# # -*-shell-script-*- # ----------------- this is now the python-3 version ---------------- # # Copyright 2004, 2005, 2006, 2007, 2008 by The University of York # Copyright 2009, 2010, 2011, 2012 by The University of York # Copyright 2012 by Paul Emsley # Copyright 2012, 2013, 2014, 2015, 2016 by Medical Reserch Council # Copyright 2014, 2015, 2016 by Medical Research Council # Author: Paul Emsley # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 3 of the License, or (at # your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA # 02110-1301, USA # # # # For instructions, read below, starting at :: NOTE :: # # # Prerequisites: sed, GNU make, libtool, wget # # libz is optional for the moment # 1.3 Put RELEASE-NOTES on web site too # 1.4 Apply both of Ezra's patches of today Wed Mar 2 22:51:36 GMT 2005 # Update clipper version (the one with shelx .fcf ability) # 1.5 Apply Ezra's gtkglarea patch and GSL patch. # Update version of FFTW and other updates from MATSUURA Takanori. # 1.6 Update to mmdb-1.0.8 [# for molrep output] # 1.7 Fix logic of fftw test # 1.8 Add the clipper edcalc patch (suggested by Ezra ages ago) # 1.9 Add Fedora Core 4 support and testing for the need to build mccp4, # mmdb and clipper. # 1.10 Tidy up nightly code. # 1.11 Add code testing the need for guile_gui and goosh. # 1.12 Tidy nightly code again. # 1.13 Don't escape the "."s in gsub for new gawk (Ward Smith). # 1.14 20050628 Test for imlib on the installation, not the system (ignore # the system). # 1.15 20050709 Add glib gstrfuncs patch # 1.16 20050709 Update to guile 1.6.7 and add lt_preloaded_symbols patch # 1.17 20050721 Added clipper status code to compiling clipper part. # Redirect stderr output? # fix build_mccp4 problem. # 1.18 20050722 Fix guile build (wrong http tar file). # Added freeglut # 1.19 20050803 Update version of guile-gtk to 0.41 # 1.20 20050815 Several updates and clean up from MATSUURA Takanori. # 1.21 20050815 Stop if wget test fails. # 1.22 20050916 Update build for freeglut to use --disable-warnings and # CFLAGS # 1.23 20050916 Move "set" so we don't see confusing default coot_version # 1.24 20051012 Do pre-release tars for a few days. # 1.25 20051017 Don't make install if Coot's makes fails. Don't make -k # 1.26 20051018 Handle clipper nxmap patch. # 1.27 20051027 [Gif, Paris] Fix tarred directory for nightly pre-release # tars. # 1.28 20051101 Fix the md5sum for nxmap.h # 1.29 20051104 Apply most of MATSUURA Takanori's fixes. # Use CCP4 libs (mtz, clipper, mmdb). # 1.30 20051109 Darwin setting of FC for CCP4 libs configure. # 1.31 20051114 Fix coot tar file problem on building pre-release (or not). # 1.32 20060205 Add scripting variable debugging (its currently not making # python tar files) # 1.33 20060214 Get wget testing tar file from YSBL, not chem.gla # 1.34 20060219 Correct the install position of libccp4c.la # 1.35 20060219 create time stamp with current time, not the time of # the previous ccp4 libs file, now the find ctime test works # as I wanted. # 1.36 20060220 Add a libmmdb.la too. # 1.37 20060222 Add Bob Nolte's proxy settings # 1.38 20060224 dylib variable for libmmdb.la and libccp4c.la # 1.39 20060225 Fix sedding of libmmdb.la and libccp4c.la # 1.40 20060323 copy over coot.py to share/coot/python (if we built with # python) # 1.41 20060401 Big changes for ccp4 5.0.2 ccp4c libs. # 1.42 20060404 Various small build debuggings. # 1.43 20060405 Fix do_nightlies syntax error and fix up glut_prefix build # problem. # 1.44 20060405 Fix the tarred directory name when this is not a pre-release # 1.45 20060406 Check for missing reference structures and monomer lib and # install them if needed. # 1.46 20060418 use install_top_dir variable to copy over coot.py (not # $coot_prefix!) # 1.47 20060419 Remove the mmdb binaries # 1.48 20060420 J. Maclean says no guile. He is right. So check install for # guile, not system. # 1.49 20060420 Replace many $AUTOBUILD_INSTALLED with $install_top_dir. # 1.50 20060421 Replace other $AUTOBUILD_INSTALLED with $install_top_dir for # tar file creation. # 1.51 20060425 net-http was installing into the wrong place because it had # been set to install_top_dir, but this was not set as a shell # (or configured) variable so it was just blank [James Murray]. # Now we export install_top_dir. # 1.52 20060427 Don't add unecessary tagging of -pre-release to tar_dir at # the end. # 1.53 20060503 Force GSL to be in $install_top_dir rather than anywhere. # 1.54 20060519 Update to extract the right coot version from the release and # pre-release directories. # 1.55 20060621 Shuffle around the test for using pre-release # 1.56 20060626 Fixes from MATSUURA Takanori. Shuffle around the usage of # install_top_dir. # 1.57 20060704 run imlib-config from the installation, not anywhere. # 1.58 20060705 Fix wrong directory to build libtiff. # 1.59 20060706 guile-config should run with an argument, otherise it # returns with exit status 1 (and we test for non-zero). # 1.60 20060706 Fix (directory for) mmdb include file test. # 1.61 20060707 Add to coot configure line the option for guile_gtk # 1.62 20060708 Fix coot_prerelease_exists typo in setting install_top_dir # (oops). # 1.63 20060708 Add jpeg dependency for imlib # 1.64 20060708 Add libungif test to installation, not system (imlib # dependency). # 1.65 20060710 Add removal of coot_wrap_guile.cc compilation when python # scripting. # 1.66 20060710 Python on a Sunday. # 1.67 20060711 Try to fix up the Makefile for PNG. # 1.68 20060723 Add in the updates to ltmain.sh, ltconfig and config.guess/sub # for Mactel build. Add build for readline. # Readline version typo fixed. # 1.69 20060724 ENABLE_PYTHON_COOT variable is tested. Don't display # a variables if we are using a proxy. # 1.70 20060728 pass CFLAGS and LDFLAGS to guile's configure # 1.71 20060730 Add test for 64-bit Linux to update config.xxxs and libtool. # Installation readline built now, not system. # 1.72 20060801 Use mmdb-1.0.8-ysbl-2, which installs includes in the include # dir. This matches clipper cif_data_io.cpp which presumes that # it is there. (And is a clean thing to do anyway). # 1.73 20060801 Use the new version of libccp4c, with some of Ralf's patches # and includes that go into include/ccp4 dir. # 1.74 20060801 Use CCP4_CXXFLAGS argument to clipper (it does the wrong thing # with --with-ccp4) # 1.75 20060801 Use -pre-2 version of SSMlib, that has -Ixxx/include/mmdb to # find mmdb include files. # 1.76 20060808 test for libjpeg.$shared_lib_ext not libjpeg.so. LTE bug. # 1.77 20060818 Force update of libtool and config files for libjpeg. Extend # the make install proceedure. Lynn Ten Eyck reported problems # here. # 1.78 20060823 Add poll fix and getpwuid fix to glib build on Intel Mac. # 1.79 20060827 Add fix for gtk-canvas from fink for Intel Mac. # 1.80 20061002 Change freeglut test to test instaltion, not system. # 1.81 20061012 The path used to find *-config files should be the same one # that new executables are added (it was $AUTOBUILD_INSTALLED) # and it should be $AUTOBUILD_INSTALLED-pre-release/bin) when # we are building a pre-release. # 1.82 20061012 Change the destination tar file so that there are nightly # and stable directories for the binary tar files on the web # server. # 1.83 20061107 cd to the clipper dir when building clipper. Pirate and # bucca are not (attempted to be) built then. # 1.84 20061107 Capture and report error status from make in GSL (intel mac # build fails). # 1.85 20061107 Use GSL version 1.8, which includes Charles Ballard's fix for # fp_regs.h # 1.86 20061108 Add fink-based args for configure of gtk for Darwin # 1.87 20061108 Fix ltmain.sh updating for Gtk (oops!). # 1.88 20061122 Fix coot tar directory now that we have revision numbers in # tar file name. # 1.89 20061123 Fix/add test for ssmlib build (now depends on mmdb build) and # libccp4c build (now depends on xxx/include/ccp4/cmtzlib.h). # 1.90 20061128 Allow the user to specify if the dependencies should be checked # on the system or only in the autobuild installed directory. # Needs more checks to use this. Currently only glib and gtk # tests. # 1.91 20061211 Don't make install for guile-gtk if the make fails - or the # dependency check for guile-gtk in coot's configure passes # when it should fail (maybe). # 1.92 20061212 Apply Charles Ballards libtool patch for Macs for imlib and # guile-gtk. # 1.93 20061212 Fiddle the env vars to compile gtk+ on Mac. # 1.94 20070104 Non-pre-release build problems, BINARY_DEST_DIR # 2.01 20070109 imlib tar gz should be downloaded from the correct directory # (sigh). # 2.02 20070117 Try to compile clipper with -fno-strict-aliasing # 2.03 20070123 Tell us where the gtkglarea include file was found. # 2.04 20070124 GCC 3.2 on RH8 machine cannot compile new clipper, so add a # patch if needed. # 2.05 20070216 Put libtiff after libjpeg and give tiff's configure command # line args to find jpeg. # 2.06 20070306 Put in the clipper<->ccp4 new dist patch. # 2.07 20070319 Remove == comparisons - Lothar Esser. # 2.08 20070424 --with-jpeg-lib-dir should be a lib dir! # 2.09 20070501 Fix the setting of coot_version when no pre-release set. # 2.10 20071002 Post install slim the binaries. Add helper functions. # 2.11 20071005 Add some debugging to make_tar. It doesn't seem to work # currently. # 2.12 20071005 Fix post_install_slim call. # 2.13 20071005 Fix slim_dir # 2.14 20071006 Adjust python scripting settings, so that it should try # to compile with python most of the time now. # 2.15 20071008 Fix extra fi, uncommented typo. # 2.16 20071010 ENABLE_PYTHON_COOT=no for now. # 2.17 20071105 Swap out DL Clipper for York clipper [whoosh, bang, kerpow!] # enable-cns # 2.18 20071105 Backpeddle to mmdb 1.08. Baah. # 2.19 20071108 Version 1.08-ysbl-3 of mmdb. # 2.20 20071118 No longer make the full fat tar file. # 2.21 20071120 Sourcefource no longer distributes libungif, now in # ysbl software/extras # 2.22 20071121 set the architecture for ubuntu systems. # 2.23 20071125 Fix typo in recent fixes. # 2.24 20071126 Fix setting of systype for MacOSX, hopefully. # 2.25 20071126 Another try to fix setting of systype for MacOSX. # 2.26 20071130 Try to enable python # 2.27 20071207 More python tinkering. Upgrade to 2.5.1 # 2.28 20071207 Add greg. If in York, use it to test before installing. # 2.29 20071208 Setup CCP4 and use it to test coot before making binaries. # 2.30 20071209 Add dewinter's ccp4 setup in setup_ccp4. # 2.31 20071212 Redirect testing output to $LOGS/$HOST-testing.log # 2.32 20071213 Copy over the ChangeLog, README and RELEASE-NOTES on good test # 2.33 20071215 Pythonize only sometimes, default off. # 2.34 20071215 Tell us some Python info # 2.35 20071215 Python settings outside the subshell. # 2.36 20071219 Set up for testing and tars on biop too. # 3.00 20080108 Gtk+-2 version # 3.01 20080118 Add GtkGlExt # 3.02 20080121 Tinker with guile build settings. # 3.03 20080124 Build GTK2 from scratch: librsvg, cairo, pango, glitz. glib, gtk+-2 # 3.04 20080128 Add a test for the existance of pygtk # 3.05 20080129 Add pkg-config and pygobject # 3.06 20080130 Add test for pycairo # 3.07 20080130 pycairo needs 1.4.12 - so test for cairo, setting build_gtk=1 on # failure # 3.08 20080130 Remove static patch (for sgi). Add test/build for freetype2 # 3.09 20080130 fontconfig added too. # 3.10 20080131 Change HOSTLOGDIR to include gtk2 to separate it from gtk1 build logs. # 3.11 20080201 Fix problem in scripting args to coot's configure. # 3.12 20080207 Add test and build of ATK, needed for gtk+2.10.x # 3.13 20080208 lib cleaning problems, add debugging. # 3.14 20080208 Try requiring gtk 2.10 # 4.00 20080208 Remove gtk2 and pkg-config building. Test for Fedora core 5. # 4.01 20080211 Remove pycairo build and fix up test for build for guile_gtk # 4.02 20080212 Add in the Neil Jerram guile-gui patch. # 4.03 20080213 Add Joseph Moran's fix for handling CC when set. # 4.04 20080213 Allow python to get through rsync filter, for PHENIX usage. # 4.05 20080226 Fix up build_guile_gtk usage. # 4.06 20080428 Apply Joseph Moran's fix correctly. # 4.07 20080518 Update the status reporting system. # 4.08 20080607 Bump version of python to 2.5.2 # 4.09 20080617 Update to guile-1.8.5 # 4.10 20080618 As per JED request, number the build logs in a more sensible way. # 4.11 20080620 Don't run the tests if not in biop or york. # 4.12 20080624 Add guile-lib to build. # 4.13 20080729 Correctly test for the up to date python version. # 4.14 20080729 Adjust test for build_guile_gtk. # 4.15 20080730 Adjust test for up to date python. # 4.16 20080730 Use old version of pyobject if pkg-config is not new enough # 4.17 20080730 Test for gtk minor version, use that to apply guile-gtk patches # if needed. # 4.18 20080730 Add Diagnosis for applying guile-gtk patch. # 4.19 20080818 use mmdb version 1.12 # 4.20 20080918 Remove references to glitz, cairo, fontconfig # 4.21 20080925 Use pygobject 2.4 if needed (e.g on CentOS 4). # 4.22 20080925 Handle typename in pygobject.h for CentOS4. # 4.23 20081007 Don't build python if python is not passed as arg. # 4.24 20081007 Back to version 2.5.1 that compiles on bragg3, 2.5.2 does not # (port 8080 already in use). # 4.25 20081008 Migrate to CCP4 version 6.0.2 for testing in York. # 4.26 20081014 Use Python 2.6 # 4.27 20081105 Adjust clipper configuration. Remove clipper-new-ccp4-install # usage, it is no longer needed, it seems. Remove configure # argument --enable-mmdbold # 4.28 20081110 Upgrade to mmdb-1.19, get it from EBI. # 4.29 20081118 Use the ccp4 libs underlay. # 4.30 20081119 Use -O not -O2 to compile coot on 64 bit machine # 4.31 20081121 Swig 1.3.34 is OK for 32 bit, I think. # 4.32 20081122 Use clipper-2.1 # 4.33 20081122 Use clipper-2.1, extra tweaks. # 4.34 20081122 Add a second test, make a holding directory for tar file before # second test is run. # 4.35 20081124 test for greg using full path to guile. # 4.36 20081130 Bump the gmp version to 4.2.4 (Does that fix the gmp.h on # intrepid problem?) # 4.37 20090220 Fix up guile-gui, post-neil-jerram patch added. # 4.38 20090423 Fix up PYTHONPATH when starting greg tests. # 4.39 20090427 Remove python and its config from bin in slimmed dir # 4.40 20090506 Upgrade to mmdb 1.21 # 4.41 20090508 add density-score-by-residue to tar ball. # 4.42 20090517 Remove standard error redirections. # 4.43 20090522 Update to guile-1.8.6 on the advice of Ed Podharski. # 4.44 20090523 Add some build info to the mmdb and clipper logs. # 4.45 20090523 build status results now go to $build_type-build-status # (not gtk2-build-status) # 4.46 20090613 Add coot revision info to build status line. # 4.47 20090617 Make a file (and transfer it if neeeded) type-binary-xxx.txt # containing the $coot_version of the just-built binary. Used # in the update-binary mechanism to find if there is a newer # version than this binary (that we are running). # 4.48 20090624 Make pre_release_server_dir be biop.ox # 4.49 20090628 On my_exit, remove the test-status file, not the build-status # file. # 4.50 20090628 Change the GSL version to 1.12 # 4.51 20090703 check exit status of wget for coot source tar file. # 4.52 20090704 mmdb-1.21 from York. # 4.53 20090706 check build dependencies when on ubuntu # 4.54 20090722 fix coot_revision typo for build status. # 4.55 20090724 make compilers_dir depend on build_type (python build logs # split out) # 4.56 20090727 Add a date for build-in-progress status # 4.57 20090728 gtk2 -> $build_type fixups for status # 4.58 20090730 remove swig from package list tested on ubuntu. # 4.59 20090913 Add a date to the fail status message # 4.60 20091001 comment out the deletion of the coot_wrap files. # 4.61 20091117 update the version of clipper. # 4.62 20091203 release server is now in oxford. # 4.63 20091208 Add curl to the build system # 4.64 20091209 Fix typo in untaring curl tar file. # 4.65 20091209 Add libidn to build (for curl). # 4.66 20091209 Test for holding dir in making tar file. # 4.67 20091209 Add LDFLAGS to args for libcurl configure. # 4.68 20091210 Add post-process-libcurl logic. # 4.69 20091216 Don't delete bin/curl, we need it for updates. (20100120 Not any more) # 4.70 20100120 debugging added to curl build (problems on bragg3). # 4.71 20100203 Remove goosh. # 4.72 20100203 Update clipper version. # 4.73 20100205 only download mmdb once. # 4.74 20100304 Fix install_top_dir typos. # 4.75 20101102 Dependency check for gtkglext patch (compatibility with gtk+ version). # 4.76 20101102 Correct directory for previoius patch. # 4.77 20110505 switch to new style Refmac library. # 4.78 20110507 Refmac mon lib to 5.29 # 4.79 20110610 biop -> lmb.bioch # 4.80 20110707 also make holding directory for stable builds. # 4.81 20110725 Add goocanvas. # 4.82 20110725 Add test for gtk and cairo before going ahead with compiling and using # goocanvas. # 4.83 20110805 On 64 bit redhat 4, building freeglut, we need to use /usr/X11R6/lib64, # not /usr/X11R6/lib, edit configure. # 4.84 20110821 Hack in a solution the the new clipper problem (new clipper with cif # tools needs new libtools/configure new ccp4 libs (underlay-2). # 4.85 20111021 Update python to 2.6, guile to 1.8.8, add guile patch. # 4.86 20111214 Update to mmdb 1.24 (new) which has working LINKRs. # 4.87 20120108 Use make not MAKE for guile-gtk. # 4.88 20120120 Don't use -j $nproc for make if we don't have memory. # 4.89 20120223 Use libccp4c-5.0.2-ysbl-3.tar.gz, that has libccp4c_la_LIBADD. # 4.90 20120713 debug $coot_dir_name link usage. # 4.91 20120808 update to handle version of debian in /etc/issue. # 4.92 20120820 Debian /etc/issue handling for wheezy. # 4.93 20120921 Update mmdb to version 1.24.2 # 4.94 20130123 Move pre-release and release server-dir to Cambridge. # 4.95 20130128 Refmac dictionary to 5.39 # 4.96 20130228 New mmdb version - 1.25.0 # 4.97 20130424 Rework (fix typo) for python include directory slimming. # 4.98 20130424 Remove ssh copying # 4.99 20130424 swig 1.3.29 is broken no matter what the architecture. # 5.00 20130425 CXX testing updates (for ubuntu). # 5.01 20130429 mmdb version bump 1.25.2 # 5.02 20130502 better diagnostic for goocanvas compile # 5.03 20130503 Remove SWIG version test (now it is not needed to build source) # 5.04 20130514 Add COOT_BUILD_INFO_STRING. # 5.05 20130604 For Release 0.7.1, change release vs pre-release logic # (MRC server). # 5.06 20130612 More tinkering to get the correct version for release from the server. # 5.07 20130707 Adjustment to build stable logic. # 5.08 20130716 Move source server to personal/pemsley. # 5.09 20130818 Use ssm-1.3 # 5.10 20130824 debugging publish # 5.11 20130826 Allow build without guile; name directory for building. # 5.12 20130909 LD_LIBRARY_PATH changes/fixup. # 5.13 20130910 Force -O usage for guile compilation. # 5.14 20130920 Publish logs. # 5.15 20140408 New version of Python. # 5.16 20140817 Python version to 2.7.8 # 5.17 20140911 SSM updates. # 5.18 20141128 Add hack bin for debian awk # 5.19 20141128 Use dist_name for debian (not systype) # 5.20 20141203 More/better Debian awk hack. # 5.21 20141203 Unset some build environment variables (including LD_LIBRARY_PATH) # 5.22 20141210 More LD_LIBRARY_PATH hacking for debian # 5.23 20141210 libreadline needs to be linked with -lcurses (on Debian) # 5.25 20141212 # 5.26 20150215 Use /opt/X11 and COOT_CCP4_PACKAGES for dependences on Darwin. # 5.27 20170925 bump libccp4 version to 6.5.1 - this has libccp4.pc for pkg-config # 5.28 20170925 Fixes for clipper and guile and gmp version update (gcc-7.2) # 5.29 20171006 Test for libgnomecanvas devel (now not available in system for Redhat 7.3) # 5.30 20180109 Update python version. # 6.00 20200812 include glm # 6.01 20210430 pkg-config tweak and no remove rdkit libs for coot configure # 6.02 20220417 add ffi into Python setup.py # 6.03 20220704 work on GLIB and python modules # 6.04 20220705 Python still doesn't build (on cluster) - add debugging # 6.05 20220706 Use https:: instead of ftp:: # 6.06 20220707 try export LD_LIBRARY_PATH=$install_top_dir/lib in Coot section # 6.07 20220710 libffi fixes for python # 6.08 20220803-PE pygobject cleanups # 6.09 20220907-PE meson adjustment for compiling glib (what a pain) script_version=6.09 echo ==================================================== add test for SWIG version echo ==================================================== add test for CMake version # :: NOTE:: # this "strange" construction of variable names: x=${x:=thing} sets the # variable x only if it has not previously been defined. # # So, the idea is that you write a wrapper for this script (defining typically # AUTOBUILD_INSTALLED, AUTOBUILD_BUILD, LOGS and build_coot_prerelease) then # source this file. That means that you (probably) don't have to edit your # version of build-it every time it changes. # ENABLE_PYTHON_COOT: if ENABLE_PYTHON_COOT is set to 0 or "no" then # python coot is not enable (guile coot is enabled). if # ENABLE_PYTHON_COOT is set, but not set to 0 or no then python coot # is enabled. If ENABLE_PYTHON_COOT is not set, the guile-coot is # enabled (python coot is not enabled). # Pythonizing coot makes non-transferable binararies (why?). Let # the pythonness be controlled on the command line: # # At the moment, if you build with Gtk2, you build with python, hence $build_type # is the same thing. # # Set the host and the OS. # Fairly fundamental. # OS=$(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} # where has gtk been installed if this is Mac OS? if test "$OS" = "Darwin" ; then if test -n "$gtk" ; then if test -d "$gtk" ; then : # pass, good else echo gtk variable must point to the directory where gtk has been installed fi else # gtk was not set, let's try to guess testdir=$HOME/gtk/inst if test -d $testdir ; then gtk=$HOME/gtk/inst else echo this build script needs to know where gtk has been installed echo \(at the moment\) echo set gtk to point to the directory where gtk has been installed exit 2 fi fi fi # 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-make-shelx-restraints \ bin/coot-dictionary-bond-distributions \ bin/lidia \ bin/curl \ $keep_lib_archs" if [ "$ENABLE_PYTHON_COOT" = yes ] ; then # 20090427 remove python and python config from bin dir (as it # interfers with system python) file_list="$file_list html \ lib/$python_version include/$python_version" fi echo rsyncing... for file in $file_list ; do dn=$(dirname $file) if [ -e $fat_dir/$file ] ; then # echo rsync -axr $fat_dir/$file $cleaned_dir/$dn rsync -axr $fat_dir/$file $cleaned_dir/$dn else echo $fat_dir/$file does not exist fi done echo done rsyncing. } function make_tar { echo in make_tar args: $1 $2 echo in make_tar: in dir: $PWD tar_dir=$1 tar_file_name=$2 cd $install_top_dir/.. if [ -e $tar_dir ] ; then echo taring nightly... from $tar_dir to $tar_file_name tar czf $tar_file_name $tar_dir status=$? if [ "$status" != 0 ] ; then echo ERROR:: tar czf $tar_file_name $tar_dir failed. echo ERROR:: while in directory $(pwd) echo ERROR:: tar failed > $tar_file_name.md5sum rm $tar_file_name else md5sum $tar_file_name > $tar_file_name.md5sum /bin/ls -l $tar_file_name >> $tar_file_name.md5sum echo done tar successfully. fi else echo ERROR:: tar target directory $tar_dir does not exist. fi } function 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 < command-line-greg.scm (use-modules (ice-9 greg)) (set! greg-tools (list "greg-tests")) (set! greg-debug #t) (set! greg-verbose 5) (let ((r (greg-test-run))) (if r (coot-real-exit 0) (coot-real-exit 1))) EOF echo $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm status=$? if [ $status = 0 ] ; then echo test_coot: coot test passed return 0 else echo test_coot: coot test failed return 1 fi else echo run_tests is not true, not testing. return 1 fi } # Return 0 on success, 1 on failure (or not tested) # # we should be in the directory where coot was untarred for building # when this function was called. # function test_coot_python { echo testing with python unittest echo testing with python unittest >&2 echo currently we are here: pwd if test "$run_tests" = true ; then # let's test our new coot # for python build we need to set COOT_PYTHON_DIR and COOT_HOME # as well as PYTHONPATH things now COOT_PYTHON_DIR=$install_top_dir/share/coot/python PYTHONPATH=$COOT_PYTHON_DIR PYTHONHOME=$install_top_dir export COOT_PYTHON_DIR export PYTHONPATH export PYTHONHOME echo $install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py $install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py status=$? if [ $status = 0 ] ; then echo test_coot_python: coot test passed return 0 else echo test_coot_python: coot test failed return 1 fi else return 1 fi } function fixup_libcurl { sed s,-L/usr/lib,, curl-config > curl-config.tmp mv curl-config.tmp curl-config sed s,-L/usr/lib,, lib/libcurl.la > lib/libcurl.la.tmp mv lib/libcurl.la.tmp lib/libcurl.la } # now we can set the gtk version gtk_version=${gtk_version:=3} build_type=gtk$gtk_version # python is implicit - we will do guile when we can # now on to some code! if [ "$use_proxy" = 1 ] ; then # establish proxy settings printf "Proxy user: " read proxy_user printf "Proxy password: " read -s proxy_pass printf "\n" http_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/" https_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/" ftp_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/" ssl_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/" export http_proxy https_proxy ftp_proxy ssl_proxy no_proxy fi # use the right (GNU) tar and provide the path to wget (needed # for downloads) and to GNU make - (which is necesary for python # at least). # # So that python and the *-configs are found when it is installed: # A bit of a kludge because we do testing for pre-release later. # It's a logical mess. # if test "$build_coot_prerelease" = 1 ; then PATH=${AUTOBUILD_INSTALLED}-pre-release-$build_type/bin:$PATH else PATH=$AUTOBUILD_INSTALLED-$build_type/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 $LOGS shared_static_flag="--disable-shared" # huh? shared_static_flag="--disable-static" shared_lib_ext=so systype=unknown # malloc.h business, Darwin does not have malloc.h # used in the gtk_canvas build have_malloc=1 if test "$OS" = "Darwin" ; then have_malloc=0 fix_ulong=1 update_libtool=1 update_config_guess_sub=1 shared_static_flag="--disable-static" shared_lib_ext=dylib 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 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 if test $OS = IRIX64 ; then osversion=`uname -r` systype=${osversion}-sgi fi if test $OS = IRIX ; then osversion=`uname -r` systype=${osversion}-sgi fi if test $OS = OSF1 ; then osversion=`uname -r | sed s/V//g` systype=${osversion}-OSF1 fi echo systype: $systype echo update_libtool: $update_libtool echo update_config_guess_sub: $update_config_guess_sub # we need these dependencies: # - libgtk-3-dev # - git # - libsqlite3-dev # needed for python compilation by jupyterlab # check dependencies for Ubuntu. case $dist_name in *ubuntu*) dep_list=' patch m4 g++ git libssl-dev libxext-dev libxmu-dev libxt-dev libc6-dev libncurses5-dev libglu1-mesa-dev libjpeg-dev mesa-common-dev libgtk-3-dev' # converted from libgtk2.0-dev - not tested # not libgtk-3-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) # python is needed to configure ninja. Sigh. flex and bison are needed for gobject-introspection dep_list='libncurses5-dev libssl-dev g++ git libxext-dev libglu1-mesa-dev mesa-common-dev python flex bison m4 cmake' # converted from dep_list='libncurses5-dev g++ libxext-dev libglu1-mesa-dev mesa-common-dev libgtk2.0-dev' # not tested for dep in $dep_list do echo $dep if dpkg-query --status $dep > /dev/null ; then echo system has $dep else echo ======== $dep is missing ====== missing_list="$missing_list $dep" fi done if [ "$missing_list" != '' ] ; then echo " " echo " " echo install these packages: $missing_list echo then re-run echo " " echo " " my_exit 2 fi ;; # centos7 needs package gtk3-devel to be installed(!) 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=$PATH:/usr/X11R6/bin export PATH fi # Do we link with sqlite (for the ligands database)? # We allow the calling script to set use_sqlite=yes use_sqlite=${use_sqlite:=no} if [ "$use_sqlite" = "yes" ] ; then sqlite_config_args=--with-sqlite3 else sqlite_config_args= fi # We want to add some compiler info in the directory name. # If CC is set, use that, # If not, try gcc, # if not, try cc # # Similarly for the c++ compiler info # If CXX is set, use that # if not, try g++ # if not, try c++ if [ -n "$CC" ] ; then # CC was set echo \$HOST is $HOST echo \$OS is is $OS gcctest=`$CC --version | awk 'NR==1 {print $2}'` echo debugging \$CC was $CC echo debugging gcctest is $gcctest and "(GCC)" is "(GCC)" if [ "$gcctest" != '(GCC)' ] ; then # but not gcc v=$CC-`$CC -v` if [ $? -ne 0 ] ; then v="missing_version" fi else # gcc v=$CC-`$CC --version | awk 'NR==1 {print $3}'` fi else # CC not set v=gcc-`gcc -dumpversion | head -1` if [ $? -ne 0 ] ; then # not gcc # try cc v=cc-`cc -v` if [ $? -ne 0 ] ; then v="missing_version" fi fi fi if [ -n "$CXX" ] ; then # CXX was set gxxtest=$($CXX --version | awk 'NR==1 {print $2}') # typically gxxtest is set to "(GCC)", but not on Ubuntu, where the line is: # g++ (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3 # Scientific Linux: # g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) # RHEL 6: # g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) echo gxxtest: $gxxtest if [ "$gxxtest" != "(GCC)" ] ; then # but not g++ (?). Maybe it was Ubuntu... case "$gxxtest" in *[Uu]buntu*) w=$($CXX --version | head -1 | awk '{print $3}' | tr -d ')') ;; *) w=$CXX-$($CXX -v | head -1 | sed 's/ / /g') if [ $? -ne 0 ] ; then w="missing_cxx_version" fi ;; esac else # g++ w=$CXX-$($CXX --version | awk 'NR==1 {print $3}') fi else # CXX not set w=g++-`g++ -dumpversion | head -1` if [ $? -ne 0 ] ; then # not g++ # try c++ w=c++-`c++ -v` if [ $? -ne 0 ] ; then # try CC w=CC-`CC -v` if [ $? -ne 0 ] ; then w="missing_c++_version" fi fi fi # note that g++ 3.2 cannot compile clipper's test_contrib.cpp. # So, if we have g++ 3.2 or less, then we need to get and apply # test_contrib.cpp.patch # add a space before argument setting awk -v version=$w 'BEGIN{ exit (version+0 >= 3.3)}' wvers=$? if [ $wvers = 0 ] ; then need_clipper_contrib_patch=true fi fi # do we actually have g++ (or c++?) if ! g++ --version ; then if ! c++ --version ; then echo no c++/g++ compiler. Exit now my_exit 2 fi fi # so now we have v and w set to something. We # need to sanitize that something. v_fid=`echo $v | sed 's/ /_/g'` w_fid=`echo $w | sed 's/ /_/g'` compilers_dir=$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=$(grep processor /proc/cpuinfo | wc -l) ; then # limit to 8 processors if [ "$np" -gt 8 ] ; then np=8 fi if [ "$HOST" = hal.lmb.internal ] ; then np=64 fi echo using $np processors in compilation MAKE="make -j$np" echo MAKE set to $MAKE fi fi fi fi if [ $OS = Darwin ] ; then np=$(system_profiler SPHardwareDataType | awk '/Total Number/ { print $NF }') MAKE="make -j$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 ######################################################################## # cmake ######################################################################## r=$(cmake --version) echo $r case $r in cmake\ version\ 3.1[0-9]*) echo found recent cmake cmake_is_good=true ;; cmake\ version\ 3.[2-9]*) echo found recent cmake cmake_is_good=true ;; cmake\ version\ 4*) echo found recent cmake cmake_is_good=true ;; esac echo cmake_is_good: $cmake_is_good if [ "$cmake_is_good" = true ] ; then echo cmake passes else echo $r echo cmake too old - Version 3.2 or later is needed. Ending now. exit 2 fi # create $AUTOBUILD_BUILD directory if [ ! -d "$AUTOBUILD_BUILD" ] ; then mkdir "$AUTOBUILD_BUILD" if [ $? -ne 0 ] ; then prev_dir=$(dirname $AUTOBUILD_BUILD) echo $prev_dir if [ ! -d "$prev_dir" ] ; then mkdir $prev_dir mkdir "$AUTOBUILD_BUILD" fi fi if [ ! -d "$AUTOBUILD_BUILD" ] ; then # echo mkdir of the AUTOBUILD_BUILD \(i.e. "$AUTOBUILD_BUILD"\) failed. my_exit 2 fi fi start_dir=$PWD echo start_dir $start_dir cd $AUTOBUILD_BUILD if [ $? -ne 0 ] ; then echo $AUTOBUILD_BUILD failed for some reason. Now in `pwd` fi # for ccp4 (20051104) compatibility, we can't use colons in the date string date=$(date -u +'%Y-%m-%d__T%H_%M_%S') echo Date: $date # now in $AUTOBUILD_BUILD BUILDING_DIR=${BUILDING_DIR:=${HOST}_$date} mkdir $BUILDING_DIR if [ $? -ne 0 ] ; then echo mkdir $BUILDING_DIR failed for some reason. Now in `pwd` fi cd $BUILDING_DIR if [ $? -ne 0 ] ; then echo cd $BUILDING_DIR failed for some reason. Now in `pwd` fi build_dir=`pwd` # test for pkg-config if type pkg-config ; then if pkg-config --atleast-pkgconfig-version 0.16 ; then build_pkg_config= echo pkg-config is new enough `pkg-config --version` else build_pkg_config=1 echo pkg-config should be built \(but won\'t be\). fi else echo pkg-config doesn\'t exist. fi echo checking wget echo which wget which wget # use -P for timestamping # Note that now wget depends on libhogweed and that depends on libgmp # but we are compiling an old version of gmp (not sure that we need # an old version) and libhogweed refers to a (now) non-existant # functions and the dynamic loading fails. # This setting of the alias fails. It works on the command line. # 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 # release_server_dir=http://www.ysbl.york.ac.uk/~emsley/software release_server_dir=http://lmb.bioch.ox.ac.uk/coot/software/source/releases release_server_dir=http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/releases/ release_server_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases # extras_place=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $release_server_dir/ ${WGETO} -O ${AUTOBUILD_SOURCES}/index-pre-release.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/ pre_release_files_html="none" if [ $build_coot_prerelease = 1 ] ; then pre_release_files_html=${AUTOBUILD_SOURCES}/index-pre-release.html fi if [ $build_coot_prerelease = yes ] ; then pre_release_files_html=${AUTOBUILD_SOURCES}/index-pre-release.html fi coot_version_tmp=$(awk ' /a href=.*.tar.gz/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \ $pre_release_files_html | tail -1) echo pre_release_files_html $pre_release_files_html echo coot_version_tmp : $coot_version_tmp : if [ -z "$coot_version_tmp" ] ; then echo clever coot_version extraction failed, using default. else coot_version=$coot_version_tmp echo clever coot_version succeeded, setting coot_version to $coot_version from extraction fi # override the switch which turns off the building of the pre-release here: # build_coot_prerelease=1 # Let's initially set coot_prerelease_exists to not-exist, then we # try to download it from the Coot web site, and if it exists we set # coot_prerelease_exists to 1. If it doesn't exist, we don't do that # of course and we also don't make the install_top_dir to be the pre-release # directory later on. coot_prerelease_exists= # coot_version_pre no longer has .tar.gz extension if test "$build_coot_prerelease" = 1 ; then echo debug:: ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/ ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/ coot_version_pre=$(awk ' /a href=.*.tar.gz/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \ ${AUTOBUILD_SOURCES}/index.html | tail -1) echo INFO:: building pre-release and coot_version_pre is $coot_version_pre if [ -z "$coot_version_pre" ] ; then # this path when there are no pre-releases to be built, i.e. build the latest release. echo trying to build pre-release coot, but failed to find pre-release version echo make a stable release then build_coot_prerelease= BINARY_TAR_DEST_DIR=$STABLE_DEST_DIR mkdir -p ${BINARY_TAR_DEST_DIR}/holding ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $release_server_dir/ echo examining release server files ${AUTOBUILD_SOURCES}/index.html # coot_version=$(awk ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { for (file in files) { final=file } ; print final } ' # have another go at latest version extraction. coot_version=$(awk '/compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[++n]=file; } END { for (file in files) print files[file]}' \ ${AUTOBUILD_SOURCES}/index.html | sort | tail -1) echo coot_version $coot_version else build_coot_prerelease=1 # belt and braces coot_prerelease_exists=1 # tinker with coot_prefix, it is generic_prefix with pre-release added to prefix dir coot_prefix="--prefix=${AUTOBUILD_INSTALLED}-pre-release-${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 ${AUTOBUILD_SOURCES}/index.html coot_version=$(awk ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { asort(files, indices) ; for (file in files) { final=file } ; print final } ' \ ${AUTOBUILD_SOURCES}/index.html | tail -1) if test -z "$coot_version" ; then # maybe it wasn't GNU awk (we can't sort the associative array), this will pick a "random" arry key -> coot_version coot_version=$(awk ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { for (file in files) { final=file } ; print final } ' \ ${AUTOBUILD_SOURCES}/index.html | tail -1) fi echo coot_version $coot_version BINARY_TAR_DEST_DIR=$STABLE_DEST_DIR mkdir -p ${BINARY_TAR_DEST_DIR} mkdir -p ${BINARY_TAR_DEST_DIR}/holding fi echo INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is $BINARY_TAR_DEST_DIR echo INFO:: coot_version_pre is $coot_version_pre echo INFO:: build_coot_prerelease is $build_coot_prerelease echo INFO:: release_server_dir is $release_server_dir echo INFO:: coot_version is $coot_version echo INFO:: build_type is $build_type # set the build prefix for installed stuff. Put everything in the # pre-release directory if we are building a pre-release. # (Perhaps this bit of code should go down lower, where we test # build_coot_prerelease again # # we need install_top_dir because we use it to copy over coot.py # to the install python directory. # Notes for SSL with python: # after configure, run this sed: # real_ssl_prefix=/usr # for mac, for PC, libs go in /usr/lib64 and # sed -i -e "s?#SSL=.*?SSL=$real_ssl_prefix?" -e 's/^#_ssl/_ssl/' -e's/^#.*-DUSE_SSL/ -DUSE_SSL/' -e 's?^#.*-L$(SSL)/lib? -L$(SSL)/lib?' Modules/Setup # also add --with-ensurepip=install # For ubuntu, you need system OpenSSL: # sudo apt-get install openssl-dev # if [ "$build_coot_prerelease" = 1 ] ; then if [ "$coot_prerelease_exists" = 1 ] ; then generic_prefix="--prefix=${AUTOBUILD_INSTALLED}-pre-release-${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 [ $(uname) != Darwin ] ; then # 20220228-PE also -L$install_top_dir/lib64 python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -Wl,--rpath=${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 [ $(uname) != Darwin ] ; then python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -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 [ $(uname) != Darwin ] ; then python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -Wl,--rpath=${AUTOBUILD_INSTALLED}-${build_type}/lib" python_ldflags="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}-${build_type}/lib" python_libs="LIBS=\"-L$install_top_dir/lib64 -lffi\"" python_libs="LIBS='""-L$install_top_dir/lib64 -lffi""'" python_libs="LIBS=-L$install_top_dir/lib64" # finds libffi python_rpath="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}-${build_type}/lib" echo python_libs is $python_libs else pv=$(sw_vers -productVersion) # e.g. 10.10 os_minor_version="${pv%.*}" python_spec_flags="MACOSX_DEPLOYMENT_TARGET=$os_minor_version" fi fi echo install_top_dir $install_top_dir # this should not be needed export PATH=$install_top_dir/bin:$PATH # Hmmm... I am not sure that I want to mess with pkg-config in the # simple version. But we do... # # This allows standard pkg-config to find gtkglext and several other # things. # # override STD_PKGCONFIG_DIR to lib64 dir if we are in 64 bit. # os_arch=x86_64-linux-gnu # for now STD_PKGCONFIG_DIR=/usr/lib/pkgconfig case "$architecture" in x86_64*) STD_PKGCONFIG_DIR=/usr/lib64/pkgconfig ;; esac echo HERE A ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH echo HERE A ppppppppppppppp with gtk $gtk echo HERE A ppppppppppppppp with os_arch $os_arch if [ -z "$PKG_CONFIG_PATH" ] ; then # I think that the standard dir is not needed. # PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$STD_PKGCONFIG_DIR # FYI packages that go into $install_top_dir/lib/$os_arch/pkgconfig: # gobject-introspection-1.0.pc # pygobject-3.0.pc # py3cairo.pc # glm.pc if test -n "$gtk" ; then PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig else PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig # glib-2.0.pc is found in $install_top_dir/lib64 PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig fi else echo HERE B ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH echo setting PKG_CONFIG_PATH: testing dir $install_top_dir/lib/$os_arch/pkgconfig if [ -d $install_top_dir/lib/$os_arch/pkgconfig ] ; then echo HERE C ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH if test -z "$gtk" ; then PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR else PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR fi echo HERE D ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH else echo HERE E ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH if test -z "$gtk" ; then echo HERE F ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR else echo HERE G ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH #PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR # glib-2.0.pc is found in $install_top_dir/lib64 PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR fi fi fi if [ -e /opt/X11/lib/pkgconfig ] ; then PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$PKG_CONFIG_PATH fi echo HERE Z ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH echo "COOT_CCP4_PACKAGES" "$COOT_CCP4_PACKAGES" if [ -n "$COOT_CCP4_PACKAGES" ] ; then # PKG_CONFIG_PATH=$COOT_CCP4_PACKAGES/lib/pkgconfig:$PKG_CONFIG_PATH PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$COOT_CCP4_PACKAGES/lib/pkgconfig fi export PKG_CONFIG_PATH echo PKG_CONFIG_PATH is now $PKG_CONFIG_PATH # Do we have freetype2? cairo depends on it. if pkg-config freetype2 ; then build_freetype2= echo system/installation has freetype2 else echo freetype2 should be built build_freetype2=1 fi # building PyGObject 3.36.1 requires glib 2.58.0 or later. # 2022-23-17-PE gobject-introspection-1.68 needs glib 2.58 or later needed_glib_version=2.58 if pkg-config --atleast-version=$needed_glib_version 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=true fi # we need to export this for net-http, because it doesn't set # variables from configure, we rely on a shell (environment) variable. export install_top_dir echo testing for install_top_dir: "$install_top_dir" if [ ! -e "$install_top_dir" ] ; then echo $install_top_dir does not exist echo making directory $install_top_dir mkdir -p $install_top_dir if [ $? -ne 0 ] ; then echo DISASTER: $install_top_dir does not exist and no way echo to make it. my_exit 2 fi else echo INFO:: $install_top_dir exists already. fi echo done testing for $install_top_dir if [ ! -e "$install_top_dir/lib" ] ; then echo making "$install_top_dir/lib" mkdir -p "$install_top_dir/lib" if [ $? -ne 0 ] ; then echo DISASTER: $install_top_dir/lib cannot be created echo to make it. my_exit 2 fi fi # # append or set LD_LIBRARY_PATH. # # this can be problematic for a distributable tar build because this can cause linkage # against ccp4's libxml2! Hmm! # # if [ -z "$LD_LIBRARY_PATH" ] ; then LD_LIBRARY_PATH=$install_top_dir/lib export LD_LIBRARY_PATH else LD_LIBRARY_PATH=$install_top_dir/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH fi #for Macs: if test "$OS" = "Darwin" ; then if [ -z "$DYLD_LIBRARY_PATH" ] ; then # DYLD_LIBRARY_PATH=$install_top_dir/lib # export DYLD_LIBRARY_PATH : else #DYLD_LIBRARY_PATH=$install_top_dir/lib:$DYLD_LIBRARY_PATH #export DYLD_LIBRARY_PATH : fi fi # # IRIX64 (on batman at least) does not seem to use LD_LIBRARY_PATH, # it uses, instead, LD_LIBRARYN32_PATH. So we set that for all # systems, hoping that it won't do any harm on other systems. # # This surely is no longer used - PE 20130909 # LD_LIBRARYN32_PATH=$LD_LIBRARY_PATH # export LD_LIBRARYN32_PATH # ccp4_system_type can be one of the following # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd # linux_compaq_compilers linux_intel_compilers generic Darwin # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers ccp4_system_type="$OS" if test "$OS" = Linux ; then ccp4_system_type=linux else if test "$OS" = IRIX64 ; then ccp4_system_type=irix64 else if test "$OS" = IRIX ; then ccp4_system_type=irix else if test "$OS" = Darwin ; then ccp4_system_type=Darwin fi fi fi fi echo ccp4_system_type $ccp4_system_type # clean up old test status: echo build-in-progress @`date +"%a_%d_%b_%H:%M"` > $LOGS/build-status echo waiting > $LOGS/test-status # ---------------------------------------------------------------------------- # ---------------------------------------------------------------------------- # which components? # ---------------------------------------------------------------------------- # ---------------------------------------------------------------------------- # # Often there are components provided by the operating system or optional # installs thereof. # build_mmdb=0 build_ssmlib=0 build_fftw=0 build_clipper= build_guile=0 build_guile_www=0 build_guile_gui=0 build_libtool=1 build_net_http=0 build_gsl=0 # build_libungif=0 # build_libtiff=0 # build_libjpeg=0 # build_libpng=0 # build_imlib=0 # build_gtk_canvas=0 build_goocanvas= build_python= build_pygobject= build_guile_gtk= 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 # ---------- test installation libidn ------------------ # if [ -e $install_top_dir/include/idn2.h ] ; then echo installation has libidn2 devel build_libidn= else echo installation does not have libidn2, libcurl should be built also build_libidn=1 build_curl=1 fi # Test the output of pkg-config gtk+-2.0 for recent enough gtk. # If not, then build it yourself. # # Experiment, to force bragg3 to compile gtk+2 # # was 2.8 needed_gtk_version=3.94 # what a mess. Needs cleaning pkg-config --atleast-version=$needed_gtk_version gtk+-2.0 gtk_pkg_config_status=$? if [ "$gtk_pkg_config_status" = 0 ] ; then echo :::::::: gtk version is at least $needed_gtk_version echo :::::::: gtk version is `pkg-config --modversion gtk+-2.0` fi echo libtool test: looking for ${install_top_dir}/include/ltdl.h ls ${install_top_dir}/include/ltdl.h if test -e ${install_top_dir}/include/ltdl.h ; then echo installation has libtool build_libtool= else echo libtool should be built fi # ============= python ================ # # python_version is the filename of the python executable. For python # 2.5.1 it is python2.5, not python2.5.1 # python_version=python3.9 pver=3.9.12 python_version_extension=3.9 # extract this # for compatibility with gtk build system # use_python_version_3_8 is not yet set anywhere. # future self: set use_python_version_3_8 when needed so that this block gets executed if [ "$use_python_version_3_8" = true ] ;then python_version=3.9 pvers=3.9.12 python_version_extension=3.8 fi # # but more modern pythons do not compile (at least on my mac) # 20201225-PE this needs checking if [ $OS = Darwin ] ; then pver=3.6.5 pver=3.8.12 fi # set build_pygobject here if [ ! -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then build_pygobject=true fi # force the GSL config to be in $install_top_dir, rather than # potenially getting it from the system # but does this compile cleanly on Mac OS X? I've forgotten. # Perhaps we will need to be more clever and potentially use # the fink GSL if it is available. $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 [ $build_gsl = 1 ] ; then echo need to build GSL build_gsl=1 else echo GSL is up to date # set build_gsl to blank: build_gsl= fi fi # test for mmdb: Does mmdb_model.h exist, and if it does, does it # contain MMDBF_IgnoreHash. If not, then build mmdb. # # CCP4 mmdb installs in the include/mmdb2 directory, # if test -e "${install_top_dir}/include/mmdb2/mmdb_model.h" ; then build_mmdb= else echo installation has no mmdb, build mmdb. build_mmdb=1 fi ssm_include_dir=ssm if [ -e $install_top_dir/include/$ssm_include_dir/ssm_align.h ] ; then if [ "$build_mmdb" = 1 ] ; then build_ssmlib=1 else # do we have SSM version 1.4 or later? if grep --silent "MINOR_VERSION = [4-9]" $install_top_dir/include/$ssm_include_dir/ssm_defs.h ; then echo SSM is found. build_ssmlib= else echo we need a newer SSM. build_ssmlib=1 fi fi else echo SSM not found - needs to be built build_ssmlib=1 fi # clipper depends on mmdb, so if mmdb was built, the so must clipper be. # likewise for fftw. # build_clipper=1 if [ -z "$build_mmdb" ] ; then # we potentially can pass the building of clipper: echo INFO:: shall we build clipper: mmdb not to be built if [ -z "$build_fftw" ] ; then echo INFO:: shall we build clipper: fftw not to be built # test for new ccp4-based clipper (for mtz and maps) if [ -e $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h ] ; then # echo $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h exist if [ -e $install_top_dir/include/clipper/contrib/sfscale.h ] ; then # echo $install_top_dir/include/clipper/contrib/sfscale.h exist build_clipper= else echo $install_top_dir/include/clipper/contrib/sfscale.h not exist, building clipper build_clipper=1 fi else echo $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h not exist, building clipper fi fi else echo mmdb needs to be built, so clipper needs building. fi # shall we build libccp4c? if [ -e $install_top_dir/lib/libccp4c.la ] ; then # 20170925 test for the pkg-config file if [ -e $install_top_dir/lib/pkgconfig/libccp4c.pc ] ; then # no need to rebuild build_ccp4c= else build_ccp4c=1 fi else build_ccp4c=1 fi if [ -e $install_top_dir/bin/python3 ] ; then if $install_top_dir/bin/python3 -V ; then # test for ctypes - was it installed correctly? if $install_top_dir/bin/python3 -c 'import ctypes' ; then echo we have python3 with working ctypes else echo python3 ctypes failure build_python=1 fi else build_python=1 fi else build_python=1 fi # ----------------------------------------------------------------------------- # ----------------------------------------------------------------------------- # build components # ----------------------------------------------------------------------------- # ----------------------------------------------------------------------------- # # # libccp4: (not fortran) if test -n "$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 # ${WGET} ftp://ftp.ccp4.ac.uk/opensource/libccp4-$libccp4_version.tar.gz ${WGET} $extras_place/libccp4-$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=2.0.20 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 ./configure $generic_prefix --enable-shared --disable-static CPPFLAGS=-I$install_top_dir/include LDFLAGS=-L$install_top_dir/lib if $MAKE ; then $MAKE install fi ) > $HOSTLOGDIR/02-ssm.txt 2>&1 else echo not building ssm: fi # fftw if test -n "$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 # patch the hkl_data.h header # sed -ibackup -e 's/int i = 0; i < list.size(); i++/unsigned int i = 0; i < list.size(); i++/' clipper/core/hkl_data.h # --- make clipper # patch clipper # fix the linking to the wrong libfftw echo patching clipper with ${AUTOBUILD_SOURCES}/clipper-configure-2.patch patch -p0 < ${AUTOBUILD_SOURCES}/clipper-configure-2.patch echo . ------------------------------------------------------------------------------ echo . " clipper " echo . ------------------------------------------------------------------------------ export CPPFLAGS=-I$install_top_dir/include export LDFLAGS=-L$install_top_dir/lib echo CPPFLAGS $CPPFLAGS echo LDFLAGS $LDFLAGS echo PKG_CONFIG_PATH $PKG_CONFIG_PATH # if /usr/lib64/lib(r)fftw.so exists, clipper will link to them # despite our having build fftw for ourselves - I need to stop # that (because of clipper's m4/fftw.m4) save_libs="$LIBS" export LIBS="-L$install_top_dir/lib:$LIBS" if [ -z "$LIBS" ] ; then save_libs= export LIBS=-L$install_top_dir/lib else save_libs="$LIBS" export LIBS=-L$install_top_dir/lib:$LIBS fi echo now we have LIBS $LIBS echo ./configure --prefix=$install_top_dir \ --enable-mmdb=$install_top_dir \ --enable-ccp4=$install_top_dir \ --enable-shared \ --enable-mmdb \ --enable-cif \ --enable-ccp4 \ --enable-minimol \ --enable-cns \ CXXFLAGS="-g -O2 -fno-strict-aliasing" ./configure --prefix=$install_top_dir \ --enable-mmdb=$install_top_dir \ --enable-ccp4=$install_top_dir \ --enable-shared \ --enable-mmdb \ --enable-cif \ --enable-ccp4 \ --enable-minimol \ --enable-cns \ CXXFLAGS="-g -O2 -fno-strict-aliasing -Wno-narrowing" export LIBS="$save_libs" # 20110921 I don't think we need these flags any longer # CCP4_CXXFLAGS=-I$install_top_dir/include CCP4_LIBS=$install_top_dir/lib/libccp4c.la # we don't want to make the clipper executables, so let's cd in to the clipper libs and # make (just) those. if $MAKE ; then $MAKE install fi ) > $HOSTLOGDIR/04-clipper.txt 2>&1 clipper_build_status=$? if [ $clipper_build_status != 0 ] ; then echo clipper build failed, exiting my_exit 2 fi else echo not building clipper: fi ############################################################################### # GEMMI is frequently updated and uses git not releases - so always install it. ############################################################################### if true ; then echo BUILDING gemmi \(installing GEMMI\) ( save_dir=$(pwd) cd $start_dir if [ -e gemmi ] ; then cd gemmi git fetch git merge cd - else git clone https://github.com/project-gemmi/gemmi.git fi cd gemmi/include # note to self: fix this for Darwin - which has a crippled cp cp -a -r gemmi $install_top_dir/include cd - cd $save_dir ) > $HOSTLOGDIR/27-gemmi.txt 2>&1 fi ####################################################################### # readline is a dependency of python and guile ####################################################################### build_readline=true if [ -e $install_top_dir/include/readline/readline.h ] ; then build_readline=false fi if test "$build_readline" = true ; then echo BUILDING readline: 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 < ${AUTOBUILD_SOURCES}/readline-5.1.patch fi if [ "$dist_name" = debian ] ; then echo applying debian sed patch for shared-lib libreadline # thanks for the quoting help tony duan @ stackoverflow sed -i '125,135 s/SHOBJ_LDFLAGS=.*/&\n SHLIB_LIBS='"'"'$(TERMCAP_LIB)'"'"'/' support/shobj-conf extra_args_for_debian="--with-curses --enable-shared" fi echo ./configure $generic_prefix $extra_args_for_debian ./configure $generic_prefix $extra_args_for_debian # single thread if make ; then make install else echo make of readline failed fi ) > $HOSTLOGDIR/10-pre-readline.txt 2>&1 else echo not building readline: fi ############################################################################### ########## build python and friends ############# ############################################################################### test_for_already_installed_dependencies=true # So that python is found when it is installed: # #this should not be needed export PATH=$install_top_dir/bin:$PATH # gobject-introspection needs libffi # meson needs libffi to be intalled before python, so that meson can find ctypes modules libffi_version=3.2.1 skip_build=false if [ $test_for_already_installed_dependencies = true ] ; then echo ffi build - testing existance $install_top_dir/lib/libffi-$libffi_version/include/fffi.h if [ -e $install_top_dir/lib/libffi-$libffi_version/include/ffi.h ] ; then skip_build=true echo installation has libffi else echo $install_top_dir/lib/libffi-$libffi_version/include does not exist fi fi if [ $skip_build = false ] ; then echo BUILDING libffi $libffi_version: ( ${WGET} https://sourceware.org/pub/libffi/libffi-$libffi_version.tar.gz gzip -dc ${AUTOBUILD_SOURCES}/libffi-$libffi_version.tar.gz | tar xf - cd libffi-$libffi_version ./configure $generic_prefix if $MAKE ; then make install fi ) > $HOSTLOGDIR/07e-libffi.txt 2>&1 fi # python # if test -n "$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 echo building in: $PWD env gzip -dc ${AUTOBUILD_SOURCES}/Python-$pver.tgz | tar xf - cd Python-$pver # stuff ffi into setup.py sed -ibackup -e 's/def detect_decimal/ ext.libraries.append("ffi")\n\n &/' setup.py ffilibdir=$install_top_dir/lib64 sed -ibackup2 -e "s?add_dir_to_list(self.compiler.library_dirs, ./usr/local/lib.)?add_dir_to_list(self.compiler.library_dirs, '$ffilibdir')?" setup.py # --with-ensurepip=install # £ echo INFO:: ./configure $generic_prefix --with-ensurepip=install --enable-shared $python_lib_flags $python_spec_flags # /Users/pemsley/ccp4/devtools/install # this should be configured openssl_prefix=$HOME/ccp4/devtools/install openssl_prefix=/usr # note to self: We need ffi.h (and lib presumably) to build the ctypes module (libffi-devel) # (or I could include it in this build script) (I don't know if ctypes is important) # 20220227-PE ctypes is crucial for meson echo INFO:: ./configure $generic_prefix --with-ensurepip=install --enable-shared --with-openssl=$openssl_prefix CFLAGS=-I$install_top_dir/lib/libffi-3.2.1/include $python_libs $python_ldflags $python_spec_flags # # do we also need to use --with-threads=dir? if ./configure $generic_prefix --with-ensurepip=install --enable-shared --with-openssl=$openssl_prefix CFLAGS=-I$install_top_dir/lib/libffi-3.2.1/include $python_libs $python_ldflags $python_spec_flags ; then echo INFO:: make for python if $MAKE ; then echo INFO:: make install for python $MAKE install fi fi # test it echo test cypes in the new python # or use this test: if $install_top_dir/bin/python3 -c 'import ctypes' ; then ... $install_top_dir/bin/python3 < $HOSTLOGDIR/07-python.txt 2>&1 ( which pip3 pip3 install --upgrade pip # pip3 install pycairo # pip3 install pygobject ) > $HOSTLOGDIR/07a-pip-upgrade.txt 2>&1 else echo not building python: fi ############################################################################### ########## meson before gobject-introspection ############# ############################################################################### # this needs to be reconsidered because gobject-intropsection needs python3 # to build. build_gobject_introspection=true if [ -e $install_top_dir/include/gobject-introspection-1.0/giversionmacros.h ] ; then build_gobject_introspection=false echo installation has gobject-introspection fi # 200918-PE install meson before using it. # ## --------------- meson --------------------------------- ## # this version of meson is too old to compile gobject-introspection (20220221) # pip3 install meson # we should have meson for pygobject, need version 0.46 or later # however, is this the way to install pygobject? Or is done with pip3? # echo testing to see if meson exists in path yet echo testing to see if meson exists in path yet 2>&1 echo which meson which meson echo meson --version meson --version if meson --version ; then echo we have meson v=$(meson --version) if [[ $v < 0.61 ]] ; then echo meson is too old, current version is $v build_meson=true else build_meson=false fi else build_meson=true fi if $build_meson = true ; then meson_version=0.61.2 echo BUILDING meson $meson_version: ( ${WGET} https://github.com/mesonbuild/meson/releases/download/$meson_version/meson-$meson_version.tar.gz tar xf ${AUTOBUILD_SOURCES}/meson-$meson_version.tar.gz cd meson-$meson_version python3 setup.py build python3 setup.py install cd - echo which meson which meson echo meson --version meson --version ) > $HOSTLOGDIR/07b-meson.txt 2>&1 else echo not building meson: fi ############################################################################### ########## ninja before glib ############# ############################################################################### build_ninja=true if [ -e $install_top_dir/bin/ninja ] ; then build_ninja=false fi if [ $build_ninja = true ] ; then echo BUILDING ninja ( # see https://github.com/ninja-build/ninja/releases ninja_version=1.10.2 ${WGET} https://github.com/ninja-build/ninja/archive/refs/tags/v$ninja_version.tar.gz tar xf ${AUTOBUILD_SOURCES}/v$ninja_version.tar.gz cd ninja-$ninja_version ./configure.py --bootstrap # builds ninja, requires python if [ -e ninja ] ; then cp ninja $install_top_dir/bin else echo configure/boostrap of ninja failed - what a surprise. fi cd - ) > $HOSTLOGDIR/07c1-ninja.txt 2>&1 fi ############################################################################### ########## glib before gobject-introspection ############# ############################################################################### if [ -e $install_top_dir/include/glib-2.0 ] ; then build_glib=false else build_glib=true fi if [ "$build_glib" = true ] ; then echo BUILDING glib: ( # without this PKG_CONFIG_PATH jiggerypokery, libz is the wrong version i.e. is the 32 bit version (on hal) export -n PKG_CONFIG_PATH export PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig echo @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ echo $PKG_CONFIG_PATH echo @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ which ninja which meson echo ninja --version ninja --version echo meson --version meson --version glib_version=2.64.3 glib_version=2.72.3 echo the following is the result of: /bin/pkg-config --modversion libffi /bin/pkg-config --modversion libffi # find new versions here: https://gitlab.gnome.org/GNOME/glib/-/releases if [ ! -e ${AUTOBUILD_SOURCES}/glib-$glib_version.tar.gz ] ; then echo ${WGET} --no-check-certificate https://gitlab.gnome.org/GNOME/glib/-/archive/2.72.3/glib-$glib_version.tar.gz ${WGET} --no-check-certificate https://gitlab.gnome.org/GNOME/glib/-/archive/2.72.3/glib-$glib_version.tar.gz fi echo tar xf ${AUTOBUILD_SOURCES}/glib-$glib_version.tar.gz tar xf ${AUTOBUILD_SOURCES}/glib-$glib_version.tar.gz cd glib-$glib_version # note to future self, when I build glib in the script then it uses a referenece to /usr/lib/libz.so # (which is the 32 bit version). When I build it by hand (as it were) outside the script, using the same # ninja and meson then it finds the *right* libz.so (/usr/lib64/libz.so). I don't have the time to # find out why now, so I installed ninja from the "hand-built" build. # # meson can't find libffi on its own, so I will export the library here export LDFLAGS=-L$install_top_dir/lib64 export CFLAGS=-I$install_top_dir/include # we install the libs in $install_top_dir (otherwise it would install in $install_top_dir/lib/x86_64-linux-gnu # and libtool would mess up and fail to properly link it (in Coot's compile) if CC=gcc meson -Dprefix=$install_top_dir -Dlibdir=$install_top_dir/lib build ; then cd build ninja ninja install cd - fi cd .. ) > $HOSTLOGDIR/07c2-glib.txt 2>&1 else echo not building glib: fi ############################################################################### ########## gobject-introspection ############# ############################################################################### if test "$build_gobject_introspection" = true ; then echo BUILDING gobject-introspection: ( # just for gobject-introspection - depends on our glib installation export PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig export LD_LIBRARY_PATH=$install_top_dir/lib64 date echo BUILDING gobject-introspection: echo environment variables echo PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ echo $PATH echo PKG_CONFIG_PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ echo $PKG_CONFIG_PATH echo LD_LIBRARY_PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ echo $LD_LIBRARY_PATH which gcc which g++ gcc --version gobject_introspection_version=1.50.0 gobject_introspection_version=1.68.0 gobject_introspection_version=1.71.0 gobject_introspection_version=1.72.0 d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.50 d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.68 d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.71 d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.72 ${WGET} $d/gobject-introspection-$gobject_introspection_version.tar.xz tar xf ${AUTOBUILD_SOURCES}/gobject-introspection-$gobject_introspection_version.tar.xz cd gobject-introspection-$gobject_introspection_version # 1.68 (probably earlier) has moved on from configure. meson baby # echo ./configure --prefix=$install_top_dir PYTHON=python3 # ./configure --prefix=$install_top_dir PYTHON=python3 # if $MAKE ; then # $MAKE install # fi echo PKG_CONFIG_PATH is... echo $PKG_CONFIG_PATH echo this is the result of /bin/pkg-config glib-2.0 /bin/pkg-config --modversion glib-2.0 /bin/pkg-config --cflags glib-2.0 /bin/pkg-config --libs glib-2.0 echo building in: pwd echo which meson which meson meson --version export CC=gcc # $install_top_dir/bin/meson is important, otherwise the wrong meson # is used. # # if $install_top_dir/bin/meson -Dprefix=$install_top_dir build ; then # # BUT... if we don't build meson because we have a new enough meson # in the path then $install_top_dir/bin/meson does not exist! if meson -Dprefix=$install_top_dir build ; then echo meson passed cd build ninja ninja install cd - else echo meson failed fi export -n CC cd .. ) > $HOSTLOGDIR/07d-gobject-introspection.txt 2>&1 fi sources_dir=${AUTOBUILD_SOURCES} # pycairo is a dependency of pygobject. Is this gtk2 stuff? pycairo_version=1.17.0 # check for a more recent version. skip_build=true if [ $test_for_already_installed_dependencies = true ] ; then # check this file name. # $install_top_dir/lib/python$python_version_extension/site-packages/pycairo-1.17.0-py3.6-linux-x86_64.egg/cairo/_cairo.py if [ -e $install_top_dir/lib/include/pycairo/py3cairo.h ] ; then skip_build=true fi fi if [ true ] ; then if [ $skip_build = false ] ; then ${WGET} https://github.com/pygobject/pycairo/releases/download/v1.17.0/pycairo-$pycairo_version.tar.gz ( if [ -e ${AUTOBUILD_SOURCES}/pycairo-$pycairo_version.tar.gz ] ; then date echo building pycairo tar xf ${AUTOBUILD_SOURCES}/pycairo-$pycairo_version.tar.gz cd pycairo-$pycairo_version python3 setup.py build python3 setup.py install cd - fi ) > $HOSTLOGDIR/07f-pycairo.txt 2>&1 else echo installation has pycairo fi fi pygobject_major_minor_version=3.29 pygobject_major_minor_version=3.30 pygobject_major_minor_version=3.36 pygobject_major_minor_version=3.42 pygobject_version=3.29.1 pygobject_version=3.30.5 pygobject_version=3.42.1 date pwd skip_build=false if [ $test_for_already_installed_dependencies = true ] ; then if [ -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then skip_build=true fi fi if [ $skip_build = false ] ; then echo BUILDING pygobject $pygobject_version: ( echo :::: PKG_CONFIG_PATH is $PKG_CONFIG_PATH ${WGET} $extras_place/PyGObject-$pygobject_version.tar.gz echo ::: trying to untar ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz if [ -e ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz ] ; then gzip -dc ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz | tar xf - cd PyGObject-$pygobject_version ### python setup.py build ### python setup.py install echo ::: which python3 which python3 echo ld_library_path $LD_LIBRARY_PATH x=$LD_LIBRARY_PATH unset LD_LIBRARY_PATH echo :::: in directory $(pwd) echo :::: building using meson -Dprefix=$install_top_dir build if meson -Dprefix=$install_top_dir build ; then echo :::: meson passed cd build echo :::: ninja ninja echo :::: ninja install ninja install else echo :::: meson failed fi export LD_LIBRARY_PATH=$x else echo ERROR:: ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz file not found. fi ) > $HOSTLOGDIR/07g-pygobject.txt 2>&1 else echo not building pygobject: echo not building pygobject: 2>&1 fi # Now we need: # * guile # * guile-www # * guile-gtk # * guile-gui # * gsl ############################################################################### ########## build guile and friends ############# ############################################################################### if [ -e $install_top_dir/include/gmp.h ] ; then build_gmp=false else build_gmp=true fi if "$build_gmp" = true ; 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 libtool_version=2.4.6 ${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libtool/libtool-$libtool_version.tar.gz (date pwd gzip -dc ${AUTOBUILD_SOURCES}/libtool-$libtool_version.tar.gz | tar xf - cd libtool-$libtool_version ./configure $generic_prefix $MAKE status=$? if [ "$status" != 0 ] ; then echo make of libtool failed else $MAKE install fi ) > $HOSTLOGDIR/09-pre-libtool.txt 2>&1 else echo not building libtool: fi ############################################################################### ########## build idn ############# ############################################################################### # we build libidn for libcurl. libcurl needs it on RHEL4 because # there is no /usr/lib/libidn.so. There is a rpm devel package, of # course, but that is more pain to install than compiling it from # scratch for coot install. if test -n "$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 ) > $HOSTLOGDIR/15-gsl.txt 2>&1 else echo not building gsl: fi ############################################################################### ########## build boost ############# ############################################################################### build_boost=true test_for_already_installed_dependencies=true if [ "$build_boost" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/boost/functional/hash.hpp ] ; then echo not building boost skip_this=true fi fi if [ $skip_this = false ] ; then boost_version=1_71_0 boost_version=1_72_0 boost_version=1_74_0 boost_server_dir=1.72.0 boost_server_dir=1.72.0 boost_server_dir=1.74.0 echo BUILDING boost $boost_version : ( echo building ========================= boost $boost_version ========================= boost_home_url=https://dl.bintray.com/boostorg/release/$boost_server_dir/source # old boost_home_url=https://boostorg.jfrog.io/artifactory/main/release/$boost_server_dir/source 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 - cd boost_$boost_version # compilation falls over # cc.compile.c++ bin.v2/libs/python/build/gcc-9/release/address-model-/python-3.6/threading-multi/visibility-hidden/long.o # In file included from ./boost/python/detail/prefix.hpp:13, # from ./boost/python/long.hpp:8, # from libs/python/src/long.cpp:5: # ./boost/python/detail/wrap_python.hpp:57:11: fatal error: pyconfig.h: No such file or directory # 57 | # include # | ^~~~~~~~~~~~ # compilation terminated. # But pyconfig.h is here: # $HOME/autobuild/Linux-penelope-pre-release-gtk3-python/include/python3.6m/pyconfig.h address_model=64 # ./bootstrap.sh --prefix=$install_top_dir --with-libraries=python,regex,serialization --without-icu pwd echo ./bootstrap.sh --prefix=$install_top_dir --with-python=python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams --without-icu echo ./bootstrap.sh --prefix=$install_top_dir --with-python=python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams --without-icu > bootstrap-command-save ./bootstrap.sh --prefix=$install_top_dir --with-python=python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams --without-icu # now edit the project-config.jam file using python line cp project-config.jam project-config.jam-orig # awk -v itd=$install_top_dir ' # /using python : 3.6/ { print " ",$1,$2,$3,$4,$5,"python3 :", itd "/include/python3.6m :", itd "/lib/libpython3.6m.so ;" } # $0 !~ "using python : 3.6 " # ' project-config.jam-orig > project-config.jam # that was flipping hard work. # 20201215-PE and now I've commented it out. # bjam no longer exists # use -Wno-deprecated-declarations echo ./b2 address-model=$address_model cflags=-fPIC -j$np cxxflags="-fPIC -I$install_top_dir/include/python$python_version_extension -Wno-maybe-uninitialized -Wno-deprecated-declarations" install > b2-command-save ./b2 address-model=$address_model cflags=-fPIC -j$np cxxflags="-fPIC -I$install_top_dir/include/python$python_version_extension -Wno-maybe-uninitialized -Wno-deprecated-declarations" install cd - ) > $HOSTLOGDIR/16-boost.txt fi fi ################################################################# # goocanvas ################################################################# # # goocanvas-2.0.pc if [ -e $install_top_dir/lib/pkgconfig/goocanvas-2.0.pc ] ; then build_goocanvas=no fi # https://download-fallback.gnome.org/sources/goocanvas/2.0/ if [ "$build_goocanvas" != "no" ] ; then goocanvas_version=2.0.4 echo BUILDING goocanvas $goocanvas_version : goocanvas_dir=https://download-fallback.gnome.org/sources/goocanvas/2.0 # or maybe http://ftp.gnome.org/pub/GNOME/sources/goocanvas/2.0 ${WGET} --no-check-certificate $goocanvas_dir/goocanvas-$goocanvas_version.tar.xz (date export PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig export LD_LIBRARY_PATH=$install_top_dir/lib64 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 tar xf ${AUTOBUILD_SOURCES}/goocanvas-$goocanvas_version.tar.xz cd goocanvas-$goocanvas_version # 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? # we don't want python 2 bindings (they find/try to install with system python) echo ./configure $generic_prefix $EXTRA_GOOCANVAS_CFLAGS if ./configure $generic_prefix --enable-python=no $EXTRA_GOOCANVAS_CFLAGS ; then if ! $MAKE ; then echo make of goocanvas failed else $MAKE install fi else echo goocanvas configure failed fi ) > $HOSTLOGDIR/17-goocanvas.txt 2>&1 else echo not building goocanvas echo not building goocanvasA 2>& 1 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 if [ ! -e ${AUTOBUILD_SOURCES}/Raster3D_$raster3d_version.tar.gz ] ; then echo missing Raster3D tar file else ( date pwd # # build libgd # if [ true ] ; 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 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 ( 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 pwd echo make linux 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 # race condition? list.mod echo make render if make render ; then echo make prefix=$install_top_dir install make prefix=$install_top_dir install # did that work? I doubt it. Let's do it by hand if [ ! -e $install_top_dir/bin/render ] ; then cp render $install_top_dir/bin/ fi else echo make render failed fi cd - else echo $install_top_dir/bin/render already exists, no build fi ) > $HOSTLOGDIR/15-raster3d.txt 2>&1 fi fi ############################################################################### ########## GLM ############# ############################################################################### if [ -e $install_top_dir/include/glm/glm.hpp ] ; then echo not building glm else echo BUILDING glm: glm_version=0.9.9.2 ${WGET} $extras_place/glm-$glm_version.tar.gz ( date pwd gzip -dc ${AUTOBUILD_SOURCES}/glm-$glm_version.tar.gz | tar xf - cd glm-$glm_version cmake . -DCMAKE_INSTALL_PREFIX=$install_top_dir if $MAKE ; then make install fi ) > $HOSTLOGDIR/17-glm.txt 2>&1 fi ############################################################################### # pygobject ############################################################################### # this needs to find gobject-introspection-1.0 >= 1.46.0 (now 1.56.0 apparently) # and it does if PKG_CONFIG_PATH is set correctly if [ -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then echo installation has pygobject else echo installing pygobject with pip3 ( echo installing pygobject echo PKG_CONFIG_PATH $PKG_CONFIG_PATH which pip3 pip3 install wheel pip3 install pygobject ) > $HOSTLOGDIR/17-pip-wheel-pygobject.txt 2>&1 fi ############################################################################### ########## build numpy ############# ############################################################################### # Let's stop at the beginning if we need a fortran compiler and don't have it. # if [ "$build_numpy" = true ] ; then if gfortran --version > /dev/null ; then echo found fortran compiler else echo fortran compiler not found. exit 2 fi fi # numpy needs system libblas (and liblapack?) - it's not clear to # me how to build them otherwise. # sudo apt-get install libblas-dev liblapack-dev # cython echo pip3 install --upgrade pip pip3 install --upgrade pip echo pip3 install cython pip3 install cython if [ true = true ] ; then skip_this=false ls -alt $install_top_dir/lib/$python_version/site-packages/numpy-*/numpy/lib/_version.py if [ -e $install_top_dir/lib/$python_version/site-packages/numpy-*/numpy/lib/_version.py ] ; then echo numpy is found, skip skip_this=true else echo not found: $install_top_dir/lib/$python_version/site-packages/numpy-*/numpy/lib/_version.py echo numpy was not found - needs building fi if [ $skip_this = false ] ; then numpy_version=1.19.4 echo building numpy $numpy_version ( echo building ========================= numpy ============================== # this needs fortran compiler gfortran # maybe get numpy from github? # https://github.com/numpy/numpy/releases/download/v1.14.1/numpy-1.14.1.tar.gz # numpy needset setuptools # https://github.com/pypa/setuptools/archive/v41.5.1.tar.gz # numpy source is now zip # ${WGET} https://pypi.python.org/packages/source/n/numpy/numpy-$numpy_version.tar.gz ${WGET} https://pypi.python.org/packages/source/n/numpy/numpy-$numpy_version.zip # if [ ! -e ${AUTOBUILD_SOURCES}/numpy-$numpy_version.zip ] ; then exit fi # tar xf ${AUTOBUILD_SOURCES}/numpy-$numpy_version.tar.gz 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 which python3 python3 setup.py build --fcompiler=gfortran python3 setup.py install if [ ! $? ] ; then echo something bad about numpy. exit 2 fi cd - ) > $HOSTLOGDIR/17-a-numpy.txt 2>&1 fi fi # this is a hack for charybdis - we need cmake version 3.1 or later export PATH=$HOME/cmake/bin:$PATH # we need to set rdkit_tar_size because the WGET doesn't skip the download if the # file exists. Amazon. # build_rdkit=true rdkit_version=2017_09_3 rdkit_version=2019_09_1 # python 3 rdkit_version=2018_09_2 # Atom pointer wrappers gone, needs coot Dec 2020 patch rdkit_version=2020_09_3 rdkit_home=https://github.com/rdkit/rdkit/archive rdkit_tar_host_file_name=Release_$rdkit_version.tar.gz rdkit_tar_download_file_name=rdkit-Release_$rdkit_version.tar.gz rdkit_tar_size=54644792 rdkit_tar_size=58598385 # 2020_09_3 if [ "$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 # skip_this=false if [ $skip_this = false ] ; then echo building rdkit $rdkit_version ( echo building ========================= rdkit ============================== # at last we get to actually compile rdkit export CC=gcc export CXX=g++ RDKIT=$install_top_dir RDBASE=$install_top_dir CMAKE_INSTALL_PREFIX=$install_top_dir export RDKIT export RDBASE export CMAKE_INSTALL_PREFIX # shall we build from github rdkit? github_rdkit=false if [ $(uname) = Darwin ] ; then echo LD_LIBRARY_FALLBACK_PATH $LD_LIBRARY_FALLBACK_PATH # what is unexport in bash? export LD_LIBRARY_PATH= fi echo ==================== LD_LIBRARY_PATH is $LD_LIBRARY_PATH if [ "$github_rdkit" = true ] ; then echo PATH A - pull if [ ! -d rdkit-github/build ] ; then mkdir -p rdkit-github/build fi echo pulling... # cd rdkit-github/rdkit && git pull && cd - cd rdkit-github/build pwd tree_from_build=../rdkit else # old wget $rdkit_home/$rdkit_tar_host_file_name -P ${AUTOBUILD_SOURCES} -O ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name echo PATH B # OK, So, AFAICS, -N doesn't work with this file. So check the size get_the_rdkit_tar_file=true echo testing for existance of ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name if [ -e ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name ] ; then which stat echo found the file ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name echo stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name size=$(stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name) echo rdkit tar ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name size from stat: $size if [ "$size" = $rdkit_tar_size ] ; then get_the_rdkit_tar_file=false fi fi echo here C with get_the_rdkit_tar_file $get_the_rdkit_tar_file if [ $get_the_rdkit_tar_file = true ] ; then $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 pwd echo tar xf ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name tar xf ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name ls if [ ! -e rdkit-Release_$rdkit_version ] ; then echo RDKit untar dir not found: rdkit-Release_$rdkit_version exit 2 fi cd rdkit-Release_$rdkit_version ${WGET} $extras_place/rdkit-maeparser.patch pwd echo patch -p0 < ${AUTOBUILD_SOURCES}/rdkit-maeparser.patch patch -p0 < ${AUTOBUILD_SOURCES}/rdkit-maeparser.patch mkdir -p build cd build pwd tree_from_build=.. fi # New (1.60) boost uses BOOST_PYTHON not Boost_PYTHON # echo which cmake which cmake # No help: -DBoost_INCLUDE_DIR=$install_top_dir/include # Cmake policy: -DMACOSX_RPATH=ON # old verisons of boost (before 1.60?) can't find boost python # with new (github Feb 2016) rdkit # -DPYTHON_LIBRARY=$install_top_dir/lib/libpython2.7.$extension_type # no help apparently # -DBoost_EXTERNAL_OBJECTS=$install_top_dir/lib/libboost_python.$extension_type # -DBoost_INCLUDE_DIR=$install_top_dir/include # # -DBOOST_ROOT=$install_top_dir # -DBoost_INCLUDE_DIR=$install_top_dir/include # -DBoost_LIBRARY_DIRS=$install_top_dir/lib # -DBoost_PYTHON_LIBRARY=$install_top_dir/lib/libboost_python.$extension_type # -DBoost_REGEX_LIBRARY=$install_top_dir/lib/libboost_regex.$extension_type # catches correctly (no need to specify) # -DPYTHON_INCLUDE_DIR=$install_top_dir/include/python2.7 if [ $(uname) = Darwin ] ; then cmake_macosx_rpath=-DCMAKE_MACOSX_RPATH=ON fi # last time I looked, the include files of RDKit MolDraw2D were wrong. # I had to hack in GraphMol/MolDraw2D into include/rdkit and copy the files # there. # -- Could NOT find InChI in system locations (missing: INCHI_LIBRARY INCHI_INCLUDE_DIR) # CMake Warning at External/INCHI-API/CMakeLists.txt:43 (message): # ** NO INCHI SOFTWARE FOUND # # InChI support will be turned off. If you want to add InChI support, please # follow the instructions inside $RDBASE/External/INCHI-API/README to # download a copy of InChI software and then rerun cmake. # # http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip # now libboost_python comes with an extended name: libboost_python27 libboost_python_ext=$python_version_extension libboost_python_ext= extension_type=so if [ $(uname) = Darwin ] ; then extension_type=dylib fi echo will configure with cmake like this: # DBoost_PYTHON39_LIBRARY_RELEASE needs to be extracted? # probblem: $install_top_dir/include/boost/python/detail/wrap_python.hpp:57:23: fatal error: pyconfig.h: No such file or directory # solution: https://github.com/rdkit/rdkit/issues/3884 # -DPYTHON_INCLUDE_DIR=$PYROOT/include/python3.8 echo cmake -DBoost_NO_BOOST_CMAKE=ON \ -DBoost_INCLUDE_DIR=$install_top_dir/include \ -DPYTHON_INCLUDE_DIR=$install_top_dir/include/python$python_version_extension \ -DBoost_PYTHON39_LIBRARY_RELEASE=$install_top_dir/lib/libpython3.so \ $cmake_macosx_rpath \ -DPYTHON_EXECUTABLE=$install_top_dir/bin/python3 \ -DCMAKE_INSTALL_PREFIX=$install_top_dir \ -DRDK_BUILD_MAEPARSER_SUPPORT=OFF \ -DRDK_BUILD_CAIRO_SUPPORT=ON \ -DRDK_INSTALL_INTREE=OFF \ $tree_from_build if cmake -DBoost_NO_BOOST_CMAKE=ON \ -DBoost_INCLUDE_DIR=$install_top_dir/include \ -DPYTHON_INCLUDE_DIR=$install_top_dir/include/python$python_version_extension \ -DBoost_PYTHON39_LIBRARY_RELEASE=$install_top_dir/lib/libpython3.so \ $cmake_macosx_rpath \ -DPYTHON_EXECUTABLE=$install_top_dir/bin/python3 \ -DCMAKE_INSTALL_PREFIX=$install_top_dir \ -DRDK_BUILD_MAEPARSER_SUPPORT=OFF \ -DRDK_BUILD_CAIRO_SUPPORT=ON \ -DRDK_INSTALL_INTREE=OFF \ $tree_from_build ; then # it seems that make -j n fails to compile (race condition?) # so use just plain make? (currently not fixed) if $MAKE ; then make install else echo problem making the RDKit. exit 1 fi else echo problem configuring the RDKit. exit 1 fi cd .. cd .. ) > $HOSTLOGDIR/18-rdkit.txt 2>&1 fi fi # silicos-it's biscu-it if [ -e $install_top_dir/lib/$python_version/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/coot/qed-python3.patch pwd tar xf ${AUTOBUILD_SOURCES}/qed-1.0.1.tar.gz cd qed-1.0.1 patch -p0 < ../qed-python3.patch # correct patch level? needs checking python3 setup.py install cd - ) > $HOSTLOGDIR/19-biscu-it.txt 2>&1 fi ############################################################################### ##################### guile and friends ####################################### ############################################################################### libffi_version=3.2.1 guile_version=3.0.5 # no g-wrap for this guile_version=2.2.7 g_wrap_version=1.9.15 libtool_version=2.4.6 gmp_version=6.1.1 gmp_version=6.2.1 unistring_version=0.9.6 unistring_version=0.9.10 guile_gnome_platform_version=2.16.5 readline_version=6.3 gc_version=8.0.4 guile_cairo_version=1.9.91 # wget http://ftp.gnu.org/pub/gnu/guile-gnome/guile-gnome-platform/guile-gnome-platform-$guile_gnome_platform_version.tar.gz # wget http://savannah.nongnu.org/download/g-wrap/g-wrap-$g_wrap_version.tar.gz # wget sourceware.org:/pub/libffi/libffi-$libffi_version.tar.gz # wget ftp://ftp.gnu.org/pub/gnu/guile/guile-2.0.12.tar.gz # wget ftp://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile/guile-2.0.12.tar.gz # wget http://ftp.heanet.ie/mirrors/gnu/libtool/libtool-$libtool_version.tar.gz # wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/gmp/gmp-$gmp_version.tar.xz # wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/libunistring/libunistring-$unistring_version.tar.gz # wget http://www.hboehm.info/gc/gc_source/gc-7.2g.tar.gz # wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/readline/readline-6.3.tar.gz # wget http://download.savannah.gnu.org/releases/guile-cairo/guile-cairo-$guile_cairo_version.tar.gz build_libffi=true build_guile=true build_g_wrap=true build_gmp=true build_unistring=true build_guile_gnome_platform=true # build_readline=true build_guile_cairo=true build_guile_lib=true if [ "$build_libffi" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/lib/pkgconfig/libffi.pc ] ; then skip_this=true fi fi if [ $skip_this = false ] ; then ( echo ========================= build libffi ================================= if [ -e ${AUTOBUILD_SOURCES}/libffi-$libffi_version.tar.gz ] ; then tar xf ${AUTOBUILD_SOURCES}/libffi-$libffi_version.tar.gz else exit fi cd libffi-$libffi_version # if ./configure --prefix=$install_top_dir --disable-multi-os-directory --enable-portable-binary --enable-shared --disable-static ; then if ./configure --prefix=$install_top_dir --enable-portable-binary --enable-shared --disable-static ; then if $MAKE ; then make install fi fi cd - ) > $HOSTLOGDIR/18-ffi.txt 2>&1 fi fi if [ "$build_unistring" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/unistr.h ] ; then skip_this=true fi fi echo libunistring skip_this $skip_this if [ $skip_this = false ] ; then echo BUILDING libunistring: ( echo ========================= build unistring ================================= if [ -e $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz ] ; then tar xf $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz else echo missing file $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz ${WGET} http://mirrorservice.org/sites/ftp.gnu.org/gnu/libunistring/libunistring-$unistring_version.tar.gz tar xf $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz fi cd libunistring-$unistring_version echo ./configure --prefix=$install_top_dir if ./configure --prefix=$install_top_dir ; then if $MAKE ; then make install fi fi cd - ) > $HOSTLOGDIR/19-libubunistring.txt 2>&1 else echo not building libunistring fi fi build_gc=true if [ "$build_gc" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/gc.h ] ; then # use the right file skip_this=true fi fi if [ $skip_this = false ] ; then ( echo BUILDING libatomic-ops: if [ ! -e $AUTOBUILD_SOURCES/libatomic_ops-7.6.12.tar.gz ] ; then ${WGET} https://github.com/ivmai/libatomic_ops/releases/download/v7.6.12/libatomic_ops-7.6.12.tar.gz fi tar xf $AUTOBUILD_SOURCES/libatomic_ops-7.6.12.tar.gz cd libatomic_ops-7.6.12 ./configure --prefix=$install_top_dir $MAKE make install cd - ) > $HOSTLOGDIR/20-libatomic-ops.txt 2>&1 fi # echo gc skip_this $skip_this if [ $skip_this = false ] ; then echo BUILDING gc: ( gc_version=7.2g gc_version_dir=7.2 gc_version=7.6.12 # needs libatomic_ops. can we find a version that doesn't need that? gc_version_dir=7.6.12 # I guess not. echo ========================= build gc ================================= if [ -e $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz ] ; then echo found gc source file $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz echo tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz else echo no file $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz ${WGET} http://www.hboehm.info/gc/gc_source/gc-$gc_version.tar.gz if [ -e $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz ] ; then tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz else echo download failed for http://www.hboehm.info/gc/gc_source/gc-$gc_version.tar.gz fi fi cd gc-$gc_version_dir echo ./configure --prefix=$install_top_dir if ./configure --prefix=$install_top_dir ; then if $MAKE ; then make install fi fi cd - ) > $HOSTLOGDIR/21-gc.txt 2>&1 else echo not building gc fi fi if [ "$build_gmp" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/gmp.h ] ; then # use the right file skip_this=true fi fi fi if [ "$build_guile" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/guile/2.2/libguile.h ] ; then # use the right file skip_this=true fi fi # echo guile skip_this $skip_this if [ $skip_this = false ] ; then echo BUILDING guile: 2>& 1 echo BUILDING guile: ( echo ========================= build guile ================================= if [ -e $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz ] ; then tar xf $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz else echo no file $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz ${WGET} https://ftp.gnu.org/pub/gnu/guile/guile-$guile_version.tar.xz tar xf ${AUTOBUILD_SOURCES}/guile-$guile_version.tar.xz fi cd guile-$guile_version # LIBFFI_LIBS=-L$install_top_dir/lib # LIBFFI_CFLAGS=-I$install_top_dir/include if ./configure --prefix=$install_top_dir \ --with-libltdl-prefix=$install_top_dir \ --with-libreadline-prefix=$install_top_dir \ LIBS=-L$install_top_dir/lib CFLAGS=-I$install_top_dir/include ; then if $MAKE ; then make install # this file causes problems on linking coot if [ -e $install_top_dir/lib/libguile-2.2.so.1.4.2-gdb.scm ] ; then mv $install_top_dir/lib/libguile-2.2.so.1.4.2-gdb.scm $install_top_dir/lib/script-libguile-2.2.so.1.4.2-gdb.scm fi fi fi cd - ) > $HOSTLOGDIR/24-guile.txt 2>&1 fi fi # ------------------------------------ template ------------------------------------- if [ "$build_template_thing" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/template.h ] ; then # use the right file skip_this=true fi fi # echo template skip_this $skip_this if [ $skip_this = false ] ; then echo ========================= build template ================================= if [ -e $AUTOBUILD_SOURCES/template-$template_version.tar.gz ] ; then tar xf $AUTOBUILD_SOURCES/template-$template_version.tar.gz else exit fi ( cd template-$template_version if ./configure --prefix=$install_top_dir ; then if $MAKE ; then make install fi fi cd - ) > $HOSTLOGDIR/2x-xx.txt 2>&1 fi fi # ------------------------------------ template end ---------------------------------- if [ "$build_g_wrap" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/g-wrap/guile-runtime.h ] ; then # use the right file skip_this=true fi fi # echo g-wrap skip_this $skip_this if [ $skip_this = false ] ; then echo BUILDING g-wrap: ( echo ========================= build g-wrap ================================= if [ -e $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz ] ; then tar xf $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz else g_wrap_version=1.9.15 ${WGET} http://savannah.nongnu.org/download/g-wrap/g-wrap-$g_wrap_version.tar.gz tar xf $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz fi if [ ! -e $install_top_dir/bin/guile ] ; then echo no guile exit fi cd g-wrap-$g_wrap_version # if ./configure --prefix=$install_top_dir # LIBFFI_LIBS=-L$install_top_dir/lib # LIBFFI_CFLAGS=-I$install_top_dir/include; then if ./configure --prefix=$install_top_dir --disable-Werror ; then if $MAKE ; then make install fi fi ) > $HOSTLOGDIR/25-g-wrap.txt 2>&1 fi fi if [ "$build_guile_cairo" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/guile-cairo/guile-cairo.h ] ; then skip_this=true fi fi if [ $skip_this = false ] ; then echo BUILDING guile-cairo ( echo ========================= build guile-cairo ================================= if [ -e $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz ] ; then tar xf $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz else echo no file $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz exit fi if [ ! -e $install_top_dir/bin/guile ] ; then echo no guile exit fi cd guile-cairo-$guile_cairo_version if ./configure --prefix=$install_top_dir ; then if $MAKE ; then make install fi fi cd - ) > $HOSTLOGDIR/26-guile-cairo.txt 2>&1 fi fi # guile-lib if test -f $install_top_dir/share/guile/site/sxml/simple.scm ; then echo installation has guile-lib build_guile_lib= else build_guile_lib=1 echo guile-lib needs to be installed fi echo some test here " " if guile-config --version ; then echo guile-config found else echo no guile-config fi guile_version=$(guile-config --version |& cut -f5 -d" ") # 2.2.7 guile_major_minor=2.2 guile_lib_version=0.2.7 if [ "$build_guile_lib" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/share/guile/site/os/process.scm ] ; then skip_this=true fi fi if [ $skip_this = false ] ; then echo ========================= build guile-lib ================================= if [ -e $AUTOBUILD_SOURCES/guile-lib-$guile_lib_version.tar.gz ] ; then tar xf $AUTOBUILD_SOURCES/template-$template_version.tar.gz else exit fi ( if [ ! -e $install_top_dir/bin/guile ] ; then echo no guile exit fi cd guile-lib-$guile_lib_version # sigh. I had to delete guile-3 installation, guile and guile-config being # correct for 2.2.7 was not enough. # (this uses PKG_CONFIG_PATH) if ./configure --prefix=$install_top_dir --with-guile-site=yes ; then if $MAKE ; then make install fi fi cd - ) > $HOSTLOGDIR/27-guile-lib.txt 2>&1 fi fi if [ "$build_guile_gnome_platform" = true ] ; then skip_this=false if [ "$test_for_already_installed_dependencies" = true ] ; then if [ -e $install_top_dir/include/guile-gnome-2/guile-gnome-gobject.h ] ; then skip_this=true fi fi echo guile-gnome-platform skip_this $skip_this if [ $skip_this = false ] ; then ( echo ========================= build guile-gnome-platform ================================= if [ -e $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz ] ; then tar xf $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz else echo no file $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz exit fi cd guile-gnome-platform-$guile_gnome_platform_version if ./configure --prefix=$install_top_dir ; then if $MAKE ; then make install fi fi ) > $HOSTLOGDIR/28-guile-gnome-platform.txt 2>&1 fi fi ############################################################################### ########## Coot is now built from git repo ############# ############################################################################### # echo 222222222222222 Now Coot..... cd $start_dir date pwd if [ -e coot ] ; then ( echo CASE 1 coot directory exists pwd cd coot echo now in this dir: pwd echo 33333333333333333333333 and about to fetch and merge... git fetch if [ -e ltmain.sh ] ; then rm ltmain.sh ; fi if [ -e config.guess ] ; then rm config.guess ; fi if [ -e config.sub ] ; then rm config.sub ; fi git merge # if [ -e ltmain.sh ] ; then # rm ltmain.sh # fi echo 44444444444444444444444 done fetch and merge rm -rf autom4te.cache echo 5555555555555555555555 bash autogen.sh echo bash autogen.sh bash autogen.sh echo 66666666666666666666 done bash autogen.sh cd - ) > $HOSTLOGDIR/30-coot-fetch-merge-autogen.txt 2>&1 else echo CASE 2 coot directory not exists in $(pwd) ( save_dir=$(pwd) echo :::: $(pwd) echo cloning coot... echo :::: git clone https://github.com/pemsley/coot.git -b gtk3 echo save_ld_library_path=$LD_LIBRARY_PATH # reset LD_LIBRARY_PATH for now. Do we need it set from now on actually? export LD_LIBRARY_PATH= if git clone https://github.com/pemsley/coot.git -b gtk3 --depth 2 ; then echo git clone https://github.com/pemsley/coot.git -b gtk3 without error status echo done clone cd coot rm -rf autom4te.cache if [ -e ltmain.sh ] ; then rm ltmain.sh ; fi if [ -e config.guess ] ; then rm config.guess ; fi if [ -e config.sub ] ; then rm config.sub ; fi bash autogen.sh else echo git clone https://github.com/pemsley/coot.git -b gtk3 failed echo done clone cd coot fi LD_LIBRARY_PATH=$save_ld_library_path cd $save_dir ) > $HOSTLOGDIR/30-clone-autogen 2>&1 fi if test -n "$glib_installed" ; then coot_extra_args="$coot_extra_args --with-glib-prefix=$install_top_dir" fi if test -n "$gtk_installed" ; then coot_extra_args="$coot_extra_args --with-gtk-prefix=$install_top_dir" fi ############################################################################### ########## build Coot ############# ############################################################################### # echo BUILDING coot echo BUILDING coot 2>& 1 ( # 20091001 should not be needed. # if [ "$ENABLE_PYTHON_COOT" = "no" ] ; then # echo INFO:: not a pythonized build # cp src/blank.cc src/coot_wrap_python.cc # else # echo INFO:: A pythonized build # fi # CXXFLAGS="-g -O" # consider getting rid of $shared_static_flag, which does a --disable-shared. # i.e. we should keep and use shared libs # $architecture is not set for Mac OS X. coot_optim_args= export CXXFLAGS="-g -O " cbis_d=$(date +'%a %d %b %H%M.%S %Z %Y') coot_build_info_string="build-host: $HOST on: $cbis_d" if [ ! -z "$libintl_cflags" ] ; then CFLAGS=$libintl_cflags CPPFLAGS="$CPPFLAGS $libintl_cflags" fi cd $start_dir if [ ! -d build-coot ] ; then mkdir build-coot fi cd build-coot export LD_LIBRARY_PATH=$install_top_dir/lib64 echo From git repo now echo building in: $PWD echo CFLAGS: $CFLAGS echo CXXFLAGS: $CXXFLAGS echo CPPFLAGS: $CPPFLAGS echo LDFLAGS: $LDFLAGS echo PATH: $PATH echo PKG_CONFIG_PATH: $PKG_CONFIG_PATH # For external use, we need to have used git checkout for # the gtk3 branch, have run autogen.sh # and have placed that directory somewhere sensible relative to here echo 33333 # 20220707-PE does this improve thie linking (get pass the problem with g_module_open_full)? export LD_LIBRARY_PATH=$install_top_dir/lib # add this when then are compiling and RDKIT is compiling # --with-enhanced-ligand-tools # ---with-rdkit-prefix=$prfx echo bash ../coot/configure $coot_prefix \ --with-fftw-prefix=$install_top_dir \ COOT_BUILD_INFO_STRING="$coot_build_info_string" \ SHELL=/bin/bash \ PYTHON=python3 \ --with-boost=$install_top_dir \ --with-boost-libdir=$install_top_dir/lib \ --with-guile \ $sqlite_config_args \ $shared_static_flag \ $coot_optim_args \ $coot_extra_args \ $extra_args_for_darwin bash ../coot/configure $coot_prefix \ --with-fftw-prefix=$install_top_dir \ SHELL=/bin/bash \ PYTHON=python3 \ COOT_BUILD_INFO_STRING="$coot_build_info_string" \ --with-boost=$install_top_dir \ --with-boost-libdir=$install_top_dir/lib \ --with-guile \ $sqlite_config_args \ $shared_static_flag \ $coot_optim_args \ $coot_extra_args \ $extra_args_for_darwin $MAKE # No rule to make target 'coot.py', needed by 'all-am'. Stop. # but it's there! Timing problems? echo === make again === make status=$? if [ "$status" != 0 ] ; then echo make failed. bad_coot_make=1 exit 2 else echo 1 --------------------------------------------------------------- echo ' ' make install echo 1 ---------------------------------------------------------------- make install echo === make install again === make install # if [ "$python_scripting" = '--with-python' ] ; then # echo copying src/coot.py $install_top_dir/share/coot/python # cp src/coot.py $install_top_dir/share/coot/python # fi fi ) > $HOSTLOGDIR/30-coot.txt 2>&1 # --with-gsl-prefix=$install_top_dir \ # --with-glib-prefix=$install_top_dir \ # --with-gtk-prefix=$install_top_dir \ # --with-gtkgl-prefix=$install_top_dir \ coot_build_status=$? if [ $coot_build_status != 0 ] ; then echo coot build failed, exiting. echo fail-build $coot_revision > $LOGS/build-status my_exit 2 $coot_revision else echo coot build was good. echo pass-build $coot_revision > $LOGS/build-status fi echo done coot build. # restore a sane environment for external programs (e.g. ftp) # unset LD_LIBRARY_PATH unset CFLAGS unset CPPFLAGS unset LDFLAGS unset PKG_CONFIG_PATH # now, do we need to add the extra data files, the refmac monomer # library and the reference structures? # 20110505 we change to Garib's new dictionary #refmac_mon_lib=refmac-monomer-library-20090929.tar.gz #refmac_mon_lib=refmac-monomer-library-20091203.tar.gz # mon_lib_dir=http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental # mon_lib_dir=http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary # refmac_mon_lib=refmac_dictionary_v5.28.tar.gz # refmac_mon_lib=refmac_dictionary_v5.29.tar.gz # refmac_mon_lib=refmac_dictionary_v5.37.tar.gz # refmac_mon_lib=refmac_dictionary_v5.38.tar.gz # refmac_mon_lib=refmac_dictionary_v5.39.tar.gz # refmac_mon_lib=refmac_dictionary_v5.41.tar.gz # new style mon_lib_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies refmac_mon_lib=refmac-monomer-library.tar.gz if [ -e $install_top_dir/share/coot/lib/data/monomers ] ; then echo INFO:: installation has refmac monomer library else echo INSTALLING refmac monomer library... echo INSTALLING refmac monomer library... >&2 $WGET $mon_lib_dir/$refmac_mon_lib mkdir -p $install_top_dir/share/coot/lib/data tar xzCf $install_top_dir/share/coot/lib/data $AUTOBUILD_SOURCES/$refmac_mon_lib fi if [ -e $install_top_dir/share/coot/reference-structures ] ; then echo INFO:: installation has reference structures else echo GETTING reference structures tar... echo GETTING reference structures tar... >&2 ${WGET} $extras_place/reference-structures.tar.gz if [ -e $AUTOBUILD_SOURCES/reference-structures.tar.gz ] ; then echo INSTALLING reference structures... tar xzCf $install_top_dir/share/coot $AUTOBUILD_SOURCES/reference-structures.tar.gz else echo FAIL wget for reference-structures.tar.gz failed. fi fi # clear up the library dependencies if [ "$build_coot_prerelease" = 1 ] ; then pre_release_str=-pre-release fi clear_up_type= if [ $shared_static_flag != "--disable-static" ] ; then clear_up_type=clear-static fi if [ $shared_static_flag != "--disable-shared" ] ; then clear_up_type=clear-dynamic fi if [ $clear_up_type != "" ] ; then if [ "$ENABLE_PYTHON_COOT" = "yes" ] ; then slim_dir=$(dirname $install_top_dir)/coot-${OS}-${systype}${pre_release_str}-${build_type}-python else slim_dir=$(dirname $install_top_dir)/coot-${OS}-${systype}${pre_release_str}-$build_type fi echo post-install slim... >&2 post_install_slim $install_top_dir $slim_dir $clear_up_type fi # clean up old status: if [ -e $LOGS/test-status ] ; then rm $LOGS/test-status fi if [ "$run_tests" = true ] ; then # run test echo running tests: echo running tests: >&2 if [ "$ENABLE_GUILE_COOT" = "yes" ] ; then echo running first test... >&2 test_coot > $LOGS/test.log 2>&1 r=$? else r=0 fi # run python tests too, maybe (i.e. if we build with python) if [ "$ENABLE_PYTHON_COOT" = "yes" ] ; then echo running python test... >&2 test_coot_python > $LOGS/test-python.log 2>&1 rp=$? else rp=0 fi # all gtk3 versions have python. No need for the python tag then if ( [ $r = 0 ] && [ $rp = 0 ] ); then echo ======================== echo ' ' first coot test passed echo ' ' first coot test passed >&2 echo ========----============ echo pass-test > $LOGS/test-status if test "$do_nightlies" = "1" ; then if [ -d $BINARY_TAR_DEST_DIR ] ; then if [ ! -d $BINARY_TAR_DEST_DIR/holding ] ; then echo WARNING:: holding directory $BINARY_TAR_DEST_DIR/holding does not exist. else # regular path # original full fat: # make_tar `basename $install_top_dir` $BINARY_TAR_DEST_DIR/${coot_version}-binary-full-${OS}-${systype}${python_tag}${gtk2}.tar.gz # slimmed: bin_tar_file=$BINARY_TAR_DEST_DIR/${coot_version}-binary-${OS}-${systype}${gtk_version}.tar.gz holding_tar_file=$BINARY_TAR_DEST_DIR/holding/${coot_version}-binary-${OS}-${systype}${gtk_version}.tar.gz make_tar $(basename $slim_dir) $holding_tar_file # Now test the tar file by un-taring it and running the # tests. Only if this test passes can we move tar file # from holding to the binary pre-release dir. if [ $run_second_test = true ] ; then cd "$build_dir" mkdir test-tar cd test-tar tar xzf $holding_tar_file echo cding into `basename $slim_dir` from `pwd` cd `basename $slim_dir` echo ln -s ../../$coot_dir_name/greg-tests . ln -s ../../$coot_dir_name/greg-tests . echo second coot test... echo running second test... >&2 test_coot bin/coot > $LOGS/test-2.log 2>&1 test2_status=$? else test2_status=0 # success fi if [ $test2_status = 0 ] ; then echo ======================== echo second coot test passed echo second coot test passed >&2 echo ======================== echo pass-2nd-test > $LOGS/test-status mv $holding_tar_file $bin_tar_file mv $holding_tar_file.md5sum $bin_tar_file.md5sum # update the description of the latest binary tar file for # this build-type. binary_type_latest=$BINARY_TAR_DEST_DIR/type-binary-${OS}-${systype}${gtk_version}-latest.txt echo $coot_version > $binary_type_latest # update the ChangeLog, README and RELEASE-NOTES cd "$build_dir" cd $coot_dir_name echo INFO:: in "$build_dir"/$coot_dir_name and about to copy over README and RELEASE-NOTES to $BINARY_TAR_DEST_DIR cp ChangeLog $BINARY_TAR_DEST_DIR cp README coot-README cp README $BINARY_TAR_DEST_DIR/coot-README cp RELEASE-NOTES $BINARY_TAR_DEST_DIR/${coot_version}-RELEASE-NOTES cp RELEASE-NOTES $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES echo about to publish files: echo about to publish files: >&2 # only copy over the binary files if they are not there # already (checked by publish executable). # # reading the git logs adding $BINARY_TAR_DEST_DIR seems to have fixed something. # Now, the transfer-to-web-server.sh scripts take the second arg # and munge it to be the correct directory for the binary (and .txt) files. echo $publish $bin_tar_file $BINARY_TAR_DEST_DIR $publish $bin_tar_file $BINARY_TAR_DEST_DIR echo $publish $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR $publish $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR # echo $publish $binary_type_latest # publish $binary_type_latest echo $publish --no-server-check ChangeLog $publish --no-server-check ChangeLog echo $publish --no-server-check coot-README $publish --no-server-check coot-README if [ -z "$build_coot_prerelease" ] ; then echo $publish --no-server-check RELEASE-NOTES $publish --no-server-check RELEASE-NOTES else echo $publish --no-server-check $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES $publish --no-server-check $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES fi echo done copy of README and RELEASE-NOTES else echo ======================== echo second coot test failed echo second coot test failed >& 2 echo ======================== echo fail-2nd-test $date > $LOGS/test-status fi fi else echo Directory for binaries $BINARY_TAR_DEST_DIR does not exist. echo Skipping tar. fi else echo not doing tar files for nightlies: $do_nightlies fi else echo ======================== echo ' ' first coot test failed echo ' ' first coot test failed >&2 echo ======================== echo greg test status: $r echo python test status: $rp if [ $r = 0 ] ; then echo fail-test greg $date > $LOGS/test-status else if [ $rp = 0 ] ; then echo fail-test python $date > $LOGS/test-status else # this should not happen, AFAICS. echo fail-test $date > $LOGS/test-status fi fi fi fi $publish_logs $LOGS echo finished. echo finished.>&2