diff options
| -rw-r--r-- | .SRCINFO | 38 | ||||
| -rw-r--r-- | PKGBUILD | 73 | ||||
| -rw-r--r-- | coot-0.8.2-desktop.patch | 21 | ||||
| -rw-r--r-- | coot-0.8.2-libtool.patch | 39 | ||||
| -rw-r--r-- | coot-0.8.2-sandbox-icons.patch | 16 | ||||
| -rw-r--r-- | coot-configure.ac.patch | 28 | ||||
| -rw-r--r-- | coot-guile.patch (renamed from coot-0.8.2-guile.patch) | 0 | ||||
| -rw-r--r-- | coot-lbg.patch | 11 | ||||
| -rw-r--r-- | coot-libguile.patch (renamed from coot-0.8.2-libguile.patch) | 0 | ||||
| -rw-r--r-- | coot-lidia.patch | 10 | ||||
| -rw-r--r-- | coot-makefile.patch | 35 | ||||
| -rw-r--r-- | coot-python.patch (renamed from coot-0.8.2-python.patch) | 0 | ||||
| -rw-r--r-- | coot-rdkit.patch | 11 | ||||
| -rw-r--r-- | coot-utils.patch | 20 |
14 files changed, 180 insertions, 122 deletions
@@ -1,9 +1,9 @@ # Generated by mksrcinfo v8 -# Tue Jan 12 02:54:27 UTC 2016 +# Thu Jun 15 19:28:55 UTC 2017 pkgbase = coot pkgdesc = Crystallographic Object-Oriented Toolkit for model building, completion and validation - pkgver = 0.8.2 - pkgrel = 2 + pkgver = 0.8.8 + pkgrel = 1 url = http://lmb.bioch.ox.ac.uk/coot/ arch = i686 arch = x86_64 @@ -33,20 +33,28 @@ pkgbase = coot depends = which depends = bc depends = sqlite - source = http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.8.2.tar.gz - source = coot-0.8.2-desktop.patch - source = coot-0.8.2-libguile.patch - source = coot-0.8.2-libtool.patch - source = coot-0.8.2-sandbox-icons.patch - source = coot-0.8.2-python.patch - source = coot-0.8.2-guile.patch - sha256sums = 2f5961ded7f2cf06b887560afe964c239aba94f9c4bf8a2a80b3ca4fbc471eee - sha256sums = 6558c17da028f47bec3480afbf85d8457e4c34bb50a6285bf0522de922a6bc89 + depends = rdkit + depends = mmdb2>=2.0.12-4 + source = http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.8.8.tar.gz + source = coot-configure.ac.patch + source = coot-makefile.patch + source = coot-guile.patch + source = coot-libguile.patch + source = coot-utils.patch + source = coot-rdkit.patch + source = coot-lbg.patch + source = coot-python.patch + source = coot-lidia.patch + sha256sums = df31ab66d7c3de6524fefcafaab6acc11e4525b930fed3b929ed773ae1776aa7 + sha256sums = 2babfbc3cb798868d9e22f19ee49d12981fac35e3dfba2d8f7318716f59f673c + sha256sums = 9ad5a56116748ab5b1f77b2a4b2e3df47847ff881579105dff6589ed60ac8eb4 + sha256sums = c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911 sha256sums = aa1e18d4ef43fb61e85aba05d13797f9aa2beb1da220405f1eb6058ac36eb60b - sha256sums = e4ba02ad24330e3df3f32772275db47caeb4f36d77d57de882f7a73d7e11e5bf - sha256sums = b93756a9ab1244573ac24427954c53ac9f14a82e7ec1f115b178897abcab42a8 + sha256sums = 059d57dc092feb8134a95e6fa452a2d807ccb3666da374f4a023e5684e3a0dfa + sha256sums = 8b1c499ce5d506419ca72f999b6a0332a2edcc30e3128b1eb0bd3d399d0d80a6 + sha256sums = 423a50d27639376c52e6987877acea908d854decb48c7c2452f7f5ecb92b60e9 sha256sums = f4747e1fc7a3387f42b6c40358f999404761a0282ee6be3c621091d9d5d88099 - sha256sums = c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911 + sha256sums = dd2eb7c66ff2fa6f68a9d1e834e1911d2a1669a76ed29b5dbd6863619edcba18 pkgname = coot @@ -1,20 +1,24 @@ # Maintainer: Alexander Minges <alexander.minges@gmail.com> pkgname=coot -pkgver=0.8.2 -pkgrel=2 +pkgver=0.8.8 +pkgrel=1 pkgdesc="Crystallographic Object-Oriented Toolkit for model building, completion and validation" arch=('i686' 'x86_64') url="http://lmb.bioch.ox.ac.uk/coot/" license=('GPL') depends=('guile1.8' 'guile1.8-lib' 'guile1.8-gtk' 'guile1.8-gui' 'gtkglext' 'libccp4' 'clipper' 'goocanvas1' 'gsl' 'libgnomecanvas' 'imlib' 'swig' - 'freeglut' 'libgl' 'gtk2' 'cairo' 'libssm>=1.4' 'zlib' 'curl' 'python2' 'pygtk' 'gtkglarea' 'which' 'bc' 'sqlite') + 'freeglut' 'libgl' 'gtk2' 'cairo' 'libssm>=1.4' 'zlib' 'curl' 'python2' 'pygtk' 'gtkglarea' 'which' 'bc' 'sqlite' 'rdkit' 'mmdb2>=2.0.12-4') source=(http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/$pkgname-$pkgver.tar.gz - coot-0.8.2-desktop.patch - coot-0.8.2-libguile.patch - coot-0.8.2-libtool.patch - coot-0.8.2-sandbox-icons.patch - coot-0.8.2-python.patch - coot-0.8.2-guile.patch) + coot-configure.ac.patch + coot-makefile.patch + coot-guile.patch + coot-libguile.patch + coot-utils.patch + coot-rdkit.patch + coot-lbg.patch + coot-python.patch + coot-lidia.patch + ) # coot-configure.in.patch # coot-user-manual.texi.patch # coot-makefile.patch @@ -22,37 +26,43 @@ source=(http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/$pkg # coot-python.patch # coot-icons.patch # coot-lidia.patch) -sha256sums=('2f5961ded7f2cf06b887560afe964c239aba94f9c4bf8a2a80b3ca4fbc471eee' - '6558c17da028f47bec3480afbf85d8457e4c34bb50a6285bf0522de922a6bc89' +sha256sums=('df31ab66d7c3de6524fefcafaab6acc11e4525b930fed3b929ed773ae1776aa7' + '2babfbc3cb798868d9e22f19ee49d12981fac35e3dfba2d8f7318716f59f673c' + '9ad5a56116748ab5b1f77b2a4b2e3df47847ff881579105dff6589ed60ac8eb4' + 'c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911' 'aa1e18d4ef43fb61e85aba05d13797f9aa2beb1da220405f1eb6058ac36eb60b' - 'e4ba02ad24330e3df3f32772275db47caeb4f36d77d57de882f7a73d7e11e5bf' - 'b93756a9ab1244573ac24427954c53ac9f14a82e7ec1f115b178897abcab42a8' + '059d57dc092feb8134a95e6fa452a2d807ccb3666da374f4a023e5684e3a0dfa' + '8b1c499ce5d506419ca72f999b6a0332a2edcc30e3128b1eb0bd3d399d0d80a6' + '423a50d27639376c52e6987877acea908d854decb48c7c2452f7f5ecb92b60e9' 'f4747e1fc7a3387f42b6c40358f999404761a0282ee6be3c621091d9d5d88099' - 'c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911') + 'dd2eb7c66ff2fa6f68a9d1e834e1911d2a1669a76ed29b5dbd6863619edcba18') build() { cd "$srcdir/$pkgname-$pkgver" - - patch -Np1 -i "$srcdir/coot-0.8.2-desktop.patch" - patch -Np1 -i "$srcdir/coot-0.8.2-libguile.patch" - patch -Np1 -i "$srcdir/coot-0.8.2-libtool.patch" - patch -Np1 -i "$srcdir/coot-0.8.2-sandbox-icons.patch" - patch -Np0 -i "$srcdir/coot-0.8.2-python.patch" - patch -Np0 -i "$srcdir/coot-0.8.2-guile.patch" - + + patch -Np0 -i "$srcdir/coot-configure.ac.patch" + patch -Np0 -i "$srcdir/coot-makefile.patch" + patch -Np0 -i "$srcdir/coot-guile.patch" + patch -Np1 -i "$srcdir/coot-libguile.patch" + patch -Np0 -i "$srcdir/coot-utils.patch" + patch -Np0 -i "$srcdir/coot-rdkit.patch" + patch -Np0 -i "$srcdir/coot-lbg.patch" + patch -Np0 -i "$srcdir/coot-python.patch" + patch -Np0 -i "$srcdir/coot-lidia.patch" + + iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README - + aclocal -I macros libtoolize --automake --copy autoconf automake --copy --add-missing --gnu - + # Work around coot's code not beeing completely standart compliant CXXFLAGS="${CXXFLAGS} -fpermissive" - + ./configure --prefix=/usr \ - --without-guile \ --with-python \ --with-guile \ --with-guile-gtk \ @@ -60,7 +70,8 @@ build() { --with-sqlite3 \ --with-boost \ --with-boost-python \ - --disable-static + --disable-static \ + --with-enhanced-ligand-tools RDKIT_LIBS="-lRDKitMolDraw2D -lRDKitForceFieldHelpers -lRDKitDescriptors -lRDKitForceField -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDistGeomHelpers -lRDKitDistGeometry -lRDKitAlignment -lRDKitEigenSolvers -lRDKitDepictor -lRDKitMolChemicalFeatures -lRDKitFileParsers -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7" RDKIT_CXXFLAGS="-I/usr/include/rdkit" make @@ -73,12 +84,12 @@ build() { # patch -Np0 -i "$srcdir/coot-lidia.patch" # iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README -# +# # aclocal -I macros # libtoolize --automake --copy # autoconf # automake --copy --add-missing --gnu -# +# # CXXFLAGS="${CXXFLAGS} -fpermissive" # CFLAGS="${CFLAGS} -fpermissive" # @@ -88,11 +99,11 @@ build() { # --with-python \ # --with-pygtk \ # --disable-static -# +# # make } package() { cd "$srcdir/$pkgname-$pkgver" make DESTDIR="$pkgdir/" install -} +} diff --git a/coot-0.8.2-desktop.patch b/coot-0.8.2-desktop.patch deleted file mode 100644 index c264dd5a7628..000000000000 --- a/coot-0.8.2-desktop.patch +++ /dev/null @@ -1,21 +0,0 @@ - coot.desktop | 7 +++---- - 1 file changed, 3 insertions(+), 4 deletions(-) - -diff --git a/coot.desktop b/coot.desktop -index 74aecf3..8668018 100644 ---- a/coot.desktop -+++ b/coot.desktop -@@ -1,10 +1,9 @@ - [Desktop Entry] - Type=Application --Encoding=UTF-8 - Name=Coot - Comment=Macromolecular model builder - Exec=coot --Icon=coot.png -+Icon=coot - Terminal=true --Categories=Science;Graphics --MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile -+Categories=Science;Graphics; -+MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile; diff --git a/coot-0.8.2-libtool.patch b/coot-0.8.2-libtool.patch deleted file mode 100644 index 10c43ad55594..000000000000 --- a/coot-0.8.2-libtool.patch +++ /dev/null @@ -1,39 +0,0 @@ - configure.ac | 2 +- - lbg/Makefile.am | 11 ----------- - 2 files changed, 1 insertion(+), 12 deletions(-) - -diff --git a/configure.ac b/configure.ac -index 73d6ed7..b04dcd6 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB - - AC_SUBST(COOT_STDTYPES) - --EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec -+eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\" - AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC) - - -diff --git a/lbg/Makefile.am b/lbg/Makefile.am -index 1277afe..a79ebe0 100644 ---- a/lbg/Makefile.am -+++ b/lbg/Makefile.am -@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh flev-annotations.hh graphics-c-interfa - lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh - pkgincludedir = $(includedir)/coot/lbg - --# 20140521 --# lidia_LDFLAGS = -Wl,--export-dynamic --# --# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic --# (but not for MacOSX, where it Does The Right Thing (hopefully)). --# We manually set the value of wl here, but maybe the Right Thing To Do for that is --# run (eval) $($LIBTOOL --config | grep ^wl). How do I do that here though? --# I don't understand. Maybe the setting of wl should be done in configure? But then --# I have to force the output of libtool. Bleugh. Hmm... --# Anyway, thankyou Gary Vaughan. --wl=-Wl, - lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC) - - # res spec output operator means we include libcoot-coord-utils diff --git a/coot-0.8.2-sandbox-icons.patch b/coot-0.8.2-sandbox-icons.patch deleted file mode 100644 index 2a9ff2d7177c..000000000000 --- a/coot-0.8.2-sandbox-icons.patch +++ /dev/null @@ -1,16 +0,0 @@ - pixmaps/icons/Makefile.am | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am -index 0c183ae..dddc11a 100644 ---- a/pixmaps/icons/Makefile.am -+++ b/pixmaps/icons/Makefile.am -@@ -11,6 +11,6 @@ install-data-local: - CONTEXT=` echo $$icon | cut -d_ -f2`; \ - SIZE=` echo $$icon | cut -d_ -f3`; \ - ICONFILE=`echo $$icon | cut -d_ -f4`; \ -- mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ -- $(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ -+ mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ -+ $(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ - done; diff --git a/coot-configure.ac.patch b/coot-configure.ac.patch new file mode 100644 index 000000000000..54ea352f0536 --- /dev/null +++ b/coot-configure.ac.patch @@ -0,0 +1,28 @@ +--- configure.ac.orig 2016-12-30 12:57:26.843081999 -0500 ++++ configure.ac 2016-12-30 12:58:11.963460565 -0500 +@@ -45,11 +45,11 @@ + + # AC_PROG_INTLTOOL, no, not today. Mac compilation problems, no perl/ XML or something. + # BL says Lets do some testing and use old style if needed +-AC_MSG_CHECKING([which libtool initialization strategy to adopt]) +-AC_MSG_RESULT([m4_ifset([LT_INIT],[LT-INIT],[AC-PROG-LIBTOOL])]) +-m4_ifset([LT_INIT], +-[LT_INIT], +-[AC_PROG_LIBTOOL]) ++# AC_MSG_CHECKING([which libtool initialization strategy to adopt]) ++# AC_MSG_RESULT([m4_ifset([LT_INIT],[LT-INIT],[AC-PROG-LIBTOOL])]) ++# m4_ifset([LT_INIT], ++# [LT_INIT], ++# [AC_PROG_LIBTOOL]) + + GNOME_COMPILE_WARNINGS + GNOME_CXX_WARNINGS +@@ -148,7 +148,7 @@ + AM_WITH_GUILE(, [echo optional guile\?],,) + if test x$coot_guile = xtrue ; then + GUILE_FLAGS +- AM_GUILE_LIB ++ # AM_GUILE_LIB + # guile-gui depends on a gui interface being present. If it is, force check for guile-gui + if test x$with_guile_gtk != x ; then + AM_GUILE_GUI diff --git a/coot-0.8.2-guile.patch b/coot-guile.patch index 44dd1462a020..44dd1462a020 100644 --- a/coot-0.8.2-guile.patch +++ b/coot-guile.patch diff --git a/coot-lbg.patch b/coot-lbg.patch new file mode 100644 index 000000000000..312737bc5c63 --- /dev/null +++ b/coot-lbg.patch @@ -0,0 +1,11 @@ +--- lbg/lbg.cc_orig 2016-11-09 21:27:32.074363190 -0500 ++++ lbg/lbg.cc 2016-11-09 21:27:47.836327788 -0500 +@@ -4873,7 +4873,7 @@ + } + } else { + +- PyObject *pName = PyString_FromString("lidia.fetch"); ++ PyObject *pName = PyString_FromString("coot.lidia.fetch"); + PyObject *pModule = PyImport_Import(pName); + if (pModule == NULL) { + std::cout << "NULL pModule" << std::endl; diff --git a/coot-0.8.2-libguile.patch b/coot-libguile.patch index cbaccefb2947..cbaccefb2947 100644 --- a/coot-0.8.2-libguile.patch +++ b/coot-libguile.patch diff --git a/coot-lidia.patch b/coot-lidia.patch new file mode 100644 index 000000000000..aeb0c933ef71 --- /dev/null +++ b/coot-lidia.patch @@ -0,0 +1,10 @@ +--- lidia-core/use-rdkit.hh.old 2017-06-15 20:46:21.245950862 +0200 ++++ lidia-core/use-rdkit.hh 2017-06-15 20:46:28.492679795 +0200 +@@ -5,6 +5,7 @@ + #include <vector> + #include <algorithm> + #include <string> ++#include <queue> + + #ifndef WINDOWS_MINGW + #define ENABLE_NLS // fixes dcgettext() header problems on including diff --git a/coot-makefile.patch b/coot-makefile.patch new file mode 100644 index 000000000000..316e0446e83b --- /dev/null +++ b/coot-makefile.patch @@ -0,0 +1,35 @@ +--- src/Makefile.am_orig 2016-11-09 16:13:53.942706012 -0500 ++++ src/Makefile.am 2016-11-09 16:15:08.263956290 -0500 +@@ -457,7 +457,9 @@ + EXTRA_DIST += coot_wrap_python_pre.cc + endif + if COOT_USE_PYTHON +- dist_python_PYTHON = coot.py coot.pth ++ # dist_python_PYTHON = coot.py coot.pth ++ pythondir = $(pkgdatadir)/python ++ dist_pkgpython_SCRIPTS = coot.py + endif + + +--- lbg/Makefile.am_orig 2016-11-09 16:46:09.161705178 -0500 ++++ lbg/Makefile.am 2016-11-09 21:51:45.630944576 -0500 +@@ -73,8 +73,8 @@ + # I don't understand. Maybe the setting of wl should be done in configure? But then + # I have to force the output of libtool. Bleugh. Hmm... + # Anyway, thankyou Gary Vaughan. +-wl=-Wl, +-lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC) ++# wl=-Wl, ++# lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC) + + # res spec output operator means we include libcoot-coord-utils + # (if that is annoying, then remove it and expand it by hand) +@@ -106,7 +106,7 @@ + test_srs_standalone_SOURCES = test-srs-standalone.cc + test_srs_standalone_LDADD = $(CCP4SRS_LIBS) $(MMDB_LIBS) + +-pkgpythondir=$(pythondir)/lidia ++pkgpythondir=$(pythondir)/coot/lidia + + dist_pkgpython_PYTHON = \ + __init__.py fetch.py diff --git a/coot-0.8.2-python.patch b/coot-python.patch index f163ed7b794b..f163ed7b794b 100644 --- a/coot-0.8.2-python.patch +++ b/coot-python.patch diff --git a/coot-rdkit.patch b/coot-rdkit.patch new file mode 100644 index 000000000000..d88e90961254 --- /dev/null +++ b/coot-rdkit.patch @@ -0,0 +1,11 @@ +--- lbg/lbg-search.cc_orig 2016-11-09 18:29:44.870809951 -0500 ++++ lbg/lbg-search.cc 2016-11-09 18:42:43.549933656 -0500 +@@ -34,7 +34,7 @@ + #include "geometry/srs-interface.hh" + #ifdef RDKIT_HAS_CAIRO_SUPPORT + #include <cairo.h> +-#include <MolDraw2DCairo.h> ++#include <GraphMol/MolDraw2D/MolDraw2DCairo.h> + #include "lidia-core/rdkit-interface.hh" + #else + #include "lidia-core/rdkit-interface.hh" diff --git a/coot-utils.patch b/coot-utils.patch new file mode 100644 index 000000000000..6342f93a7952 --- /dev/null +++ b/coot-utils.patch @@ -0,0 +1,20 @@ +--- coot-utils/coot-shelx.hh_orig 2016-04-07 22:05:10.753625059 -0400 ++++ coot-utils/coot-shelx.hh 2016-04-07 22:05:43.366973568 -0400 +@@ -33,6 +33,7 @@ + + #include <mmdb2/mmdb_manager.h> + #include "clipper/core/cell.h" ++#include "coot-coord-utils.hh" + + namespace coot { + +--- coot-utils/coot-hole.hh_orig 2016-04-07 22:05:55.561054355 -0400 ++++ coot-utils/coot-hole.hh 2016-04-07 22:06:16.954432665 -0400 +@@ -4,6 +4,7 @@ + #include "clipper/core/xmap.h" + #include "clipper/core/nxmap.h" + ++#include "coot-map-utils.hh" + #include "utils/coot-utils.hh" + #include "geometry/protein-geometry.hh" + |