' in the input arguments corresponds to
# anything. Note that some of the given directories may be empty (no
# software installed).
@@ -1385,9 +1406,9 @@ echo `.local/bin/date` > $finaltarget
# The configuration is now complete, we can inform the user on the next
# step(s) to take.
if [ x$reproducible_paper_group_name = x ]; then
- buildcommand="./project prepare -j8"
+ buildcommand="./project make -j8"
else
- buildcommand="./project prepare --group=$reproducible_paper_group_name -j8"
+ buildcommand="./project make --group=$reproducible_paper_group_name -j8"
fi
cat <<EOF
diff --git a/reproduce/software/bash/git-post-checkout b/reproduce/software/shell/git-post-checkout
index f6366dc..f6366dc 100755
--- a/reproduce/software/bash/git-post-checkout
+++ b/reproduce/software/shell/git-post-checkout
diff --git a/reproduce/software/bash/git-pre-commit b/reproduce/software/shell/git-pre-commit
index 9d550db..9d550db 100755
--- a/reproduce/software/bash/git-pre-commit
+++ b/reproduce/software/shell/git-pre-commit