#!/bin/bash
#
# -*-shell-script-*-
# Local Variables:
# mode: shell-script
# sh-shell: bash
# End:
# ----------------- this is now the python-3 version ----------------
#
# Copyright 2004, 2005, 2006, 2007, 2008 by The University of York
# Copyright 2009, 2010, 2011, 2012 by The University of York
# Copyright 2012 by Paul Emsley
# Copyright 2012, 2013, 2014, 2015, 2016 by Medical Reserch Council
# Copyright 2014, 2015, 2016, 2017, 2018 by Medical Reserch Council
# Copyright 2019, 2020, 2021, 2022, 2023, 2024 by Medical Research Council
# Author: Paul Emsley
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
#
#
#
# For instructions, read below, starting at :: NOTE ::
#
#
# Prerequisites: sed, GNU make, libtool, wget
#
# libz is optional for the moment
# 1.3 Put RELEASE-NOTES on web site too
# 1.4 Apply both of Ezra's patches of today Wed Mar 2 22:51:36 GMT 2005
# Update clipper version (the one with shelx .fcf ability)
# 1.5 Apply Ezra's gtkglarea patch and GSL patch.
# Update version of FFTW and other updates from MATSUURA Takanori.
# 1.6 Update to mmdb-1.0.8 [# for molrep output]
# 1.7 Fix logic of fftw test
# 1.8 Add the clipper edcalc patch (suggested by Ezra ages ago)
# 1.9 Add Fedora Core 4 support and testing for the need to build mccp4,
# mmdb and clipper.
# 1.10 Tidy up nightly code.
# 1.11 Add code testing the need for guile_gui and goosh.
# 1.12 Tidy nightly code again.
# 1.13 Don't escape the "."s in gsub for new gawk (Ward Smith).
# 1.14 20050628 Test for imlib on the installation, not the system (ignore
# the system).
# 1.15 20050709 Add glib gstrfuncs patch
# 1.16 20050709 Update to guile 1.6.7 and add lt_preloaded_symbols patch
# 1.17 20050721 Added clipper status code to compiling clipper part.
# Redirect stderr output?
# fix build_mccp4 problem.
# 1.18 20050722 Fix guile build (wrong http tar file).
# Added freeglut
# 1.19 20050803 Update version of guile-gtk to 0.41
# 1.20 20050815 Several updates and clean up from MATSUURA Takanori.
# 1.21 20050815 Stop if wget test fails.
# 1.22 20050916 Update build for freeglut to use --disable-warnings and
# CFLAGS
# 1.23 20050916 Move "set" so we don't see confusing default coot_version
# 1.24 20051012 Do pre-release tars for a few days.
# 1.25 20051017 Don't make install if Coot's makes fails. Don't make -k
# 1.26 20051018 Handle clipper nxmap patch.
# 1.27 20051027 [Gif, Paris] Fix tarred directory for nightly pre-release
# tars.
# 1.28 20051101 Fix the md5sum for nxmap.h
# 1.29 20051104 Apply most of MATSUURA Takanori's fixes.
# Use CCP4 libs (mtz, clipper, mmdb).
# 1.30 20051109 Darwin setting of FC for CCP4 libs configure.
# 1.31 20051114 Fix coot tar file problem on building pre-release (or not).
# 1.32 20060205 Add scripting variable debugging (its currently not making
# python tar files)
# 1.33 20060214 Get wget testing tar file from YSBL, not chem.gla
# 1.34 20060219 Correct the install position of libccp4c.la
# 1.35 20060219 create time stamp with current time, not the time of
# the previous ccp4 libs file, now the find ctime test works
# as I wanted.
# 1.36 20060220 Add a libmmdb.la too.
# 1.37 20060222 Add Bob Nolte's proxy settings
# 1.38 20060224 dylib variable for libmmdb.la and libccp4c.la
# 1.39 20060225 Fix sedding of libmmdb.la and libccp4c.la
# 1.40 20060323 copy over coot.py to share/coot/python (if we built with
# python)
# 1.41 20060401 Big changes for ccp4 5.0.2 ccp4c libs.
# 1.42 20060404 Various small build debuggings.
# 1.43 20060405 Fix do_nightlies syntax error and fix up glut_prefix build
# problem.
# 1.44 20060405 Fix the tarred directory name when this is not a pre-release
# 1.45 20060406 Check for missing reference structures and monomer lib and
# install them if needed.
# 1.46 20060418 use install_top_dir variable to copy over coot.py (not
# $coot_prefix!)
# 1.47 20060419 Remove the mmdb binaries
# 1.48 20060420 J. Maclean says no guile. He is right. So check install for
# guile, not system.
# 1.49 20060420 Replace many $AUTOBUILD_INSTALLED with $install_top_dir.
# 1.50 20060421 Replace other $AUTOBUILD_INSTALLED with $install_top_dir for
# tar file creation.
# 1.51 20060425 net-http was installing into the wrong place because it had
# been set to install_top_dir, but this was not set as a shell
# (or configured) variable so it was just blank [James Murray].
# Now we export install_top_dir.
# 1.52 20060427 Don't add unecessary tagging of -pre-release to tar_dir at
# the end.
# 1.53 20060503 Force GSL to be in $install_top_dir rather than anywhere.
# 1.54 20060519 Update to extract the right coot version from the release and
# pre-release directories.
# 1.55 20060621 Shuffle around the test for using pre-release
# 1.56 20060626 Fixes from MATSUURA Takanori. Shuffle around the usage of
# install_top_dir.
# 1.57 20060704 run imlib-config from the installation, not anywhere.
# 1.58 20060705 Fix wrong directory to build libtiff.
# 1.59 20060706 guile-config should run with an argument, otherise it
# returns with exit status 1 (and we test for non-zero).
# 1.60 20060706 Fix (directory for) mmdb include file test.
# 1.61 20060707 Add to coot configure line the option for guile_gtk
# 1.62 20060708 Fix coot_prerelease_exists typo in setting install_top_dir
# (oops).
# 1.63 20060708 Add jpeg dependency for imlib
# 1.64 20060708 Add libungif test to installation, not system (imlib
# dependency).
# 1.65 20060710 Add removal of coot_wrap_guile.cc compilation when python
# scripting.
# 1.66 20060710 Python on a Sunday.
# 1.67 20060711 Try to fix up the Makefile for PNG.
# 1.68 20060723 Add in the updates to ltmain.sh, ltconfig and config.guess/sub
# for Mactel build. Add build for readline.
# Readline version typo fixed.
# 1.69 20060724 ENABLE_PYTHON_COOT variable is tested. Don't display
# a variables if we are using a proxy.
# 1.70 20060728 pass CFLAGS and LDFLAGS to guile's configure
# 1.71 20060730 Add test for 64-bit Linux to update config.xxxs and libtool.
# Installation readline built now, not system.
# 1.72 20060801 Use mmdb-1.0.8-ysbl-2, which installs includes in the include
# dir. This matches clipper cif_data_io.cpp which presumes that
# it is there. (And is a clean thing to do anyway).
# 1.73 20060801 Use the new version of libccp4c, with some of Ralf's patches
# and includes that go into include/ccp4 dir.
# 1.74 20060801 Use CCP4_CXXFLAGS argument to clipper (it does the wrong thing
# with --with-ccp4)
# 1.75 20060801 Use -pre-2 version of SSMlib, that has -Ixxx/include/mmdb to
# find mmdb include files.
# 1.76 20060808 test for libjpeg.$shared_lib_ext not libjpeg.so. LTE bug.
# 1.77 20060818 Force update of libtool and config files for libjpeg. Extend
# the make install proceedure. Lynn Ten Eyck reported problems
# here.
# 1.78 20060823 Add poll fix and getpwuid fix to glib build on Intel Mac.
# 1.79 20060827 Add fix for gtk-canvas from fink for Intel Mac.
# 1.80 20061002 Change freeglut test to test instaltion, not system.
# 1.81 20061012 The path used to find *-config files should be the same one
# that new executables are added (it was $AUTOBUILD_INSTALLED)
# and it should be $AUTOBUILD_INSTALLED-pre-release/bin) when
# we are building a pre-release.
# 1.82 20061012 Change the destination tar file so that there are nightly
# and stable directories for the binary tar files on the web
# server.
# 1.83 20061107 cd to the clipper dir when building clipper. Pirate and
# bucca are not (attempted to be) built then.
# 1.84 20061107 Capture and report error status from make in GSL (intel mac
# build fails).
# 1.85 20061107 Use GSL version 1.8, which includes Charles Ballard's fix for
# fp_regs.h
# 1.86 20061108 Add fink-based args for configure of gtk for Darwin
# 1.87 20061108 Fix ltmain.sh updating for Gtk (oops!).
# 1.88 20061122 Fix coot tar directory now that we have revision numbers in
# tar file name.
# 1.89 20061123 Fix/add test for ssmlib build (now depends on mmdb build) and
# libccp4c build (now depends on xxx/include/ccp4/cmtzlib.h).
# 1.90 20061128 Allow the user to specify if the dependencies should be checked
# on the system or only in the autobuild installed directory.
# Needs more checks to use this. Currently only glib and gtk
# tests.
# 1.91 20061211 Don't make install for guile-gtk if the make fails - or the
# dependency check for guile-gtk in coot's configure passes
# when it should fail (maybe).
# 1.92 20061212 Apply Charles Ballards libtool patch for Macs for imlib and
# guile-gtk.
# 1.93 20061212 Fiddle the env vars to compile gtk+ on Mac.
# 1.94 20070104 Non-pre-release build problems, BINARY_DEST_DIR
# 2.01 20070109 imlib tar gz should be downloaded from the correct directory
# (sigh).
# 2.02 20070117 Try to compile clipper with -fno-strict-aliasing
# 2.03 20070123 Tell us where the gtkglarea include file was found.
# 2.04 20070124 GCC 3.2 on RH8 machine cannot compile new clipper, so add a
# patch if needed.
# 2.05 20070216 Put libtiff after libjpeg and give tiff's configure command
# line args to find jpeg.
# 2.06 20070306 Put in the clipper<->ccp4 new dist patch.
# 2.07 20070319 Remove == comparisons - Lothar Esser.
# 2.08 20070424 --with-jpeg-lib-dir should be a lib dir!
# 2.09 20070501 Fix the setting of coot_version when no pre-release set.
# 2.10 20071002 Post install slim the binaries. Add helper functions.
# 2.11 20071005 Add some debugging to make_tar. It doesn't seem to work
# currently.
# 2.12 20071005 Fix post_install_slim call.
# 2.13 20071005 Fix slim_dir
# 2.14 20071006 Adjust python scripting settings, so that it should try
# to compile with python most of the time now.
# 2.15 20071008 Fix extra fi, uncommented typo.
# 2.16 20071010 ENABLE_PYTHON_COOT=no for now.
# 2.17 20071105 Swap out DL Clipper for York clipper [whoosh, bang, kerpow!]
# enable-cns
# 2.18 20071105 Backpeddle to mmdb 1.08. Baah.
# 2.19 20071108 Version 1.08-ysbl-3 of mmdb.
# 2.20 20071118 No longer make the full fat tar file.
# 2.21 20071120 Sourcefource no longer distributes libungif, now in
# ysbl software/extras
# 2.22 20071121 set the architecture for ubuntu systems.
# 2.23 20071125 Fix typo in recent fixes.
# 2.24 20071126 Fix setting of systype for MacOSX, hopefully.
# 2.25 20071126 Another try to fix setting of systype for MacOSX.
# 2.26 20071130 Try to enable python
# 2.27 20071207 More python tinkering. Upgrade to 2.5.1
# 2.28 20071207 Add greg. If in York, use it to test before installing.
# 2.29 20071208 Setup CCP4 and use it to test coot before making binaries.
# 2.30 20071209 Add dewinter's ccp4 setup in setup_ccp4.
# 2.31 20071212 Redirect testing output to $LOGS/$HOST-testing.log
# 2.32 20071213 Copy over the ChangeLog, README and RELEASE-NOTES on good test
# 2.33 20071215 Pythonize only sometimes, default off.
# 2.34 20071215 Tell us some Python info
# 2.35 20071215 Python settings outside the subshell.
# 2.36 20071219 Set up for testing and tars on biop too.
# 3.00 20080108 Gtk+-2 version
# 3.01 20080118 Add GtkGlExt
# 3.02 20080121 Tinker with guile build settings.
# 3.03 20080124 Build GTK2 from scratch: librsvg, cairo, pango, glitz. glib, gtk+-2
# 3.04 20080128 Add a test for the existance of pygtk
# 3.05 20080129 Add pkg-config and pygobject
# 3.06 20080130 Add test for pycairo
# 3.07 20080130 pycairo needs 1.4.12 - so test for cairo, setting build_gtk=1 on
# failure
# 3.08 20080130 Remove static patch (for sgi). Add test/build for freetype2
# 3.09 20080130 fontconfig added too.
# 3.10 20080131 Change HOSTLOGDIR to include gtk2 to separate it from gtk1 build logs.
# 3.11 20080201 Fix problem in scripting args to coot's configure.
# 3.12 20080207 Add test and build of ATK, needed for gtk+2.10.x
# 3.13 20080208 lib cleaning problems, add debugging.
# 3.14 20080208 Try requiring gtk 2.10
# 4.00 20080208 Remove gtk2 and pkg-config building. Test for Fedora core 5.
# 4.01 20080211 Remove pycairo build and fix up test for build for guile_gtk
# 4.02 20080212 Add in the Neil Jerram guile-gui patch.
# 4.03 20080213 Add Joseph Moran's fix for handling CC when set.
# 4.04 20080213 Allow python to get through rsync filter, for PHENIX usage.
# 4.05 20080226 Fix up build_guile_gtk usage.
# 4.06 20080428 Apply Joseph Moran's fix correctly.
# 4.07 20080518 Update the status reporting system.
# 4.08 20080607 Bump version of python to 2.5.2
# 4.09 20080617 Update to guile-1.8.5
# 4.10 20080618 As per JED request, number the build logs in a more sensible way.
# 4.11 20080620 Don't run the tests if not in biop or york.
# 4.12 20080624 Add guile-lib to build.
# 4.13 20080729 Correctly test for the up to date python version.
# 4.14 20080729 Adjust test for build_guile_gtk.
# 4.15 20080730 Adjust test for up to date python.
# 4.16 20080730 Use old version of pyobject if pkg-config is not new enough
# 4.17 20080730 Test for gtk minor version, use that to apply guile-gtk patches
# if needed.
# 4.18 20080730 Add Diagnosis for applying guile-gtk patch.
# 4.19 20080818 use mmdb version 1.12
# 4.20 20080918 Remove references to glitz, cairo, fontconfig
# 4.21 20080925 Use pygobject 2.4 if needed (e.g on CentOS 4).
# 4.22 20080925 Handle typename in pygobject.h for CentOS4.
# 4.23 20081007 Don't build python if python is not passed as arg.
# 4.24 20081007 Back to version 2.5.1 that compiles on bragg3, 2.5.2 does not
# (port 8080 already in use).
# 4.25 20081008 Migrate to CCP4 version 6.0.2 for testing in York.
# 4.26 20081014 Use Python 2.6
# 4.27 20081105 Adjust clipper configuration. Remove clipper-new-ccp4-install
# usage, it is no longer needed, it seems. Remove configure
# argument --enable-mmdbold
# 4.28 20081110 Upgrade to mmdb-1.19, get it from EBI.
# 4.29 20081118 Use the ccp4 libs underlay.
# 4.30 20081119 Use -O not -O2 to compile coot on 64 bit machine
# 4.31 20081121 Swig 1.3.34 is OK for 32 bit, I think.
# 4.32 20081122 Use clipper-2.1
# 4.33 20081122 Use clipper-2.1, extra tweaks.
# 4.34 20081122 Add a second test, make a holding directory for tar file before
# second test is run.
# 4.35 20081124 test for greg using full path to guile.
# 4.36 20081130 Bump the gmp version to 4.2.4 (Does that fix the gmp.h on
# intrepid problem?)
# 4.37 20090220 Fix up guile-gui, post-neil-jerram patch added.
# 4.38 20090423 Fix up PYTHONPATH when starting greg tests.
# 4.39 20090427 Remove python and its config from bin in slimmed dir
# 4.40 20090506 Upgrade to mmdb 1.21
# 4.41 20090508 add density-score-by-residue to tar ball.
# 4.42 20090517 Remove standard error redirections.
# 4.43 20090522 Update to guile-1.8.6 on the advice of Ed Podharski.
# 4.44 20090523 Add some build info to the mmdb and clipper logs.
# 4.45 20090523 build status results now go to $build_type-build-status
# (not gtk2-build-status)
# 4.46 20090613 Add coot revision info to build status line.
# 4.47 20090617 Make a file (and transfer it if neeeded) type-binary-xxx.txt
# containing the $coot_version of the just-built binary. Used
# in the update-binary mechanism to find if there is a newer
# version than this binary (that we are running).
# 4.48 20090624 Make pre_release_server_dir be biop.ox
# 4.49 20090628 On my_exit, remove the test-status file, not the build-status
# file.
# 4.50 20090628 Change the GSL version to 1.12
# 4.51 20090703 check exit status of wget for coot source tar file.
# 4.52 20090704 mmdb-1.21 from York.
# 4.53 20090706 check build dependencies when on ubuntu
# 4.54 20090722 fix coot_revision typo for build status.
# 4.55 20090724 make compilers_dir depend on build_type (python build logs
# split out)
# 4.56 20090727 Add a date for build-in-progress status
# 4.57 20090728 gtk2 -> $build_type fixups for status
# 4.58 20090730 remove swig from package list tested on ubuntu.
# 4.59 20090913 Add a date to the fail status message
# 4.60 20091001 comment out the deletion of the coot_wrap files.
# 4.61 20091117 update the version of clipper.
# 4.62 20091203 release server is now in oxford.
# 4.63 20091208 Add curl to the build system
# 4.64 20091209 Fix typo in untaring curl tar file.
# 4.65 20091209 Add libidn to build (for curl).
# 4.66 20091209 Test for holding dir in making tar file.
# 4.67 20091209 Add LDFLAGS to args for libcurl configure.
# 4.68 20091210 Add post-process-libcurl logic.
# 4.69 20091216 Don't delete bin/curl, we need it for updates. (20100120 Not any more)
# 4.70 20100120 debugging added to curl build (problems on bragg3).
# 4.71 20100203 Remove goosh.
# 4.72 20100203 Update clipper version.
# 4.73 20100205 only download mmdb once.
# 4.74 20100304 Fix install_top_dir typos.
# 4.75 20101102 Dependency check for gtkglext patch (compatibility with gtk+ version).
# 4.76 20101102 Correct directory for previoius patch.
# 4.77 20110505 switch to new style Refmac library.
# 4.78 20110507 Refmac mon lib to 5.29
# 4.79 20110610 biop -> lmb.bioch
# 4.80 20110707 also make holding directory for stable builds.
# 4.81 20110725 Add goocanvas.
# 4.82 20110725 Add test for gtk and cairo before going ahead with compiling and using
# goocanvas.
# 4.83 20110805 On 64 bit redhat 4, building freeglut, we need to use /usr/X11R6/lib64,
# not /usr/X11R6/lib, edit configure.
# 4.84 20110821 Hack in a solution the the new clipper problem (new clipper with cif
# tools needs new libtools/configure new ccp4 libs (underlay-2).
# 4.85 20111021 Update python to 2.6, guile to 1.8.8, add guile patch.
# 4.86 20111214 Update to mmdb 1.24 (new) which has working LINKRs.
# 4.87 20120108 Use make not MAKE for guile-gtk.
# 4.88 20120120 Don't use -j $nproc for make if we don't have memory.
# 4.89 20120223 Use libccp4c-5.0.2-ysbl-3.tar.gz, that has libccp4c_la_LIBADD.
# 4.90 20120713 debug $coot_dir_name link usage.
# 4.91 20120808 update to handle version of debian in /etc/issue.
# 4.92 20120820 Debian /etc/issue handling for wheezy.
# 4.93 20120921 Update mmdb to version 1.24.2
# 4.94 20130123 Move pre-release and release server-dir to Cambridge.
# 4.95 20130128 Refmac dictionary to 5.39
# 4.96 20130228 New mmdb version - 1.25.0
# 4.97 20130424 Rework (fix typo) for python include directory slimming.
# 4.98 20130424 Remove ssh copying
# 4.99 20130424 swig 1.3.29 is broken no matter what the architecture.
# 5.00 20130425 CXX testing updates (for ubuntu).
# 5.01 20130429 mmdb version bump 1.25.2
# 5.02 20130502 better diagnostic for goocanvas compile
# 5.03 20130503 Remove SWIG version test (now it is not needed to build source)
# 5.04 20130514 Add COOT_BUILD_INFO_STRING.
# 5.05 20130604 For Release 0.7.1, change release vs pre-release logic
# (MRC server).
# 5.06 20130612 More tinkering to get the correct version for release from the server.
# 5.07 20130707 Adjustment to build stable logic.
# 5.08 20130716 Move source server to personal/pemsley.
# 5.09 20130818 Use ssm-1.3
# 5.10 20130824 debugging publish
# 5.11 20130826 Allow build without guile; name directory for building.
# 5.12 20130909 LD_LIBRARY_PATH changes/fixup.
# 5.13 20130910 Force -O usage for guile compilation.
# 5.14 20130920 Publish logs.
# 5.15 20140408 New version of Python.
# 5.16 20140817 Python version to 2.7.8
# 5.17 20140911 SSM updates.
# 5.18 20141128 Add hack bin for debian awk
# 5.19 20141128 Use dist_name for debian (not systype)
# 5.20 20141203 More/better Debian awk hack.
# 5.21 20141203 Unset some build environment variables (including LD_LIBRARY_PATH)
# 5.22 20141210 More LD_LIBRARY_PATH hacking for debian
# 5.23 20141210 libreadline needs to be linked with -lcurses (on Debian)
# 5.25 20141212
# 5.26 20150215 Use /opt/X11 and COOT_CCP4_PACKAGES for dependences on Darwin.
# 5.27 20170925 bump libccp4 version to 6.5.1 - this has libccp4.pc for pkg-config
# 5.28 20170925 Fixes for clipper and guile and gmp version update (gcc-7.2)
# 5.29 20171006 Test for libgnomecanvas devel (now not available in system for Redhat 7.3)
# 5.30 20180109 Update python version.
# 6.00 20200812 include glm
# 6.01 20210430 pkg-config tweak and no remove rdkit libs for coot configure
# 6.02 20220417 add ffi into Python setup.py
# 6.03 20220704 work on GLIB and python modules
# 6.04 20220705 Python still doesn't build (on cluster) - add debugging
# 6.05 20220706 Use https:: instead of ftp::
# 6.06 20220707 try export LD_LIBRARY_PATH=$install_top_dir/lib in Coot section
# 6.07 20220710 libffi fixes for python
# 6.08 20220803-PE pygobject cleanups
# 6.09 20220907-PE meson adjustment for compiling glib (what a pain)
# 6.10 20230603-PE remove goocanvas
# 6.11 20231113-PE print out the script_version
# 6.12 20240105-PE link $HOME/data/greg-data for the testing step
# 6.13 20240216-PE Install Darwin OpenSSL in $install_top_dir
# 6.14 20240220-PE Set the C++ flags for Catch2 (needed for macOS/clang) and build with CMake
# 6.15 20240220-PE OpenSSL and python apiflags and boost bjam updates
# 6.16 20240228-PE Add status of FFTW building
# 6.17 20240229-PE Portentious day. Adding in gettext for libintl for python and rdkit
# 6.18 20240304-PE Remove the --pydebug from Python's configuration
# 6.19 20240306-PE Don't build gettext on anything other than Darwin
# 6.20 20240326-PE Add cairo
# 6.21 20240327-PE Reposition the cairo build (after ninja)
# 6.22 20240427-PE Fix-ups for building on fedora (partial)
# 6.23 20250214-PE Remove build_type (gtk4) from directory names
script_version=6.22
echo ==================================================== add test for SWIG version
echo ==================================================== add test for CMake version
echo this is script version $script_version
# :: NOTE::
# this "strange" construction of variable names: x=${x:=thing} sets the
# variable x only if it has not previously been defined.
#
# So, the idea is that you write a wrapper for this script (defining typically
# AUTOBUILD_INSTALLED, AUTOBUILD_BUILD, LOGS and build_coot_prerelease) then
# source this file. That means that you (probably) don't have to edit your
# version of build-it every time it changes.
# ENABLE_PYTHON_COOT: if ENABLE_PYTHON_COOT is set to 0 or "no" then
# python coot is not enable (guile coot is enabled). if
# ENABLE_PYTHON_COOT is set, but not set to 0 or no then python coot
# is enabled. If ENABLE_PYTHON_COOT is not set, the guile-coot is
# enabled (python coot is not enabled).
# Pythonizing coot makes non-transferable binararies (why?). Let
# the pythonness be controlled on the command line:
#
# At the moment, if you build with Gtk2, you build with python, hence $build_type
# is the same thing.
#
# Set the host and the OS.
# Fairly fundamental.
#
# arch needs inetutils for hostname
OS=$(uname)
HOST=$(hostname)
# Do we need to use a proxy server to get documents from the web? (set
# to 1 if we do)
use_proxy=${use_proxy:=}
# if we do need a proxy then we should give the proxy host and port too:
proxy_host=${proxy_host:=myproxy.com}
proxy_port=${proxy_port:=800}
no_proxy=${no_proxy:=".corp.net.com"}
# set this to true if you want to run the test suite and make binary
# bundles (needs test data and the CCP4 suite):
#
run_tests=${run_tests:=false}
# run the second test? Almost always passes and takes up lots of
# disk space
#
run_second_test=${run_second_test:=true}
# This is where the compiled binaries/libraries/data get installed:
# Note that the directory name must NOT end in a /
#
AUTOBUILD_INSTALLED=${AUTOBUILD_INSTALLED:=${HOME}/autobuild/${OS}-${HOST}}
if test x$GITHUB_ENV = x ; then
: # we are not in a hithub actions build
else
if [ "$CHAPI_ONLY" = true ] ; then
if [ $OS = Darwin ] ; then
AUTOBUILD_INSTALLED=$HOME/install/chapi-Darwin-macos
else
AUTOBUILD_INSTALLED=$HOME/install/chapi-Linux-ubuntu
fi
else
AUTOBUILD_INSTALLED=$HOME/install/coot-Linux-ubuntu
fi
fi
# or perhaps, for the adventurous:
#AUTOBUILD_INSTALLED=$CCP4_MASTER
# This is where the actual build (compilation) master directory is:
# a temporary or scratch directory would be sensible.
#
# AUTOBUILD_BUILD=${HOME}/autobuild
# I'm putting my build on "scratch space"
AUTOBUILD_BUILD=${AUTOBUILD_BUILD:=$HOME/autobuild/building}
# This is where the build logs go:
# suggested value:
# LOGS=$AUTOBUILD_BUILD/logs
# but I want to put my log file on the web, so I put them here:
LOGS=${LOGS:=$HOME/public_html/build-logs/${OS}-${HOST}}
# set this to "no" if you don't want to compile the pre-release code.
# build_coot_prerelease=
build_coot_prerelease=${build_coot_prerelease:=1}
# get build specials, e.g. change the compiler or the compiler options
# (e.g build for debugging), extra libraries etc setup LD_LIBRARY_PATH
# (or whatever) to include the autobuild library dir so that
# intermediate (configure compile) programs run and the addition to
# the path of GNU make and wget.
#
# use this to specify config_extras
#
# options are: GL_prefix, e.g. SunOS has Mesa Graphics - this is
# where to find them:
# glut_prefix, optionally can use freeglut
#
# Suggested value: comment out this line
specs=${specs:=$HOME/autobuild/build-scripts/${HOST}-specials}
# if we are not in chapi mode, we ask
# where has gtk been installed if this is Mac OS?
# (this was from when gtk3 could be installed on macOS).
# I should add /usr/local of course these days
if test "$CHAPI_ONLY" = true ; then
:
else
if test "$OS" = "Darwin" ; then
if test -n "$gtk" ; then
if test -d "$gtk" ; then
: # pass, good
else
echo gtk variable must point to the directory where gtk has been installed
fi
else
# gtk was not set, let's try to guess
testdir=$HOME/gtk/inst
if test -d $testdir ; then
gtk=$HOME/gtk/inst
else
echo this build script needs to know where gtk has been installed
echo \(at the moment\)
echo set gtk to point to the directory where gtk has been installed
exit 2
fi
fi
fi
fi
# Make nightly binary tarballs?
# You probably don't want to do this, so recommended is do_nightlies=0
do_nightlies=${do_nightlies:=1}
# if you do want to build them where should they go?
# NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
NIGHTLY_DEST_DIR=${NIGHTLY_DEST_DIR:=${HOME}/public_html/software/binaries/nightlies/pre-release}
# if we are not building a nightly/pre-release, i.e. this is a binary
# for a stable release, they go somewhere else:
#
STABLE_DEST_DIR=${STABLE_DEST_DIR:=${HOME}/public_html/software/binaries/stable}
# this is given args: arg1(dir) arg2(file-name)
# how do we transfer the file on the build host to the web server?
# Some systems we can simply copy the files. For others, we now have
# this "publish" mechanism (to be overwritten as needed)
publish=${publish:=:}
publish_logs=${publish_logs:=:}
# if umask was not set, then use 0022
# umask 0022
if [ -z "$umask" ] ; then
umask 0022
else
umask "$umask"
fi
# When we fail to extract the correct tar file from the web site, what
# shall we build instead?
#
fallback_coot_version=coot-0.4
# ----------------------------------------------------------------
# End of tinkering with parameters.
# ----------------------------------------------------------------
# First, check that this is bash.
#
if [ "$BASH" = "" ] ; then
echo this shell is not bash\!
echo this script must be run with bash\!
exit
fi
# now the functions:
function mkdir_maybe {
dir=$1
if [ ! -e "$dir" ] ; then
mkdir "$dir"
fi
}
# Give args: prefix-dir and (based on is-static-flag) either
# "clear-static" or "clear-dynamic"
#
function post_install_slim {
echo we are slimming directory "$1"
fat_dir="$1"
cleaned_dir="$2"
clear_type="$3"
echo fat_dir is "$fat_dir"
echo clear_type is "$clear_type"
echo cleaned_dir is "$cleaned_dir"
mkdir_maybe "$cleaned_dir"
mkdir_maybe "$cleaned_dir"/bin
mkdir_maybe "$cleaned_dir"/lib
# and this for pyconfig.h
if [ "$ENABLE_PYTHON_COOT" = yes ] ; then
mkdir_maybe "$cleaned_dir"/include
mkdir_maybe "$cleaned_dir"/include/$python_version
fi
lib_sos=`cd $fat_dir && ls -1 lib/lib*.so*`
lib_as=`cd $fat_dir && ls -1 lib/lib*.a`
if [ "$clear_type" = "clear-dynamic" ] ; then
keep_lib_archs="$lib_as"
fi
if [ "$clear_type" = "clear-static" ] ; then
keep_lib_archs="$lib_sos"
fi
file_list="etc info man share libexec \
libexec/coot-bin \
libexec/findwaters-bin \
libexec/findligand-bin \
libexec/mini-rsr-bin \
libexec/density-score-by-residue-bin \
bin/coot \
bin/findwaters \
bin/findligand \
bin/guile \
bin/coot-density-score-by-residue \
bin/coot-available-comp-id \
bin/coot-compare-dictionaries \
bin/coot-make-shelx-restraints \
bin/coot-dictionary-bond-distributions \
bin/lidia \
bin/curl \
$keep_lib_archs"
if [ "$ENABLE_PYTHON_COOT" = yes ] ; then
# 20090427 remove python and python config from bin dir (as it
# interfers with system python)
file_list="$file_list html \
lib/$python_version include/$python_version"
fi
echo rsyncing...
for file in $file_list ;
do
dn=$(dirname $file)
if [ -e $fat_dir/$file ] ; then
# echo rsync -axr $fat_dir/$file $cleaned_dir/$dn
rsync -axr $fat_dir/$file $cleaned_dir/$dn
else
echo $fat_dir/$file does not exist
fi
done
echo done rsyncing.
}
function make_tar {
echo in make_tar args: $1 $2
echo in make_tar: in dir: $PWD
tar_dir=$1
tar_file_name=$2
cd $install_top_dir/..
if [ -e $tar_dir ] ; then
echo taring nightly... from $tar_dir to $tar_file_name
tar czf $tar_file_name $tar_dir
status=$?
if [ "$status" != 0 ] ; then
echo ERROR:: tar czf $tar_file_name $tar_dir failed.
echo ERROR:: while in directory $(pwd)
echo ERROR:: tar failed > $tar_file_name.md5sum
rm $tar_file_name
else
md5sum $tar_file_name > $tar_file_name.md5sum
/bin/ls -l $tar_file_name >> $tar_file_name.md5sum
echo done tar successfully.
fi
else
echo ERROR:: tar target directory $tar_dir does not exist.
fi
}
function setup_ccp4 {
# we have access to $OS and $arch.
if test "$OS" = Linux ; then
setup_file=/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/include/ccp4.setup-sh
if test -e $setup_file ; then
. $setup_file
else
if [ "$systype" = x86_64-centos-6 ] ; then
setup_file=/home/emsley/ccp4/setup-scripts/sh/ccp4.setup
else
if [ "$systype" = x86_64-centos-5 ] ; then
setup_file=/home/emsley/ccp4/ccp4-6.2.0/include/ccp4.setup-sh
else
setup_file=setup-ccp4
fi
fi
if test -e $setup_file ; then
echo evaluating $setup_file
. $setup_file
else
echo WARNING:: ccp4 setup file $setup_file does not exist.
fi
fi
fi
if test "$OS" = Darwin ; then
. /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh
fi
}
# exit
function my_exit {
exit_arg=$1
shift
extra_args=$*
# echo fail-build $extra_args > $LOGS/$build-status
if [ -e $LOGS/$test-status ] ; then
rm $LOGS/$test-status
fi
exit $exit_arg
}
# Return 0 on success, 1 on failure (or not tested)
#
#
# This can only be run when the coot tar file and greg tests have been
# untared (in this particular build)
#
# we should be in the directory where coot was untarred for building
# when this function was called.
#
function test_coot {
echo testing with greg
echo testing with greg >&2
echo currently we are here:
pwd
date
if [ "$1" != "" ] ; then
coot_binary=$1
else
coot_binary=$install_top_dir/libexec/coot-bin
fi
if test "$run_tests" = true ; then
# let's test our new coot
# for python build we need to set COOT_PYTHON_DIR and COOT_HOME
# as well as PYTHONPATH things now, because we do a "proper"
# import * from coot, which needs to find coot.py the
# conventional/pythonic way. If pythonic coot doesn't start properly,
# the greg tests fail.
COOT_PYTHON_DIR=$install_top_dir/share/coot/python
PYTHONPATH=$COOT_PYTHON_DIR
PYTHONHOME=$install_top_dir
export COOT_PYTHON_DIR
export PYTHONPATH
export PYTHONHOME
# the greg tests are where the coot source code was untarred.
#
# if it's not there, then let's link it.
if [ ! -d greg-tests ] ; then
echo greg-tests dir missing in this directory:
pwd
echo trying to link
if [ -d ~/data/greg-data ] ; then
ln -s ~/data/greg-data .
else
echo $HOME/data/greg-data data files are not in place
fi
return 1
fi
setup_ccp4
cat <<EOF > command-line-greg.scm
(use-modules (ice-9 greg))
(set! greg-tools (list "greg-tests"))
(set! greg-debug #t)
(set! greg-verbose 5)
(let ((r (greg-test-run)))
(if r
(coot-real-exit 0)
(coot-real-exit 1)))
EOF
echo $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm
$install_top_dir/bin/coot --no-graphics --script command-line-greg.scm
status=$?
if [ $status = 0 ] ; then
echo test_coot: coot test passed
return 0
else
echo test_coot: coot test failed
return 1
fi
else
echo run_tests is not true, not testing.
return 1
fi
}
# Return 0 on success, 1 on failure (or not tested)
#
# we should be in the directory where coot was untarred for building
# when this function was called.
#
function test_coot_python {
echo testing with python unittest
echo testing with python unittest >&2
echo currently we are here:
pwd
if test "$run_tests" = true ; then
# let's test our new coot
# for python build we need to set COOT_PYTHON_DIR and COOT_HOME
# as well as PYTHONPATH things now
COOT_PYTHON_DIR=$install_top_dir/share/coot/python
PYTHONPATH=$COOT_PYTHON_DIR
PYTHONHOME=$install_top_dir
export COOT_PYTHON_DIR
export PYTHONPATH
export PYTHONHOME
echo $install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py
$install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py
status=$?
if [ $status = 0 ] ; then
echo test_coot_python: coot test passed
return 0
else
echo test_coot_python: coot test failed
return 1
fi
else
return 1
fi
}
function fixup_libcurl {
sed s,-L/usr/lib,, curl-config > curl-config.tmp
mv curl-config.tmp curl-config
sed s,-L/usr/lib,, lib/libcurl.la > lib/libcurl.la.tmp
mv lib/libcurl.la.tmp lib/libcurl.la
}
# now we can set the gtk version
gtk_version=${gtk_version:=4}
build_type="" # python and gtk4 are implicit - we will do guile when we can
# now on to some code!
if [ "$use_proxy" = 1 ] ; then
# establish proxy settings
printf "Proxy user: "
read proxy_user
printf "Proxy password: "
read -s proxy_pass
printf "\n"
http_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
https_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
ftp_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
ssl_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
export http_proxy https_proxy ftp_proxy ssl_proxy no_proxy
fi
# use the right (GNU) tar and provide the path to wget (needed
# for downloads) and to GNU make - (which is necesary for python
# at least).
#
# So that python and the *-configs are found when it is installed:
# A bit of a kludge because we do testing for pre-release later.
# It's a logical mess.
#
if test "$build_coot_prerelease" = 1 ; then
PATH=${AUTOBUILD_INSTALLED}-pre-release/bin:$PATH
else
PATH=$AUTOBUILD_INSTALLED/bin:$PATH
fi
PATH=$PATH:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin:
PATH=$PATH:/etc:/usr/etc
#
# This is where the sources downloaded from network go:
AUTOBUILD_SOURCES=${AUTOBUILD_BUILD}/sources
if (! test -d ${AUTOBUILD_SOURCES}) ; then
mkdir -p ${AUTOBUILD_SOURCES}
fi
export PATH
echo PATH is now: $PATH
echo LOGS is $LOGS
echo AUTOBUILD_SOURCES is $AUTOBUILD_SOURCES
echo AUTOBUILD_BUILD is $AUTOBUILD_BUILD
echo AUTOBUILD_INSTALLED is $AUTOBUILD_INSTALLED
echo GITHUB_ENV $GITHUB_ENV
echo GITHUB_WORKSPACE $GITHUB_WORKSPACE
# now make the build logs directory
mkdir -p $LOGS
shared_static_flag="--disable-shared" # huh?
shared_static_flag="--disable-static"
shared_lib_ext=so
systype=unknown
# malloc.h business, Darwin does not have malloc.h
# used in the gtk_canvas build
have_malloc=1
if test "$OS" = "Darwin" ; then
have_malloc=0
fix_ulong=1
update_libtool=1
update_config_guess_sub=1
shared_static_flag="--disable-static"
shared_lib_ext=dylib
# what happens if I do this?
# need_readline_patch=1
# uname -a gives processor type in last field on Darwin
processor=$(uname -a | awk '{print $(NF)}')
need_gtk_imlib_libtool_fix=1
if test "$processor" = "i386" ; then
need_glib_getpwuid_fix=1
need_glib_poll_fix=1
fi
osversion=$(sw_vers -productVersion)
systype=MacOSX-${osversion}-${processor}
fi
# redirect the output.
#
# exec 2>&1 > $LOGS/$HOST.log
# Try not to redirect standard out so that it goes to
# the sub-shell log? (testing)
if [ -n "$TEE_STDOUT" ]; then
echo INFO:: std output will be both printed here and written to $LOGS/build-gtk4.log
exec > >(tee $LOGS/build-gtk4.log)
else
if test "$CHAPI_ONLY" = true ; then
echo INFO:: redirecting std output to $LOGS/build-chapi.log
exec > $LOGS/build-chapi.log
else
echo INFO:: redirecting std output to $LOGS/build-gtk4.log
exec > $LOGS/build-gtk4.log
fi
fi
date
#
if [ -n "$specs" ] ; then
if [ -e "$specs" ] ; then
echo running these extras:
echo . --------------------------------
cat "$specs"
. "$specs"
echo . --------------------------------
fi
fi
#initially unset:
if test $OS = Linux ; then
architecture=$(uname -i)
# uname -i and uname -p (strangely) return unknown on my ubuntu
if test $architecture = unknown ; then
architecture=$(uname -m)
fi
fi
# now architecture is something like i386 or x86_64
# now test for 64 bit Linux:
if test "$OS" = "Linux" ; then
processor=$(uname -a | awk '{print $NF}')
# on my Redhat i386, uname returns:
# Linux kalypso 2.6.12-1.1398_FC4 #1 Fri Jul 15 00:52:32 EDT 2005 i686 athlon i386 GNU/Linux
# 64 bit Ubuntu:
# Linux kalypso 2.6.22-14-generic #1 SMP Sun Oct 14 21:45:15 GMT 2007 x86_64 GNU/Linux
# from that I presume we need $(NF-2) to get the arch (not NF-1). Eh?
# arch=`uname -a | awk '{print $(NF-1)}'`
arch=$(uname -a | awk '{print $(NF-1)}')
echo currently architecture is $architecture
if test "$architecture" = x86_64 -o "$architecture" = ia64 ; then
update_libtool=1
update_config_guess_sub=1
else
echo this is not a 64 bit machine
fi
fi
if test $OS = Linux ; then
if [ -e /bin/rpm ] ; then
if rpm -a ; then
if test -e /etc/os-release ; then
# 20240914 strip quote marks also now
dist_name=$(grep ^ID= /etc/os-release | sed -e 's/ID=//' -e 's/"//g')
dist_ver=$(grep ^VERSION_ID /etc/os-release | sed -e 's/VERSION_ID=//')
else
for i in fedora-release redhat-release redhat-release-workstation centos-release sl-release openSUSE-release ; do
rpm -q --qf '%{name}' ${i}
dist=`rpm -q --qf '%{name}' ${i}`
echo dist is $dist
dist=`rpm -q --qf '%{name}' ${i}`
if test $? = 0 ; then
echo passes with dist $dist
dist_name=$(echo ${dist} | sed -e 's/\-release//g' -e 's/\-workstation//g')
dist_ver=$(rpm -q --qf '%{version}' ${i})
break
else
echo does not pass
dist_name='unknown'
fi
done
fi
else
dist_name='unknown'
fi
else
if test -e /etc/os-release ; then
# 20240914 strip quote marks also now
dist_name=$(grep ^ID= /etc/os-release | sed -e 's/ID=//' -e 's/"//g')
dist_ver=$(grep ^VERSION_ID /etc/os-release | sed -e 's/VERSION_ID=//')
if grep BUILD_ID=rolling /etc/os-release ; then
dist_ver=rolling
fi
fi
fi
echo here 2222 with dist_name $dist_name
echo here 2222 with dist_ver $dist_ver
case ${dist_name} in
redhat* )
case ${dist_ver} in
[0-9] | [0-9].[0-9]* )
systype=${architecture}-redhat-${dist_ver}
;;
* )
systype=${architecture}-rhel-$(echo ${dist_ver} | sed s/[A-Za-z]//g)
if [ $arch = x86_64 ] ; then
if [ $dist_ver = 4WS ] ; then
echo RedHat 4 Linux x86_64 detected. need to update libtool
update_libtool=1
# stupid la file of libcur puts /usr/lib in the link path (early). This causes link
# problems on 64 bit RHEL4. So lets fix curl-config and libcurl.la
post_process_libcurl=1
fi
fi
;;
esac
;;
fedora | centos | openSUSE | rocky | almalinux)
systype=${architecture}-${dist_name}-${dist_ver}
;;
sl )
systype=${architecture}-scientific-linux-${dist_ver}
;;
arch )
systype=${architecture}-arch
;;
* )
if test -r /etc/issue; then
echo this fallback case............
dist_name=$(awk 'NR==1{print tolower($1)}' /etc/issue)
if [ "$dist_name" = "debian" ] ; then
dist_ver=$(awk 'NR==1{x=tolower($2); y=tolower($3); gsub("/","-",x); gsub("/","-",y); print x "-" y}' /etc/issue)
else
dist_ver=$(awk 'NR==1{x=tolower($2); gsub("/","-",x); print x}' /etc/issue)
fi
systype=${architecture}-${dist_name}-${dist_ver}
else
systype=${architecture}-unknown-Linux
fi
;;
esac
fi
echo dist_name $dist_name
echo systype $systype
if test $OS = IRIX64 ; then
osversion=`uname -r`
systype=${osversion}-sgi
fi
if test $OS = IRIX ; then
osversion=`uname -r`
systype=${osversion}-sgi
fi
if test $OS = OSF1 ; then
osversion=`uname -r | sed s/V//g`
systype=${osversion}-OSF1
fi
echo systype: $systype
echo update_libtool: $update_libtool
echo update_config_guess_sub: $update_config_guess_sub
# we need these dependencies:
# - libgtk-3-dev
# - git
# - libsqlite3-dev # needed for python compilation by jupyterlab
# check dependencies for Ubuntu.
case $dist_name in
*ubuntu*)
dep_list='
patch
m4
g++
git
libtool
cmake
swig
flex
bison
gfortran
autoconf
automake
libssl-dev
libblas-dev
liblapack-dev
libc6-dev
libncurses5-dev
libjpeg-dev
libgtk-4-dev'
# gfortran is for numpy
for dep in $dep_list
do
echo $dep
if dpkg-query --status $dep > /dev/null ; then
echo system has $dep
else
echo ======== $dep is missing ======
missing_list="$missing_list $dep"
fi
done
if [ "$missing_list" != '' ] ; then
echo " "
echo " "
echo install these packages: $missing_list
echo then re-run
echo " "
echo " "
my_exit 2
fi
# swig is special. On 6.06 it is not new enough. So Kevin compiled his own.
# swig is tested for later separately.
;;
debian)
# python is needed to configure ninja. Sigh. flex and bison are needed for gobject-introspection
# libbz2-dev is for building python so that torchvision can be installed.
# libsqlite3-dev is needed for ipython (so that Python is compiled "correctly")
dep_list='wget pkg-config libgtk-4-dev build-essential libdw-dev libvorbis-dev libncurses5-dev libssl-dev g++ git libxext-dev libglu1-mesa-dev mesa-common-dev flex bison m4 cmake autoconf gfortran rsync libbz2-dev'
# converted from dep_list='libncurses5-dev g++ libxext-dev libglu1-mesa-dev mesa-common-dev libgtk2.0-dev'
# not tested
for dep in $dep_list
do
echo $dep
if dpkg-query --status $dep > /dev/null ; then
echo system has $dep
else
echo ======== $dep is missing ======
missing_list="$missing_list $dep"
fi
done
if [ "$missing_list" != '' ] ; then
echo " "
echo " "
echo install these packages: $missing_list
echo then re-run
echo " "
echo " "
my_exit 2
fi
;;
# centos7 needs package gtk3-devel to be installed(!)
# fedora needs automake
esac
# 20240305 too noisy
# give us some diagnostic shell information:
# (what extra things did $specs give us?)
#
# if [ "$use_proxy" = 1 ] ; then
# echo no diagnostic variables, we are using a proxy.
# else
# set
# fi
# On 64 bit redhat 4, we (might) need to add X11 to the path for freeglut configure.
#
echo \n\n ============================================ start ============================
echo INFO:: MACHTYPE is $MACHTYPE
echo INFO:: systype is $systype
if [ "$systype" = x86_64-rhel-4 ] ; then
PATH=$PATH:/usr/X11R6/bin
export PATH
fi
# Do we link with sqlite (for the ligands database)?
# We allow the calling script to set use_sqlite=yes
use_sqlite=${use_sqlite:=no}
if [ "$use_sqlite" = "yes" ] ; then
sqlite_config_args=--with-sqlite3
else
sqlite_config_args=
fi
# We want to add some compiler info in the directory name.
# If CC is set, use that,
# If not, try gcc,
# if not, try cc
#
# Similarly for the c++ compiler info
# If CXX is set, use that
# if not, try g++
# if not, try c++
if [ -n "$CC" ] ; then
# CC was set
echo \$HOST is $HOST
echo \$OS is is $OS
gcctest=`$CC --version | awk 'NR==1 {print $2}'`
echo debugging \$CC was $CC
echo debugging gcctest is $gcctest and "(GCC)" is "(GCC)"
if [ "$gcctest" != '(GCC)' ] ; then
# but not gcc
v=$CC-`$CC -v`
if [ $? -ne 0 ] ; then
v="missing_version"
fi
else
# gcc
v=$CC-`$CC --version | awk 'NR==1 {print $3}'`
fi
else
# CC not set
v=gcc-`gcc -dumpversion | head -1`
if [ $? -ne 0 ] ; then
# not gcc
# try cc
v=cc-`cc -v`
if [ $? -ne 0 ] ; then
v="missing_version"
fi
fi
fi
if [ -n "$CXX" ] ; then
# CXX was set
gxxtest=$($CXX --version | awk 'NR==1 {print $2}')
# typically gxxtest is set to "(GCC)", but not on Ubuntu, where the line is:
# g++ (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3
# Scientific Linux:
# g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
# RHEL 6:
# g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
echo gxxtest: $gxxtest
if [ "$gxxtest" != "(GCC)" ] ; then
# but not g++ (?). Maybe it was Ubuntu...
case "$gxxtest" in
*[Uu]buntu*)
w=$($CXX --version | head -1 | awk '{print $3}' | tr -d ')')
;;
*)
w=$CXX-$($CXX -v | head -1 | sed 's/ / /g')
if [ $? -ne 0 ] ; then
w="missing_cxx_version"
fi
;;
esac
else
# g++
w=$CXX-$($CXX --version | awk 'NR==1 {print $3}')
fi
else
# CXX not set
w=g++-`g++ -dumpversion | head -1`
if [ $? -ne 0 ] ; then
# not g++
# try c++
w=c++-`c++ -v`
if [ $? -ne 0 ] ; then
# try CC
w=CC-`CC -v`
if [ $? -ne 0 ] ; then
w="missing_c++_version"
fi
fi
fi
# note that g++ 3.2 cannot compile clipper's test_contrib.cpp.
# So, if we have g++ 3.2 or less, then we need to get and apply
# test_contrib.cpp.patch
# add a space before argument setting
awk -v version=$w 'BEGIN{ exit (version+0 >= 3.3)}'
wvers=$?
if [ $wvers = 0 ] ; then
need_clipper_contrib_patch=true
fi
fi
# do we actually have g++ (or c++?)
if ! g++ --version ; then
if ! c++ --version ; then
echo no c++/g++ compiler. Exit now
my_exit 2
fi
fi
# so now we have v and w set to something. We
# need to sanitize that something.
v_fid=`echo $v | sed 's/ /_/g'`
w_fid=`echo $w | sed 's/ /_/g'`
compilers_dir=gtk4-coot-${v_fid}_and_${w_fid}
if test "$CHAPI_ONLY" = true ; then
compilers_dir=chapi-${v_fid}_and_${w_fid}
fi
HOSTLOGDIR=$LOGS/$compilers_dir
if [ ! -e $HOSTLOGDIR ] ; then
mkdir -p $HOSTLOGDIR
if [ $? -ne 0 ] ; then
#
echo DISASTER: could not make directory $HOSTLOGDIR
echo exiting.
my_exit 2
fi
fi
# 20120223 Whether or not we need to patch guile depends on the
# version of the compiler (or so I currently believe). So here we do
# a string comparison vs "4.5". If greater than this (e.g. "4.5.1") then
# we do need the patch.
#
if awk -v v_fid=$v_fid 'BEGIN{if (v_fid > "gcc-4.5") exit 1 ; else exit 0}' ; then
echo gcc version: $v_fid
else
need_guile_unused_values_patch=true
echo new version path
fi
echo need_guile_unused_values_patch is $need_guile_unused_values_patch
# need to add test that make is GNU make, and set number of processor if we have
# enough memory and cpus...
#
echo "Testing version of make"
MAKE=make
if make --version ; then
# let's try to set some args
if [ -e /proc/meminfo ] ; then
memory_kb=$(awk '/MemTotal:/ {print $2} ' /proc/meminfo)
if [ "$memory_kb" -gt 2000512 ] ; then
if [ -e /proc/cpuinfo ] ; then
if np=$(grep processor /proc/cpuinfo | wc -l) ; then
# limit to 8 processors
if [ "$np" -gt 8 ] ; then
np=8
fi
if [ "$HOST" = hal.lmb.internal ] ; then
np=64
fi
echo using $np processors in compilation
MAKE="make -j$np"
echo MAKE set to $MAKE
fi
fi
fi
fi
if [ $OS = Darwin ] ; then
np=$(system_profiler SPHardwareDataType | awk '/Total Number/ { print $5 }')
MAKE="make -j$np"
fi
else
# definately not GNU make
# Try gmake then....
gmake --version
if [ $? -ne 0 ] ; then
nomake=1
else
MAKE=gmake
nomake=0
fi
if [ $nomake -eq 1 ] ; then
echo Ooops. Your make '(' `which make` ')' is not GNU make and gmake not found.
echo Exiting now.
my_exit 2
fi
fi
echo number of processors for compiling: $np
echo testing for patch
patch --version > /dev/null
if [ $? -ne 0 ] ; then
echo no patch - exit now
my_exit 2
fi
echo testing awk type \(prefer GNU awk\)
if awk --version ; then
echo good, you have an awk from GNU.
else
echo WARNING:: awk is not a GNU awk, trouble ahead possibly.
fi
########################################################################
# cmake
########################################################################
r=$(cmake --version)
echo $r
case $r in
cmake\ version\ 3.1[0-9]*)
echo found recent cmake
cmake_is_good=true
;;
cmake\ version\ 3.[2-9]*)
echo found recent cmake
cmake_is_good=true
;;
cmake\ version\ 4*)
echo found recent cmake
cmake_is_good=true
;;
esac
echo cmake_is_good: $cmake_is_good
if [ "$cmake_is_good" = true ] ; then
echo cmake passes
else
echo $r
echo cmake too old - Version 3.2 or later is needed. Ending now.
exit 2
fi
# create $AUTOBUILD_BUILD directory
if [ ! -d "$AUTOBUILD_BUILD" ] ; then
mkdir "$AUTOBUILD_BUILD"
if [ $? -ne 0 ] ; then
prev_dir=$(dirname $AUTOBUILD_BUILD)
echo $prev_dir
if [ ! -d "$prev_dir" ] ; then
mkdir $prev_dir
mkdir "$AUTOBUILD_BUILD"
fi
fi
if [ ! -d "$AUTOBUILD_BUILD" ] ; then
# echo mkdir of the AUTOBUILD_BUILD \(i.e. "$AUTOBUILD_BUILD"\) failed.
my_exit 2
fi
fi
start_dir=$PWD
echo start_dir $start_dir
cd $AUTOBUILD_BUILD
if [ $? -ne 0 ] ; then
echo $AUTOBUILD_BUILD failed for some reason. Now in `pwd`
fi
# for ccp4 (20051104) compatibility, we can't use colons in the date string
date=$(date -u +'%Y-%m-%d__T%H_%M_%S')
echo Date: $date
# now in $AUTOBUILD_BUILD
BUILDING_DIR=${BUILDING_DIR:=${HOST}_$date}
mkdir $BUILDING_DIR
if [ $? -ne 0 ] ; then
echo mkdir $BUILDING_DIR failed for some reason. Now in `pwd`
fi
cd $BUILDING_DIR
if [ $? -ne 0 ] ; then
echo cd $BUILDING_DIR failed for some reason. Now in `pwd`
fi
build_dir=`pwd`
# test for pkg-config
if type pkg-config ; then
if pkg-config --atleast-pkgconfig-version 0.16 ; then
build_pkg_config=
echo pkg-config is new enough `pkg-config --version`
else
build_pkg_config=1
echo pkg-config should be built \(but won\'t be\).
fi
else
echo pkg-config doesn\'t exist.
fi
echo checking wget
echo which wget
which wget
# use -P for timestamping
# Note that now wget depends on libhogweed and that depends on libgmp
# but we are compiling an old version of gmp (not sure that we need
# an old version) and libhogweed refers to a (now) non-existant
# functions and the dynamic loading fails.
# This setting of the alias fails. It works on the command line.
# -nv is means not-verbose (but not quiet)
# WGET="LD_LIBRARY_PATH=/usr/lib wget -N -P ${AUTOBUILD_SOURCES}"
# WGETO="LD_LIBRARY_PATH=/usr/lib wget -P ${AUTOBUILD_SOURCES}"
WGET="wget -nv -N -P ${AUTOBUILD_SOURCES}"
WGETO="wget -nv -P ${AUTOBUILD_SOURCES}"
# latest version (without .tar.gz extension)
coot_version=$fallback_coot_version
pre_release_server_dir=http://www.ysbl.york.ac.uk/~emsley/software/pre-release/
pre_release_server_dir=http://lmb.bioch.ox.ac.uk/coot/software/source/pre-releases/
pre_release_server_dir=http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/
pre_release_server_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases
#
release_server_dir=http://www.ysbl.york.ac.uk/~emsley/software
release_server_dir=http://lmb.bioch.ox.ac.uk/coot/software/source/releases
release_server_dir=http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/releases/
release_server_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases
#
extras_place=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies
${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $release_server_dir/
${WGETO} -O ${AUTOBUILD_SOURCES}/index-pre-release.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/
pre_release_files_html="none"
if [ $build_coot_prerelease = 1 ] ; then
pre_release_files_html=${AUTOBUILD_SOURCES}/index-pre-release.html
fi
if [ $build_coot_prerelease = yes ] ; then
pre_release_files_html=${AUTOBUILD_SOURCES}/index-pre-release.html
fi
coot_version_tmp=$(awk ' /a href=.*.tar.gz/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \
$pre_release_files_html | tail -1)
echo pre_release_files_html $pre_release_files_html
echo coot_version_tmp : $coot_version_tmp :
if [ -z "$coot_version_tmp" ] ; then
echo clever coot_version extraction failed, using default.
else
coot_version=$coot_version_tmp
echo clever coot_version succeeded, setting coot_version to $coot_version from extraction
fi
# override the switch which turns off the building of the pre-release here:
# build_coot_prerelease=1
# Let's initially set coot_prerelease_exists to not-exist, then we
# try to download it from the Coot web site, and if it exists we set
# coot_prerelease_exists to 1. If it doesn't exist, we don't do that
# of course and we also don't make the install_top_dir to be the pre-release
# directory later on.
coot_prerelease_exists=
# coot_version_pre no longer has .tar.gz extension
if test "$build_coot_prerelease" = 1 ; then
echo debug:: ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/
${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/
coot_version_pre=$(awk ' /a href=.*.tar.gz/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \
${AUTOBUILD_SOURCES}/index.html | tail -1)
echo INFO:: building pre-release and coot_version_pre is $coot_version_pre
if [ -z "$coot_version_pre" ] ; then
# this path when there are no pre-releases to be built, i.e. build the latest release.
echo trying to build pre-release coot, but failed to find pre-release version
echo make a stable release then
build_coot_prerelease=
BINARY_TAR_DEST_DIR=$STABLE_DEST_DIR
mkdir -p ${BINARY_TAR_DEST_DIR}/holding
${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $release_server_dir/
echo examining release server files ${AUTOBUILD_SOURCES}/index.html
# coot_version=$(awk ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { for (file in files) { final=file } ; print final } '
# have another go at latest version extraction.
coot_version=$(awk '/compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[++n]=file; } END { for (file in files) print files[file]}' \
${AUTOBUILD_SOURCES}/index.html | sort | tail -1)
echo coot_version $coot_version
else
build_coot_prerelease=1 # belt and braces
coot_prerelease_exists=1
# tinker with coot_prefix, it is generic_prefix with pre-release added to prefix dir
coot_prefix="--prefix=${AUTOBUILD_INSTALLED}-pre-release ${config_extras:-}"
coot_source_tar_file=${pre_release_server_dir}/$coot_version_pre.tar.gz
echo DEBUG:: set coot_source_tar_file to $coot_source_tar_file
coot_version=`echo $coot_version_pre | sed s/\.tar.gz//`
BINARY_TAR_DEST_DIR=$NIGHTLY_DEST_DIR
mkdir -p ${NIGHTLY_DEST_DIR}
mkdir -p ${BINARY_TAR_DEST_DIR}/holding
echo INFO:: set the target destination for binary tar file \(BINARY_TAR_DEST_DIR\) to $NIGHTLY_DEST_DIR
fi
else
# this is a stable release
echo ============= This is a stable build ==============
${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $release_server_dir/
echo examining release server files ${AUTOBUILD_SOURCES}/index.html
coot_version=$(awk ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { asort(files, indices) ; for (file in files) { final=file } ; print final } ' \
${AUTOBUILD_SOURCES}/index.html | tail -1)
if test -z "$coot_version" ; then
# maybe it wasn't GNU awk (we can't sort the associative array), this will pick a "random" arry key -> coot_version
coot_version=$(awk ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { for (file in files) { final=file } ; print final } ' \
${AUTOBUILD_SOURCES}/index.html | tail -1)
fi
echo coot_version $coot_version
BINARY_TAR_DEST_DIR=$STABLE_DEST_DIR
mkdir -p ${BINARY_TAR_DEST_DIR}
mkdir -p ${BINARY_TAR_DEST_DIR}/holding
fi
echo INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is $BINARY_TAR_DEST_DIR
echo INFO:: coot_version_pre is $coot_version_pre
echo INFO:: build_coot_prerelease is $build_coot_prerelease
echo INFO:: release_server_dir is $release_server_dir
echo INFO:: coot_version is $coot_version
echo INFO:: build_type is $build_type
# set the build prefix for installed stuff. Put everything in the
# pre-release directory if we are building a pre-release.
# (Perhaps this bit of code should go down lower, where we test
# build_coot_prerelease again
#
# we need install_top_dir because we use it to copy over coot.py
# to the install python directory.
# Notes for SSL with python:
# after configure, run this sed:
# real_ssl_prefix=/usr # for mac, for PC, libs go in /usr/lib64 and
# sed -i -e "s?#SSL=.*?SSL=$real_ssl_prefix?" -e 's/^#_ssl/_ssl/' -e's/^#.*-DUSE_SSL/ -DUSE_SSL/' -e 's?^#.*-L$(SSL)/lib? -L$(SSL)/lib?' Modules/Setup
# also add --with-ensurepip=install
# For ubuntu, you need system OpenSSL:
# sudo apt-get install openssl-dev
#
if [ "$build_coot_prerelease" = 1 ] ; then
if [ "$coot_prerelease_exists" = 1 ] ; then
generic_prefix="--prefix=${AUTOBUILD_INSTALLED}-pre-release ${config_extras:-}"
coot_prefix="$generic_prefix"
install_top_dir=${AUTOBUILD_INSTALLED}-pre-release
# python seems to link OK on Darwin, so no need for this jiggery pokery
if [ $(uname) != Darwin ] ; then
# 20220228-PE also -L$install_top_dir/lib64
python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release/lib"
python_ldflags="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release/lib"
python_libs="LIBS=\"-L$install_top_dir/lib64 -lffi\""
python_libs="LIBS='""-L$install_top_dir/lib64 -lffi""'"
python_libs="LIBS=-L$install_top_dir/lib64" # finds libffi
python_rpath="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release/lib"
else
pv=$(sw_vers -productVersion)
# e.g. 10.10
os_minor_version="${pv%.*}"
python_spec_flags="MACOSX_DEPLOYMENT_TARGET=$os_minor_version"
fi
else
# don't use pre-release
generic_prefix="--prefix=$AUTOBUILD_INSTALLED ${config_extras:-}"
coot_prefix="$generic_prefix"
install_top_dir=${AUTOBUILD_INSTALLED}
if [ $(uname) != Darwin ] ; then
python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release/lib"
fi
fi
else
# not pre-release
generic_prefix="--prefix=$AUTOBUILD_INSTALLED ${config_extras:-}"
install_top_dir=${AUTOBUILD_INSTALLED}
coot_prefix="$generic_prefix"
if [ $(uname) != Darwin ] ; then
python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -Wl,--rpath=${AUTOBUILD_INSTALLED}/lib"
python_ldflags="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}/lib"
python_libs="LIBS=\"-L$install_top_dir/lib64 -lffi\""
python_libs="LIBS='""-L$install_top_dir/lib64 -lffi""'"
python_libs="LIBS=-L$install_top_dir/lib64" # finds libffi
python_rpath="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}/lib"
echo python_libs is $python_libs
else
pv=$(sw_vers -productVersion)
# e.g. 10.10
os_minor_version="${pv%.*}"
python_spec_flags="MACOSX_DEPLOYMENT_TARGET=$os_minor_version"
fi
fi
echo install_top_dir $install_top_dir
# this should not be needed
export PATH=$install_top_dir/bin:$PATH
# Hmmm... I am not sure that I want to mess with pkg-config in the
# simple version. But we do...
#
# This allows standard pkg-config to find gtkglext and several other
# things.
#
# override STD_PKGCONFIG_DIR to lib64 dir if we are in 64 bit.
#
os_arch=x86_64-linux-gnu # for now
STD_PKGCONFIG_DIR=/usr/lib/pkgconfig
case "$architecture" in
x86_64*)
STD_PKGCONFIG_DIR=/usr/lib64/pkgconfig
;;
esac
echo HERE A ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
echo HERE A ppppppppppppppp with gtk $gtk
echo HERE A ppppppppppppppp with os_arch $os_arch
if [ -z "$PKG_CONFIG_PATH" ] ; then
# I think that the standard dir is not needed.
# PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$STD_PKGCONFIG_DIR
# FYI packages that go into $install_top_dir/lib/$os_arch/pkgconfig:
# gobject-introspection-1.0.pc
# pygobject-3.0.pc
# py3cairo.pc
# glm.pc
if test -n "$gtk" ; then
PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig
else
PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig
# glib-2.0.pc is found in $install_top_dir/lib64
PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig
fi
else
echo HERE B ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
echo setting PKG_CONFIG_PATH: testing dir $install_top_dir/lib/$os_arch/pkgconfig
if [ -d $install_top_dir/lib/$os_arch/pkgconfig ] ; then
echo HERE C ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
if test -z "$gtk" ; then
PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
else
PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
fi
echo HERE D ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
else
echo HERE E ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
if test -z "$gtk" ; then
echo HERE F ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
else
echo HERE G ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
#PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
# glib-2.0.pc is found in $install_top_dir/lib64
PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
fi
fi
fi
if [ -e /opt/X11/lib/pkgconfig ] ; then
PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$PKG_CONFIG_PATH
fi
echo HERE Z ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
echo "COOT_CCP4_PACKAGES" "$COOT_CCP4_PACKAGES"
if [ -n "$COOT_CCP4_PACKAGES" ] ; then
# PKG_CONFIG_PATH=$COOT_CCP4_PACKAGES/lib/pkgconfig:$PKG_CONFIG_PATH
PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$COOT_CCP4_PACKAGES/lib/pkgconfig
fi
export PKG_CONFIG_PATH
echo PKG_CONFIG_PATH is now $PKG_CONFIG_PATH
# Do we have freetype2? cairo depends on it.
if pkg-config freetype2 ; then
build_freetype2=
echo system/installation has freetype2
else
echo freetype2 should be built
build_freetype2=1
fi
if command -v swig -version ; then
echo swig found
else
echo swig is needed
exit 2
fi
# we need to export this for net-http, because it doesn't set
# variables from configure, we rely on a shell (environment) variable.
export install_top_dir
echo testing for install_top_dir: "$install_top_dir"
if [ ! -e "$install_top_dir" ] ; then
echo $install_top_dir does not exist
echo making directory $install_top_dir
mkdir -p $install_top_dir
if [ $? -ne 0 ] ; then
echo DISASTER: $install_top_dir does not exist and no way
echo to make it.
my_exit 2
fi
else
echo INFO:: $install_top_dir exists already.
fi
echo done testing for $install_top_dir
if [ ! -e "$install_top_dir/lib" ] ; then
echo making "$install_top_dir/lib"
mkdir -p "$install_top_dir/lib"
if [ $? -ne 0 ] ; then
echo DISASTER: $install_top_dir/lib cannot be created
echo to make it.
my_exit 2
fi
fi
#
# append or set LD_LIBRARY_PATH.
#
# this can be problematic for a distributable tar build because this can cause linkage
# against ccp4's libxml2! Hmm!
#
#
if [ -z "$LD_LIBRARY_PATH" ] ; then
LD_LIBRARY_PATH=$install_top_dir/lib
export LD_LIBRARY_PATH
else
LD_LIBRARY_PATH=$install_top_dir/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH
fi
#for Macs:
if test "$OS" = "Darwin" ; then
if [ -z "$DYLD_LIBRARY_PATH" ] ; then
# DYLD_LIBRARY_PATH=$install_top_dir/lib
# export DYLD_LIBRARY_PATH
:
else
#DYLD_LIBRARY_PATH=$install_top_dir/lib:$DYLD_LIBRARY_PATH
#export DYLD_LIBRARY_PATH
:
fi
fi
#
# IRIX64 (on batman at least) does not seem to use LD_LIBRARY_PATH,
# it uses, instead, LD_LIBRARYN32_PATH. So we set that for all
# systems, hoping that it won't do any harm on other systems.
#
# This surely is no longer used - PE 20130909
# LD_LIBRARYN32_PATH=$LD_LIBRARY_PATH
# export LD_LIBRARYN32_PATH
# ccp4_system_type can be one of the following
# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
# linux_compaq_compilers linux_intel_compilers generic Darwin
# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
ccp4_system_type="$OS"
if test "$OS" = Linux ; then
ccp4_system_type=linux
else
if test "$OS" = IRIX64 ; then
ccp4_system_type=irix64
else
if test "$OS" = IRIX ; then
ccp4_system_type=irix
else
if test "$OS" = Darwin ; then
ccp4_system_type=Darwin
fi
fi
fi
fi
echo ccp4_system_type $ccp4_system_type
# clean up old test status:
# echo build-in-progress @`date +"%a_%d_%b_%H:%M"` > $LOGS/build-status
# echo waiting > $LOGS/test-status
# ----------------------------------------------------------------------------
# ----------------------------------------------------------------------------
# which components?
# ----------------------------------------------------------------------------
# ----------------------------------------------------------------------------
#
# Often there are components provided by the operating system or optional
# installs thereof.
#
build_mmdb=0
build_ssmlib=0
build_fftw=0
build_clipper=
build_guile=0
build_guile_www=0
build_guile_gui=0
build_libtool=1
build_net_http=0
build_gsl=0
# build_libungif=0
# build_libtiff=0
# build_libjpeg=0
# build_libpng=0
# build_imlib=0
build_python=
build_pygobject=
build_guile_gtk=
# build_readline=
build_curl=
build_libidn=
# In Gtk2, we presume that glib, gtk2 and gnomecanvas are available.
# We shall test for these, but not build them.
# Where might the "system" components be?
#
non_standard_dir_list="/usr/freeware /sw /opt/gnome $install_top_dir"
dir_list="/usr /usr/X11R6 /usr/local $non_standard_dir_list"
# fftw
# We can eventually get fancy on this... but then clipper configure
# needs changing.
# The test is -n, i.e. a non-zero string length to build things.
#
# We need to test the $AUTOBUILD_INSTALLED directory for fftw because any
# other place could quite well have the fftw that is compiled with doubles.
#
if test -e $install_top_dir/include/fftw.h ; then
echo installation has fftw
build_fftw=
fi
if test -n "$build_fftw" ; then
echo fftw should be built
build_fftw=1
fi
if [ -e $install_top_dir/include/curl/curl.h ] ; then
echo installation has curl/libcurl
else
echo curl should be built
build_curl=1
fi
# ---------- test installation libidn ------------------
#
if [ -e $install_top_dir/include/idn2.h ] ; then
echo installation has libidn2 devel
build_libidn=
else
echo installation does not have libidn2, libcurl should be built also
build_libidn=1
build_curl=1
fi
# Test the output of pkg-config gtk+-2.0 for recent enough gtk.
# If not, then build it yourself.
#
# Experiment, to force bragg3 to compile gtk+2
#
# was 2.8
needed_gtk_version=3.94
# what a mess. Needs cleaning
pkg-config --atleast-version=$needed_gtk_version gtk+-2.0
gtk_pkg_config_status=$?
if [ "$gtk_pkg_config_status" = 0 ] ; then
echo :::::::: gtk version is at least $needed_gtk_version
echo :::::::: gtk version is `pkg-config --modversion gtk+-2.0`
fi
echo libtool test: looking for ${install_top_dir}/include/ltdl.h
if test -e ${install_top_dir}/include/ltdl.h ; then
echo installation has libtool
build_libtool=
else
echo libtool should be built
fi
# ============= python ================
#
# python_version is the filename of the python executable. For python
# 2.5.1 it is python2.5, not python2.5.1
#
python_version=python3.11
pver=3.11.4
python_version_extension=3.11 # extract this
# I think that for python to be compatible with Blender, we don't want the debug version
# python_abiflags=d # because we use --with-pydebug on the command line for Python configure
python_version_squish=311
# for Blender 4 in 2024, we want Python 3.10.13, so uncomment the 3 lines below:
if [ "$CHAPI_ONLY" = true ] ; then
python_version=python3.10
pver=3.10.13
python_version_extension=3.10
python_version_squish=310
# python_version=python3.12
# pver=3.12.7
# python_version_extension=3.12
# python_version_squish=312
fi
# for compatibility with gtk build system
# use_python_version_3_8 is not yet set anywhere.
# future self: set use_python_version_3_8 when needed so that this block gets executed
if [ "$use_python_version_3_8" = true ] ;then
python_version=3.9
pvers=3.9.12
python_version_extension=3.8
fi
# 20240203-PE I don't want version 3.8.
# but more modern pythons do not compile (at least on my mac)
# 20201225-PE this needs checking
# if [ $OS = Darwin ] ; then
# pver=3.6.5
# pver=3.8.12
# fi
# set build_pygobject here
if [ ! -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then
build_pygobject=true
fi
# force the GSL config to be in $install_top_dir, rather than
# potenially getting it from the system
# but does this compile cleanly on Mac OS X? I've forgotten.
# Perhaps we will need to be more clever and potentially use
# the fink GSL if it is available.
# 20240302-PE "fink"? Blimey.
if test -e $install_top_dir/bin/gsl-config ; then
if test $dist_name = arch ; then
unset LD_LIBRARY_PATH
fi
echo $install_top_dir/bin/gsl-config --prefix
$install_top_dir/bin/gsl-config --prefix 2>&1
$install_top_dir/bin/gsl-config --prefix
if test $? != 0 ; then
echo gsl should be built
build_gsl=1
else
gsl_version=`gsl-config --version`
# if you change this, change also gsl_version below.
needed_gsl_version=1.11
needed_gsl_version=1.12
needed_gsl_version=1.15
needed_gsl_version=1.16
needed_gsl_version=2.7
if [ -e $install_top_dir/include/gsl/gsl_version.h ] ; then
build_gsl=
fi
echo installation has the GSL version $gsl_version
if [ "$build_gsl" = 1 ] ; then
echo need to build GSL
else
echo GSL is up to date
fi
fi
else
build_gsl=1
fi
# test for mmdb: Does mmdb_model.h exist, and if it does, does it
# contain MMDBF_IgnoreHash. If not, then build mmdb.
#
# CCP4 mmdb installs in the include/mmdb2 directory,
#
if test -e "${install_top_dir}/include/mmdb2/mmdb_model.h" ; then
build_mmdb=
else
echo installation has no mmdb, build mmdb.
build_mmdb=1
fi
ssm_include_dir=ssm
if [ -e $install_top_dir/include/$ssm_include_dir/ssm_align.h ] ; then
if [ "$build_mmdb" = 1 ] ; then
build_ssmlib=1
else
# do we have SSM version 1.4 or later?
if grep --silent "MINOR_VERSION = [4-9]" $install_top_dir/include/$ssm_include_dir/ssm_defs.h ; then
echo SSM is found.
build_ssmlib=
else
echo we need a newer SSM.
build_ssmlib=1
fi
fi
else
echo SSM not found - needs to be built
build_ssmlib=1
fi
# clipper depends on mmdb, so if mmdb was built, the so must clipper be.
# likewise for fftw.
#
build_clipper=1
if [ -z "$build_mmdb" ] ; then
# we potentially can pass the building of clipper:
echo INFO:: shall we build clipper: mmdb not to be built
if [ -z "$build_fftw" ] ; then
echo INFO:: shall we build clipper: fftw not to be built
# test for new ccp4-based clipper (for mtz and maps)
if [ -e $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h ] ; then
# echo $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h exist
if [ -e $install_top_dir/include/clipper/contrib/sfscale.h ] ; then
# echo $install_top_dir/include/clipper/contrib/sfscale.h exist
build_clipper=
else
echo $install_top_dir/include/clipper/contrib/sfscale.h not exist, building clipper
build_clipper=1
fi
else
echo $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h not exist, building clipper
fi
fi
else
echo mmdb needs to be built, so clipper needs building.
fi
# shall we build libccp4c?
if [ -e $install_top_dir/lib/libccp4c.la ] ; then
# 20170925 test for the pkg-config file
if [ -e $install_top_dir/lib/pkgconfig/libccp4c.pc ] ; then
# no need to rebuild
build_ccp4c=
else
build_ccp4c=1
fi
else
build_ccp4c=1
fi
if [ -e $install_top_dir/bin/$python_version ] ; then
if ${install_top_dir}/bin/$python_version -V ; then
# test for ctypes - was it installed correctly?
ld_lib_path_backup=$LD_LIBRARY_PATH
unset LD_LIBRARY_PATH
if [ "$(${install_top_dir}/bin/$python_version -V)" = "Python $pver" ] ; then
echo found version of Python `${install_top_dir}/bin/$python_version -V` 2>&1
if ${install_top_dir}/bin/$python_version -c 'import ctypes' ; then
echo we have $python_version with working ctypes
else
echo $python_version ctypes failure
build_python=1
fi
else
echo wrong version of Python - needs rebuild
${install_top_dir}/bin/$python_version -V
fi
export LD_LIBRARY_PATH=$ld_lib_path_backup
else
build_python=1
fi
else
build_python=1
fi
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
# build components
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
#
#
# libccp4: (not fortran)
if test -n "$build_ccp4c" ; then
libccp4_version=6.5.1
echo BUILDING libccp4: $libccp4_version
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/libccp4c-5.0.2-ysbl-2.tar.gz
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/libccp4c-5.0.2-ysbl-3.tar.gz
#${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/martyn-extras.tar.gz
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/libccp4c-5.0.2-ysbl-3.tar.gz
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/martyn-extras.tar.gz
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/ccp4-libs-underlay-2.tar.gz
# ${WGET} $extras_place/libccp4c-5.0.2-ysbl-3.tar.gz
# ${WGET} $extras_place/martyn-extras.tar.gz
# ${WGET} $extras_place/ccp4-libs-underlay-2.tar.gz
# ${WGET} $extras_place/libccp4-6.4.0.tar.gz
# ${WGET} ftp://ftp.ccp4.ac.uk/opensource/libccp4-$libccp4_version.tar.gz
${WGET} $extras_place/libccp4-$libccp4_version.tar.gz
echo BUILDING libccp4 $libccp4_version >&2
(
date
gzip -dc ${AUTOBUILD_SOURCES}/libccp4-$libccp4_version.tar.gz | tar xf -
cd libccp4-$libccp4_version
if ./configure $generic_prefix --enable-shared --disable-static --disable-fortran ; then
if $MAKE ; then
$MAKE install
fi
fi
) > $HOSTLOGDIR/01-libccp4.txt 2>&1
echo done libccp4 $libccp4_version >&2
else
echo not building libccp4:
fi
#
# mmdb
#
#
# mmdb
#
if test -n "$build_mmdb" ; then
echo BUILDING mmdb:
#
# mmdb_version=1.0.10. Not yet.
# mmdb_version=1.0.8-ysbl-3
mmdb_version=1.11
mmdb_version=1.12
mmdb_version=1.19
mmdb_version=1.21
mmdb_version=1.22
mmdb_version=1.23
mmdb_version=1.23.2
mmdb_version=1.24
mmdb_version=1.24.2
mmdb_version=1.25.0
mmdb_version=1.25.2
mmdb_version=1.25.3
mmdb_version=2.0.1
mmdb_version=2.0.2
mmdb_version=2.0.5
mmdb_version=2.0.11
mmdb_version=2.0.16
mmdb_version=2.0.19
mmdb_version=2.0.20
mmdb_version=2.0.22
# mmdb_server_dir=ftp://ftp.ccp4.ac.uk/opensource
mmdb_server_dir=$extras_place
${WGET} $mmdb_server_dir/mmdb2-$mmdb_version.tar.gz
echo BUILDING mmdb $mmdb_version >&2
(
date
gzip -dc ${AUTOBUILD_SOURCES}/mmdb2-$mmdb_version.tar.gz | tar xf -
echo gzip -dc ${AUTOBUILD_SOURCES}/mmdb2-$mmdb_version.tar.gz
cd mmdb2-$mmdb_version
pwd
# patch to read long lines in a cif file
# 20091110 this patch is not available, above says that it is badly formed.
# Needs fixing.
# add the following 2 touches because centos 4.6 jackal gives LIBTOOL
# problems on `make'.
# if configure.in newer than aclocal.m4 -> rebuild aclocal.m4
# if aclocal.m4 newer than Makefile.in -> rebuild Makfile.in
# mmdb 1.21 has configure.in newer than aclocal.m4 for some reason.
# must make sure that next version does not.
# touch aclocal.m4
# sleep 2
# touch Makefile.in
./configure $generic_prefix --enable-shared --disable-static
if $MAKE ; then
make install
fi
) > $HOSTLOGDIR/02-mmdb.txt 2>&1
echo done mmdb $mmdb_version >&2
else
echo not building mmdb:
fi
if test -n "$build_ssmlib" ; then
echo BUILDING SSM $ssm_version
echo BUILDING SSM $ssm_version >&2
#
# ssm_version=0.0-pre-2-ysbl
ssm_version=1.4
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/SSMlib-$ssmlib_version.tar.gz
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/SSMlib-$ssmlib_version.tar.gz
# ${WGET} $extras_place/SSMlib-$ssmlib_version.tar.gz
# ${WGET} ftp://ftp.ccp4.ac.uk/opensource/ssm-1.3.tar.bz2
# ${WGET} ftp://ftp.ccp4.ac.uk/opensource/ssm-1.3.tar.bz2
${WGET} $extras_place/ssm-$ssm_version.tar.gz
(
date
# gzip -dc ${AUTOBUILD_SOURCES}/ssm-1.3.tar.bz2 | tar xf -
tar xf ${AUTOBUILD_SOURCES}/ssm-$ssm_version.tar.gz
cd ssm-$ssm_version
./configure $generic_prefix --enable-shared --disable-static CPPFLAGS=-I$install_top_dir/include LDFLAGS=-L$install_top_dir/lib
if $MAKE ; then
$MAKE install
fi
) > $HOSTLOGDIR/02-ssm.txt 2>&1
echo done SSM $ssm_version >&2
else
echo not building ssm:
fi
# fftw
if test -n "$build_fftw" ; then
echo BUILDING fftw:
echo BUILDING fftw 2.1.5: >&2
#
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/fftw-2.1.5.tar.gz
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/fftw-configure-stuff.tar.gz
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/fftw-2.1.5.tar.gz
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/fftw-configure-stuff.tar.gz
${WGET} $extras_place/fftw-2.1.5.tar.gz
# ${WGET} $extras_place/fftw-configure-stuff.tar.gz # Don't need
(
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/fftw-2.1.5.tar.gz | tar xf -
# gzip -dc ${AUTOBUILD_SOURCES}/fftw-configure-stuff.tar.gz | tar xf - # don't need.
cd fftw-2.1.5
if ./configure $generic_prefix --enable-shared --enable-float ; then
if $MAKE ; then
$MAKE install
fi
fi
) > $HOSTLOGDIR/03-fftw.txt 2>&1
echo done fftw >&2
else
echo not building fftw:
fi
# # clipper
# #
# #
if test -n "$build_clipper" ; then
# clipper: we use the ccp4 version of clipper now.
# (it uses configure, not scons)
#
echo BUILDING clipper:
# clipper_version is for the file name on the server, clipper_dir_version is the directory
# that files untars into (20160713 with Marcin in control of the tar dist now they are the
# same, it seems?).
clipper_version=20ac
clipper_version=2.1-081118-ac
clipper_version=2.1-081201-ac
clipper_version=2.1-090210-ac
clipper_version=2.1-090522-ac
clipper_version=2.1-090826-ac
clipper_version=2.1-091215-ac
clipper_version=2.1-100511-ac
clipper_version=2.1
clipper_version=2.1.20160708
clipper_dir_version=2.1
clipper_dir_version=$clipper_version
# ${WGET} http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper-$clipper_version.tar.gz
# 20110921 hack in a temporary solution, while Kevin's new clipper
# is not available yet from his site.
clipper_hack_version=2.1-110915-fixup-2
clipper_hack_version=2.1-140110-fixup
clipper_hack_version=2.1-20170202.tar.gz
# ${WGET} $extras_place/clipper-$clipper_hack_version.tar.gz
# now clipper has all the bits.
# ${WGET} $extras_place/clipper-$clipper_version.tar.gz
# ${WGET} ftp://ftp.ccp4.ac.uk/opensource/clipper-$clipper_version.tar.gz
# Bernie made this tarball
clipper_version=2.1.20180802
clipper_version_dir=2.1
${WGET} $extras_place/clipper-$clipper_version.tar.gz
${WGET} $extras_place/clipper-configure-2.patch
echo BUILDING clipper $clipper_version >&2
(
gzip -dc ${AUTOBUILD_SOURCES}/clipper-$clipper_version.tar.gz | tar xf -
cd clipper-$clipper_version_dir
pwd
date
# patch the hkl_data.h header
# sed -ibackup -e 's/int i = 0; i < list.size(); i++/unsigned int i = 0; i < list.size(); i++/' clipper/core/hkl_data.h
# --- make clipper
# patch clipper
# fix the linking to the wrong libfftw
echo patching clipper with ${AUTOBUILD_SOURCES}/clipper-configure-2.patch
patch -p0 < ${AUTOBUILD_SOURCES}/clipper-configure-2.patch
echo . ------------------------------------------------------------------------------
echo . " clipper "
echo . ------------------------------------------------------------------------------
export CPPFLAGS=-I$install_top_dir/include
export LDFLAGS=-L$install_top_dir/lib
echo CPPFLAGS $CPPFLAGS
echo LDFLAGS $LDFLAGS
echo PKG_CONFIG_PATH $PKG_CONFIG_PATH
# if /usr/lib64/lib(r)fftw.so exists, clipper will link to them
# despite our having build fftw for ourselves - I need to stop
# that (because of clipper's m4/fftw.m4)
save_libs="$LIBS"
export LIBS="-L$install_top_dir/lib:$LIBS"
if [ -z "$LIBS" ] ; then
save_libs=
export LIBS=-L$install_top_dir/lib
else
save_libs="$LIBS"
export LIBS=-L$install_top_dir/lib:$LIBS
fi
echo now we have LIBS $LIBS
echo ./configure --prefix=$install_top_dir \
--enable-mmdb=$install_top_dir \
--enable-ccp4=$install_top_dir \
--enable-shared \
--enable-mmdb \
--enable-cif \
--enable-ccp4 \
--enable-minimol \
--enable-cns \
CXXFLAGS="-g -O2 -fno-strict-aliasing"
./configure --prefix=$install_top_dir \
--enable-mmdb=$install_top_dir \
--enable-ccp4=$install_top_dir \
--enable-shared \
--enable-mmdb \
--enable-cif \
--enable-ccp4 \
--enable-minimol \
--enable-cns \
CXXFLAGS="-g -O2 -fno-strict-aliasing -Wno-narrowing"
export LIBS="$save_libs"
# 20110921 I don't think we need these flags any longer
# CCP4_CXXFLAGS=-I$install_top_dir/include CCP4_LIBS=$install_top_dir/lib/libccp4c.la
# we don't want to make the clipper executables, so let's cd in to the clipper libs and
# make (just) those.
if $MAKE ; then
$MAKE install
fi
) > $HOSTLOGDIR/04-clipper.txt 2>&1
clipper_build_status=$?
if [ $clipper_build_status != 0 ] ; then
echo clipper build failed, exiting
my_exit 2
fi
echo done clipper >&2
else
echo not building clipper:
fi
###############################################################################
# GEMMI is frequently updated and uses git not releases - so always install it.
###############################################################################
if true ; then
echo BUILDING gemmi from git repo \(and installing GEMMI\)
echo BUILDING gemmi from git repo \(and installing GEMMI\) >&2
pwd >&2
echo start_dir is $start_dir
(
save_dir=$(pwd)
cd $start_dir
needs_rebuild=false
if [ -e gemmi ] ; then
pwd
echo path A
cd gemmi
git remote update
git status -uno
needs_rebuild=false
if git status -uno | grep -q "branch is behind" ; then
needs_rebuild=true
git fetch
git merge
fi
echo needs rebuild: $needs_rebuild
cd -
else
pwd
echo path B
git clone https://github.com/project-gemmi/gemmi.git
needs_rebuild=true
fi
# cd gemmi/include
# note to self: fix this for Darwin - which has a crippled cp
# cp -a -r gemmi $install_top_dir/include
# cd -
# cd $save_dir
echo gemmi needs rebuild: $needs_rebuild
echo gemmi needs rebuild: $needs_rebuild > $start_dir/gemmi-rebuild.txt
if $needs_rebuild = true ; then
if [ -d build-gemmi ] ; then
:
else
mkdir build-gemmi
fi
cd build-gemmi
pwd
# add -DUSE_PYTHON=1 here at some stage.
cmake -DCMAKE_INSTALL_PREFIX=$install_top_dir -DBUILD_SHARED_LIBS=ON ../gemmi
if $MAKE ; then
make install
fi
fi
) > $HOSTLOGDIR/05-gemmi.txt 2>&1
cat $start_dir/gemmi-rebuild.txt 2>&1
echo done gemmi
echo done gemmi >&2
fi
#######################################################################
# readline is a dependency of python and guile
#######################################################################
build_readline=true
if [ -e $install_top_dir/include/readline/readline.h ] ; then
build_readline=false
fi
if test "$build_readline" = true ; then
echo BUILDING readline:
echo BUILDING readline: >&2
readline_version=6.2
readline_version=6.3
readline_version=8.2
${WGET} https://ftp.gnu.org/gnu/readline/readline-$readline_version.tar.gz
${WGET} $extras_place/readline-5.1.patch
(
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/readline-$readline_version.tar.gz | tar xf -
cd readline-$readline_version
if test -n "$need_readline_patch" ; then
ls -l
echo patching readline...
# need a patch (for debian only) to add curses to the additional libs line
echo patch -p0 input-from ${AUTOBUILD_SOURCES}/readline-5.1.patch
ls -l ${AUTOBUILD_SOURCES}/readline-5.1.patch
patch -p0 < ${AUTOBUILD_SOURCES}/readline-5.1.patch
fi
if [ "$dist_name" = debian ] ; then
echo applying debian sed patch for shared-lib libreadline
# thanks for the quoting help tony duan @ stackoverflow
sed -i '125,135 s/SHOBJ_LDFLAGS=.*/&\n SHLIB_LIBS='"'"'$(TERMCAP_LIB)'"'"'/' support/shobj-conf
extra_args_for_debian="--with-curses --enable-shared"
fi
if [ "$dist_name" = arch ] ; then
echo in arch block, applying debian sed patch for shared-lib libreadline
# thanks for the quoting help tony duan @ stackoverflow
sed -i '125,135 s/SHOBJ_LDFLAGS=.*/&\n SHLIB_LIBS='"'"'$(TERMCAP_LIB)'"'"'/' support/shobj-conf
extra_args_for_debian="--with-curses --enable-shared"
fi
echo ./configure $generic_prefix $extra_args_for_debian
./configure $generic_prefix $extra_args_for_debian
# single thread
if make ; then
make install
else
echo make of readline failed
fi
) > $HOSTLOGDIR/08-readline.txt 2>&1
else
echo not building readline:
fi
###############################################################################
########## build python and friends #############
###############################################################################
test_for_already_installed_dependencies=true
# So that python3 is found when it is installed:
#
#this should not be needed
export PATH=$install_top_dir/bin:$PATH
# gobject-introspection needs libffi
# meson needs libffi to be intalled before python, so that meson can find ctypes modules
libffi_version=3.2.1
# libffi_version=3.4.3 is available now 20231021-PE
libffi_version=3.4.6
skip_build=false
if [ $test_for_already_installed_dependencies = true ] ; then
if [ -e $install_top_dir/include/ffi.h ] ; then
skip_build=true
echo installation has libffi
else
echo $install_top_dir/include/ffi.h does not exist
fi
fi
if [ $skip_build = false ] ; then
echo BUILDING libffi from libffi-master.zip
echo BUILDING libffi from libffi-master.zip >&2
(
unset LD_LIBRARY_PATH
pwd
echo ${WGET} https://github.com/libffi/libffi/archive/refs/heads/master.zip
${WGET} https://github.com/libffi/libffi/archive/refs/heads/master.zip
ls -l
mv ${AUTOBUILD_SOURCES}/master.zip ${AUTOBUILD_SOURCES}/libffi-master.zip
unzip ${AUTOBUILD_SOURCES}/libffi-master.zip
cd libffi-master
bash autogen.sh
# this was from the other build:
# ./configure --prefix=$install_top_dir --disable-multi-os-directory --enable-portable-binary --enable-shared --disable-static
# where --disable-multi-os-directory was commented out
./configure --prefix="$install_top_dir"
make -j 4
make install
cd -
) > $HOSTLOGDIR/09-libffi.txt 2>&1
else
echo not building libffi >&2
fi
echo post libffi with LD_LIBRARY_PATH $LD_LIBRARY_PATH
echo post libffi with LD_LIBRARY_PATH $LD_LIBRARY_PATH >&2
############## 09b-libffi #####################
build_libffi=true
echo ================= here with build_libffi $build_libffi
#
if [ "$build_libffi" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/lib/pkgconfig/libffi.pc ] ; then
skip_this=true
fi
fi
if [ $skip_this = false ] ; then
echo ========================= build 09b-libffi =================================
(
unset LD_LIBRARY_PATH # or otherwise UP in libreadline problems
echo ========================= build 09b-libffi =================================
echo BUILDING libffi $libffi_version >&2
${WGET} https://github.com/libffi/libffi/releases/download/v$libffi_version/libffi-$libffi_version.tar.gz
if [ -e ${AUTOBUILD_SOURCES}/libffi-$libffi_version.tar.gz ] ; then
tar xf ${AUTOBUILD_SOURCES}/libffi-$libffi_version.tar.gz
else
exit
fi
cd libffi-$libffi_version
# if ./configure --prefix=$install_top_dir --disable-multi-os-directory --enable-portable-binary --enable-shared --disable-static ; then
if ./configure --prefix=$install_top_dir --enable-portable-binary --enable-shared --disable-static ; then
if $MAKE ; then
make install
fi
fi
cd -
) > $HOSTLOGDIR/09b-libffi.txt 2>&1
fi
fi
build_openssl=false
if [ $OS = Darwin ] ; then
if [ -e $install_top_dir/include/openssl ] ; then
echo OpenSSL is installed
build_openssl=false
else
build_openssl=true
fi
else
# what about rocky here also?
if test "$dist_name" = fedora ; then
if [ -e $install_top_dir/include/openssl ] ; then
build_openssl=false
else
build_openssl=true
fi
fi
fi
if [ $build_openssl = true ] ; then
echo BUILDING OpenSSL
echo BUILDING OpenSSL >&2
(
openssl_version=3.2.1
${WGET} https://github.com/openssl/openssl/releases/download/openssl-$openssl_version/openssl-$openssl_version.tar.gz
ls -alt ${AUTOBUILD_SOURCES}
tar xf ${AUTOBUILD_SOURCES}/openssl-$openssl_version.tar.gz
ls -alt
cd openssl-$openssl_version
./Configure --prefix=$install_top_dir --openssldir=$install_top_dir '-Wl,-rpath,$(LIBRPATH)'
$MAKE && make install
cd -
) > $HOSTLOGDIR/10-openssl.txt 2>&1
echo done OpenSSL
echo done OpenSSL >&2
fi
# gettext provides -lintl - which is needed for python on macOS
build_gettext=true
if test $OS = Darwin ; then
if test -e $install_top_dir/include/libintl.h ; then
build_gettext=false
else
echo where is libintl.h in $install_top_dir/include question-mark
ls -l $install_top_dir/include
echo $install_top_dir/include/libintl.h does not exist - hence build_gettext $build_gettext
fi
else
echo gettext: this is $OS, not Darwin
build_gettext=false
fi
if $build_gettext = true ; then
gettext_version=0.22.5
echo BUILDING gettext
echo BUILDING gettext $gettext_version >&2
(
unset LD_LIBRARY_PATH # or otherwise UP in libreadline problems
${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gettext/gettext-$gettext_version.tar.gz
tar xf $AUTOBUILD_SOURCES/gettext-$gettext_version.tar.gz
cd gettext-$gettext_version
./configure --prefix=$install_top_dir --disable-java
$MAKE && make install
cd -
) > $HOSTLOGDIR/11-gettext.txt 2>&1
echo done gettext >&2
else
echo not building gettext >&2
fi
# python
#
if test -n "$build_python" ; then
echo BUILDING Python ${pver}:
echo BUILDING Python ${pver}: >&2
echo ${WGET} http://www.python.org/ftp/python/$pver/Python-$pver.tgz
# hacking in --no-check-certificate is not the right way to do it.
# This is a problem with old(?) wgets. In future, we should remove this.
if ${WGET} --no-check-certificate http://www.python.org/ftp/python/$pver/Python-$pver.tgz ; then
echo got Python-$pver.tgz
else
echo problem getting Python-$pver.tgz
fi
(
date
echo building in: $PWD
unset LD_LIBRARY_PATH
# test raw awk
which awk
awk --version
env
gzip -dc ${AUTOBUILD_SOURCES}/Python-$pver.tgz | tar xf -
cd Python-$pver
# stuff ffi into setup.py
sed -ibackup -e 's/def detect_decimal/ ext.libraries.append("ffi")\n\n &/' setup.py
ffilibdir=$install_top_dir/lib64
sed -ibackup2 -e "s?add_dir_to_list(self.compiler.library_dirs, ./usr/local/lib.)?add_dir_to_list(self.compiler.library_dirs, '$ffilibdir')?" setup.py
# --with-ensurepip=install
# echo INFO:: ./configure $generic_prefix --with-ensurepip=install --enable-shared $python_lib_flags $python_spec_flags
# /Users/pemsley/ccp4/devtools/install
# this should be configured
# note to self: We need ffi.h (and lib presumably) to build the ctypes module (libffi-devel)
# (or I could include it in this build script) (I don't know if ctypes is important)
# 20220227-PE ctypes is crucial for meson
# remove --with-pydebug for now because __PyNegativeRefcount problem on trying to load this into Blender
#
# do we also need to use --with-threads=dir?
if test "$dist_name" = fedora ; then
python_install_top_dir=$HOME/building-python
python_install_top_dir=$HOME/building-python-tt
python_install_top_dir=$install_top_dir
ssl_top_dir=$HOME/building-python
ffi_top_dir=$HOME/building-python
ssl_top_dir=$install_top_dir
ffi_top_dir=$install_top_dir
# INFO:: ./configure --prefix=/home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4 \
# --with-ensurepip=install --enable-shared --with-openssl=/usr \
# CFLAGS=-I/home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib/libffi-3.2.1/include \
# LIBS=-L/home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib64 \
# LDFLAGS=-Wl,--rpath=/home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib
echo ./configure --prefix="$python_install_top_dir" --with-ensurepip=install --enable-shared \
--with-openssl="$ssl_top_dir" \
LIBS=-L$install_top_dir/lib64 LDFLAGS="-Wl,--rpath=$install_top_dir/lib"
if ./configure --prefix="$python_install_top_dir" --with-ensurepip=install --enable-shared \
--with-openssl="$ssl_top_dir" \
LIBS=-L$install_top_dir/lib64 LDFLAGS="-Wl,--rpath=$install_top_dir/lib" ; then
echo INFO:: make for python
if $MAKE ; then
echo INFO:: make install for python
$MAKE install
fi
fi
else
openssl_prefix=/usr
if [ $OS = Darwin ] ; then
openssl_prefix=$install_top_dir
fi
echo INFO:: ./configure $generic_prefix --with-ensurepip=install --enable-shared --with-openssl=$openssl_prefix \
CFLAGS=-I$install_top_dir/lib/libffi-3.2.1/include $python_libs $python_ldflags $python_spec_flags
if ./configure $generic_prefix --with-ensurepip=install --enable-shared --with-openssl=$openssl_prefix \
CFLAGS=-I$install_top_dir/lib/libffi-3.2.1/include $python_libs $python_ldflags $python_spec_flags ; then
echo INFO:: make for python
if $MAKE ; then
echo INFO:: make install for python
$MAKE install
fi
fi
fi
# test it
echo test cypes in the new python
# or use this test: if $install_top_dir/bin/python3 -c 'import ctypes' ; then ...
$install_top_dir/bin/python3 <<EOF
import ctypes
print(dir(ctypes))
print('post ctypes test')
EOF
) > $HOSTLOGDIR/12-python.txt 2>&1
# we need this because boost configuration runs "python" - at least on my Mac
# (finding the correct python(3) doesn't seem to be a problem on the PC).
# The better way is to use cmd-or-prefix, it seems:
# https://www.phind.com/search?cache=z8ao21y6rh5grg4wezeybr06
# try this:
# add
# echo "using python : 3.10 : $install_top_dir/bin/python3 ;" > user-config.jam
if [ -e $install_top_dir/bin/python3 ] ; then
echo linking python to python3
if [ -e $install_top_dir/bin/python ] ; then
rm $install_top_dir/bin/python
fi
ln -s $install_top_dir/bin/python3 $install_top_dir/bin/python
fi
echo BUILDING: Python $pver done >&2
echo Upgrading pip
(
which pip3
pip3 install --upgrade pip
# pip3 install pycairo
# pip3 install pygobject
) > $HOSTLOGDIR/13-pip-upgrade.txt 2>&1
echo Pip update done >&2
else
echo not building python
echo not building python >&2
fi
############ test python, exit on failure ##################
$install_top_dir/bin/$python_version <<EOF
import ctypes
print(dir(ctypes))
EOF
if [ $? = 0 ] ; then
echo Good Python
else
echo Python not working
exit 2
fi
###############################################################################
########## meson before gobject-introspection #############
###############################################################################
# this needs to be reconsidered because gobject-intropsection needs python3
# to build.
build_gobject_introspection=true
if [ -e $install_top_dir/include/gobject-introspection-1.0/giversionmacros.h ] ; then
build_gobject_introspection=false
echo installation has gobject-introspection
fi
# 200918-PE install meson before using it.
#
## --------------- meson ---------------------------------
##
# this version of meson is too old to compile gobject-introspection (20220221)
# pip3 install meson
# we should have meson for pygobject, need version 0.46 or later
# however, is this the way to install pygobject? Or is done with pip3?
#
build_meson=true
if command -v meson --version ; then
echo meson --version
which meson >&2
echo meson --version >&2
meson --version >&2
if meson --version ; then
echo we have meson
v=$(meson --version)
if [[ $v < 1.2.3 ]] ; then
echo meson is too old, current version is $v
build_meson=true
else
build_meson=false
fi
else
build_meson=true
fi
fi
if $build_meson = true ; then
meson_version=1.2.3
meson_version=1.7.0
echo BUILDING: meson $meson_version:
echo BUILDING: meson $meson_version: >&2
(
${WGET} https://github.com/mesonbuild/meson/releases/download/$meson_version/meson-$meson_version.tar.gz
tar xf ${AUTOBUILD_SOURCES}/meson-$meson_version.tar.gz
cd meson-$meson_version
python3 setup.py build
python3 setup.py install
cd -
echo which meson
which meson
echo meson --version
meson --version
) > $HOSTLOGDIR/14-meson.txt 2>&1
else
echo not building meson:
fi
###############################################################################
########## ninja before glib #############
###############################################################################
build_ninja=true
if [ -e $install_top_dir/bin/ninja ] ; then
build_ninja=false
fi
if [ $build_ninja = true ] ; then
echo BUILDING ninja
(
# see https://github.com/ninja-build/ninja/releases
unset LD_LIBRARY_PATH
ninja_version=1.10.2
${WGET} https://github.com/ninja-build/ninja/archive/refs/tags/v$ninja_version.tar.gz
tar xf ${AUTOBUILD_SOURCES}/v$ninja_version.tar.gz
cd ninja-$ninja_version
python3 ./configure.py --bootstrap # builds ninja, requires python
if [ -e ninja ] ; then
cp ninja $install_top_dir/bin
else
echo configure/boostrap of ninja failed - what a surprise.
fi
cd -
) > $HOSTLOGDIR/15-ninja.txt 2>&1
fi
#######################################################################
# Pixman
#######################################################################
# cairo depends on pixman. So let's install that too.
if test -e $install_top_dir/include/pixman-1/pixman.h ; then
echo installation has pixman
else
unset LD_LIBRARY_PATH
pixman_version=0.43.4
echo BUILDING: pixman $pixman_version
echo BUILDING: pixman $pixman_version >&2
(
${WGET} https://www.cairographics.org/releases/pixman-$pixman_version.tar.gz
tar xf $AUTOBUILD_SOURCES/pixman-$pixman_version.tar.gz
cd pixman-$pixman_version
pwd
mkdir build
cd build
# put /usr/lib64 at the front of PKG_CONFIG_PATH so that meson
# picks up the correct version of libpng
export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:$PKG_CONFIG_PATH
echo PKG_CONFIG_PATH is $PKG_CONFIG_PATH
echo meson setup -Dprefix=$install_top_dir ..
meson setup -Dprefix=$install_top_dir ..
ninja
ninja install
) > $HOSTLOGDIR/16-a-pixman.txt
fi
#######################################################################
# Cairo - needed for RKit molecule drawing - which can be used by chapi
#######################################################################
# 20240326-PE
if [ -e $install_top_dir/include/cairo/cairo.h ] ; then
echo installation has cairo
else
# we need modern cairo - because that is what is used by GTK4.
# in fact, perhaps we should build cairo at all on arch...
if test "$dist_name" = arch ; then
(
cairo_version=1.18.2
echo BUILDING: cairo $cairo_version
echo BUILDING: cairo $cairo_version >&2
${WGET} https://www.cairographics.org/releases/cairo-$cairo_version.tar.xz
tar xf $AUTOBUILD_SOURCES/cairo-$cairo_version.tar.xz
cd cairo-$cairo_version
meson setup -Dprefix=$install_top_dir build
cd build
ninja
# ninja install
echo no install of cairo in this path at the moment.
cd ..
cd ..
) > $HOSTLOGDIR/16-b-cairo-by-ninja.txt 2>&1
else
cairo_version=1.16.0 # not meson/ninja
echo BUILDING: cairo $cairo_version
echo BUILDING: cairo $cairo_version >&2
(
unset LD_LIBRARY_PATH
${WGET} https://www.cairographics.org/releases/cairo-$cairo_version.tar.xz
tar xf $AUTOBUILD_SOURCES/cairo-$cairo_version.tar.xz
cd cairo-$cairo_version
pwd
# meson/ninja
# mkdir build
# cd build
# meson -Dprefix=$install_top_dir ..
# ninja
# ninja install
# cd ..
# cd ..
# standard
./configure --prefix=$install_top_dir
if $MAKE ; then
make install
fi
) > $HOSTLOGDIR/16-b-cairo.txt 2>&1
fi
fi
###############################################################################
########## build guile and friends #############
###############################################################################
if test -n "$build_libtool" ; then
echo BUILDING libtool:
# libtool_version=1.5.24
libtool_version=2.4.6
${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libtool/libtool-$libtool_version.tar.gz
(date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/libtool-$libtool_version.tar.gz | tar xf -
unset LD_LIBRARY_PATH
cd libtool-$libtool_version
./configure $generic_prefix
$MAKE
status=$?
if [ "$status" != 0 ] ; then
echo make of libtool failed
else
$MAKE install
fi
) > $HOSTLOGDIR/17-libtool.txt 2>&1
else
echo not building libtool:
fi
###############################################################################
########## build idn #############
###############################################################################
# we build libidn for libcurl. libcurl needs it on RHEL4 because
# there is no /usr/lib/libidn.so. There is a rpm devel package, of
# course, but that is more pain to install than compiling it from
# scratch for coot install.
if test -n "$build_libidn" ; then
echo BUILDING: libidn:
echo BUILDING: libidn: >&2
(
unset LD_LIBRARY_PATH
libidn_version=1.15
libidn_version=2.2.0
# ${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libidn/libidn-$libidn_version.tar.gz
${WGET} https://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libidn/libidn2-$libidn_version.tar.gz
gzip -dc ${AUTOBUILD_SOURCES}/libidn2-$libidn_version.tar.gz | tar xf -
cd libidn2-$libidn_version
./configure $generic_prefix
if $MAKE ; then
$MAKE install
fi
) > $HOSTLOGDIR/18-libidn2.txt 2>&1
else
echo not building libidn2:
fi
# note: libpsl depends on libunistring. If I compile on the command line
# libpsl#s configure finds a library for u8_tolower. From this script
# it does (did) not. Hence move this build up before libpsl
###############################################################################
########## build unistring #############
###############################################################################
build_unistring=true
unistring_version=0.9.6
unistring_version=0.9.10
if [ "$build_unistring" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/unistr.h ] ; then
skip_this=true
fi
fi
echo libunistring skip_this $skip_this
if [ $skip_this = false ] ; then
echo BUILDING libunistring $unistring_version >&2
echo BUILDING libunistring:
(
unset LD_LIBRARY_PATH
echo ========================= build unistring =================================
if [ -e $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz ] ; then
tar xf $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz
else
echo missing file $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz
${WGET} http://mirrorservice.org/sites/ftp.gnu.org/gnu/libunistring/libunistring-$unistring_version.tar.gz
tar xf $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz
fi
cd libunistring-$unistring_version
echo ./configure --prefix=$install_top_dir
if ./configure --prefix=$install_top_dir ; then
if $MAKE ; then
make install
fi
fi
cd -
) > $HOSTLOGDIR/18-libubunistring.txt 2>&1
echo done libunistring $unistring_version >&2
else
echo not building libunistring
fi
fi
#
###############################################################################
########## build libpsl #############
###############################################################################
#
# curl depends on libpsl - should we build that?
# https://github.com/rockdaboot/libpsl/releases/download/0.21.5/libpsl-0.21.5.tar.gz
# seems straightforward...
build_libpsl=true
if test -e $install_top_dir/include/libpsl.h ; then
build_libpsl=false
fi
if test $build_libpsl = true ; then
libpsl_version=0.21.5
echo BUILDING: libpsl $libpsl_version
echo BUILDING: libpsl $libpsl_version >&2
(
pwd
unset LD_LIBRARY_PATH
${WGET} https://github.com/rockdaboot/libpsl/releases/download/0.21.5/libpsl-0.21.5.tar.gz
tar xf ${AUTOBUILD_SOURCES}/libpsl-0.21.5.tar.gz
cd libpsl-$libpsl_version
./configure --prefix=$install_top_dir
$MAKE && make install
) > $HOSTLOGDIR/18-libpsl.txt
fi
#
###############################################################################
########## build curl #############
###############################################################################
#
if test -n "$build_curl" ; then
# curl version 8.10.1 has a build problem on Alma 9.4 (at least). Let's
# try the latest version: 8.11.1
libcurl_version=7.65.3
libcurl_version=8.10.1
libcurl_version=8.11.1
libcurl_version_directory=7_65_3
libcurl_version_directory=8_10_1
libcurl_version_directory=8_11_1
echo BUILDING: curl $libcurl_version
echo BUILDING: curl $libcurl_version >&2
(
# get libcurl from here:
# libcurl_version=7.19.7
# libcurl_version=7.25.0
# libcurl_version=7.27.0
# libcurl_version=7.32.0
# ${WGET} http://curl.haxx.se/download/curl-$libcurl_version.tar.gz
${WGET} https://github.com/curl/curl/releases/download/curl-$libcurl_version_directory/curl-$libcurl_version.tar.gz
gzip -dc ${AUTOBUILD_SOURCES}/curl-$libcurl_version.tar.gz | tar xf -
cd curl-$libcurl_version
echo from tar file ${AUTOBUILD_SOURCES}/curl-$libcurl_version.tar.gz
echo building in: $PWD
unset LD_LIBRARY_PATH
# libcurl has problems with putting the libraries ine right order when we specify
# --with-libidn (it puts the libidn prefix libs at the end of its LDFLAGS and that
# is bad because /usr/lib gets in front, and /usr/lib/libidn.so is missing). So here
# we force the libidn libs at the front of LDFLAGS. Problem found on RHEL4-64bit
# (lemur).
#
# this implicitly uses OpenSSL if it can be configured via pkg-config
#
# 20191211-PE on modern ubuntu: apt install libssl-dev, so that curl's configure finds it
# It's OK to depend on system libssl rather than build it myself.
# Make sure (here) that system has OpenSSL
# on Ubuntu: install it like this:
# apt-get install libssl-dev
#
echo ./configure $generic_prefix --enable-versioned-symbols --with-libidn2=$install_top_dir LDFLAGS=-L$install_top_dir/lib --with-openssl
./configure $generic_prefix --enable-versioned-symbols --with-libidn2=$install_top_dir LDFLAGS=-L$install_top_dir/lib --with-openssl
if $MAKE ; then
if [ -n $post_process_libcurl ] ; then
fixup_libcurl
fi
$MAKE install
# argh! This is such a hack! `make install' installs a broken (see post_process_libcurl
# comments) even though it is fixed by the sed in fixup_libcurl. So *after* the install
# let's install the corrected libcurl.la. Wonderful stuff.
#
if [ -n "$post_process_libcurl" ] ; then
/usr/bin/install -c 'libcurl.la' $install_top_dir/lib/libcurl.la
fi
fi
) > $HOSTLOGDIR/19-curl.txt 2>&1
echo BUILDING: done curl: >&2
else
echo not building curl:
fi
###############################################################################
########## build gsl #############
###############################################################################
#
if test -n "$build_gsl" ; then
# wget http://www.mirror.ac.uk/sites/ftp.gnu.org/gnu/gsl/gsl-1.5.tar.gz
# wget http://ftp.gnu.org/gnu/gsl/gsl-1.6.tar.gz
# if you change this, change needed_gsl_version above
gsl_version=1.12
gsl_version=1.15
gsl_version=1.16
gsl_version=2.7
echo BUILDING: gsl $gsl_version
echo BUILDING: gsl $gsl_version >&2
#
# ${WGET} http://ftp.gnu.org/gnu/gsl/gsl-$gsl_version.tar.gz
# ${WGET} http://ftp.gnu.org/gnu/gsl/gsl-$gsl_version.tar.gz
${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gsl/gsl-$gsl_version.tar.gz
(
date
pwd
unset LD_LIBRARY_PATH
gzip -dc ${AUTOBUILD_SOURCES}/gsl-$gsl_version.tar.gz | tar xf -
cd gsl-$gsl_version
./configure $generic_prefix
$MAKE
status=$?
if [ "$status" != 0 ] ; then
echo ERROR:: GSL make failed.
exit 2
else
echo 1 ---------------------------------------------------------------
echo ' ' make install
echo 1 ----------------------------------------------------------------
$MAKE install
fi
) > $HOSTLOGDIR/20-gsl.txt 2>&1
echo BUILDING: done gsl >&2
else
echo not building gsl:
fi
###############################################################################
########## GLM #############
###############################################################################
if [ -e $install_top_dir/include/glm/glm.hpp ] ; then
echo not building glm
else
echo where is glm/include question-mark
ls $install_top_dir/include
# The glm version is 0.9.9.5 because glm.pc was deleted after that.
# thanks sayurlinux.
# ${WGET} $extras_place/glm-$glm_version.tar.gz
# However, that fails to compile:
# In file included from /Users/runner/autobuild/building/Mac-1710037648402.local_2024-03-10__T03_03_05/glm-0.9.9.5/glm/gtc/random.hpp:82:
# /Users/runner/autobuild/building/Mac-1710037648402.local_2024-03-10__T03_03_05/glm-0.9.9.5/glm/gtc/random.inl:25:17: error: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Werror,-Wimplicit-int-conversion]
# so let's try 0.9.8
glm_version=0.9.9.2
glm_version=1.0.0
glm_version=0.9.9.5
glm_version=0.9.9.8
glm_version=1.0.0
echo BUILDING glm $glm_version:
echo BUILDING glm $glm_version: >&2
# echo fetching https://github.com/g-truc/glm/archive/refs/tags/$glm_version.tar.gz >&2
${WGET} https://github.com/g-truc/glm/archive/refs/tags/$glm_version.tar.gz
echo cp ${AUTOBUILD_SOURCES}/$glm_version.tar.gz ${AUTOBUILD_SOURCES}/glm-$glm_version.tar.gz
cp ${AUTOBUILD_SOURCES}/$glm_version.tar.gz ${AUTOBUILD_SOURCES}/glm-$glm_version.tar.gz
echo ${WGET} $extras_place/glm-CMakeLists-for-glm.pc.patch
${WGET} $extras_place/glm-CMakeLists-for-glm.pc.patch
(
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/glm-$glm_version.tar.gz | tar xf -
cd glm-$glm_version
# restore glm.pc
echo 'prefix=@CMAKE_INSTALL_PREFIX@
includedir=${prefix}/include
Name: GLM
Description: OpenGL Mathematics
Version: @GLM_VERSION@
Cflags: -I${includedir}' > cmake/glm.pc.in
cat cmake/glm.pc.in
echo patch from ${AUTOBUILD_SOURCES}/glm-CMakeLists-for-glm.pc.patch
patch < ${AUTOBUILD_SOURCES}/glm-CMakeLists-for-glm.pc.patch
echo cmake . -DCMAKE_INSTALL_PREFIX=$install_top_dir
cmake . -DCMAKE_INSTALL_PREFIX=$install_top_dir
if $MAKE ; then
make install
fi
) > $HOSTLOGDIR/22-glm.txt 2>&1
echo INFO:: glm-build-sub-shell-status $? >&2
echo done glm: >&2
fi
###############################################################################
########## build numpy #############
###############################################################################
# Let's stop if we need a fortran compiler and don't have it.
#
if [ "$build_numpy" = true ] ; then
if gfortran --version > /dev/null ; then
echo found fortran compiler
else
echo fortran compiler not found.
exit 2
fi
else
echo debug:: build_numpy was $build_numpy
fi
# numpy needs system libblas (and liblapack?) - it's not clear to
# me how to build them otherwise.
# sudo apt-get install libblas-dev liblapack-dev
echo command -v pip3
command -v pip3
# cython
echo pip3 install --upgrade pip
pip3 install --upgrade pip
echo pip3 install cython
pip3 install cython
if test -d $install_top_dir/lib/$python_version/site-packages/nanobind ; then
:
else
echo pip3 install nanobind
echo pip3 install nanobind >&2
pip3 install nanobind
echo pip3 install nanobind done >&2
fi
if [ true = true ] ; then
skip_this=false
# ls -alt $install_top_dir/lib/$python_version/site-packages/numpy/lib/_version.py
if [ -e $install_top_dir/lib/$python_version/site-packages/numpy/lib/_version.py ] ; then
echo numpy is found, skip
skip_this=true
else
echo numpy test file not found: $install_top_dir/lib/$python_version/site-packages/numpy/lib/_version.py
echo numpy was not found - needs building
fi
if [ $skip_this = false ] ; then
# numpy_version=1.19.4
# 20240127-PE Using 1.19.4 I am getting an error installing with Python 3.10 [errno #1].
# So let's try the latest numpy - 1.26.3
numpy_version=1.26.3
# still compilation errors:
# numpy-1.26.3/numpy/core/src/npysort/simd_qsort.dispatch.cpp:11:14: fatal error: x86 -simd-sort/src/avx512-32bit-qsort.hpp: No such file or directory
# 11 | #include "x86-simd-sort/src/avx512-32bit-qsort.hpp"
# | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# compilation terminated.
# numpy_version=2.2.2 # hellish build complexity
numpy_version=1.26.4
echo BUILDING numpy $numpy_version
echo BUILDING numpy $numpy_version >&2
(
echo this gfortran:
command -v gfortran
echo $PATH
# this needs fortran compiler gfortran
# maybe get numpy from github?
# https://github.com/numpy/numpy/releases/download/v1.14.1/numpy-1.14.1.tar.gz
# numpy needset setuptools
# https://github.com/pypa/setuptools/archive/v41.5.1.tar.gz
# numpy source is now zip
# ${WGET} https://pypi.python.org/packages/source/n/numpy/numpy-$numpy_version.tar.gz
# ${WGET} https://pypi.python.org/packages/source/n/numpy/numpy-$numpy_version.zip
# echo Fetching https://github.com/numpy/numpy/archive/refs/tags/v$numpy_version.tar.gz >&2
# ${WGET} https://github.com/numpy/numpy/archive/refs/tags/v$numpy_version.tar.gz
echo ${WGET} https://github.com/numpy/numpy/releases/download/v$numpy_version/numpy-$numpy_version.tar.gz
${WGET} https://github.com/numpy/numpy/releases/download/v$numpy_version/numpy-$numpy_version.tar.gz
#
tar xf ${AUTOBUILD_SOURCES}/numpy-$numpy_version.tar.gz
cd numpy-$numpy_version/
# we need to check that we have a fortran compiler, in this case gnu95
#
if gfortran --version ; then
echo found fortran compiler
else
echo fortran compiler not found.
exit 2
fi
which python3
# OK, back to compiling...
$python_version setup.py build --fcompiler=gfortran
$python_version setup.py install
if [ ! $? ] ; then
echo something bad about numpy.
exit 2
fi
cd -
# let's just try to install it using pip! Maybe that will do good things?
$python_version -m pip install numpy==$numpy_version --force-reinstall
) > $HOSTLOGDIR/23-numpy.txt 2>&1
echo BUILDING numpy $numpy_version finished >&2
fi
fi
###############################################################################
########## build boost - after numpy #############
###############################################################################
# which messes up the log numbering
# there is something wrong here - boost needs to come after numpy
# rdkit needs boost-numpy
build_boost=true
test_for_already_installed_dependencies=true
if [ "$build_boost" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/boost/functional/hash.hpp ] ; then
echo not building boost
skip_this=true
fi
fi
if [ $skip_this = false ] ; then
# 20241002-PE
# try 1.86.0 becausee 1.83 doesn't compile - like this:
# https://github.com/bambulab/BambuStudio/issues/3957
# They fixed the problem by udating the boost - let's try that
boost_version=1_71_0
boost_version=1_72_0
boost_version=1_74_0
boost_version=1_83_0
boost_version=1_86_0
boost_version=1_87_0
boost_server_dir=1.72.0
boost_server_dir=1.72.0
boost_server_dir=1.74.0
boost_server_dir=1.82.0
boost_server_dir=1.83.0
boost_server_dir=1.86.0
boost_server_dir=1.87.0
echo BUILDING boost $boost_version :
echo BUILDING boost $boost_version >&2
boost_home_url=https://dl.bintray.com/boostorg/release/$boost_server_dir/source # old
boost_home_url=https://boostorg.jfrog.io/artifactory/main/release/$boost_server_dir/source
boost_home_url=https://archives.boost.io/release/$boost_server_dir/source/
echo wgetting $boost_home_url/boost_$boost_version.tar.gz
echo ${WGET} $boost_home_url/boost_$boost_version.tar.gz 2>&1
${WGET} $boost_home_url/boost_$boost_version.tar.gz
echo done ${WGET} $boost_home_url/boost_$boost_version.tar.gz 2>&1
echo fetch of $boost_home_url/boost_$boost_version.tar.gz complete.. compiling...
(
echo building ========================= boost $boost_version =========================
gzip -dc ${AUTOBUILD_SOURCES}/boost_$boost_version.tar.gz | tar xf -
cd boost_$boost_version
# compilation falls over
# cc.compile.c++ bin.v2/libs/python/build/gcc-9/release/address-model-/python-3.6/threading-multi/visibility-hidden/long.o
# In file included from ./boost/python/detail/prefix.hpp:13,
# from ./boost/python/long.hpp:8,
# from libs/python/src/long.cpp:5:
# ./boost/python/detail/wrap_python.hpp:57:11: fatal error: pyconfig.h: No such file or directory
# 57 | # include <pyconfig.h>
# | ^~~~~~~~~~~~
# compilation terminated.
# But pyconfig.h is here:
# $HOME/autobuild/Linux-penelope-pre-release-gtk3-python/include/python3.6m/pyconfig.h
address_model=64
pwd
# echo "using python : 3.10 : $install_top_dir/bin/python3 ;" > user-config.jam
echo "using python : $python_version_extension : $install_top_dir/bin/python3 ;" > user-config.jam
echo ./bootstrap.sh --prefix=$install_top_dir --with-python=$install_top_dir/bin/python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams,program_options --without-icu
echo ./bootstrap.sh --prefix=$install_top_dir --with-python=$install_top_dir/bin/python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams,program_options --without-icu > bootstrap-command-save
./bootstrap.sh --prefix=$install_top_dir --with-python=$install_top_dir/bin/python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams,program_options --without-icu
echo boostrap.sh done
# now edit the project-config.jam file using python line
cp project-config.jam project-config.jam-orig
# awk -v itd=$install_top_dir '
# /using python : 3.6/ { print " ",$1,$2,$3,$4,$5,"python3 :", itd "/include/python3.6m :", itd "/lib/libpython3.6m.so ;" }
# $0 !~ "using python : 3.6 "
# ' project-config.jam-orig > project-config.jam
# that was flipping hard work.
# 20201215-PE and now I've commented it out.
# bjam no longer exists
# use -Wno-deprecated-declarations
echo ./b2 address-model=$address_model --debug-configuration cflags=-fPIC -j$np cxxflags="-fPIC -I$install_top_dir/include/python$python_version_extension$python_abiflags -Wno-maybe-uninitialized -Wno-deprecated-declarations" install > b2-command-save
./b2 address-model=$address_model --debug-configuration cflags=-fPIC -j$np cxxflags="-fPIC -I$install_top_dir/include/python$python_version_extension$python_abiflags -Wno-maybe-uninitialized -Wno-deprecated-declarations" install
cd -
) > $HOSTLOGDIR/23-boost.txt
echo done boost $boost_version >&2
fi
fi
################## python diagnostics #########################################
if [ -e $install_top_dir/lib/libboost_python$python_version_squish.a ] ; then
echo libboost_python $install_top_dir/lib/libboost_python$python_version_squish.a was installed
else
echo libboost_python $install_top_dir/lib/libboost_python$python_version_squish.a was not installed
echo libboost_python $install_top_dir/lib/libboost_python$python_version_squish.a was not installed >&2
exit
fi
# this is a hack for charybdis - we need cmake version 3.1 or later
# export PATH=$HOME/cmake/bin:$PATH
############################### eigen ##########################################
eigen_version=3.3.9
if [ -e $install_top_dir/include/eigen3 ] ; then
echo eigen3 is installed
echo eigen3 is installed >&2
else
echo BUILDING eigen $eigen_version
echo BUILDING eigen $eigen_version >&2
(
${WGET} https://gitlab.com/libeigen/eigen/-/archive/$eigen_version/eigen-$eigen_version.tar.gz
tar xf $AUTOBUILD_SOURCES/eigen-$eigen_version.tar.gz
mkdir -p build-eigen
cd build-eigen
cmake -DCMAKE_INSTALL_PREFIX=$install_top_dir ../eigen-$eigen_version
make install
cd -
) > $HOSTLOGDIR/24-eigen.txt 2>&1
echo BUILDING eigen finished >&2
fi
############################### catch2 ##########################################
# rdkit needs catch2 (C++ testing framework).
if [ -e $install_top_dir/include/catch2/catch_config.hpp ] ; then
echo Catch2 is installed
echo Catch2 is installed >&2
else
catch2_version=3.5.2
echo BUILDING catch2 $catch2_version
${WGET} https://github.com/catchorg/Catch2/archive/refs/tags/v$catch2_version.tar.gz
(
unset LD_LIBRARY_PATH
tar xf $AUTOBUILD_SOURCES/v$catch2_version.tar.gz
echo cd Catch2-$catch2_version
cd Catch2-$catch2_version
# meson setup -Dcpp_std=c++17 -Dprefix=$install_top_dir build
# cd build
# ninja
# ninja install
# cd ..
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=$install_top_dir ..
echo $MAKE && make install
$MAKE && make install
cd ..
cd ..
) > $HOSTLOGDIR/25-catch2.txt 2>&1
fi
if [ -d $install_top_dir/include/catch2 ] ; then
echo OK, Catch2 is installed
else
echo FAIL BUILDING Catch2
echo FAIL BUILDING Catch2 >&2
exit
fi
############################### rdkit ##########################################
# we need to set rdkit_tar_size because the WGET doesn't skip the download if the
# file exists. Amazon.
#
build_rdkit=true
rdkit_version=2017_09_3
rdkit_version=2019_09_1 # python 3
rdkit_version=2018_09_2 # Atom pointer wrappers gone, needs coot Dec 2020 patch
rdkit_version=2020_09_3
rdkit_version=2023_03_1
rdkit_version=2023_09_4
rdkit_version=2024_09_4
rdkit_version=2024_09_5
# see https://github.com/rdkit/rdkit/releases
rdkit_home=https://github.com/rdkit/rdkit/archive
rdkit_tar_host_file_name=Release_$rdkit_version.tar.gz
rdkit_tar_download_file_name=rdkit-Release_$rdkit_version.tar.gz
rdkit_tar_size=54644792
rdkit_tar_size=58598385 # 2020_09_3
rdkit_tar_size=79454133 # 2023_03_1
rdkit_tar_size=80212603 # 2023_09_4
rdkit_tar_size=82055856 # 2024_09_4
rdkit_tar_size=82181626 # 2024_09_5
if [ "$build_rdkit" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
# this file is in 2018_09 but not in 2017_09
if [ -e $install_top_dir/include/rdkit/GraphMol/StereoGroup.h ] ; then
echo not building rdkit:
echo not building rdkit: >&2
skip_this=true
fi
fi
# hack
# skip_this=false
if [ $skip_this = false ] ; then
echo BUILDING: RDKit $rdkit_version
echo BUILDING: RDKit $rdkit_version >&2
(
echo building ========================= rdkit ==============================
# at last we get to actually compile rdkit
export CC=gcc
export CXX=g++
RDKIT=$install_top_dir
RDBASE=$install_top_dir
CMAKE_INSTALL_PREFIX=$install_top_dir
export RDKIT
export RDBASE
export CMAKE_INSTALL_PREFIX
# shall we build from github rdkit?
github_rdkit=false
if [ $(uname) = Darwin ] ; then
echo LD_LIBRARY_FALLBACK_PATH $LD_LIBRARY_FALLBACK_PATH
# what is unexport in bash?
export LD_LIBRARY_PATH=
fi
echo ==================== LD_LIBRARY_PATH is $LD_LIBRARY_PATH
if [ "$github_rdkit" = true ] ; then
echo PATH A - pull
if [ ! -d rdkit-github/build ] ; then
mkdir -p rdkit-github/build
fi
echo pulling...
# cd rdkit-github/rdkit && git pull && cd -
cd rdkit-github/build
pwd
tree_from_build=../rdkit
else
# old wget $rdkit_home/$rdkit_tar_host_file_name -P ${AUTOBUILD_SOURCES} -O ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
echo PATH B
# OK, So, AFAICS, -N doesn't work with this file. So check the size
get_the_rdkit_tar_file=true
echo testing for existance of ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
if [ -e ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name ] ; then
which stat
echo found the file ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
if [ $OS = Darwin ] ; then
echo stat -f%z ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
stat -f%z ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
size=$(stat -f%z ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name)
echo rdkit tar ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name size from stat: $size
else
echo stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
size=$(stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name)
echo rdkit tar ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name size from stat: $size
fi
if [ "$size" = $rdkit_tar_size ] ; then
get_the_rdkit_tar_file=false
fi
fi
echo here C with get_the_rdkit_tar_file $get_the_rdkit_tar_file
if [ $get_the_rdkit_tar_file = true ] ; then
echo $WGET $rdkit_home/$rdkit_tar_host_file_name -O ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
$WGET $rdkit_home/$rdkit_tar_host_file_name -O ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
do_rdkit_download=true
if [ -e ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name ] ; then
echo here D
if [ $OS = Darwin ] ; then
s=$(stat -f%z ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name)
else
s=$(stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name)
fi
if [ "$s" = $rdkit_tar_size ] ; then
do_rdkit_download=false
fi
fi
if [ $do_rdkit_download = true ] ; then
echo here E
echo $WGET $rdkit_home/$rdkit_tar_host_file_name
if ${WGET} $rdkit_home/$rdkit_tar_host_file_name ; then
if [ -e ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name ] ; then
cp ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name ${AUTOBUILD_SOURCES}/rdkit-$rdkit_tar_host_file_name
else
echo $rdkit_tar_host_file_name does not exist after download
fi
fi
fi
fi
pwd
echo tar xf ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
tar xf ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
ls
if [ ! -e rdkit-Release_$rdkit_version ] ; then
echo RDKit untar dir not found: rdkit-Release_$rdkit_version
exit 2
fi
cd rdkit-Release_$rdkit_version
${WGET} $extras_place/rdkit-maeparser.patch
pwd
echo patch -p0 < ${AUTOBUILD_SOURCES}/rdkit-maeparser.patch
patch -p0 < ${AUTOBUILD_SOURCES}/rdkit-maeparser.patch
# now fix for modern boost:
# Code/RDGeneral/RDValue-taggedunion.h needs numeric_cast.hpp
mkdir -p build
cd build
pwd
tree_from_build=..
fi
# New (1.60) boost uses BOOST_PYTHON not Boost_PYTHON
#
echo which cmake
which cmake
# No help: -DBoost_INCLUDE_DIR=$install_top_dir/include
# Cmake policy: -DMACOSX_RPATH=ON
# old verisons of boost (before 1.60?) can't find boost python
# with new (github Feb 2016) rdkit
# -DPYTHON_LIBRARY=$install_top_dir/lib/libpython2.7.$extension_type
# no help apparently
# -DBoost_EXTERNAL_OBJECTS=$install_top_dir/lib/libboost_python.$extension_type
# -DBoost_INCLUDE_DIR=$install_top_dir/include
#
# -DBOOST_ROOT=$install_top_dir
# -DBoost_INCLUDE_DIR=$install_top_dir/include
# -DBoost_LIBRARY_DIRS=$install_top_dir/lib
# -DBoost_PYTHON_LIBRARY=$install_top_dir/lib/libboost_python.$extension_type
# -DBoost_REGEX_LIBRARY=$install_top_dir/lib/libboost_regex.$extension_type
# catches correctly (no need to specify)
# -DPYTHON_INCLUDE_DIR=$install_top_dir/include/python2.7
if [ $(uname) = Darwin ] ; then
cmake_macosx_rpath=-DCMAKE_MACOSX_RPATH=ON
fi
# last time I looked, the include files of RDKit MolDraw2D were wrong.
# I had to hack in GraphMol/MolDraw2D into include/rdkit and copy the files
# there.
# -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR)
# CMake Warning at External/INCHI-API/CMakeLists.txt:43 (message):
# ** NO INCHI SOFTWARE FOUND
#
# InChI support will be turned off. If you want to add InChI support, please
# follow the instructions inside $RDBASE/External/INCHI-API/README to
# download a copy of InChI software and then rerun cmake.
#
# http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip
# now libboost_python comes with an extended name: libboost_python27
libboost_python_ext=$python_version_extension
libboost_python_ext=
extension_type=so
python_arch=x86_64-linux-gnu
if [ $(uname) = Darwin ] ; then
extension_type=dylib
python_arch=darwin
fi
if test "$dist_name" = debian ; then
echo don.t mess with LDFLAGS here on debian
else
if test "$dist_name" = ubuntu ; then
echo don.t mess with LDFLAGS here on ubuntu
else
if test "$dist_name" = almalinux ; then
echo don.t mess with LDFLAGS on almalinux
else
if test "$dist_name" = arch ; then
echo don.t mess with LDFLAGS here on arch
else
export LDFLAGS="-L$install_top_dir/lib -lintl"
fi
fi
fi
fi
echo AAAAAAAAAAAAAAAAAAAAAAAA LDFLAGS is $LDFLAGS
# echo will configure with cmake like this:
# DBoost_PYTHON39_LIBRARY_RELEASE needs to be extracted?
# probblem: $install_top_dir/include/boost/python/detail/wrap_python.hpp:57:23: fatal error: pyconfig.h: No such file or directory
# solution: https://github.com/rdkit/rdkit/issues/3884
# -DPYTHON_INCLUDE_DIR=$PYROOT/include/python3.8
# -DBoost_PYTHON39_LIBRARY_RELEASE=$install_top_dir/lib/libpython3.so
# -DCMAKE_CXX_STANDARD_LIBRARIES="-lintl -dl"
# -DCMAKE_SHARED_LINKER_FLAGS="-lintl -dl"
# libpython is linking with /usr/local/opt/gettext/lib:
# otool -L ~/autobuild/build-chapi-gtk4/lib/libpython3.10d.dylib | grep libint
# /usr/local/opt/gettext/lib/libintl.8.dylib (compatibility version 13.0.0, current version 13.0.0)
# no help
# -DCMAKE_C_STANDARD_LIBRARIES="-lintl -ldl -framework CoreFoundation" \
# remove to see if this fixes the non-Darwin build.
# -DCMAKE_STATIC_LINKER_FLAGS="$install_top_dir/lib/libintl.a"
echo cmake \
-DCMAKE_PREFIX_PATH=$install_top_dir \
-DCatch2_DIR=$install_top_dir \
-DPYTHON_INCLUDE_DIR=$install_top_dir/include/python$python_version_extension$python_abiflags \
$cmake_macosx_rpath \
-DPYTHON_EXECUTABLE=$install_top_dir/bin/python3 \
-DPYTHON_LIBRARY=$install_top_dir/lib/python$python_version_extension/config-${python_version_extension}$python_abiflags-$python_arch/libpython$python_version_extension$python_abiflags.a \
-DCMAKE_INSTALL_PREFIX=$install_top_dir \
-DRDK_BUILD_MAEPARSER_SUPPORT=OFF \
-DRDK_BUILD_CAIRO_SUPPORT=ON \
-DRDK_INSTALL_INTREE=OFF \
-DRDK_INSTALL_COMIC_FONTS=OFF \
-DCatch2_DIR=$install_top_dir \
$tree_from_build
if cmake \
-DCMAKE_PREFIX_PATH=$install_top_dir \
-DCatch2_DIR=$install_top_dir \
-DPYTHON_INCLUDE_DIR=$install_top_dir/include/python$python_version_extension$python_abiflags \
$cmake_macosx_rpath \
-DPYTHON_EXECUTABLE=$install_top_dir/bin/python3 \
-DPYTHON_LIBRARY=$install_top_dir/lib/python$python_version_extension/config-${python_version_extension}$python_abiflags-$python_arch/libpython$python_version_extension$python_abiflags.a \
-DCMAKE_INSTALL_PREFIX=$install_top_dir \
-DRDK_BUILD_MAEPARSER_SUPPORT=OFF \
-DRDK_BUILD_CAIRO_SUPPORT=ON \
-DRDK_INSTALL_INTREE=OFF \
-DRDK_INSTALL_COMIC_FONTS=OFF \
-DCatch2_DIR=$install_top_dir \
$tree_from_build ; then
# now patch rapidjson document.h
sed -i.backup -e 's/const SizeType length/SizeType length/' ../External/rapidjson-1.1.0/include/rapidjson/document.h
# it seems that make -j n fails to compile (race condition?)
# so use just plain make? (currently not fixed)
if $MAKE ; then
make install
else
echo problem making the RDKit.
exit 1
fi
else
echo problem configuring the RDKit.
exit 1
fi
cd ..
cd ..
) > $HOSTLOGDIR/26-rdkit.txt 2>&1
echo BUILDING rdkit finished
echo BUILDING rdkit finished >&2
wc $HOSTLOGDIR/26-rdkit.txt >&2
fi
fi
###############################################################################
# exit here for the chapi-dependencies build
###############################################################################
if [ "$CHAPI_ONLY" = true ] ; then
echo done CHAPI_ONLY
exit
fi
###############################################################################
########## gmp #############
###############################################################################
if [ -e $install_top_dir/include/gmp.h ] ; then
build_gmp=false
else
build_gmp=true
fi
if "$build_gmp" = true ; then
# gmp_version=4.2.4
# gmp_version=5.1.2
# gmp_version=6.0.0a # it doesn't untar into this directory
# gmp_version=5.1.3
gmp_version=6.1.2
echo BUILDING gmp $gmp_version
echo BUILDING gmp $gmp_version >&2
${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gmp/gmp-$gmp_version.tar.bz2
(date
pwd
unset LD_LIBRARY_PATH
tar xf ${AUTOBUILD_SOURCES}/gmp-$gmp_version.tar.bz2
cd gmp-$gmp_version
./configure $generic_prefix
$MAKE
status=$?
if [ "$status" != 0 ] ; then
echo make of gmp failed
else
$MAKE install
fi
) > $HOSTLOGDIR/27-gmp.txt 2>&1
echo done gmp $gmp_version >&2
else
echo not building gmp:
fi
# glib was removed because glib is a dependency of gtk-4 and we don't build gtk-4,
# so if we want to use glib for other packages, we need to use the same glib that
# gtk-4 used.
# we need python3 to have packaging
python3 -m pip install packaging
###### pcre2 is needed for glib. glib is compiled by gobject-introspection
###### (that doesn't seem good). Let's install pcre2 and see what happens
if test -e $install_top_dir/include/pcre2.h ; then
echo installation has pcre2
echo installation has pcre2 >&2
else
pcre2_version=10.43
echo BUILDING: pcre2 $pcre2_version
echo BUILDING: pcre2 $pcre2_version >&2
(
unset LD_LIBRARY_PATH
d=https://github.com/PCRE2Project/pcre2/releases/download/pcre2-$pcre2_version
${WGET} $d/pcre2-$pcre2_version.tar.gz
tar xf $AUTOBUILD_SOURCES/pcre2-$pcre2_version.tar.gz
cd pcre2-$pcre2_version
./configure --prefix=$install_top_dir
if $MAKE ; then
make install
fi
cd -
) > $HOSTLOGDIR/28-pcre2.txt 2>&1
fi
###############################################################################
########## gobject-introspection #############
###############################################################################
# hack to use system library:
build_gobject_introspection=false
if test "$build_gobject_introspection" = true ; then
echo BUILDING gobject-introspection:
echo BUILDING gobject-introspection: >&2
(
# just for gobject-introspection - depends on our glib installation
export PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig
export LD_LIBRARY_PATH=$install_top_dir/lib64:$install_top_dir/lib
date
echo BUILDING gobject-introspection:
# or else very annoying:
# symbol lookup error: /home/paule/autobuild/Linux-penelope-arch-gtk4/lib/libreadline.so.8: undefined symbol: UP
if test $dist_name = arch ; then
unset LD_LIBRARY_PATH
fi
echo environment variables
echo PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
echo $PATH
echo PKG_CONFIG_PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
echo $PKG_CONFIG_PATH
echo LD_LIBRARY_PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
echo $LD_LIBRARY_PATH
which gcc
which g++
gcc --version
gobject_introspection_version=1.50.0
gobject_introspection_version=1.68.0
gobject_introspection_version=1.71.0
gobject_introspection_version=1.72.0
gobject_introspection_version=1.80.0
gobject_introspection_version_stub=1.80
# 20220820-PE note to self: 1.73.0 is now avaliable
# https://download.gnome.org/sources/gobject-introspection/1.73/
d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.50
d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.68
d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.71
d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.72
d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.72
d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/$gobject_introspection_version_stub
${WGET} $d/gobject-introspection-$gobject_introspection_version.tar.xz
tar xf ${AUTOBUILD_SOURCES}/gobject-introspection-$gobject_introspection_version.tar.xz
cd gobject-introspection-$gobject_introspection_version
# 1.68 (probably earlier) has moved on from configure. meson baby
# echo ./configure --prefix=$install_top_dir PYTHON=python3
# ./configure --prefix=$install_top_dir PYTHON=python3
# if $MAKE ; then
# $MAKE install
# fi
echo PKG_CONFIG_PATH is...
echo $PKG_CONFIG_PATH
echo this is the result of /bin/pkg-config glib-2.0
/bin/pkg-config --modversion glib-2.0
/bin/pkg-config --cflags glib-2.0
/bin/pkg-config --libs glib-2.0
echo building in:
pwd
echo which meson
which meson
meson --version
export CC=gcc
# $install_top_dir/bin/meson is important, otherwise the wrong meson
# is used.
#
# if $install_top_dir/bin/meson -Dprefix=$install_top_dir build ; then
#
# BUT... if we don't build meson because we have a new enough meson
# in the path then $install_top_dir/bin/meson does not exist!
# how about setting --libdir?
# if meson setup -Dprefix=$install_top_dir --libdir=$install_top_dir/lib64 build ; then
if meson setup -Dprefix=$install_top_dir build ; then
echo meson passed
cd build
ninja
ninja install
cd -
else
echo meson failed
fi
export -n CC
cd ..
) > $HOSTLOGDIR/29-gobject-introspection.txt 2>&1
echo done gobject-introspection: >&2
fi
sources_dir=${AUTOBUILD_SOURCES}
# pycairo is a dependency of pygobject. Is this gtk2 stuff?
pycairo_version=1.17.0 # check for a more recent version.
skip_build=true
if [ $test_for_already_installed_dependencies = true ] ; then
# check this file name.
# $install_top_dir/lib/python$python_version_extension/site-packages/pycairo-1.17.0-py3.6-linux-x86_64.egg/cairo/_cairo.py
if [ -e $install_top_dir/lib/include/pycairo/py3cairo.h ] ; then
skip_build=true
fi
fi
if [ true ] ; then
if [ $skip_build = false ] ; then
${WGET} https://github.com/pygobject/pycairo/releases/download/v1.17.0/pycairo-$pycairo_version.tar.gz
(
if [ -e ${AUTOBUILD_SOURCES}/pycairo-$pycairo_version.tar.gz ] ; then
date
echo BUILDING pycairo
echo BUILDING pycairo >&2
tar xf ${AUTOBUILD_SOURCES}/pycairo-$pycairo_version.tar.gz
cd pycairo-$pycairo_version
python3 setup.py build
python3 setup.py install
cd -
fi
) > $HOSTLOGDIR/30-pycairo.txt 2>&1
else
echo installation has pycairo
fi
fi
# https://pypi.org/project/PyGObject/#files
# https://download.gnome.org/sources/pygobject
pygobject_major_minor_version=3.29
pygobject_major_minor_version=3.30
pygobject_major_minor_version=3.36
pygobject_major_minor_version=3.42
pygobject_version=3.29.1
pygobject_version=3.30.5
pygobject_version=3.42.1
# pygobject_version=3.42.2 add me to the extras place!
# https://download.gnome.org/sources/pygobject/3.42/pygobject-3.42.2.tar.xz
date
pwd
skip_build=false
if [ $test_for_already_installed_dependencies = true ] ; then
if [ -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then
skip_build=true
fi
fi
if [ /usr/include/pygobject-3.0 ] ; then
skip_build=true
fi
echo /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-gtk4/bin/glib-compile-schemas --targetdir tests ../tests
/lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-gtk4/bin/glib-compile-schemas --targetdir tests ../tests
if [ $skip_build = false ] ; then
echo BUILDING pygobject $pygobject_version:
echo BUILDING pygobject $pygobject_version: >&2
(
echo :::: PKG_CONFIG_PATH is $PKG_CONFIG_PATH
unset LD_LIBRARY_PATH
echo /lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-gtk4/bin/glib-compile-schemas --targetdir tests ../tests
/lmb/home/pemsley/autobuild/Linux-hal.lmb.internal-gtk4/bin/glib-compile-schemas --targetdir tests ../tests
${WGET} $extras_place/PyGObject-$pygobject_version.tar.gz
echo ::: trying to untar ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz
if [ -e ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz ] ; then
gzip -dc ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz | tar xf -
cd PyGObject-$pygobject_version
### python setup.py build
### python setup.py install
echo ::: which python3
which python3
echo ld_library_path $LD_LIBRARY_PATH
x=$LD_LIBRARY_PATH
# unset LD_LIBRARY_PATH # I want LD_LIBRARY_PATH so that libffi.so is found
echo :::: in directory $(pwd)
echo :::: building using meson -Dprefix=$install_top_dir build
if meson setup -Dprefix=$install_top_dir build ; then
echo :::: meson passed
cd build
echo :::: ninja
if ninja ; then
echo :::: ninja install
ninja install
else
echo ninja failed
fi
else
echo :::: meson failed
fi
export LD_LIBRARY_PATH=$x
else
echo ERROR:: ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz file not found.
fi ) > $HOSTLOGDIR/31-pygobject.txt 2>&1
echo BUILDING: done pygobject $pygobject_version: >&2
else
echo not building pygobject:
echo not building pygobject: 2>&1
fi
# restore Raster3D here at some stage
# When you do, make it work with transparent density and ribbons/surfaces
# (look up how to send the triangles)
###############################################################################
# pygobject
###############################################################################
# this needs to find gobject-introspection-1.0 >= 1.46.0 (now 1.56.0 apparently)
# and it does if PKG_CONFIG_PATH is set correctly
if [ -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then
echo installation has pygobject
else
echo installing pygobject with pip3
echo installing pygobject with pip3 >&2
(
echo installing pygobject
echo PKG_CONFIG_PATH $PKG_CONFIG_PATH
which pip3
pip3 install wheel
pip3 install pygobject
) > $HOSTLOGDIR/34-pip-wheel-pygobject.txt 2>&1
echo BUILDING: done install pygobject with pip3 >&2
fi
# silicos-it's biscu-it (QED) is now part of RDKit main.
###############################################################################
##################### guile and friends #######################################
###############################################################################
# libffi_version=3.2.1 built above (for python)
guile_version=3.0.5 # no g-wrap for this
guile_version=2.2.7
g_wrap_version=1.9.15
libtool_version=2.4.6
gmp_version=6.1.1
gmp_version=6.2.1
guile_gnome_platform_version=2.16.5
readline_version=6.3
gc_version=8.0.4
guile_cairo_version=1.9.91
# wget http://ftp.gnu.org/pub/gnu/guile-gnome/guile-gnome-platform/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
# wget http://savannah.nongnu.org/download/g-wrap/g-wrap-$g_wrap_version.tar.gz
# wget sourceware.org:/pub/libffi/libffi-$libffi_version.tar.gz
# wget ftp://ftp.gnu.org/pub/gnu/guile/guile-2.0.12.tar.gz
# wget ftp://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile/guile-2.0.12.tar.gz
# wget http://ftp.heanet.ie/mirrors/gnu/libtool/libtool-$libtool_version.tar.gz
# wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/gmp/gmp-$gmp_version.tar.xz
# wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/libunistring/libunistring-$unistring_version.tar.gz
# wget http://www.hboehm.info/gc/gc_source/gc-7.2g.tar.gz
# wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/readline/readline-6.3.tar.gz
# wget http://download.savannah.gnu.org/releases/guile-cairo/guile-cairo-$guile_cairo_version.tar.gz
build_guile=true
build_g_wrap=true
build_gmp=true
build_guile_gnome_platform=true
# build_readline=true
build_guile_cairo=true
build_guile_lib=true
build_gc=true
if [ "$build_gc" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/gc.h ] ; then # use the right file
skip_this=true
fi
fi
if [ $skip_this = false ] ; then
echo BUILDING libatomic-ops:
echo BUILDING libatomic-ops: >&2
(
unset LD_LIBRARY_PATH
if [ ! -e $AUTOBUILD_SOURCES/libatomic_ops-7.6.12.tar.gz ] ; then
${WGET} https://github.com/ivmai/libatomic_ops/releases/download/v7.6.12/libatomic_ops-7.6.12.tar.gz
fi
tar xf $AUTOBUILD_SOURCES/libatomic_ops-7.6.12.tar.gz
cd libatomic_ops-7.6.12
./configure --prefix=$install_top_dir
$MAKE
make install
cd -
) > $HOSTLOGDIR/37-libatomic-ops.txt 2>&1
echo BUILDING: done libatomic-ops: >&2
fi
# echo gc skip_this $skip_this
if [ $skip_this = false ] ; then
gc_version=7.2g
gc_version_dir=7.2
gc_version=7.6.12 # needs libatomic_ops. can we find a version that doesn't need that?
gc_version_dir=7.6.12 # I guess not.
gc_version=8.2.4
gc_version_dir=8.2.4
echo BUILDING: gc $gc_version
echo BUILDING: gc $gc_version >&2
(
echo ========================= build gc =================================
unset LD_LIBRARY_PATH
echo PKG_CONFIG_PATH is $PKG_CONFIG_PATH
echo testing for presence of tar file $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
if [ -e $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz ] ; then
echo Here build-gc A
echo found gc source file $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
echo Here build-gc B
echo tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
echo Here build-gc B2
else
echo no file $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
echo ${WGET} http://www.hboehm.info/gc/gc_source/gc-$gc_version.tar.gz
${WGET} http://www.hboehm.info/gc/gc_source/gc-$gc_version.tar.gz
# this file is double-gzipped!
# 2024-08-23 no more. It's been fixed
# mv $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz.gz
# gunzip $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz.gz
if [ -e $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz ] ; then
tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
else
echo download failed for http://www.hboehm.info/gc/gc_source/gc-$gc_version.tar.gz
fi
fi
echo Here build-gc C
cd gc-$gc_version_dir
pwd
echo ./configure --prefix=$install_top_dir
echo Here D
if ./configure --prefix=$install_top_dir ; then
if $MAKE ; then
make install
fi
fi
cd -
) > $HOSTLOGDIR/38-gc.txt 2>&1
echo BUILDING: done gc $gc_version >&2
else
echo not building gc
fi
fi
if [ "$build_gmp" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/gmp.h ] ; then # use the right file
skip_this=true
fi
fi
fi
if [ "$build_guile" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/guile/2.2/libguile.h ] ; then # use the right file
skip_this=true
fi
fi
# echo guile skip_this $skip_this
if [ $skip_this = false ] ; then
echo BUILDING guile:
echo BUILDING guile $guile_version >&2
(
unset LD_LIBRARY_PATH
echo ========================= build guile =================================
if [ -e $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz ] ; then
tar xf $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz
else
echo no file $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz
${WGET} https://ftp.gnu.org/pub/gnu/guile/guile-$guile_version.tar.xz
tar xf ${AUTOBUILD_SOURCES}/guile-$guile_version.tar.xz
fi
cd guile-$guile_version
# LIBFFI_LIBS=-L$install_top_dir/lib
# LIBFFI_CFLAGS=-I$install_top_dir/include
if ./configure --prefix=$install_top_dir \
--with-libltdl-prefix=$install_top_dir \
--with-libreadline-prefix=$install_top_dir \
LIBS=-L$install_top_dir/lib CFLAGS=-I$install_top_dir/include ; then
if $MAKE ; then
make install
# this file causes problems on linking coot
if [ -e $install_top_dir/lib/libguile-2.2.so.1.4.2-gdb.scm ] ; then
mv $install_top_dir/lib/libguile-2.2.so.1.4.2-gdb.scm $install_top_dir/lib/script-libguile-2.2.so.1.4.2-gdb.scm
fi
fi
fi
cd -
) > $HOSTLOGDIR/39-guile.txt 2>&1
echo done guile:
fi
else
echo not building guile:
fi
# ------------------------------------ template -------------------------------------
if [ "$build_template_thing" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/template.h ] ; then # use the right file
skip_this=true
fi
fi
# echo template skip_this $skip_this
template_version=1.2.3
server_for_template=https://thing
if [ $skip_this = false ] ; then
echo ========================= build template =================================
if [ -e $AUTOBUILD_SOURCES/template-$template_version.tar.gz ] ; then
tar xf $AUTOBUILD_SOURCES/template-$template_version.tar.gz
else
${WGET} $server_for_template/template-$template_version.tar.gz
tar xf $AUTOBUILD_SOURCES/template-$template_version.tar.gz
fi
(
cd template-$template_version
if ./configure --prefix=$install_top_dir ; then
if $MAKE ; then
make install
fi
fi
cd -
) > $HOSTLOGDIR/2x-xx.txt 2>&1
fi
fi
# ------------------------------------ template end ----------------------------------
if [ "$build_g_wrap" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/g-wrap/guile-runtime.h ] ; then # use the right file
skip_this=true
fi
fi
# echo g-wrap skip_this $skip_this
if [ $skip_this = false ] ; then
echo BUILDING: g-wrap:
echo BUILDING: g-wrap $g_wrap_version >&2
(
unset LD_LIBRARY_PATH
echo ========================= build g-wrap =================================
if [ -e $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz ] ; then
tar xf $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz
else
g_wrap_version=1.9.15
${WGET} http://savannah.nongnu.org/download/g-wrap/g-wrap-$g_wrap_version.tar.gz
tar xf $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz
fi
if [ ! -e $install_top_dir/bin/guile ] ; then
echo no guile
exit
fi
cd g-wrap-$g_wrap_version
# if ./configure --prefix=$install_top_dir
# LIBFFI_LIBS=-L$install_top_dir/lib
# LIBFFI_CFLAGS=-I$install_top_dir/include; then
if ./configure --prefix=$install_top_dir --disable-Werror ; then
if $MAKE ; then
make install
fi
fi
) > $HOSTLOGDIR/40-g-wrap.txt 2>&1
echo BUILDING: g-wrap done >&2
fi
else
echo not building g_wrap
fi
if [ "$build_guile_cairo" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/guile-cairo/guile-cairo.h ] ; then
skip_this=true
fi
fi
if [ $skip_this = false ] ; then
echo BUILDING guile-cairo:
echo BUILDING guile-cairo $guile_cairo_version >&2
(
unset LD_LIBRARY_PATH
echo ========================= build guile-cairo =================================
if [ -e $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz ] ; then
tar xf $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz
else
echo fetching file $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz
${WGET} http://download.savannah.gnu.org/releases/guile-cairo/guile-cairo-$guile_cairo_version.tar.gz
tar xf $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz
fi
if [ ! -e $install_top_dir/bin/guile ] ; then
echo no guile
exit
fi
cd guile-cairo-$guile_cairo_version
if ./configure --prefix=$install_top_dir ; then
if $MAKE ; then
make install
fi
fi
cd -
) > $HOSTLOGDIR/41-guile-cairo.txt 2>&1
echo BUILDING: guile-cairo done >&2
fi
else
echo not building guile-cairo:
fi
# guile-lib
if test -f $install_top_dir/share/guile/site/sxml/simple.scm ; then
echo installation has guile-lib
build_guile_lib=
else
build_guile_lib=1
echo guile-lib needs to be installed
fi
echo some test here " "
if guile-config --version ; then
echo guile-config found
else
echo no guile-config
fi
guile_version=$(guile-config --version |& cut -f5 -d" ") # 2.2.7
guile_major_minor=2.2
guile_lib_version=0.2.7
if [ "$build_guile_lib" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/share/guile/site/os/process.scm ] ; then
skip_this=true
fi
fi
if [ $skip_this = false ] ; then
echo ========================= build guile-lib =================================
if [ -e $AUTOBUILD_SOURCES/guile-lib-$guile_lib_version.tar.gz ] ; then
tar xf $AUTOBUILD_SOURCES/guile-lib-$guile_lib_version.tar.gz
else
exit
fi
(
if [ ! -e $install_top_dir/bin/guile ] ; then
echo no guile
exit
fi
cd guile-lib-$guile_lib_version
# sigh. I had to delete guile-3 installation, guile and guile-config being
# correct for 2.2.7 was not enough.
# (this uses PKG_CONFIG_PATH)
if ./configure --prefix=$install_top_dir --with-guile-site=yes ; then
if $MAKE ; then
make install
fi
fi
cd -
) > $HOSTLOGDIR/42-guile-lib.txt 2>&1
fi
else
echo not building guile-lib:
fi
if [ "$build_guile_gnome_platform" = true ] ; then
skip_this=false
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/guile-gnome-2/guile-gnome-gobject.h ] ; then
skip_this=true
fi
fi
echo guile-gnome-platform skip_this $skip_this
if [ $skip_this = false ] ; then
echo BUILDING: gnome-gnome-platform
echo BUILDING: gnome-gnome-platform $guile_gnome_platform_version >&2
(
unset LD_LIBRARY_PATH
echo ========================= build guile-gnome-platform =================================
if [ -e $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz ] ; then
tar xf $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
else
echo no file $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
${WGET} http://ftp.gnu.org/pub/gnu/guile-gnome/guile-gnome-platform/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
tar xf $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
fi
cd guile-gnome-platform-$guile_gnome_platform_version
if ./configure --prefix=$install_top_dir ; then
if $MAKE ; then
make install
fi
fi
) > $HOSTLOGDIR/43-guile-gnome-platform.txt 2>&1
echo BUILDING gnome-gnome-platform finished
fi
else
echo not building guile-gnome-platform
fi
###############################################################################
########## Coot is now built from git repo #############
###############################################################################
#
if test x$GITHUB_ENV = x ; then
: # we are not in a hithub actions build
else
# stop here because we build coot outside of this script in github actions
exit
fi
echo Now Coot..... >&2
cd $start_dir
echo GITHUB_WORKSPACE is $GITHUB_WORKSPACE
date >&2
pwd >&2
if [ -e coot ] ; then
echo CASE 1 coot directory exists
echo CASE 1 coot directory exists >&2
(
pwd
cd coot
echo now in this dir:
pwd
echo 33333333333333333333333 and about to fetch and merge...
git fetch
if [ -e ltmain.sh ] ; then rm ltmain.sh ; fi
if [ -e config.guess ] ; then rm config.guess ; fi
if [ -e config.sub ] ; then rm config.sub ; fi
git merge
# if [ -e ltmain.sh ] ; then
# rm ltmain.sh
# fi
rm -rf autom4te.cache
echo bash autogen.sh
bash autogen.sh
cd -
) > $HOSTLOGDIR/50-coot-fetch-merge-autogen.txt 2>&1
echo BUILDING: done merge
else
echo CASE 2 coot directory not exists in $(pwd)
echo CASE 2 coot directory not exists in $(pwd) >&2
(
save_dir=$(pwd)
echo :::: $(pwd)
echo cloning coot...
echo cloning coot... >&2
echo :::: git clone https://github.com/pemsley/coot.git -b main
echo save_ld_library_path=$LD_LIBRARY_PATH
# reset LD_LIBRARY_PATH for now. Do we need it set from now on actually?
export LD_LIBRARY_PATH=
if git clone https://github.com/pemsley/coot.git -b main --depth 2 ; then
echo git clone https://github.com/pemsley/coot.git -b main without error status
echo done clone
cd coot
rm -rf autom4te.cache
if [ -e ltmain.sh ] ; then rm ltmain.sh ; fi
if [ -e config.guess ] ; then rm config.guess ; fi
if [ -e config.sub ] ; then rm config.sub ; fi
bash autogen.sh
else
echo git clone https://github.com/pemsley/coot.git -b main failed
echo done clone
cd coot
fi
LD_LIBRARY_PATH=$save_ld_library_path
cd $save_dir
) > $HOSTLOGDIR/50-clone-autogen.txt 2>&1
echo BUILDING: done checkout
fi
if test -n "$glib_installed" ; then
coot_extra_args="$coot_extra_args --with-glib-prefix=$install_top_dir"
fi
if test -n "$gtk_installed" ; then
coot_extra_args="$coot_extra_args --with-gtk-prefix=$install_top_dir"
fi
###############################################################################
########## build Coot #############
###############################################################################
#
echo BUILDING: coot
echo BUILDING: coot >&2
(
# 20091001 should not be needed.
# if [ "$ENABLE_PYTHON_COOT" = "no" ] ; then
# echo INFO:: not a pythonized build
# cp src/blank.cc src/coot_wrap_python.cc
# else
# echo INFO:: A pythonized build
# fi
# CXXFLAGS="-g -O"
# consider getting rid of $shared_static_flag, which does a --disable-shared.
# i.e. we should keep and use shared libs
# $architecture is not set for Mac OS X.
coot_optim_args=
export CXXFLAGS="-g -O "
cbis_d=$(date +'%a %d %b %H%M.%S %Z %Y')
coot_build_info_string="build-host: $HOST on: $cbis_d"
if [ ! -z "$libintl_cflags" ] ; then
CFLAGS=$libintl_cflags
CPPFLAGS="$CPPFLAGS $libintl_cflags"
fi
cd $start_dir
if [ ! -d build-coot ] ; then
mkdir build-coot
fi
cd build-coot
export LD_LIBRARY_PATH=$install_top_dir/lib64
unset LD_LIBRARY_PATH
echo From git repo now
echo building in: $PWD
echo CFLAGS: $CFLAGS
echo CXXFLAGS: $CXXFLAGS
echo CPPFLAGS: $CPPFLAGS
echo LDFLAGS: $LDFLAGS
echo PATH: $PATH
echo PKG_CONFIG_PATH: $PKG_CONFIG_PATH
# For external use, we need to have used git checkout for
# the gtk3 branch, have run autogen.sh
# and have placed that directory somewhere sensible relative to here
echo 33333
# 20220707-PE does this improve thie linking (get pass the problem with g_module_open_full)?
# We get checking dynamic linker characteristics... awk: symbol lookup error: /home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib/libreadline.so.8: undefined symbol: UP
# on fedora if LD_LIBRARY_PATH is set
if [ "$dist_name" = fedora ] ; then
:
else
if [ "$dist_name" = arch ] ; then
:
else
export LD_LIBRARY_PATH=$install_top_dir/lib
fi
fi
# add this when then are compiling and RDKIT is compiling
# if compiling with sound on ubuntu libvorbis-dev libasound2-dev
unset LD_LIBRARY_PATH
echo :::::::::::::::::::::::::::::::::::::::::::::::::::::::
echo LD_LIBRARY_PATH $LD_LIBRARY_PATH
echo :::::::::::::::::::::::::::::::::::::::::::::::::::::::
echo bash ../coot/configure $coot_prefix \
--with-fftw-prefix=$install_top_dir \
COOT_BUILD_INFO_STRING="$coot_build_info_string" \
SHELL=/bin/bash \
PYTHON=python3 \
--with-boost=$install_top_dir \
--with-boost-libdir=$install_top_dir/lib \
--with-enhanced-ligand-tools \
--with-rdkit-prefix=$install_top_dir \
--with-guile \
$sqlite_config_args \
$shared_static_flag \
$coot_optim_args \
$coot_extra_args \
$extra_args_for_darwin
bash ../coot/configure $coot_prefix \
--with-fftw-prefix=$install_top_dir \
SHELL=/bin/bash \
PYTHON=python3 \
COOT_BUILD_INFO_STRING="$coot_build_info_string" \
--with-boost=$install_top_dir \
--with-boost-libdir=$install_top_dir/lib \
--with-enhanced-ligand-tools \
--with-rdkit-prefix=$install_top_dir \
--with-guile \
$sqlite_config_args \
$shared_static_flag \
$coot_optim_args \
$coot_extra_args \
$extra_args_for_darwin
$MAKE
# No rule to make target 'coot.py', needed by 'all-am'. Stop.
# but it's there! Timing problems?
echo === make again ===
make
status=$?
if [ "$status" != 0 ] ; then
echo make failed.
bad_coot_make=1
exit 2
else
echo 1 ---------------------------------------------------------------
echo ' ' make install
echo 1 ----------------------------------------------------------------
make install
echo === make install again ===
make install
# if [ "$python_scripting" = '--with-python' ] ; then
# echo copying src/coot.py $install_top_dir/share/coot/python
# cp src/coot.py $install_top_dir/share/coot/python
# fi
fi
) > $HOSTLOGDIR/50-coot.txt 2>&1
# --with-gsl-prefix=$install_top_dir \
# --with-glib-prefix=$install_top_dir \
# --with-gtk-prefix=$install_top_dir \
# --with-gtkgl-prefix=$install_top_dir \
coot_build_status=$?
if [ $coot_build_status != 0 ] ; then
echo coot build failed, exiting.
# echo fail-build $coot_revision > $LOGS/build-status
my_exit 2 $coot_revision
else
echo coot build was good.
# echo pass-build $coot_revision > $LOGS/build-status
fi
echo done coot build.
# restore a sane environment for external programs (e.g. ftp)
#
unset LD_LIBRARY_PATH
unset CFLAGS
unset CPPFLAGS
unset LDFLAGS
unset PKG_CONFIG_PATH
# now, do we need to add the extra data files, the refmac monomer
# library and the reference structures?
# 20110505 we change to Garib's new dictionary
#refmac_mon_lib=refmac-monomer-library-20090929.tar.gz
#refmac_mon_lib=refmac-monomer-library-20091203.tar.gz
# mon_lib_dir=http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental
# mon_lib_dir=http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary
# refmac_mon_lib=refmac_dictionary_v5.28.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.29.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.37.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.38.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.39.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.41.tar.gz
# new style
mon_lib_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies
refmac_mon_lib=refmac-monomer-library.tar.gz
if [ -e $install_top_dir/share/coot/lib/data/monomers ] ; then
echo INFO:: installation has refmac monomer library
else
echo INSTALLING refmac monomer library...
echo INSTALLING refmac monomer library... >&2
$WGET $mon_lib_dir/$refmac_mon_lib
mkdir -p $install_top_dir/share/coot/lib/data
tar xzCf $install_top_dir/share/coot/lib/data $AUTOBUILD_SOURCES/$refmac_mon_lib
fi
if [ -e $install_top_dir/share/coot/reference-structures ] ; then
echo INFO:: installation has reference structures
else
echo GETTING reference structures tar...
echo GETTING reference structures tar... >&2
${WGET} $extras_place/reference-structures.tar.gz
if [ -e $AUTOBUILD_SOURCES/reference-structures.tar.gz ] ; then
echo INSTALLING reference structures...
tar xzCf $install_top_dir/share/coot $AUTOBUILD_SOURCES/reference-structures.tar.gz
else
echo FAIL wget for reference-structures.tar.gz failed.
fi
fi
# clear up the library dependencies
if [ "$build_coot_prerelease" = 1 ] ; then
pre_release_str=-pre-release
fi
clear_up_type=
if [ $shared_static_flag != "--disable-static" ] ; then
clear_up_type=clear-static
fi
if [ $shared_static_flag != "--disable-shared" ] ; then
clear_up_type=clear-dynamic
fi
if [ $clear_up_type != "" ] ; then
if [ "$ENABLE_PYTHON_COOT" = "yes" ] ; then
slim_dir=$(dirname $install_top_dir)/coot-${OS}-${systype}${pre_release_str}-gtk4-python
else
slim_dir=$(dirname $install_top_dir)/coot-${OS}-${systype}${pre_release_str}-gtk4
fi
echo post-install slim... >&2
post_install_slim $install_top_dir $slim_dir $clear_up_type
fi
# clean up old status:
if [ -e $LOGS/test-status ] ; then
rm $LOGS/test-status
fi
if [ "$run_tests" = true ] ; then
# run test
echo running tests:
echo running tests: >&2
if [ "$ENABLE_GUILE_COOT" = "yes" ] ; then
echo running first test... >&2
test_coot > $LOGS/test.log 2>&1
r=$?
else
r=0
fi
# run python tests too, maybe (i.e. if we build with python)
if [ "$ENABLE_PYTHON_COOT" = "yes" ] ; then
echo running python test... >&2
test_coot_python > $LOGS/test-python.log 2>&1
rp=$?
else
rp=0
fi
# all gtk3 versions have python. No need for the python tag then
if ( [ $r = 0 ] && [ $rp = 0 ] ); then
echo ========================
echo ' ' first coot test passed
echo ' ' first coot test passed >&2
echo ========----============
echo pass-test > $LOGS/test-status
if test "$do_nightlies" = "1" ; then
if [ -d $BINARY_TAR_DEST_DIR ] ; then
if [ ! -d $BINARY_TAR_DEST_DIR/holding ] ; then
echo WARNING:: holding directory $BINARY_TAR_DEST_DIR/holding does not exist.
else
# regular path
# original full fat:
# make_tar `basename $install_top_dir` $BINARY_TAR_DEST_DIR/${coot_version}-binary-full-${OS}-${systype}${python_tag}${gtk2}.tar.gz
# slimmed:
bin_tar_file=$BINARY_TAR_DEST_DIR/${coot_version}-binary-${OS}-${systype}${gtk_version}.tar.gz
holding_tar_file=$BINARY_TAR_DEST_DIR/holding/${coot_version}-binary-${OS}-${systype}${gtk_version}.tar.gz
make_tar $(basename $slim_dir) $holding_tar_file
# Now test the tar file by un-taring it and running the
# tests. Only if this test passes can we move tar file
# from holding to the binary pre-release dir.
if [ $run_second_test = true ] ; then
cd "$build_dir"
mkdir test-tar
cd test-tar
tar xzf $holding_tar_file
echo cding into `basename $slim_dir` from `pwd`
cd `basename $slim_dir`
echo ln -s ../../$coot_dir_name/greg-tests .
ln -s ../../$coot_dir_name/greg-tests .
echo second coot test...
echo running second test... >&2
test_coot bin/coot > $LOGS/test-2.log 2>&1
test2_status=$?
else
test2_status=0 # success
fi
if [ $test2_status = 0 ] ; then
echo ========================
echo second coot test passed
echo second coot test passed >&2
echo ========================
echo pass-2nd-test > $LOGS/test-status
mv $holding_tar_file $bin_tar_file
mv $holding_tar_file.md5sum $bin_tar_file.md5sum
# update the description of the latest binary tar file for
# this build-type.
binary_type_latest=$BINARY_TAR_DEST_DIR/type-binary-${OS}-${systype}${gtk_version}-latest.txt
echo $coot_version > $binary_type_latest
# update the ChangeLog, README and RELEASE-NOTES
cd "$build_dir"
cd $coot_dir_name
echo INFO:: in "$build_dir"/$coot_dir_name and about to copy over README and RELEASE-NOTES to $BINARY_TAR_DEST_DIR
cp ChangeLog $BINARY_TAR_DEST_DIR
cp README coot-README
cp README $BINARY_TAR_DEST_DIR/coot-README
cp RELEASE-NOTES $BINARY_TAR_DEST_DIR/${coot_version}-RELEASE-NOTES
cp RELEASE-NOTES $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES
echo about to publish files:
echo about to publish files: >&2
# only copy over the binary files if they are not there
# already (checked by publish executable).
#
# reading the git logs adding $BINARY_TAR_DEST_DIR seems to have fixed something.
# Now, the transfer-to-web-server.sh scripts take the second arg
# and munge it to be the correct directory for the binary (and .txt) files.
echo $publish $bin_tar_file $BINARY_TAR_DEST_DIR
$publish $bin_tar_file $BINARY_TAR_DEST_DIR
echo $publish $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR
$publish $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR
# echo $publish $binary_type_latest
# publish $binary_type_latest
echo $publish --no-server-check ChangeLog
$publish --no-server-check ChangeLog
echo $publish --no-server-check coot-README
$publish --no-server-check coot-README
if [ -z "$build_coot_prerelease" ] ; then
echo $publish --no-server-check RELEASE-NOTES
$publish --no-server-check RELEASE-NOTES
else
echo $publish --no-server-check $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES
$publish --no-server-check $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES
fi
echo done copy of README and RELEASE-NOTES
else
echo ========================
echo second coot test failed
echo second coot test failed >& 2
echo ========================
echo fail-2nd-test $date > $LOGS/test-status
fi
fi
else
echo Directory for binaries $BINARY_TAR_DEST_DIR does not exist.
echo Skipping tar.
fi
else
echo not doing tar files for nightlies: $do_nightlies
fi
else
echo ========================
echo ' ' first coot test failed
echo ' ' first coot test failed >&2
echo ========================
echo greg test status: $r
echo python test status: $rp
if [ $r = 0 ] ; then
echo fail-test greg $date > $LOGS/test-status
else
if [ $rp = 0 ] ; then
echo fail-test python $date > $LOGS/test-status
else
# this should not happen, AFAICS.
echo fail-test $date > $LOGS/test-status
fi
fi
fi
fi
$publish_logs $LOGS
echo finished.
echo finished.>&2