#
# -*-shell-script-*-
#
# 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, 2019, 2020, 2021 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.
# 5.31 20180822 gdkshapes.c in gtkglext
# 5.32 20180924 bump the clipper version (pre-Pro)
# 5.33 20181214 bump the mmdb2 version (pdbx_ins_code)
# 5.34 20181215 clipper patch fixes
# 5.35 20190401 clipper configure fftw patch
# 5.36 20200415 Updates for Release 0.9 - a bit delayed
# 5.37 20200514 redirect numpy output
# 5.38 20200921 Add clustalw2
# 5.39 20201203 Add use_system_gnomecanvas_if_possible, default no.
# 5.40 20210109 change the args to boost's build
# 5.41 20210110 change the boost build log output
# 5.42 20210110 Rework the build of numpy, boost and rdkit
# 5.43 20210110 Add unzip to build dependencies
# 5.44 20210110 Bump the python version, rework the readline configure command line
# 5.45 20210110 Bump the python version again - no2 2.7.18
# 5.46 20210110 Add a test for the version of cmake
# 5.47 20210111 Use the correct name for the libtinfo dev package
# 5.48 20210407 Add to the PKG_CONFIG_PATH for 64 bit builds
# 5.49 20210407 find mmdb libs in lib64 maybe for SSM.
# 5.50 20210407 fix previous fix
# 5.51 20210407 adjust LIBS for clipper configure for lib64 usage
# 5.52 20210511 rework the coot configure
# 5.53 20210706 use jfrog.io for boost
# 5.54 20210706 build sqllite3
# 5.55 20210727 shared-static flag --enable-shared - what *was* I thinking? Modern clipper test
# 5.56 20210816 Put libsqlite3 build into the proper log/txt file. Boost 1.72.0
# 5.57 20211019 add another make for guile-lib. Add texinfo to the dependencies for debian
# 5.58 20211019 Add a sort to the awk result when determining the tar file for the stable release
# 5.59 20220708 Use https:: instead of ftp:: for libccp4 and readline
script_version=5.59
# :: 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.
#
if [ "$1" = "no-python" ] ; then
ENABLE_PYTHON_COOT=no
ENABLE_GUILE_COOT=yes
build_type=gtk2
else
if [ "$1" = "no-guile" ] ; then
ENABLE_PYTHON_COOT=yes
ENABLE_GUILE_COOT=no
build_type=gtk2-noguile
else
ENABLE_PYTHON_COOT=yes
ENABLE_GUILE_COOT=yes
build_type=gtk2-python
fi
fi
# Set the host and the OS.
# Fairly fundamental.
#
OS=$(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}-${HOST}}
# or perhaps, for the adventurous:
#AUTOBUILD_INSTALLED=$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}
# 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)
BINARY_INSTALL_CMD=www-placement
# 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-dictionary-bond-distributions \
bin/coot-make-shelx-restraints \
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 ssh_copy {
# bin_tar_file=$1
# if [ "$domainname" = "biop" ] ; then
# do_ssh_copy=true
# fi
if [ "$do_ssh_copy" = true ] ; then
dir=public_html/software/binaries/nightlies/pre-release/
echo ssh_copy copying over files using $HOME/bin/sput-with-dir $bin_tar_file $dir
$HOME/bin/sput-with-dir $bin_tar_file $dir
if [ -e $bin_tar_file.md5sum ] ; then
$HOME/bin/sput-with-dir $bin_tar_file.md5sum dir
fi
else
echo Not ssh copying file to York, $domainname
fi
}
function ssh_copy_to_biop {
bin_tar_file=$1
if [ "$do_ssh_biop_copy" = true ] ; then
target_dir=public_html/coot/software/binaries/pre-releases/
echo copying over files to Biop: $HOME/bin/sput-with-dir $bin_tar_file $target_dir
$HOME/bin/sput-with-dir $bin_tar_file $target_dir
if [ -e $bin_tar_file.md5sum ] ; then
echo and also: $HOME/bin/sput-with-dir $bin_tar_file.md5sum $target_dir
$HOME/bin/sput-with-dir $bin_tar_file.md5sum $target_dir
fi
else
echo Not ssh copying file to biop
fi
}
function ssh_copy_logs_to_biop {
local_log_dir=$1
target_dir=$2
if [ "$do_ssh_biop_copy" = true ] ; then
echo copying over log files to Biop...
target_dir=$2
$HOME/bin/sput-with-dir $local_log_dir $target_dir
else
echo Not ssh copying log files to biop
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 [ ! -d greg-tests ] ; then
echo greg-tests dir missing in this directory:
pwd
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 [ $status = 0 ] ; then
echo test_coot_python: coot test passed
return 0
else
echo test_coot_python: coot test failed
return 1
fi
else
return 1
fi
}
function fixup_libcurl {
sed s,-L/usr/lib,, curl-config > curl-config.tmp
mv curl-config.tmp curl-config
sed s,-L/usr/lib,, lib/libcurl.la > lib/libcurl.la.tmp
mv lib/libcurl.la.tmp lib/libcurl.la
}
# now on to some code!
if [ "$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
#intltool-update for libgnomecanvas is here /usr/share/intltool-debian/intltool-update on ubuntu
# it's in /usr/bin on RHEL
PATH=/usr/share/intltool-debian:$PATH
# use the right (GNU) tar and provide the path to wget (needed
# for downloads) and to GNU make - (which is necesary for python
# at least).
#
# So that python and the *-configs are found when it is installed:
# A bit of a kludge because we do testing for pre-release later.
# It's a logical mess.
#
if test "$build_coot_prerelease" = 1 ; then
PATH=${AUTOBUILD_INSTALLED}-pre-release-gtk2/bin:$PATH
else
PATH=$AUTOBUILD_INSTALLED-gtk2/bin:$PATH
fi
PATH=$PATH:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin:
PATH=$PATH:/etc:/usr/etc
#
export PATH
echo PATH is now: $PATH
echo AUTOBUILD_BUILD is $AUTOBUILD_BUILD
# This is where the sources downloaded from network go:
AUTOBUILD_SOURCES=${AUTOBUILD_BUILD}/sources
echo AUTOBUILD_SOURCES is $AUTOBUILD_SOURCES
if (! test -d ${AUTOBUILD_SOURCES}) ; then
mkdir -p ${AUTOBUILD_SOURCES}
fi
# now make the build logs directory
mkdir -p $LOGS
shared_static_flag="--disable-shared" # what!? 20210727-PE
shared_static_flag="--enable-shared"
shared_lib_ext=so
systype=unknown
# malloc.h business, Darwin does not have malloc.h
# used in the gtk_canvas build
have_malloc=1
if test "$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
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
need_gtk_canvas_patch=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)
echo INFO:: redirecting std output to $LOGS/build.log
exec > $LOGS/build.log
# local tinkering because our sgi runs out of room on /tmp on compiling
if [ $HOST = batman ] ; then
TMPDIR=$HOME/tmp
export TMPDIR
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
# From Christoph Buhlheller:
# Guide for CentOS8 to install Coot:
# yum install libXt-devel
# yum install gtk2-devel
# yum install mesa-*
# yum install gcc-gfortran
if test $OS = Linux ; then
if [ -e /bin/rpm ] ; then
if rpm -a ; then
for i in fedora-release redhat-release redhat-release-workstation centos-release sl-release openSUSE-release ; do
dist=`rpm -q --qf '%{name}' ${i}`
echo dist is $dist
dist=`rpm -q --qf '%{name}' ${i}`
if test $? = 0 ; then
dist_name=$(echo ${dist} | sed -e 's/\-release//g' -e 's/\-workstation//g')
dist_ver=$(rpm -q --qf '%{version}' ${i})
break
else
dist_name='unknown'
fi
done
else
dist_name='unknown'
fi
fi
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 [ $dist_ver = 4WS ] ; then
echo RedHat 4 Linux x86_64 detected. need to update libtool
update_libtool=1
# stupid la file of libcur puts /usr/lib in the link path (early). This causes link
# problems on 64 bit RHEL4. So lets fix curl-config and libcurl.la
post_process_libcurl=1
fi
fi
;;
esac
;;
fedora | centos | openSUSE )
systype=${architecture}-${dist_name}-${dist_ver}
;;
sl )
systype=${architecture}-scientific-linux-${dist_ver}
;;
* )
if test -r /etc/issue; then
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=${architecture}-unknown-Linux
fi
;;
esac
fi
a=$(cmake --version)
have_new_enough_cmake=false
case $a in
# old versions of cmake don't find Boost (FindBoost) when configuring the RDKit.
cmake?version?3.1[5-9].*) # 3.15.x is inferred! 3.18 is new enough, 3.10 is not.
# https://cmake.org/cmake/help/latest/release/3.15.html
have_new_enough_cmake=true
;;
cmake?version?3.[2-9][0-9].*)
have_new_enough_cmake=true
;;
*)
echo cmake version fallback: $a
;;
esac
echo have_new_enough_cmake: $have_new_enough_cmake
if [ $have_new_enough_cmake = false ] ; then
echo update your cmake and try again
my_exit 2
fi
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
# Fedora required package libXt-devel which provides X11/Intrinsic.h (for gtktlext)
# and libgnomecanvas-devel (which is probably a mistake)
# check dependencies for Ubuntu.
case $dist_name in
*ubuntu*)
dep_list='
patch
unzip
rsync
m4
g++
libxext-dev
libxmu-dev
libxt-dev
libc6-dev
libtinfo-dev
libncurses5-dev
libssl-dev
libglu1-mesa-dev
libjpeg-dev
mesa-common-dev
libgtk2.0-dev
libgnomecanvas2-dev'
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)
# note from Dirk Kostrewa 20211018-PE:
#
# cmake libncurses5-dev libxext-dev libglu1-mesa-dev mesa-common-dev libgtk2.0-dev
# libgnomecanvas2-dev libxt-dev libjpeg-dev
# 20211019-PE also texinfo (for makeinfo for guile-lib)
dep_list='rsync m4 unzip patch libncurses-dev g++ libxext-dev libxt-dev libglu1-mesa-dev mesa-common-dev libgtk2.0-dev libgnomecanvas2-dev unzip texinfo cmake libjpeg-dev'
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
;;
esac
# 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 INFO:: MACHTYPE is $MACHTYPE
echo INFO:: systype is $systype
if [ "$systype" = x86_64-rhel-4 ] ; then
PATH=$PATH:/usr/X11R6/bin
export PATH
fi
sqlite_config_args=--with-sqlite3
# We want to add some compiler info in the directory name.
# If CC is set, use that,
# If not, try gcc,
# if not, try cc
#
# Similarly for the c++ compiler info
# If CXX is set, use that
# if not, try g++
# if not, try c++
if [ -n "$CC" ] ; then
# CC was set
gcctest=`$CC --version | awk 'NR==1 {print $2}'`
if [ "$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 $w | sed 's/ /_/g'`
compilers_dir=$build_type-${v_fid}_and_${w_fid}
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_raw=$(grep processor /proc/cpuinfo | wc -l) ; then
# limit to 8 processors
np=$np_raw # cooked
if [ "$np" -gt 8 ] ; then
np=8
fi
if [ "$np_raw" = 224 ] ; then
np=64 # teehee!
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 $NF }')
MAKE="make -j$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 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
# 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
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`
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.
# WGET="LD_LIBRARY_PATH=/usr/lib wget -N -P ${AUTOBUILD_SOURCES}"
# WGETO="LD_LIBRARY_PATH=/usr/lib wget -P ${AUTOBUILD_SOURCES}"
WGET="wget -N -P ${AUTOBUILD_SOURCES}"
WGETO="wget -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
pre_release_server_dir=https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases/0.9-pre
pre_release_server_dir=https://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
echo doing the awk on the html $pre_release_files_html
awk ' /a href=.*.tar.gz/ {split($2, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' $pre_release_files_html
coot_version_tmp=$(awk ' /a href=.*.tar.gz/ {split($2, 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
echo =========================== build_coot_prerelease currently is $build_coot_prerelease ========================
if test "$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=$2; split(f, 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 NNX:: trying to build pre-release coot, but failed to find pre-release version
echo NNX:: make a stable release then
build_coot_prerelease=no
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 NNX:: 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.
# 20200415-PE - man this is fragile code. Don't need to sort now.
awk '/.*a href=.coot/ {f=$2; split(f, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[++n]=file; } END { for (file in files) print files[file]}' ${AUTOBUILD_SOURCES}/index.html
coot_version=$(awk '/.*a href=.coot/ {f=$2; split(f, 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)
coot_version=coot-0.9.8.5
coot_version=coot-0.9.8.6
coot_version=coot-0.9.8.7
coot_version=coot-0.9.8.8
coot_version=coot-0.9.8.9
coot_version=coot-0.9.8.91
coot_version=coot-0.9.8.92
echo NNX:: 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-${build_type} ${config_extras:-}"
coot_source_tar_file=${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
echo ========== awk results:
awk ' /a href=.*.tar.gz/ {f=$2; split(f, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \
${AUTOBUILD_SOURCES}/index.html
echo ==== sorted awk results ==========
awk ' /a href=.*.tar.gz/ {f=$2; split(f, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \
${AUTOBUILD_SOURCES}/index.html | sort
echo ==== with tail ==========
awk ' /a href=.*.tar.gz/ {f=$2; split(f, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \
${AUTOBUILD_SOURCES}/index.html | sort | tail -1
echo =========== from ${AUTOBUILD_SOURCES}/index.html
cat ${AUTOBUILD_SOURCES}/index.html
echo ==============
coot_version=$(awk ' /a href=.*.tar.gz/ {f=$2; split(f, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \
${AUTOBUILD_SOURCES}/index.html | sort | tail -1)
coot_version=coot-0.9.8.3 # the other one is used
if test -z "$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 ' /.*a href=/ {f=$2; split(f, 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 coot_version_pre is $coot_version_pre
echo build_coot_prerelease: $build_coot_prerelease
echo release_server_dir $release_server_dir
echo coot_version $coot_version
# exit # for testing release version extraction
# set the build prefix for installed stuff. Put everything in the
# pre-release directory if we are building a pre-release.
# (Perhaps this bit of code should go down lower, where we test
# build_coot_prerelease again
#
# we need install_top_dir because we use it to copy over coot.py
# to the install python directory.
# Notes for SSL with python:
# after configure, run this sed:
# real_ssl_prefix=/usr # for mac, for PC, libs go in /usr/lib64 and
# sed -i -e "s?#SSL=.*?SSL=$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=${AUTOBUILD_INSTALLED}-pre-release-${build_type} ${config_extras:-}"
coot_prefix="$generic_prefix"
install_top_dir=${AUTOBUILD_INSTALLED}-pre-release-${build_type}
# python seems to link OK on Darwin, so no need for this jiggery pokery
if [ $(uname) != Darwin ] ; then
python_lib_flags=LDFLAGS="-Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release-${build_type}/lib"
else
pv=$(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=$AUTOBUILD_INSTALLED-${build_type} ${config_extras:-}"
coot_prefix="$generic_prefix"
install_top_dir=${AUTOBUILD_INSTALLED}-${build_type}
if [ $(uname) != Darwin ] ; then
python_lib_flags=LDFLAGS="-Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release-${build_type}/lib"
fi
fi
else
# not pre-release
generic_prefix="--prefix=$AUTOBUILD_INSTALLED-${build_type} ${config_extras:-}"
install_top_dir=${AUTOBUILD_INSTALLED}-${build_type}
coot_prefix="$generic_prefix"
if [ $(uname) != Darwin ] ; then
python_lib_flags=LDFLAGS="-Wl,--rpath=${AUTOBUILD_INSTALLED}-${build_type}/lib"
else
pv=$(sw_vers -productVersion)
# e.g. 10.10
os_minor_version="${pv%.*}"
python_spec_flags="MACOSX_DEPLOYMENT_TARGET=$os_minor_version"
fi
fi
PATH=$install_top_dir/bin:$PATH
# 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=0
build_net_http=0
build_gsl=0
# build_libungif=0
# build_libtiff=0
# build_libjpeg=0
# build_libpng=0
# build_imlib=0
# build_gtk_canvas=0
build_goocanvas=
build_python=
build_pygobject=
build_guile_gtk=
build_gtkglext=
build_freeglut=0
build_glib=
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
# using system idn is no longer allowed.
# ---- test installation libidn -------------------------------
if [ -e $install_top_dir/include/idn2.h ] ; then
echo installation has libidn
else
echo installation does not have libidn, libcurl should be built also
build_libidn=1
build_curl=1
fi
# 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
# 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.
#
STD_PKGCONFIG_DIR=/usr/lib/pkgconfig
case "$architecture" in
x86_64*)
STD_PKGCONFIG_DIR=/usr/lib64/pkgconfig
;;
esac
if [ -z "$PKG_CONFIG_PATH" ] ; then
# I think that the standard dir is not needed.
# PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$STD_PKGCONFIG_DIR
PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig
case "$architecture" in
x86_64*)
PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib64/pkgconfig
;;
esac
else
PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
case "$architecture" in
x86_64*)
PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib64/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
;;
esac
fi
if [ -e /opt/X11/lib/pkgconfig ] ; then
PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$PKG_CONFIG_PATH
fi
echo "COOT_CCP4_PACKAGES" "$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 $PKG_CONFIG_PATH
# Do we have freetype2? cairo depends on it.
if pkg-config freetype2 ; then
build_freetype2=
echo system/installation has freetype2
else
echo freetype2 should be built
build_freetype2=1
fi
if pkg-config --atleast-version=2.14.5 glib ; then
# have glib
echo glib is up to date
build_glib=
else
echo glib is not up to date, rebuild glib - maybe.
build_glib=1
fi
# Test the output of pkg-config gtk+-2.0 for recent enough gtk.
# If not, then build it yourself.
#
# Experiment, to force bragg3 to compile gtk+2
#
# was 2.8
needed_gtk_version=2.10
#
pkg-config --atleast-version=$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
# guilegtk2.1 need version 2.8 of gtk to compile out of the box. If
# we have less than that then we need to apply a fix
#
gtk_version=`pkg-config --modversion gtk+-2.0`
if pkg-config --atleast-version=2.8 gtk+-2.0 ; then
echo gtk is new enough for guile-gtk
gtk_new_enough_for_guilegtk=true
else
echo guile-gtk needs fixing up
gtk_new_enough_for_guilegtk=false
fi
# freeglut
# for dir in ${dir_list} ; do
if [ "$OS" = Darwin ] ; then
if [ -e /opt/X11/lib/libglut.dylib ] ; then
build_freeglut=
fi
fi
if test -e ${install_top_dir}/include/GL/freeglut_std.h ; then
echo installation has Freeglut
build_freeglut=
glut_prefix="--with-glut-prefix=${install_top_dir}"
fi
# done
if test -n "$build_freeglut" ; then
echo freeglut should be built
build_freeglut=1
glut_prefix="--with-glut-prefix=$install_top_dir"
fi
build_libtool=1
if test -e ${install_top_dir}/lib/libltdl.so.3 ; then
build_libtool=
fi
if test -e ${install_top_dir}/lib/libltdl.la ; then
build_libtool=
fi
if test -z "$build_libtool" ; then
echo installation has libtool
else
echo libtool should be built
fi
# If this is unset, it means the same as "no"
if test -z "$use_system_gnomecanvas_if_possible" ; then
use_system_gnomecanvas_if_possible=no
fi
# test for libgnomecanvas
if test "$use_system_gnomecanvas_if_possible" = yes ; then
if test -e /usr/include/libgnomecanvas-2.0/libgnomecanvas/gnome-canvas-line.h ; then
echo system has libgnomecanvas
else
if test -e ${install_top_dir}/include/libgnomecanvas-2.0/libgnomecanvas/gnome-canvas-line.h ; then
echo installation has libgnomecanvas - you clever fellow
else
build_libgnomecanvas=1
fi
fi
else
if test -e ${install_top_dir}/include/libgnomecanvas-2.0/libgnomecanvas/gnome-canvas-line.h ; then
echo installation has libgnomecanvas - you clever fellow
else
build_libgnomecanvas=1
fi
fi
# ========== guile etc ==========
# FIXME indent
if [ $ENABLE_GUILE_COOT = yes ] ; then
# using install_top_dir's libgmp causes selinux problems on some systems. Therefore, if
# libgmp-dev is installed in the system lib dir /usr/$acl_libdirstem/libgmp.so.la we should
# use that rather than building. Users of that build will have to install their own libgmp
# then. So be it.
build_gmp=1
if test -e ${install_top_dir}/lib/libgmp.so.3 ; then
echo installation has gmp
build_gmp=
else
if test -e ${install_top_dir}/lib/libgmp.la ; then
echo installation has gmp
build_gmp=
else
echo gmp should be built
fi
fi
build_readline=1
#
# guile dependency readline. chihiro has bad build in
# guile-1.6.7/guile-readline/readline.c:107 'rl_pending_input' undeclared
# So installation needs to build readline (sigh).
#
if test -e ${install_top_dir}/include/readline/chardefs.h ; then
build_readline=
fi
if test -z "$build_readline" ; then
echo installation has readline
else
echo readline needs to be built
fi
# Darwin currently has guile-1.6 and guile (which is an older version)
# we want to use guile-1.6 if it exists.
# This need to be fixed for Macs I guess. We need 1.8.3 not 1.6
#
# echo guile-1.6-config will fail on non-fink non-mac systems
# guile-1.6-config --version
# if test $? = 0 ; then
# echo linking in fink 1.6 guile...
# rm -f $install_top_dir/bin/guile
# rm -f $install_top_dir/bin/guile-config
# rm -f $install_top_dir/bin/guile-snarf
# ln -s /sw/bin/guile-1.6 $install_top_dir/bin/guile
# ln -s /sw/bin/guile-1.6-config $install_top_dir/bin/guile-config
# ln -s /sw/bin/guile-1.6-snarf $install_top_dir/bin/guile-snarf
# fi
if [ -e $install_top_dir/bin/guile-config ] ; then
if $install_top_dir/bin/guile-config --version ; then
# We have a seen a situation somehow where bin/guile-config is installed
# but include/libguile.h is not. Strange. Let's test for libguile.h too.
#
if test -e $install_top_dir/include/libguile.h ; then
echo installation has guile
build_guile=
else
echo no include/libguile.h. guile should be built
echo no include/libguile.h. guile-gtk should be built
build_guile_gtk=1
build_guile=1
fi
else
echo guile-config failed. guile should be built
build_guile=1
build_guile_gtk=1
fi
else
echo guile-config missing. guile should be built
build_guile=1
build_guile_gtk=1
fi
# guile-gui
if test -f $install_top_dir/share/guile/gui/paren-match.scm ; then
echo installation has guile-gui
build_guile_gui=
else
echo guile-gui needs to be installed
build_guile_gui=1
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
# do we have greg?
# LD_LIBRARY_PATH has been set by now
if [ -e $install_top_dir/bin/guile ] ; then
$install_top_dir/bin/guile -c '(use-modules (ice-9 greg))'
status=$?
echo guile greg status $status
if test $status = 0 ; then
echo installation has greg
build_greg=
else
echo greg should be built
build_greg=1
fi
else
build_greg=1
fi
fi # ENABLE_GUILE_COOT
# ============= 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=python2.7
pver=2.7.18 # this is it - the final version of Python 2
numpy_version=1.7.1
numpy_version=1.16.6
# for an upgrade of numpy to work, the old numpy must be deleted from site-packages
#
# but more modern pythons do not compile (at least on my mac)
if [ $OS = Darwin ] ; then
pver=2.7.8
fi
if [ $ENABLE_PYTHON_COOT = yes ] ; then
$install_top_dir/bin/python -V
if test $? != 0 ; then
echo python should be built
build_python=1
build_pygtk=1
build_pygobject=1
else
python_version_installed=`python -V 2>&1`
python_target_version="Python $pver"
case "$python_version_installed" in
"$python_target_version")
echo installation has python, $python_version_installed
which python
build_python=
build_pygtk=
;;
*)
echo python $python_version_installed installed but not up to date...
echo python should be built
build_python=1
build_pygobject=1
build_pygtk=1
;;
esac
fi
fi
# test for pygobject
if [ $ENABLE_PYTHON_COOT = yes ] ; then
if test -z "$build_pygobject" ; then
if test -e $install_top_dir/include/pygtk-2.0/pygobject.h ; then
echo installation has pygobject
build_pygobject=
else
echo pygobject NOT exists, pygobject should be built
build_pygobject=1
build_pygtk=1
fi
fi
fi
# test for pygtk
if [ $ENABLE_PYTHON_COOT = yes ] ; then
if test -z "$build_pygtk" ; then
if test -e $install_top_dir/lib/pygtk/2.0/pygtk-demo.py ; then
echo pygtk demo exists, no build pygtk
else
echo pygtk demo NOT exists, pygtk should be built
build_pygtk=1
fi
fi
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.
$install_top_dir/bin/gsl-config --prefix
if test $? != 0 ; then
echo gsl should be built
build_gsl=1
else
gsl_version=`gsl-config --version`
# if you change this, change also gsl_version below.
needed_gsl_version=1.11
needed_gsl_version=1.12
needed_gsl_version=1.15
needed_gsl_version=1.16
# tmp value. This uses awk. It need not do.
# You can do the comparison with test.
build_gsl=`awk -v A=$gsl_version -v N=$needed_gsl_version 'BEGIN{x = ((A+0) != (N+0)) ; print x}'`
echo system/installation has the GSL version $gsl_version
echo build_gsl is $build_gsl
if [ $build_gsl = 1 ] ; then
echo need to build GSL
build_gsl=1
else
echo GSL is up to date
# set build_gsl to blank:
build_gsl=
fi
fi
# ##############################################################
# test for GtkGLExt
# ##############################################################
build_gtkglext=1
if test -e ${install_top_dir}/include/gtkglext-1.0/gdk/glext/glext.h ; then
build_gtkglext=
fi
if [ -n "$COOT_CCP4_PACKAGES" ] ; then
if test -e ${COOT_CCP4_PACKAGES}/include/gtkglext-1.0/gdk/glext/glext.h ; then
echo INFO:: found ${COOT_CCP4_PACKAGES}/include/gtkglext-1.0/gdk/glext/glext.h
build_gtkglext=
fi
fi
if test -z "$build_gtkglext" ; then
echo installation has gtkglext
else
echo gtkglext should be built
fi
# ##############################################################
# test for guile-gtk
# ##############################################################
# guile-gtk, only look in installation, not system.
# if we are not building gtk, perhaps we should not build
# guile-gtk also?
if test -e "${install_top_dir}/include/guile-gtk.h" ; then
echo installation has guile-gtk
if [ "$build_guile" != 1 ] ; then
build_guile_gtk=
else
echo guile needs building, so guile-gtk needs building.
build_guile_gtk=1
fi
else
echo installation does not have guile-gtk
build_guile_gtk=1
fi
if test -n "${build_guile_gtk}" ; then
echo guile-gtk.h not found, guile-gtk should be built
build_guile_gtk=1
else
echo guile-gtk should not be built
fi
# ##############################################################
# test for gnomecanvas
# ##############################################################
# on new Scientific Linux (7.3) we need to test for libgnomecanvas, not libgnomecanvas-2.0
#
# test for libgnomecanvas here
if pkg-config --modversion libgnomecanvas-2.0 ; then
:
else
# echo pkg-config does not find libgnomecanvas-2.0. Exiting.
# pkg_hnd=yum
# if [ "$dist_name" = debian ] ; then
# pkg_hnd=apt-get
# fi
# if [ "$dist_name" = ubuntu ] ; then
# pkg_hnd=apt-get
# fi
# echo consider: $pkg_hnd install libgnomecanvas-devel
# my_exit 2
echo ================ set build_libgnomecanvas=1
build_libgnomecanvas=1
fi
# ##############################################################
# test for goocanvas
# ##############################################################
if [ "$build_goocanvas" = "" ] ; then
# has it been installed?
#
if [ -e "${install_top_dir}/include/goocanvas-1.0/goocanvaswidget.h" ] ; then
build_goocanvas=no
goocanvas_args="--with-goocanvas-prefix=$install_top_dir"
fi
# is it compilable? (do we have the right gtk (etc) version?)
#
if pkg-config gtk+-2.0 --atleast-version 2.12 ; then
echo goocanvas: recent enough gtk+ version
if pkg-config cairo --atleast-version 1.4 ; then
echo goocanvas: recent enough cairo version
# yes, compilable
goocanvas_args="--with-goocanvas-prefix=$install_top_dir"
else
echo goocanvas: Cairo is too old. Goocanvas needs cairo 1.4 or later. You have:
pkg-config cairo --modversion
build_goocanvas=no
fi
else
echo goocanvas: gtk+-2.0 too old. Goocanvas needs 2.12 or later. You have:
pkg-config gtk+-2.0 --modversion
build_goocanvas=no
fi
fi
echo goocanvas: goocanvas_args set to $goocanvas_args
# test for mmdb: Does mmdb_model.h exist, and if it does, does it
# contain MMDBF_IgnoreHash. If not, then build mmdb.
#
# CCP4 mmdb installs in the include/mmdb2 directory,
#
if test -e "${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
if [ -e $install_top_dir/include/clipper/contrib/sfscale.h ] ; then
if grep PrePro2 $install_top_dir/include/clipper/core/ramachandran.h ; then
build_clipper=
else
echo $install_top_dir/include/clipper/core/ramachandran.h is old, building clipper
build_clipper=1
fi
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 $install_top_dir/lib/pkgconfig/libccp4c.pc ] ; then
# no need to rebuild
build_ccp4c=
else
build_ccp4c=1
fi
else
build_ccp4c=1
fi
# Here we can force the building of clipper because we don't
# know if the dependency libccp4c.la was from 6.0 or 5.0.2
# But, let's not do that any more.
# build_clipper=
# build_ccp4c=
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
# build components
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
#
#
# libccp4: (not fortran)
if test -n "$build_ccp4c" ; then
echo BUILDING: libccp4
libccp4_version=6.5.1
# ${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
${WGET} https://ftp.ccp4.ac.uk/opensource/libccp4-$libccp4_version.tar.gz
(
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
) > $HOSTLOGDIR/01-libccp4.txt 2>&1
else
echo not building libccp4:
fi
#
# mmdb
#
#
# mmdb
#
if test -n "$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=2.0.22
# mmdb_server_dir=ftp://ftp.ccp4.ac.uk/opensource
mmdb_server_dir=$extras_place
echo ${WGET} $mmdb_server_dir/mmdb2-$mmdb_version.tar.gz
${WGET} $mmdb_server_dir/mmdb2-$mmdb_version.tar.gz
(
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
) > $HOSTLOGDIR/02-mmdb.txt 2>&1
else
echo not building mmdb:
fi
if test -n "$build_ssmlib" ; then
echo BUILDING SSM:
#
# 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-$ssm_version
mmdb_lib_dir=$install_top_dir/lib
if [ -e $install_top_dir/lib64/libmmdb2.so ] ; then
mmdb_lib_dir=$install_top_dir/lib64
fi
./configure $generic_prefix --enable-shared --disable-static CPPFLAGS=-I$install_top_dir/include LDFLAGS=-L$mmdb_lib_dir
if $MAKE ; then
$MAKE install
fi
) > $HOSTLOGDIR/02-ssm.txt 2>&1
else
echo not building ssm:
fi
# fftw
if test -n "$build_fftw" ; then
echo BUILDING fftw:
#
# ${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
) > $HOSTLOGDIR/03-fftw.txt 2>&1
else
echo not building fftw:
fi
# # clipper
# #
# #
if test -n "$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
(
gzip -dc ${AUTOBUILD_SOURCES}/clipper-$clipper_version.tar.gz | tar xf -
cd clipper-$clipper_version_dir
pwd
date
# this seems to have already been applied in 2.1.20180802
# patch the hkl_data.h header
# needs testing
# 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
if [ -e $install_top_dir/lib64 ] ; then
export LIBS="-L$install_top_dir/lib64 -L$install_top_dir/lib"
fi
else
save_libs="$LIBS"
export LIBS=-L$install_top_dir/lib:$LIBS
if [ -e $install_top_dir/lib64 ] ; then
export LIBS="-L$install_top_dir/lib64 -L$install_top_dir/lib $LIBS"
fi
fi
echo for clipper configure 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
else
echo not building clipper:
fi
if [ -e $install_top_dir/lib/libsqlite3.so ] ; then
echo libsqlite3 is installed
else
echo building libsqlite3
${WGET} https://www.sqlite.org/2021/sqlite-autoconf-3360000.tar.gz
(
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/sqlite-autoconf-3360000.tar.gz | tar xf -
cd sqlite-autoconf-3360000
if ./configure --prefix=$install_top_dir ; then
$MAKE
make install
fi
cd -
) > $HOSTLOGDIR/05a-libsqlite3.txt 2>&1
fi
# freeglut
if test -n "$build_freeglut" ; then
echo BUILDING freeglut:
${WGET} $extras_place/freeglut-2.4.0.tar.gz
(
date
pwd
save_CFLAGS="$CFLAGS"
CFLAGS="$CFLAGS -I/usr/X11R6/include"
export CFLAGS
gzip -dc ${AUTOBUILD_SOURCES}/freeglut-2.4.0.tar.gz | tar xf -
cd freeglut-2.4.0
# On 64 bit redhat 4, we need to use /usr/X11R6/lib64, not /usr/X11R6/lib.
echo INFO:: MACHTYPE is $MACHTYPE
echo INFO:: systype is $systype
if [ "$systype" = x86_64-rhel-4 ] ; then
echo patching freeglut configure for lib64.
cp configure configure.orig
if sed -i -e 's?/usr/X11R6/lib?/usr/X11R6/lib64?' configure ; then
echo patching went OK.
else
echo patching failed.
my_exit 1
fi
fi
./configure $generic_prefix --disable-warnings
build_status=$?
echo INFO:: freeglut configure status $build_status
if [ $build_status -eq 0 ] ; then
$MAKE
build_status=$?
echo INFO:: freeglut make status $build_status
if [ $build_status -eq 0 ] ; then
echo INFO:: freeglut make installing...
$MAKE install
glut_prefix="--with-glut-prefix=$install_top_dir"
echo INFO:: setting glut_prefix to $glut_prefix
fi
fi
CFLAGS="$save_CFLAGS"
export CFLAGS
) > $HOSTLOGDIR/05-freeglut.txt 2>&1
else
echo not building freeglut:
fi
if [ "$build_gtkglext" = 1 ] ; then
echo BUILDING gtkglext:
gtkglext_version=1.2.0
# this host? disappeared.
# ${WGET} http://surfnet.dl.sourceforge.net/sourceforge/gtkglext/gtkglext-$gtkglext_version.tar.gz
# ${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/gtkglext-$gtkglext_version.tar.gz
${WGET} $extras_place/gtkglext-$gtkglext_version.tar.gz
(date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/gtkglext-$gtkglext_version.tar.gz | tar xf -
# now, for some (newer) versions of GTK+ the gtkglext needs to be
# tweaked so that it fixes out of date function usage:
cd gtkglext-$gtkglext_version
echo gtk+-2.0 version:
pkg-config gtk+-2.0 --modversion
# gtk+ 2.20 needs converting GTK_WIDGET_REALIZED to gtk_widget_get_realised, but
# gtk+ 2.18 does not (it fails if we add that patch), so use a simpler one.
if pkg-config gtk+-2.0 --atleast-version 2.16 ; then
patch_file_1=gtk-gtkglwidget.c-for-modern-gtk-for-2.18.patch
patch_file_2=gtkglext-context-finalize.diff
patch_file_3=gtkglext-multisample.patch.patch
patch_file_4=gtkglext-pangox.patch
patch_file_5=gtkglext-gdkglfont.patch
if pkg-config gtk+-2.0 --atleast-version 2.20 ; then
patch_file_1=gtk-gtkglwidget.c-for-modern-gtk.patch
fi
echo we have sufficiently new version of gtk+, we need to patch gtkglext with $patch_file_1
# when in the gtkglext dir, patch patch_file_2 with -p0 and patch_file_3 with -p1
${WGET} $extras_place/$patch_file_1
${WGET} $extras_place/$patch_file_2
${WGET} $extras_place/$patch_file_3
${WGET} $extras_place/$patch_file_4
${WGET} $extras_place/$patch_file_5
# we need extra patch to get rid of pangox dependency in
# configure and stop gdkglfont-x11.c getting compiled by
# removing references to it and its object from
# gdk/x11/Makefile. Either that or get a nice new gtkglext by
# doing make dist from git (see hal Project).
if patch -p0 < ${AUTOBUILD_SOURCES}/$patch_file_1 ; then
echo gtkglext patched patch_file_1 good.
else
echo gtkglext patch_file_1 failed.
my_exit 2
fi
if patch -p0 < ${AUTOBUILD_SOURCES}/$patch_file_2 ; then
echo gtkglext patched patch_file_2 good.
else
echo gtkglext patch_file_2 failed.
my_exit 2
fi
if patch -p1 < ${AUTOBUILD_SOURCES}/$patch_file_3 ; then
echo gtkglext patched patch_file_3 good.
else
echo gtkglext patch_file_3 failed.
my_exit 2
fi
# 20180822 I also found on Ubuntu 18.04 gtk 2.24.32 that we need to fix up gdkglshapes.c
sed -e 's/static int index/static int index_xx/' \
-e 's/drawtriangle(i, idata, index/drawtriangle(i, idata, index_xx/' \
gdk/gdkglshapes.c > shapes-tmp
mv shapes-tmp gdk/gdkglshapes.c
else
echo version of gtk is old, no need to patch gtkglext.
fi
# get rid of font stuff.
if patch -p0 < ${AUTOBUILD_SOURCES}/$patch_file_4 ; then
echo gtkglext patched patch_file_4 good.
else
echo gtkglext patch_file_4 failed.
my_exit 2
fi
if patch -p0 < ${AUTOBUILD_SOURCES}/$patch_file_5 ; then
echo gtkglext patched patch_file_5 good.
else
echo gtkglext patch_file_5 failed.
my_exit 2
fi
if [ $OS = Darwin ] ; then
if [ -e /opt/X11 ] ; then
extra_gtkglext_args="CPPFLAGS=-I/opt/X11/include LDFLAGS=-L/opt/X11/lib"
fi
fi
echo PKG_CONFIG_PATH: $PKG_CONFIG_PATH
echo ./configure $generic_prefix $extra_gtkglext_args
if ./configure $generic_prefix $extra_gtkglext_args ; then
if [ "$update_libtool" = 1 ] ; then
cp $install_top_dir/bin/libtool .
fi
# do this on 64 bit systems. FIXME
# Use uname -p being x84_64
# sed -i 's#sys_lib_search_path_spec="#sys_lib_search_path_spec="/usr/lib64#' libtool
$MAKE
status=$?
if [ "$status" != 0 ] ; then
echo make of gtkglext failed
else
$MAKE install
fi
else
echo : ----------------------------------------------------------------
echo gtkglext configure failed
echo : ----------------------------------------------------------------
echo here is config.log:
echo " "
cat config.log
status=2
fi
exit $status
) > $HOSTLOGDIR/06-pre-gtkglext.txt 2>&1
# capture the status from the subshell, if an error, exit the main shell too.
status=$?
echo status from gtkglext build was $status
if [ $status = 2 ] ; then
echo that\'s an error.
echo perhaps libXt-devel is missing\?
my_exit 2
fi
else
echo not building gtkglext:
fi
##################### libgnome #####################################
#
# for SuSe 11.3, we need to install the following:
# g++ patch m4 make libgnomecanvas-dev gtk-dev swig
# Redhat 7.3 doesn't have libgnomecanvas*-devel because they don't support
# development using this lib. Move to libcairo they say (I think).
# Well, maybe later.
# Get libgnomecanvas here if needed:
# http://ftp.gnome.org/pub/gnome/sources/libgnomecanvas/2.30/libgnomecanvas-2.30.3.tar.bz2
# depends on
# https://ftp.gnome.org/pub/gnome/sources/libart_lgpl/2.3/libart_lgpl-2.3.21.tar.gz
# test for libgnomecanvas and if the system doesn't have it then
# build it
if [ "$build_libgnomecanvas" = 1 ] ; then
# do both libart_lgpl and libgnomecanvas
libart_lgpl_version=2.3.21
if [ -e $install_top_dir/include/libart-2.0/libart_lgpl/libart.h ] ; then
echo not building libart_lgpl_version
else
(
${WGET} https://ftp.gnome.org/pub/gnome/sources/libart_lgpl/2.3/libart_lgpl-2.3.21.tar.gz
tar xf ${AUTOBUILD_SOURCES}/libart_lgpl-2.3.21.tar.gz
cd libart_lgpl-$libart_lgpl_version
./configure $generic_prefix
${MAKE} && make install
cd -
) > $HOSTLOGDIR/06-libart_lgpl.txt 2>&1
fi
# not to self: it seems, from my centos7 build that libgnomecanvas doesn't
# correctly pick up the libart above - I did a system install of libart before I thought about it.
if [ -e $install_top_dir/include/libgnomecanvas-2.0/libgnomecanvas/libgnomecanvas.h ] ; then
echo not building libgnomecanvas
else
libgnomecanvas_version=2.30.3
(
${WGET} http://ftp.gnome.org/pub/gnome/sources/libgnomecanvas/2.30/libgnomecanvas-$libgnomecanvas_version.tar.bz2
tar xf ${AUTOBUILD_SOURCES}/libgnomecanvas-$libgnomecanvas_version.tar.bz2
cd libgnomecanvas-$libgnomecanvas_version
./configure $generic_prefix
${MAKE} && make install
cd -
) > $HOSTLOGDIR/06-libgnomecanvas.txt 2>&1
fi
fi
##################### goocanvas #####################################
if [ "$build_goocanvas" != "no" ] ; then
echo BUILDING goocanvas
${WGET} http://ftp.gnome.org/pub/GNOME/sources/goocanvas/1.0/goocanvas-1.0.0.tar.gz
(date
echo building in: $PWD
echo PKG_CONFIG_PATH is $PKG_CONFIG_PATH
echo CFLAGS: $CFLAGS
echo CXXFLAGS: $CXXFLAGS
echo CPPFLAGS: $CPPFLAGS
echo LDFLAGS: $LDFLAGS
pwd
gzip -dc ${AUTOBUILD_SOURCES}/goocanvas-1.0.0.tar.gz | tar xf -
cd goocanvas-1.0.0
# on my Mac, glib depends on libintl.h and that is installed by the ccp4 dir
# but that is not added by pkg-config glib-2.0 --cflags. glib bug?
if ./configure $generic_prefix $EXTRA_GOOCANVAS_CFLAGS ; then
if ! $MAKE ; then
echo make of goocanvas failed
else
$MAKE install
fi
else
echo goocanvas configure failed
echo here is config.log
cat config.log
fi
) > $HOSTLOGDIR/06-pre-goocanvas.txt 2>&1
fi
##################### readline #####################################
if test -n "$build_readline" ; then
echo BUILDING readline:
readline_version=6.2
readline_version=6.3
${WGET} https://ftp.gnu.org/gnu/readline/readline-$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
echo patching readline...
# need a patch (for debian only) to add curses to the additional libs line
patch -p0 < ${AUTOBUILD_SOURCES}/readline-5.1.patch
fi
apply_shared_lib_sed_fix=true
# when don't we want to apply the sed fix?
# ....
#
if [ $apply_shared_lib_sed_fix = true ] ; then
echo applying sed patch for shared-lib libreadline
# thanks for the quoting help tony duan @ stackoverflow
sed -i '125,135 s/SHOBJ_LDFLAGS=.*/&\n SHLIB_LIBS='"'"'$(TERMCAP_LIB)'"'"'/' support/shobj-conf
fi
echo ./configure $generic_prefix --with-curses --enable-shared
./configure $generic_prefix --with-curses --enable-shared
# single thread
if make ; then
make install
# no more missing functions hopefully!
# undefined symbol: UP (/home/paule/autobuild/Linux-penelope-gtk2-python/lib/libreadline.so)
ldd -r $install_top_dir/lib/libreadline.so
else
echo make of readline failed
fi
) > $HOSTLOGDIR/06-pre-readline.txt 2>&1
else
echo not building readline:
fi
###############################################################################
########## build python and friends #############
###############################################################################
# So that python is found when it is installed:
#
PATH=$install_top_dir/bin:$PATH
export PATH
# python
#
if test -n "$build_python" ; then
echo BUILDING Python ${pver}:
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
gzip -dc ${AUTOBUILD_SOURCES}/Python-$pver.tgz | tar xf -
cd Python-$pver
# --with-ensurepip=install
echo INFO:: ./configure $generic_prefix --enable-shared --with-ensurepip=install $python_lib_flags $python_spec_flags for python
#
# do we also need to use --with-threads=dir?
if ./configure $generic_prefix --enable-shared --with-ensurepip=install $python_lib_flags $python_spec_flags ; then
echo INFO:: make for python
if $MAKE ; then
echo INFO:: make install for python
$MAKE install
fi
fi
) > $HOSTLOGDIR/07-python.txt 2>&1
# We need these otherwise python moans about not finding the libraries.
#
# 20140903 I have my doubts this is true now. Comment out
#
# echo setting PYTHONHOME
# PYTHONHOME=$install_top_dir
# export PYTHONHOME
# echo PYTHONHOME is now $PYTHONHOME
echo post linking python to $python_version
#
if [ ! -e $install_top_dir/bin/$python_version ] ; then
echo Oops\! $python_version does not exist.
# only python dependencies from now on
echo exiting...
my_exit 2
fi
if [ -e $install_top_dir/bin/python ] ; then
echo removing old python
rm $install_top_dir/bin/python
fi
current_dir=`pwd`
cd $install_top_dir/bin
echo linking new...
ln -s $python_version python
if [ $? -ne 0 ] ; then
echo Opps: failed: ln -s $install_top_dir/bin/$python_version \
$install_top_dir/bin/python
fi
cd $current_dir
echo done python linking.
# now we have "python" in our path - no need to rehash -
# clever old Bourne shell (or do I mean bash?).
else
echo not building python:
fi
#################################################################
#################################################################
# should I use pip to install other packages? (skilearn)
if test -n "$build_pygobject" ; then
echo BUILDING pygobject:
#
pygobject_major_minor_version=2.14
pygobject_version=2.14.1
# new (2.4+) versions of pygobject do not compile with older
# versions of GLIB and pkgconfig.
if pkg-config --atleast-pkgconfig-version 0.16 ; then
echo INFO:: pkg-config is new enough to build pygobject
pygobject_major_minor_version=2.8
pygobject_version=2.8.0
echo path 1 ${WGET} http://ftp.gnome.org/pub/GNOME/sources/pygobject/$pygobject_major_minor_version/pygobject-$pygobject_version.tar.gz
if ${WGET} http://ftp.gnome.org/pub/GNOME/sources/pygobject/$pygobject_major_minor_version/pygobject-$pygobject_version.tar.gz ; then
echo OK got pygobject-$pygobject_version.tar.gz
else
echo PROBLEM:: wget for pygobject-$pygobject_version.tar.gz
fi
else
if pkg-config --atleast-pkgconfig-version 0.15.1 ; then
pygobject_major_minor_version=2.8
pygobject_version=2.8.0
echo path 2 ${WGET} http://ftp.gnome.org/pub/GNOME/sources/pygobject/$pygobject_major_minor_version/pygobject-$pygobject_version.tar.gz
if ${WGET} http://ftp.gnome.org/pub/GNOME/sources/pygobject/$pygobject_major_minor_version/pygobject-$pygobject_version.tar.gz ; then
echo OK got pygobject-$pygobject_version.tar.gz
else
echo PROBLEM:: wget for pygobject-$pygobject_version.tar.gz
fi
else
# centos4 can't build 2.8, because glib is not new enough (it is 2.3.5)
# centos4 pkg-config version is 0.15.0
pygobject_major_minor_version=2.4
pygobject_version=2.4.0
# ftp.gnome.org does not distribute 2.4.x Baah. Get it from extras
${WGET} $extras_place/pygobject-2.4.0.tar.gz
fi
echo INFO:: pkg-config is NOT new enough to build pygobject 2.14
echo downgrading pygobject to $pygobject_version
fi
(
date
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-$pygobject_version
# typename is a variable name to a function in the pygobject header.
# it causes the compiler on CentOS4 to fail with a syntax error.
# so substitute the name.
echo about to sed
sed -e 's/typename/s_typename/' gobject/pygobject.h > gobject/pygobject.h.tmp
echo about to mv gobject/pygobject.h.tmp gobject/pygobject.h
mv gobject/pygobject.h.tmp gobject/pygobject.h
save_dllp=$DYLD_LIBRARY_PATH
unset DYLD_LIBRARY_PATH
echo about to bash configure ./configure $generic_prefix
# on MacOSX we need to bash this or some sort of crappy apple crash in configure here.
bash ./configure $generic_prefix
echo about to make
$MAKE
pygobject_status=$?
if [ "$pygobject_status" != 0 ] ; then
echo make of pygobject failed
else
$MAKE install
fi
export DYLD_LIBRARY_PATH=$save_dllp
else
echo ERROR:: ${AUTOBUILD_SOURCES}/pygobject-$pygobject_version.tar.gz file not found.
fi
) > $HOSTLOGDIR/07-pygobject.txt 2>&1
else
echo not building pygobject:
fi
# http://ftp.gnome.org/pub/GNOME/sources/pygtk/2.12/pygtk-2.12.1.tar.gz
if test -n "$build_pygtk" ; then
echo BUILDING pygtk:
#
# py_gtk_version=2.12.1
# pygtk_version=2.8.6 # too recent, need 'pango >= 1.10.0' but version of Pango is 1.8.1
# Requested 'pygobject-2.0 >= 2.9' but version of PyGObject is 2.6.0
# GTK... Requested 'gtk+-2.0 >= 2.7' but version of GTK+ is 2.6.7
# GTK... Requested 'gtk+-2.0 >= 2.8.0' but version of GTK+ is 2.6.7
# GLIB - version >= 2.8.0
pygtk_version=2.6.3
# FIXME
# 20090824
# 2.6.3 is too hight for CentOS 4 series, because it complains that
# GLIB2 needs to be 2.6.0 or greater and (system) is only 2.4.2
# Red Hat Enterprise Linux was released 2005-02-15. Find a version of pygtk that
# is compatible with that.
${WGET} http://ftp.gnome.org/pub/GNOME/sources/pygtk/2.6/pygtk-$pygtk_version.tar.gz
(
date
gzip -dc ${AUTOBUILD_SOURCES}/pygtk-$pygtk_version.tar.gz | tar xf -
cd pygtk-$pygtk_version
if [ ! -z "$libintl_cflags" ] ; then
export CFLAGS=$libintl_cflags
export CPPFLAGS="$CPPFLAGS $libintl_cflags"
fi
save_dllp=$DYLD_LIBRARY_PATH
unset DYLD_LIBRARY_PATH
./configure $generic_prefix --with-pango --with-pangocairo PYGOBJECT_CFLAGS=-I$install_top_dir/include/pygtk-2.0 PYGOBJECT_LIBS=-L$install_top_dir/lib
$MAKE
pygtk_status=$?
if [ "$pygtk_status" != 0 ] ; then
echo make of pygtk failed
else
$MAKE install
fi
export DYLD_LIBRARY_PATH=$save_dllp
) > $HOSTLOGDIR/07-pygtk.txt 2>&1
else
echo not building pygtk:
fi
###############################################################################
########## build boost #############
###############################################################################
build_boost=true
test_for_already_installed_dependencies=true
if [ "$test_for_already_installed_dependencies" = true ] ; then
if [ -e $install_top_dir/include/boost/functional/hash.hpp ] ; then
echo not building boost:
build_boost=false
fi
fi
if [ "$build_boost" = true ] ; then
boost_version=1_72_0
echo building boost $boost_version # to build.log
echo building boost $boost_version 1>&2 # to the terminal
(
echo building ========================= boost $boost_version =========================
address_model=64
python_version_extention=2.7 # extract this
boost_home_url=https://dl.bintray.com/boostorg/release/1.72.0/source
boost_home_url=https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source
echo wgetting $boost_home_url/boost_$boost_version.tar.gz
${WGET} $boost_home_url/boost_$boost_version.tar.gz
gzip -dc ${AUTOBUILD_SOURCES}/boost_$boost_version.tar.gz | tar xf -
if [ -e boost_$boost_version ] ; then
cd boost_$boost_version
# ./bootstrap.sh --prefix=$install_top_dir --with-libraries=python,regex,serialization --without-icu
./bootstrap.sh --prefix=$install_top_dir --with-libraries=python,regex,thread,serialization --without-icu
# bjam no longer exists
./b2 address-model=$address_model -j2 cflags=-fPIC cxxflags="-fPIC -I$install_top_dir/include/python$python_version_extention -Wno-maybe-uninitialized -Wno-deprecated-declarations" install
echo b2 install into $install_top_dir complete
cd -
else
echo boost untar failed - maybe download failed.
fi
) > $HOSTLOGDIR/16-boost.txt 2>&1
fi
build_numpy=true
# Let's stop at the beginning if we need a fortran compiler and don't have it.
#
if [ "$build_numpy" = true ] ; then
if gfortran --version > /dev/null ; then
:
else
echo fortran compiler not found.
exit 2
fi
fi
if [ true = true ] ; then
skip_this=false
arch=linux
if [ -e $install_top_dir/lib/python2.7/site-packages/numpy-$numpy_version-py2.7-$arch-x86_64.egg/numpy/core/include/numpy/halffloat.h ] ; then
echo not building numpy:
skip_this=true
fi
if [ $skip_this = false ] ; then
echo building numpy
(
echo building ========================= numpy ==============================
pwd
# 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
pythonhosted_magic_number=b7/6f/24647f014eef9b67a24adfcbcd4f4928349b4a0f8393b3d7fe648d4d2de3
${WGET} https://files.pythonhosted.org/packages/$pythonhosted_magic_number/numpy-$numpy_version.zip
#
unzip ${AUTOBUILD_SOURCES}/numpy-$numpy_version.zip
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
python setup.py build --fcompiler=gfortran
python setup.py install
if [ $? ] ; then
:
else
echo something bad about numpy.
exit 2
fi
cd -
) > $HOSTLOGDIR/16-b-numpy.txt 2>&1
fi
fi
# need to install Pillow (for depictions to work):
# https://files.pythonhosted.org/packages/b3/d0/a20d8440b71adfbf133452d4f6e0fe80de2df7c2578c9b498fb812083383/Pillow-6.2.2.tar.gz
if [ -e $install_top_dir/lib/python2.7/site-packages/Pillow-6.2.2.dist-info ] ; then
build_pillow=no
else
build_pillow=yes
fi
if [ -e $install_top_dir/lib/python2.7/site-packages/Pillow-6.2.2-py2.7-linux-x86_64.egg ] ; then
build_pillow=no
fi
if [ "$build_pillow" = no ] ; then
echo not building Pillow:
else
pillow_url=https://files.pythonhosted.org/packages/b3/d0/a20d8440b71adfbf133452d4f6e0fe80de2df7c2578c9b498fb812083383/Pillow-6.2.2.tar.gz
${WGET} --no-if-modified-since $pillow_url
if [ -e ${AUTOBUILD_SOURCES}/Pillow-6.2.2.tar.gz ] ; then
(
tar xf ${AUTOBUILD_SOURCES}/Pillow-6.2.2.tar.gz
cd Pillow-6.2.2
python setup.py build
python setup.py install
cd -
) > $HOSTLOGDIR/17-pillow.txt 2>&1
fi
fi
# this is a hack for charybdis - we need cmake version 3.1 or later
export PATH=$HOME/cmake/bin:$PATH
build_rdkit=true
rdkit_version=2017_09_3
# rdkit_version=2019_09_1 # python 3
rdkit_version=2018_09_3 # Atom pointers gone, needs coot update
rdkit_home=https://github.com/rdkit/rdkit/archive
rdkit_tar_host_file_name=Release_$rdkit_version.tar.gz
rdkit_tar_download_file_name=rdkit-Release_$rdkit_version.tar.gz
if [ "$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:
skip_this=true
fi
fi
# hack - force RDKit build
# skip_this=false
if [ $skip_this = false ] ; then
echo building rdkit $rdkit_version
(
echo building ========================= rdkit ==============================
# at last we get to actually compile rdkit
RDKIT=$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
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
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
echo found the file ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
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: $size
if [ "$size" = 54644917 ] ; 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
# $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
s=$(stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name)
if [ "$s" = $rdkit_tar_size ] ; then
do_rdkit_download=false
fi
fi
if [ $do_rdkit_download = true ] ; then
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
echo tar xf ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
tar xf ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
pwd
ls
if [ ! -e rdkit-Release_$rdkit_version ] ; then
echo RDKit untar dir not find: rdkit-Release_$rdkit_version
exit 2
fi
cd rdkit-Release_$rdkit_version
mkdir -p build
cd build
pwd
tree_from_build=..
fi
# New (1.60) boost uses BOOST_PYTHON not Boost_PYTHON
#
echo which cmake
which cmake
# No help: -DBoost_INCLUDE_DIR=$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_pthon_ext=27
libboost_pthon_ext=
extension_type=so
if [ $(uname) = Darwin ] ; then
extension_type=dylib
else
extension_type=so
fi
echo will configure with cmake like this:
echo cmake -DRDK_INSTALL_INTREE=0 \
-DPYTHON_EXECUTABLE=$install_top_dir/bin/python \
-DPYTHON_LIBRARY=$install_top_dir/lib/libpython2.7.$extension_type \
-DPYTHON_INCLUDE_DIR=$install_top_dir/include/python2.7 \
-DRDK_BUILD_CAIRO_SUPPORT=ON \
-DRDK_TEST_MULTITHREADED=OFF \
-DRDK_BUILD_THREADSAFE_SSS=OFF \
-DRDK_BUILD_INCHI_SUPPORT=OFF \
$cmake_macosx_rpath \
-DCMAKE_INSTALL_PREFIX=$install_top_dir $tree_from_build
if cmake -DRDK_INSTALL_INTREE=0 \
-DPYTHON_EXECUTABLE=$install_top_dir/bin/python \
-DPYTHON_LIBRARY=$install_top_dir/lib/libpython2.7.$extension_type \
-DPYTHON_INCLUDE_DIR=$install_top_dir/include/python2.7 \
-DRDK_BUILD_CAIRO_SUPPORT=ON \
-DRDK_TEST_MULTITHREADED=OFF \
-DRDK_BUILD_THREADSAFE_SSS=OFF \
-DRDK_BUILD_INCHI_SUPPORT=OFF \
$cmake_macosx_rpath \
-DCMAKE_INSTALL_PREFIX=$install_top_dir $tree_from_build ; then
pwd
echo ls -l
ls -l
echo ls -l ../External
ls -l ../External
echo ls -l ../External/catch
ls -l ../External/catch
echo ls -l ../External/catch/catch
ls -l ../External/catch/catch
# linusheinz: glibc changed SIGSTKSZ to be a syscall instead
# of being constant
#
# External/catch/catch/single_include/catch.hpp:7320 needs a patch
# 7320 // char FatalConditionHandler::altStackMem[SIGSTKSZ] = {};
# 7321 char FatalConditionHandler::altStackMem[32768] = {};
sed -i.backup -e 's/char FatalConditionHandler::altStackMem.SIGSTKSZ./char FatalConditionHandler::altStackMem[32768]/' ../External/catch/catch/single_include/catch.hpp
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/17-rdkit.txt 2>&1
fi
fi
# silicos-it's biscu-it
if [ -e $install_top_dir/lib/python2.7/site-packages/silicos_it/descriptors/qed.py ] ; then
echo not building biscu-it:
else
echo building QED
(date
# ${WGET} http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/_downloads/qed-1.0.1.tar.gz
${WGET} $extras_place/qed-1.0.1.tar.gz
pwd
tar xf ${AUTOBUILD_SOURCES}/qed-1.0.1.tar.gz
cd qed-1.0.1
python setup.py install
cd -
) > $HOSTLOGDIR/19-biscu-it.txt 2>&1
fi
# Now we need:
# * guile
# * guile-www
# * guile-gtk
# * guile-gui
# * gsl
###############################################################################
########## build guile and friends #############
###############################################################################
if test -n "$build_gmp" ; then
echo BUILDING gmp:
# 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
${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gmp/gmp-$gmp_version.tar.bz2
(date
pwd
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
) > $HOSTLOGDIR/08-pre-gmp.txt 2>&1
else
echo not building gmp:
fi
if test -n "$build_libtool" ; then
echo BUILDING libtool:
libtool_version=1.5.24
${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libtool/libtool-$libtool_version.tar.gz
(date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/libtool-$libtool_version.tar.gz | tar xf -
cd libtool-$libtool_version
./configure $generic_prefix
$MAKE
status=$?
if [ "$status" != 0 ] ; then
echo make of libtool failed
else
$MAKE install
fi
) > $HOSTLOGDIR/09-pre-libtool.txt 2>&1
else
echo not building libtool:
fi
# $ guile
# Backtrace:
# In unknown file:
# ?: 133* [#<procedure #f ()>]
# ?: 134* [load-file #<primitive-procedure primitive-load> ...]
# ?: 135* [save-module-excursion #<procedure #f ()>]
# ?: 136 (let (# #) (dynamic-wind # thunk #))
# ?: 137 [dynamic-wind #<procedure #f ()> #<procedure #f ()> #<procedure #f ()>]
# ?: 138* [#<procedure #f ()>]
# ?: 139* [primitive-load "/home/xxx/autobuild/Linux-host-pre-release-gtk2-python/share/guile/1.8/ice-9/debug.scm"]
# In /home/xxx/autobuild/Linux-host-pre-release-gtk2-python/share/guile/1.8/ice-9/debug.scm:
# 22: 140* (define-module (ice-9 debug) :export ...)
# In unknown file:
# ?: 141* [copy-tree ...
# ?: 142* [apply #<procedure #f args> (# :export #)]
# ?: 143 [#<procedure #f args> (ice-9 debug) :export ...]
# ?: 144 (quasiquote (eval-case (# #) (else #)))
# ?: 145* [compile-define-module-args (# :export #)]
# ?: 146 [loop ((quote #)) (:export (frame-number->index trace untrace ...))]
# ...
# ?: 147 [loop ((quote (ice-9 debug))) ...
# ?: 148* [cons ...
# ?: 149* [keyword-like-symbol->keyword :export]
# ?: 150 [symbol->keyword ...
# ?: 151* [string->symbol ...
# ?: 152* (substring (symbol->string sym) 1)
#
# then compile guile with -O (it defaults to -O2 if you do not add this, I think)
# 20130910 force -O2 for every target.
# <unnamed port>: In expression (substring (symbol->string sym) 1):
# <unnamed port>: Stack overflow
if test -n "$build_guile" ; then
echo BUILDING guile:
#
guile_version=1.8.8
guile_version_dir=$guile_version
if test "$OS" = "Darwin" ; then
guile_version=1.8.8-marcin-fix
fi
# mirror has gone/moved.
# ${WGET} http://mirror.ac.uk/mirror/ftp.gnu.org/gnu/guile/guile-${guile_version}.tar.gz
# ${WGET} http://ftp.gnu.org/gnu/guile/guile-${guile_version}.tar.gz
# ${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile/guile-${guile_version}.tar.gz
# Marcin-fix version
${WGET} $extras_place/guile-${guile_version}.tar.gz
${WGET} $extras_place/guile-1.8.7-updated.patch
${WGET} $extras_place/guile-1.8.8-gc-segment.c.patch
${WGET} $extras_place/guile-fink.patch
${WGET} $extras_place/guile-configure.patch
# if debian, unset LD_LIBRARY_PATH and set it back again when done.
if [ "$dist_name" = "debian" ] ; then
llp_save=$LD_LIBRARY_PATH
unset LD_LIBRARY_PATH
extra_flags_for_debian="LD_LIBRARY_PATH=$llp_save --disable-error-on-warning"
fi
if [ $OS = Darwin ] ; then
extra_flags_for_darwin="--disable-rpath --disable-error-on-warning --enable-silent-rules --enable-shared --disable-static"
fi
(
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/guile-${guile_version}.tar.gz | tar xf -
cd guile-${guile_version_dir}
# we need to pass CFLAGS and LDFLAGS because there is no --with-readline-prefix
# note that for guile's guile-readline module to compile correctly,
# ncurses-dev needs to be installed (that is on this Fed 15 machine,
# at least - I presume others also).
if [ "$need_guile_unused_values_patch" = true ] ; then
# 20130820-PE Ubuntu 12.04 also needs -Wno-unused-result
additional_unused_arg="-Wno-unused-but-set-variable -Wno-unused-result"
else
additional_unused_arg=
fi
export GUILE_ERROR_ON_WARNING=no
# arg to guile's configure
./configure $generic_prefix \
$extra_flags_for_darwin \
CFLAGS="-I$install_top_dir/include $additional_unused_arg -O -Wno-deprecated-declarations -Wno-unused-but-set-variable" \
LDFLAGS=-L$install_top_dir/lib \
CPPFLAGS=-P \
$extra_flags_for_debian
# Multilib fix for procedures.txt
echo =========== post-configure patching threads.doc ====================
perl -pi -e 's|threads.doc||' `find . -name Makefile`
if [ "$need_guile_unused_values_patch" = true ] ; then
echo =========== post-configure patching for unused-values ====================
patch -p0 < ${AUTOBUILD_SOURCES}/guile-1.8.7-updated.patch
else
echo not applying guile unused values patch
fi
# fedora 24 doesn't like the parethenses around a particular if expression
# gcc 6.1.1 - harmless for others
#
patch -p0 < ${AUTOBUILD_SOURCES}/guile-1.8.8-gc-segment.c.patch
# patch -p0 < ${AUTOBUILD_SOURCES}/guile-fink.patch
# patch -p0 < ${AUTOBUILD_SOURCES}/guile-configure.patch
echo =========== make ====================
$MAKE
status=$?
if [ "$status" != 0 ] ; then
echo guile make failed.
guile_build_status=$status
exit 2
else
echo 1 ---------------------------------------------------------------------
echo ' ' make install
echo 1 ---------------------------------------------------------------------
$MAKE install
fi
# Debian gawk work-around
if [ "$dist_name" = "debian" ] ; then
export LD_LIBRARY_PATH=$llp_save
fi
exit $status
) > $HOSTLOGDIR/11-guile.txt 2>&1
# -> 1: command not found
if [ ! $? = 0 ] ; then
echo guile build failed
fi
# outer
else
echo not building guile:
fi
if test -n "$build_greg" ; then
echo building greg:
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/greg-2.0.0-pe.tar.gz
${WGET} $extras_place/greg-2.0.0-pe.tar.gz
(
date
gzip -dc ${AUTOBUILD_SOURCES}/greg-2.0.0-pe.tar.gz | tar xf -
cd greg-2.0.0-pe
./configure $generic_prefix
$MAKE
$MAKE install
) > $HOSTLOGDIR/11c-greg.txt 2>&1
else
echo not building greg:
fi
if test -n "$build_guile_gtk" ; then
echo BUILDING guile-gtk:
#
guile_gtk_version=2.1
${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile-gtk/guile-gtk-$guile_gtk_version.tar.gz
# now, if we have gtk version 2.4 then we need guile-gtk patches.
gtk_minor_version=`awk -F '[()]' '/define GTK_MINOR_VERSION/ {print $(NF-1)} ' /usr/include/gtk-2.0/gtk/gtkversion.h`
if [ "$gtk_minor_version" = "4" ] ; then
echo guile-gtk needs to be patched, gtk MINOR version is 4.
apply_guile_gtk_patches=1
# ${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/guile-gtk-2.1-for-gtk-2.4.patch
${WGET} $extras_place/guile-gtk-2.1-for-gtk-2.4.patch
else
echo GTK minor version is good enough, $gtk_minor_version
fi
(
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/guile-gtk-$guile_gtk_version.tar.gz | tar xf -
cd guile-gtk-$guile_gtk_version
if [ "$apply_guile_gtk_patches" = 1 ]; then
echo patch -p0 ..from.. ${AUTOBUILD_SOURCES}/guile-gtk-2.1-for-gtk-2.4.patch
patch -p0 < ${AUTOBUILD_SOURCES}/guile-gtk-2.1-for-gtk-2.4.patch
else
echo info:: not patching guile-gtk for gtk 2.4
fi
./configure $generic_prefix --without-gtkgl --with-glade=no
# now patch the libtool if needed:
# fix ulong if needed:
# sed 's/(ulong)/(unsigned long)/g' guile-gtk.c > tmp.c
# mv tmp.c guile-gtk.c
# apply gtk_dialog_get_response_for_widget fix up if needed
if [ $gtk_new_enough_for_guilegtk = false ] ; then
echo fixing up guile-gtk
cp gtk-glue.c glue.tmp.c
awk '
$0 !~ " gtk_dialog_get_response_for_widget"
/ gtk_dialog_get_response_for_widget/ { print " cr_ret = 0;"; }
' glue.tmp.c > gtk-glue.c
fi
# make not MAKE (using multiprocessors seems to fail).
make
status=$?
guile_gtk_status=$status
if [ "$guile_gtk_status" != 0 ] ; then
echo Oooops guile-gtk make failed
else
echo 1 -------------------------------------------------------------------------
echo ' ' make install
echo 1 -------------------------------------------------------------------------
# $MAKE install
make install
fi
) > $HOSTLOGDIR/12-guile-gtk.txt 2>&1
else
echo not building guile-gtk:
fi
if test -n "$build_guile_gui" ; then
echo BUILDING guile-gui:
#
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/guile-gui-0.2.tar.gz
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/neil-jerram.guile-gui.patch
# ${WGET} http://lmb.bioch.ox.ac.uk/coot/extras/guile-gui-0.3.tar.gz
${WGET} $extras_place/guile-gui-0.3.tar.gz
#
# guile-gui-patch-post-neil.patch is the same as
# neil-jerram.guile-gui.patch except guile-gui-patch-post-neil.patch
# has the correct file names. Hmm...
#
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/guile-gui-patch-post-neil.patch
(
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/guile-gui-0.3.tar.gz | tar xf -
# patch -p0 < ${AUTOBUILD_SOURCES}/neil-jerram.guile-gui.patch # this is for 0.2
cd guile-gui-0.3
./configure $generic_prefix
$MAKE install
) > $HOSTLOGDIR/13-guile-gui.txt 2>&1
else
echo not building guile-gui:
fi
# on Darwin, I have to cd to $install_top_dir/lib and
# ln -s libgreg.2.0.0.dylib libgreg.so
# ln -s libguilegtk-2.0.dylib libguilegtk-2.0.so
if [ $OS = Darwin ] ; then
cd $install_top_dir/lib
if [ -e libgreg.2.0.0.dylib ] ; then
ln -s libgreg.2.0.0.dylib libgreg.so
fi
if [ -e libguilegtk-2.0.dylib ] ; then
ln -s libguilegtk-2.0.dylib libguilegtk-2.0.so
fi
cd -
fi
if test -n "$build_guile_lib" ; then
echo BUILDING guile-lib:
#
guile_lib_version=0.1.6
guile_lib_version=0.2.1
# guile-lib has moved
# ${WGET} http://download.gna.org/guile-lib/guile-lib-$guile_lib_version.tar.gz
# ${WGET} http://download.savannah.gnu.org/releases/guile-lib/guile-lib-$guile_lib_version.tar.gz
${WGET} $extras_place/guile-lib-$guile_lib_version.tar.gz
(
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/guile-lib-$guile_lib_version.tar.gz | tar xf -
cd guile-lib-$guile_lib_version
# the prefix for guile-lib must be the prefix of guile, or else the sxml and
# other library files will not be found
# 20211019-PE strangely the second make seems to pass after the first one has failed
# (in the doc directory)
./configure $generic_prefix
$MAKE
make
$MAKE install
) > $HOSTLOGDIR/14-guile-lib.txt 2>&1
else
echo not building guile-lib
fi
###############################################################################
########## build idn #############
###############################################################################
# we build libidn for libcurl. libcurl needs it on RHEL4 because
# there is no /usr/lib/libidn.so. There is a rpm devel package, of
# course, but that is more pain to install than compiling it from
# scratch for coot install.
if test -n "$build_libidn" ; then
echo BUILDING libidn:
(
# get libcurl from here:
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
) > $HOSTLOGDIR/15-a-libidn2.txt 2>&1
else
echo not building libidn2:
fi
#
###############################################################################
########## build curl #############
###############################################################################
#
if test -n "$build_curl" ; then
echo BUILDING curl:
(
# get libcurl from here:
# libcurl_version=7.19.7
# libcurl_version=7.25.0
# libcurl_version=7.27.0
# libcurl_version=7.32.0
libcurl_version=7.65.3
libcurl_version_directory=7_65_3
# ${WGET} http://curl.haxx.se/download/curl-$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
# 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 $generic_prefix --with-libidn2=$install_top_dir LDFLAGS=-L$install_top_dir/lib
./configure $generic_prefix --with-libidn2=$install_top_dir LDFLAGS=-L$install_top_dir/lib
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
) > $HOSTLOGDIR/15-b-curl.txt 2>&1
else
echo not building curl:
fi
###############################################################################
########## build gsl #############
###############################################################################
#
if test -n "$build_gsl" ; then
echo BUILDING gsl:
#
# 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
# ${WGET} http://ftp.gnu.org/gnu/gsl/gsl-$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
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/15-gsl.txt 2>&1
else
echo not building gsl:
fi
#################################################################
# Clustalw2
#################################################################
#
if test -e $install_top_dir/bin/clustalw2 ; then
echo not building clustalw2
else
${WGET} ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/clustalw-2.1.tar.gz
if [ ! -e ${AUTOBUILD_SOURCES}/clustalw-2.1.tar.gz ] ; then
echo failed to download clustalw2
else
# happy path
(
tar xf ${AUTOBUILD_SOURCES}/clustalw-2.1.tar.gz
cd clustalw-2.1/
./configure --prefix=$install_top_dir
if ${MAKE} ; then
make install
else
echo make for clustalw-2.1 failed. Boo.
fi
) > $HOSTLOGDIR/18-clustalw.txt 2>&1
fi
fi
#################################################################
# Raster3D
#################################################################
#
if [ -e $install_top_dir/bin/render ] ; then
echo not building Raster3D render
else
raster3d_version=3.0-3
raster3d_version=3.0-7
# raster3d depends on libgd to make png images
# ${WGET} http://skuld.bmsc.washington.edu/raster3d/Raster3D_$raster3d_version.tar.gz
${WGET} http://www.bmsc.washington.edu/raster3d/Raster3D_$raster3d_version.tar.gz
if [ ! -e ${AUTOBUILD_SOURCES}/Raster3D_$raster3d_version.tar.gz ] ; then
echo missing Raster3D tar file
else
echo libgd...............
(
date
pwd
# build libgd
#
system_has_libgd=false
if [ -e /usr/include/gd.h ] ; then
system_has_libgd=true
fi
echo system_has_libgd: $system_has_libgd
if [ "$system_has_libgd" = false ] ; then
echo checking for existance of $install_top_dir/include/gd.h
if [ ! -e $install_top_dir/include/gd.h ] ; then
echo get and build libgd...
# Amazon file names too long, so force output name with -O
${WGET} https://github.com/libgd/libgd/releases/download/gd-2.1.1/libgd-2.1.1.tar.gz -O ${AUTOBUILD_SOURCES}/libgd-2.1.1.tar.gz
gzip -dc ${AUTOBUILD_SOURCES}/libgd-2.1.1.tar.gz | tar xf -
cd libgd-2.1.1
# don't use /bin/sh as shell to run libtool (on Ubuntu it's a problem)
bash ./configure --prefix=$install_top_dir SHELL=/bin/bash
if $MAKE ; then
make install
else
echo info: $MAKE failed for libgd
fi
cd -
else
echo $install_top_dir/include/gd.h exists - skip libgd build
fi
else
echo /usr/include/gd.h exists - skip libgd build
fi
) > $HOSTLOGDIR/15-libgd.txt 2>&1
echo build render...............
(
date
pwd
# build render
#
system_has_libgd=false
if [ -e /usr/include/gd.h ] ; then
system_has_libgd=true
fi
if [ ! -e $install_top_dir/bin/render ] ; then
# now build it.
gzip -dc ${AUTOBUILD_SOURCES}/Raster3D_$raster3d_version.tar.gz | tar xf -
cd Raster3D_$raster3d_version
make linux # FIXME for Darwin
# compiling libgd so that render links against it depend on libjpeg-turbo-devel
# having been installed. i.e. /usr/lib/libjpeg.so should exist
# add the gd support directory
#
system_has_libgd=false
if [ -e /usr/include/gd.h ] ; then
system_has_libgd=true
fi
echo system_has_libgd: $system_has_libgd
if [ "$system_has_libgd" = false ] ; then
sed -ibackup \
-e "s?=.-lgd?= -L$install_top_dir/lib -lgd?" \
-e "s?=.-DGD_SUPPORT?= -DGD_SUPPORT -I$install_top_dir/include?" \
-e 's/ TDEFS =.*/ TDEFS =/' \
-e 's/ TLIBS =.*/ TLIBS =/' \
Makefile.incl
fi
echo about to do this: $MAKE render
make render
ls -l render
if make render ; then
make prefix=$install_top_dir install
# did that work? I doubt it. Let's do it by hand
if [ ! -e $install_top_dir/bin/render ] ; then
echo Hand copy: cp render $install_top_dir/bin/
cp render $install_top_dir/bin/
fi
else
echo INFO:: make failed for render
# warning make exit status false, but the binary may well have been built
if [ -e render ] ; then
if [ ! -e $install_top_dir/bin/render ] ; then
echo Hand copy: cp render $install_top_dir/bin/
cp render $install_top_dir/bin/
fi
else
echo no render built in `pwd`
fi
fi
cd -
else
echo $install_top_dir/bin/render already exists, no build
fi
) > $HOSTLOGDIR/15-raster3d.txt 2>&1
fi
fi
###############################################################################
########## get Coot #############
###############################################################################
#
echo BUILDING coot: version $coot_version, guile=$ENABLE_GUILE_COOT, python=$ENABLE_PYTHON_COOT
if [ -z "$coot_version" ] ; then
echo coot_version is empty - exit now
my_exit 2 coot_version not set
fi
if [ "$build_coot_prerelease" != 1 ] ; then
# normal release coot
${WGET} $release_server_dir/$coot_version.tar.gz
if [ ! $? = 0 ] ; then
echo failed to wget $coot_version.tar.gz
my_exit 2 wget-fail-coot-source
fi
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/coot-static.patch
else
# If we are building pre-release coot_source_tar_file is set only if we can find
# a pre-release source tar in the pre-release directory, otherwise it is not set
if [ -n "$coot_source_tar_file" ] ; then
${WGET} $coot_source_tar_file
if [ ! $? = 0 ] ; then
echo failed to wget $coot_source_tar_file
my_exit 2 wget-fail-coot-source
fi
else
# compile release code then:
echo compile RELEASE code then, getting $release_server_dir/$coot_version.tar.gz
${WGET} $release_server_dir/$coot_version.tar.gz
if [ ! $? = 0 ] ; then
echo failed to wget $release_server_dir/$coot_version.tar.gz
my_exit 2 wget-fail-coot-source
fi
fi
coot_revision=`echo $coot_version | awk '{a=$1; i=index(a,"revision"); print substr(a,i)}'`
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/coot-static.patch
fi
# get the cxxsurface patch - not sure if/when it's needed.
# It seems to be needed for g++ 9.2.1 on Ubuntu 19.10
# but not on 4.8.5 on Scientific Linux
# ${WGET} $extras_place/cxxsurface-for-openmp-v1.patch
# reset this (set it to "yes") if needed, depending on the OS/compiler
# need_cxxsurface_for_openmp_patch=no
# if [ "$w_fid" = g++-9 ] ; then
# echo we need the CXXSurface OpenMP patch
# need_cxxsurface_for_openmp_patch=yes
# fi
echo using coot version $coot_version
ls -ls ${AUTOBUILD_SOURCES}/$coot_version.tar.gz
if [ -e ${AUTOBUILD_SOURCES}/$coot_version.tar.gz ] ; then
echo good ${AUTOBUILD_SOURCES}/$coot_version.tar.gz exists
else
echo badness ${AUTOBUILD_SOURCES}/$coot_version.tar.gz does not exist.
echo nothing left to do then. Goodbye.
my_exit 2 $coot_version.tar.gz not found
fi
date
pwd
gzip -dc ${AUTOBUILD_SOURCES}/$coot_version.tar.gz | tar xf -
coot_dir_name=`echo $coot_version | sed 's/-revision.*//'`
cd $coot_dir_name
# if [ $need_cxxsurface_for_openmp_patch = yes ] ; then
# echo patching from ${AUTOBUILD_SOURCES}/cxxsurface-for-openmp-v1.patch
# patch -p0 < ${AUTOBUILD_SOURCES}/cxxsurface-for-openmp-v1.patch
# fi
if test -n "$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=$install_top_dir"
fi
if [ "$ENABLE_GUILE_COOT" != "no" ] ; then
guile_scripting="--with-guile --with-guile-gtk --with-guile-gtk-prefix=$install_top_dir"
fi
# if ENABLE_PYTHON_COOT is not set, then we choose a day of the week
# to build a python version.
# if ENABLE_PYTHON_COOT is set, then if it is set to 0 or no then we
# do not build a python version, otherwise we do build a python
# version
if [ -n "$ENABLE_PYTHON_COOT" ] ; then
# it was set to something
if [ "$ENABLE_PYTHON_COOT" != "0" ] ; then
if [ "$ENABLE_PYTHON_COOT" != "no" ] ; then
python_scripting='--with-python --with-pygtk'
fi
fi
else
# if ENABLE_PYTHON_COOT was not set, then turn on python scripting
python_scripting='--with-python --with-pygtk'
fi
# no longer makes sense now that python is in by default
# else
# time_date=`date`
# if [ ${time_date:0:3} = "Sun" ] ; then
# scripting='--with-python'
# fi
# if [ ${time_date:0:3} = "Sun" ] ; then
# scripting='--with-python'
# fi
# fi
###############################################################################
########## build Coot #############
###############################################################################
#
echo BUILDING coot: version $coot_version, python=$ENABLE_PYTHON_COOT
# set the python tag outside the compile/install sub-shell.
if [ "$ENABLE_PYTHON_COOT" = "no" ] ; then
python_tag=
else
python_tag=-python
fi
(
# 20091001 should not be needed.
# if [ "$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
# $architecture is not set for Mac OS X.
coot_optim_args=
if [ "$architecture" = x86_64 ] ; then
# This could well be too general a test, certainly on 64 bit CentOS 5 we need this,
# and possibly on 64 bit Gutsy.
# There is a problem quoting this, e.g.
# coot_optim_args="CXXFLAGS='\"-g -O\"'" fails in configure
#coot_optim_args="CXXFLAGS=-gO"
#coot_optim_args="CXXFLAGS=\"-g -O\""
export CXXFLAGS="-g -O3 -ffast-math"
# unset CXXFLAGS
fi
cbis_d=$(date +'%a %d %b %H%M.%S %Z %Y')
if /usr/bin/finger ; then
cbis_n=$(finger $USER | head -1 | sed 's/.*Name: //')
coot_build_info_string="built by: $cbis_n build-host: $HOST on: $cbis_d"
else
coot_build_info_string="build-host: $HOST on: $cbis_d by $USER"
fi
# We no longer need this because clipper is found using pkg-config
# --with-clipper-prefix=$install_top_dir
if [ $OS = Darwin ] ; then
if [ -d /opt/X11 ] ; then
export CPPFLAGS=-I/opt/X11/include
# I think this is needed for COOT_OPENGL_LIBS to be correctly found/set in configure.ac on Mac
extra_args_for_darwin="LIBS=-L/opt/X11/lib"
fi
fi
if [ ! -z "$libintl_cflags" ] ; then
CFLAGS=$libintl_cflags
CPPFLAGS="$CPPFLAGS $libintl_cflags"
fi
echo From tar file: ${AUTOBUILD_SOURCES}/$coot_version.tar.gz
echo building in: $PWD
echo CFLAGS: $CFLAGS
echo CXXFLAGS: $CXXFLAGS
echo CPPFLAGS: $CPPFLAGS
echo LDFLAGS: $LDFLAGS
echo PATH: $PATH
echo using this guile:
which guile
# I want to compile with no-strict-aliasing for the python files output by swig. How do I do that?
echo ./configure $coot_prefix \
--with-fftw-prefix=$install_top_dir \
$goocanvas_args \
$glut_prefix \
COOT_BUILD_INFO_STRING="$coot_build_info_string" \
$guile_scripting \
$python_scripting \
$sqlite_config_args \
--with-enhanced-ligand-tools \
--with-boost=$install_top_dir \
--with-boost-libdir=$install_top_dir/lib \
--with-rdkit-prefix=$install_top_dir \
$shared_static_flag \
$coot_optim_args \
$coot_extra_args \
$extra_args_for_darwin
./configure $coot_prefix \
--with-fftw-prefix=$install_top_dir \
$goocanvas_args \
$glut_prefix \
COOT_BUILD_INFO_STRING="$coot_build_info_string" \
$guile_scripting \
$python_scripting \
$sqlite_config_args \
--with-enhanced-ligand-tools \
--with-boost=$install_top_dir \
--with-boost-libdir=$install_top_dir/lib \
--with-rdkit-prefix=$install_top_dir \
$shared_static_flag \
$coot_optim_args \
$coot_extra_args \
$extra_args_for_darwin
# 20230907-PE There is a problem on Fedora now, it seems - possibly/probably before
# also, when installing the python files. They are compiled with ../py-compile
# but using ../py-compile --destdir "" fails, i.e. when DESTDIR is not defined,
# as is the case when one dose "make install"
# So I will convert that to say just "../py-compile"
#
sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile)/' pyrogen/Makefile
sed -ibackup -e 's/am__py_compile.*destdir.*/am__py_compile)/' python/Makefile
# these are no longer used
# --with-mmdb-prefix=$install_top_dir
# --with-ssmlib-prefix=$install_top_dir
# consider adding -DCOOT_SYS_TYPE=systype (or something like that)
# here, so that coot --version-info/full returns it.
# HACK out libtool updating for coot
#if [ "$update_libtool" = 1 ] ; then
# echo need to update libtool here $PWD
# cp $install_top_dir/bin/libtool .
#else
# echo NO need to update libtool $PWD
#fi
# 20091001 should not be needed
# rm src/coot_wrap_guile_pre.cc
# rm src/coot_wrap_python_pre.cc
$MAKE
status=$?
if [ "$status" != 0 ] ; then
echo make failed.
bad_coot_make=1
exit 2
else
echo 1 ---------------------------------------------------------------
echo ' ' make install
echo 1 ----------------------------------------------------------------
$MAKE DESTDIR=/ install
if [ "$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
) > $HOSTLOGDIR/20-coot.txt 2>&1
# --with-gsl-prefix=$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 coot build failed, exiting. 1>&2
echo fail-build $coot_revision > $LOGS/build-status
my_exit 2 $coot_revision
else
echo coot build was good.
echo coot build was good. 1>&2
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
# refmac_mon_lib=refmac-monomer-library.tar.gz
# refmac_mon_lib=refmac-monomer-library-20210105.tar.gz
# new style
mon_lib_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies
ccp4_mon_lib=monomers-2023-01-02-23:57:29.tar.gz
if [ -e $install_top_dir/share/coot/lib/data/monomers ] ; then
echo INFO:: installation has refmac monomer library
else
echo INSTALLING CCP4 monomer library...
echo INSTALLING CCP4 monomer library... >&2
$WGET $mon_lib_dir/$ccp4_mon_lib
mkdir -p $install_top_dir/share/coot/lib/data
tar xzCf $install_top_dir/share/coot/lib/data $AUTOBUILD_SOURCES/$ccp4_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 = "--enable-shared" ] ; then
clear_up_type=clear-static
fi
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}-gtk2-python
else
slim_dir=$(dirname $install_top_dir)/coot-${OS}-${systype}${pre_release_str}-gtk2
fi
echo post-install slim... with clear-up type $clear_up_type >&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" = "disablethisfornow" ] ; then
echo running python test... >&2
test_coot_python > $LOGS/test-python.log 2>&1
rp=$?
else
rp=0
fi
gtk2=-gtk2
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}${python_tag}${gtk2}.tar.gz
holding_tar_file=$BINARY_TAR_DEST_DIR/holding/${coot_version}-binary-${OS}-${systype}${python_tag}${gtk2}.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}${python_tag}${gtk2}-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