From fb08c80032540e0ca37f049cebc368c289338d62 Mon Sep 17 00:00:00 2001 From: Till Maas Date: Tue, 31 May 2016 23:18:48 +0200 Subject: [PATCH 1/7] 2016-05-31: Retired because of broken deps in preparation of Fedora 24 Reference: https://fedorahosted.org/rel-eng/ticket/6416 --- .gitignore | 14 -- __init__.py | 1 - coot-appdata.patch | 24 --- coot-configure.ac.patch | 11 -- coot-guile.patch | 27 --- coot-makefile.patch | 43 ----- coot-unistd.patch | 12 -- coot-user-manual.texi.patch | 33 ---- coot-utils.patch | 31 ---- coot.desktop | 10 -- coot.in | 62 ------- coot.png | Bin 1271 -> 0 bytes coot.spec | 349 ------------------------------------ dead.package | 3 + sources | 2 - 15 files changed, 3 insertions(+), 619 deletions(-) delete mode 100644 .gitignore delete mode 100644 __init__.py delete mode 100644 coot-appdata.patch delete mode 100644 coot-configure.ac.patch delete mode 100644 coot-guile.patch delete mode 100644 coot-makefile.patch delete mode 100644 coot-unistd.patch delete mode 100644 coot-user-manual.texi.patch delete mode 100644 coot-utils.patch delete mode 100644 coot.desktop delete mode 100755 coot.in delete mode 100644 coot.png delete mode 100644 coot.spec create mode 100644 dead.package delete mode 100644 sources diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 576b573..0000000 --- a/.gitignore +++ /dev/null @@ -1,14 +0,0 @@ -coot-0.6.1-20100127svn2740.tar.gz -coot-reference-structures.tar.gz -/coot-reference-structures.tar.gz -/coot-0.6.2-20101012svn3213.tar.gz -/coot-0.6.2-20110225svn3399.tar.gz -/coot-0.6.2-20110328svn3442.tar.gz -/coot-0.6.2-20110421svn3461.tar.gz -/coot-0.6.2-20110715svn3566.tar.gz -/coot-0.7-20120929svn4458.tar.gz -/coot-0.7-20120929svn4458.tar.xz -/coot-0.7.2.tar.gz -/reference-structures.tar.gz -/coot-0.8.1.tar.gz -/coot-0.8.2.tar.gz diff --git a/__init__.py b/__init__.py deleted file mode 100644 index 83d04e7..0000000 --- a/__init__.py +++ /dev/null @@ -1 +0,0 @@ -# File to allow this directory to be treated as a python package. diff --git a/coot-appdata.patch b/coot-appdata.patch deleted file mode 100644 index d472d3d..0000000 --- a/coot-appdata.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- coot.appdata.xml_orig 2015-06-28 23:45:07.527132520 -0400 -+++ coot.appdata.xml 2015-06-29 23:44:38.374147150 -0400 -@@ -1,10 +1,11 @@ - - -- -- Coot.desktop -+ -+ coot.desktop - GFDL-1.3 -- GPL-2.0+ and GPL-3.0+ and LGPL-3.0+ -- Macromolecular model builder -+ GPLv3+ and LGPLv2+ -+ Coot -+ Protein model building and validation for X-ray crystallographic data - -

- Coot is a powerful macromolecular model-building tool for -@@ -26,4 +27,4 @@ - - http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ - pemsley _at_ mrc dash lmb.cam.ac.uk -- -+ diff --git a/coot-configure.ac.patch b/coot-configure.ac.patch deleted file mode 100644 index c9a35b3..0000000 --- a/coot-configure.ac.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- configure.ac_orig 2015-01-31 15:55:07.102736249 -0500 -+++ configure.ac 2015-02-01 13:23:47.715379636 -0500 -@@ -135,7 +135,7 @@ - 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-guile.patch b/coot-guile.patch deleted file mode 100644 index e79a6a9..0000000 --- a/coot-guile.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- macros/guile_orig.m4 2013-07-31 00:25:19.715073145 -0700 -+++ macros/guile.m4 2013-07-31 00:27:01.763927099 -0700 -@@ -72,21 +72,21 @@ - # The variables are marked for substitution, as by @code{AC_SUBST}. - # - AC_DEFUN([GUILE_PROGS], -- [AC_PATH_PROG(GUILE,guile) -+ [AC_PATH_PROG(GUILE,guile1.8) - if test x$with_guile = xyes ; then - if test "$GUILE" = "" ; then - AC_MSG_ERROR([guile required but not found]) - fi - fi - AC_SUBST(GUILE) -- AC_PATH_PROG(GUILE_CONFIG,guile-config) -+ AC_PATH_PROG(GUILE_CONFIG,guile1.8-config) - if test x$with_guile = xyes ; then - if test "$GUILE_CONFIG" = "" ; then - AC_MSG_ERROR([guile-config required but not found]) - fi - fi - AC_SUBST(GUILE_CONFIG) -- AC_PATH_PROG(GUILE_TOOLS,guile-tools) -+ AC_PATH_PROG(GUILE_TOOLS,guile1.8-tools) - AC_SUBST(GUILE_TOOLS) - ]) - diff --git a/coot-makefile.patch b/coot-makefile.patch deleted file mode 100644 index 2188a96..0000000 --- a/coot-makefile.patch +++ /dev/null @@ -1,43 +0,0 @@ ---- src/Makefile.am_orig 2015-06-29 23:10:49.500572880 -0400 -+++ src/Makefile.am 2015-06-29 23:11:33.041822617 -0400 -@@ -27,9 +27,8 @@ - #__init__.py: coot.py - # cp coot.py __init__.py - -- --dist_python_SCRIPTS = coot.py coot.pth -- -+pythondir = $(pkgdatadir)/python -+dist_pkgpython_SCRIPTS = coot.py - - endif - ---- pixmaps/icons/Makefile.am_orig 2015-06-29 23:11:55.713911249 -0400 -+++ pixmaps/icons/Makefile.am 2015-06-29 23:26:22.902239461 -0400 -@@ -11,6 +11,6 @@ - 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; ---- lbg/Makefile.am_orig 2015-09-24 23:04:49.843200580 -0400 -+++ lbg/Makefile.am 2015-09-24 23:10:03.355713678 -0400 -@@ -1,4 +1,3 @@ -- - lib_LTLIBRARIES=libcoot-lidia.la - - AM_CPPFLAGS = \ -@@ -53,8 +52,8 @@ - # 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) diff --git a/coot-unistd.patch b/coot-unistd.patch deleted file mode 100644 index a91efcb..0000000 --- a/coot-unistd.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- utils/coot-utils.cc_orig 2012-09-29 19:16:39.050470149 -0700 -+++ utils/coot-utils.cc 2012-09-29 19:18:01.609169266 -0700 -@@ -48,9 +48,7 @@ - - #include // for mkdir - #include --#if defined WINDOWS_MINGW - #include // BL says: in windows needed for mkdir --#endif // MINGW - - // #include "clipper/core/hkl_compute.h" - diff --git a/coot-user-manual.texi.patch b/coot-user-manual.texi.patch deleted file mode 100644 index c4ad336..0000000 --- a/coot-user-manual.texi.patch +++ /dev/null @@ -1,33 +0,0 @@ ---- doc/coot-user-manual.texi_orig 2013-12-27 15:59:56.897931023 -0800 -+++ doc/coot-user-manual.texi 2013-12-27 16:22:22.207559590 -0800 -@@ -47,7 +47,7 @@ - - @vskip 10mm - --@image{coot-plain-2,127mm} -+@c @image{coot-plain-2,127mm} - - - @c The following two commands start the copyright page. -@@ -4951,10 +4951,10 @@ - @c note that texi2html (and makeinfo) requires that this c-interface texi file be in the - @c same directory as this file (user-manual.texi) NOT the directory that - @c texi2html is run in. --@include c-interface.h.texi -+@c @include c-interface.h.texi - @node More Scripting Functions - @chapter More Scripting Functions --@include cc-interface.hh.texi -+@c @include cc-interface.hh.texi - - - -@@ -4972,7 +4972,7 @@ - @c nodes (mutate, povray) and (e.g.) `tips-gui', but has no menu entry for this node - @c - --@include coot-scheme-functions.texi -+@c @include coot-scheme-functions.texi - - - diff --git a/coot-utils.patch b/coot-utils.patch deleted file mode 100644 index 458835e..0000000 --- a/coot-utils.patch +++ /dev/null @@ -1,31 +0,0 @@ ---- coot-utils/Makefile.am_orig 2015-09-24 22:00:00.826912149 -0400 -+++ coot-utils/Makefile.am 2015-09-24 22:02:42.329117367 -0400 -@@ -116,7 +116,7 @@ - - - # test-agg-clust --check_PROGRAMS = test-h-bonds testshelxreader testcootutils test-hole test-elastic test-spherical glyco-torsions test-tt-morph -+check_PROGRAMS = test-h-bonds testshelxreader testcootutils test-hole test-elastic test-spherical glyco-torsions - - # testshelxreader fails to link for some reason! coot::protein_geometry::get_h_bond_type - # testcootutils also. 20100812 Fixed now - added libcoot-geometry.la ---- coot-utils/coot-shelx.hh_orig 2015-09-24 22:00:31.889296059 -0400 -+++ coot-utils/coot-shelx.hh 2015-09-24 22:01:54.006864161 -0400 -@@ -33,6 +33,7 @@ - - #include - #include "clipper/core/cell.h" -+#include "coot-coord-utils.hh" - - namespace coot { - ---- coot-utils/coot-hole.hh_orig 2015-09-24 22:00:39.574533094 -0400 -+++ coot-utils/coot-hole.hh 2015-09-24 22:02:06.645417847 -0400 -@@ -3,6 +3,7 @@ - #include "clipper/core/coords.h" - #include "clipper/core/nxmap.h" - -+#include "coot-map-utils.hh" - #include "utils/coot-utils.hh" - #include "geometry/protein-geometry.hh" - diff --git a/coot.desktop b/coot.desktop deleted file mode 100644 index 79a76c6..0000000 --- a/coot.desktop +++ /dev/null @@ -1,10 +0,0 @@ -[Desktop Entry] -Encoding=UTF-8 -Name=coot -GenericName=coot -Comment=macromolecular model builder -Exec=coot -Icon=coot -Terminal=false -Type=Application -Categories=Graphics;Science diff --git a/coot.in b/coot.in deleted file mode 100755 index 7c2b35f..0000000 --- a/coot.in +++ /dev/null @@ -1,62 +0,0 @@ -#!/bin/sh -# -*-shell-script-*- -# coot wrapper script -# Copyright 2004, 2005, 2006, 2007 University of York -# written by Paul Emsley - -COOT_PREFIX="@prefix@" -current_exe_dir="@libexecdir@" - -coot_real=$current_exe_dir/coot-bin -# echo coot-real is at $coot_real - -# ---------------------------------------------------------------------------- -# ---------------------------------------------------------------------------- -# If the COOT_PREFIX is correct, then these should not need modification -# i.e. nothing below here need be changed. -# ---------------------------------------------------------------------------- -# ---------------------------------------------------------------------------- -# -prefix=$COOT_PREFIX - -SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib -COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme -COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb -COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps -COOT_DATA_DIR=$COOT_PREFIX/share/coot -COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc -COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures -COOT_PYTHON_DIR= -COOT_REFMAC_LIB_DIR= - -PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR - -GUILE_WARN_DEPRECATED=no - -if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then - GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH - export GUILE_LOAD_PATH -fi - -# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH - -export SYMINFO -export COOT_PREFIX -export COOT_STANDARD_RESIDUES -export COOT_REFMAC_LIB_DIR -export COOT_PYTHON_DIR -export PYTHONPATH -export COOT_SCHEME_DIR -export COOT_REF_STRUCTS -export COOT_RESOURCES_FILE -export COOT_PIXMAPS_DIR -export COOT_DATA_DIR - -echo $coot_real $* -$coot_real $* -status=$? - -if [ $status != 0 ] ; then - @bindir@/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real -fi - diff --git a/coot.png b/coot.png deleted file mode 100644 index 9e6ded7e24754bfa77ee5fe584fd2df36be6e86e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1271 zcmVPx#24YJ`L;(K){{a7>y{D4^000SaNLh0L01FcU01FcV0GgZ_00007bV*G`2iOY| z7cwAl4qK}L00ehQL_t(o!|j$^h*nh;$A4?>v(Gv6&FyO@P0Y-$hK1E+NifDss}%$!X@howHXD-}g<^ zMNP{J@_#scpR@O7t^ZnkueBE(#$o&)AcFoYiX+_3UZNo{&YXx%@9BB$pHnVwiGr!r z-xkGYo;}STU-{@+2Q9SVS~^pSZ;A2iJgyvxS|nQbM4v{u6%M_DRN_?9$q~*JY&41M zF1^TON7f@&i(w5|1m8EKiB^n8-ZNBAi92Im9B=61>Gk7U2eB{5$nIHAPI} z^HYzT^umnOPJQD0_qOi(>a&mE`(>N<0iXCZt;9>fZZph-Aqa+H1Z?En>W2+Q37uf) z3epram=~jypPzMRM>hSA`GadeTKCe16>sg+Vi$Q|q+?zeom;yphAuj-NV|2=W^EL# zmDCC(mJ*Lx?s3*aVhORuBV&;{+y_m$eQ&P3;`RA+i@!doqtGqIg^{^An&}ip)i56j zy91#mAaTH4KpWNv0yJ6>q~Q|~X!yhs$eQvir~Gu(MNhppuvY@XtYFwU#W{f>NLA6A zVMBqC)QN;NAd#U`r=blBVU+S_YZzgu_u>0``lr@T7##ZXi0$7jJ7?T6i#9ZMjwA?C z*S&|K0mZlHSZhWo*2s#1kO-1H+_1;*^7tP-ezzm4*6mgl0krX@jnO6@R!zMArVqa! 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Coot uses professional (and free) widgets (with the -GUI builder glade), mmdb, clipper, and OpenGL, together with a new -approach to map contouring and importing/creation and other modeling -and building operations. - -%package devel -Summary: Header files and library for developing programs with coot -Requires: %{name} = %{version}-%{release} -Group: Development/Libraries - -%description devel - -This package contains libraries and header files needed for program -development using the coot macromolecular model building package. - -%package doc -Summary: documentation PDF files for coot -Requires: %{name} = %{version}-%{release} -Group: Applications/Engineering - -%description doc - -the coot-doc package contains information concerning the use and -button/key shortcuts for the coot macromolecular model building -package. - -%prep -%setup -q -a 1 -%patch0 -p0 -%patch1 -p0 -%patch2 -p0 -%patch3 -p0 -%patch4 -p0 -%patch5 -p0 - -cp %{SOURCE2} ./src/ -cp %{SOURCE3} . - -# various cleanups -iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README - -aclocal -I macros -libtoolize --automake --copy -autoconf -automake --copy --add-missing --gnu - -%build -mkdir guile -# -D_GLIBCXX_USE_CXX11_ABI=0 ? -std=c++11 -%configure --with-guile --with-python --with-pygtk --with-goocanvas-prefix=/usr --disable-static CPPFLAGS="-I/usr/include/mmdb2 -I/usr/include/ssm" CXXFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing" GUILE_LOAD_PATH="$GUILE_LOAD_PATH:/tmp/guile" -sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool -sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool - -make %{?_smp_mflags} -pushd doc -texi2pdf coot-user-manual.texi -make coot-keys-and-buttons.pdf -popd - -%install -rm -rf %{buildroot} -make install DESTDIR=%{buildroot} INSTALL='install -p' - -mv reference-structures %{buildroot}%{_datadir}/coot/ - -sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=%{python_sitelib}/coot|' src/coot -sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=%{_datadir}/%{refmac_dictionary}|' src/coot -install -p -m 755 src/coot %{buildroot}%{_bindir}/ - -# remove unpackaged files from the buildroot -rm -f %{buildroot}%{_libdir}/*.la - -# headers -# mkdir %{buildroot}%{_includedir}/coot -# mv %{buildroot}%{_includedir}/*.h %{buildroot}%{_includedir}/coot/ -# mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/ - -# python stuff -# mkdir -p %{buildroot}%{python_sitelib}/coot -# mv %{buildroot}%{_datadir}/coot/python/* %{buildroot}%{python_sitelib}/coot/ -for lib in $(find %{buildroot}%{python_sitelib}/coot/ -name "*.py"); do - sed '/\/usr\/bin\/env/d' $lib > $lib.new && - touch -r $lib $lib.new && - mv $lib.new $lib -done -cp %{SOURCE4} %{buildroot}%{python_sitelib}/coot/ -chmod 644 %{buildroot}%{python_sitelib}/coot/coot.py - -# desktop file -desktop-file-install --vendor='' --dir=%{buildroot}%{_datadir}/applications coot.desktop -appstream-util validate-relax --nonet %{buildroot}/%{_datadir}/appdata/*.appdata.xml - -%clean -rm -rf %{buildroot} - -%check -make check -# %{buildroot}%{_bindir}/coot-real --no-graphics --script python-tests/coot_unittest.py - -%post -/sbin/ldconfig -/bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null || : - -%postun -/sbin/ldconfig -if [ $1 -eq 0 ] ; then - /bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null - /usr/bin/gtk-update-icon-cache %{_datadir}/icons/hicolor &>/dev/null || : -fi - -%posttrans -/usr/bin/gtk-update-icon-cache %{_datadir}/icons/hicolor &>/dev/null || : - -%files -%defattr(-,root,root,-) -%doc AUTHORS README COPYING -%{_bindir}/* -%{_libexecdir}/* -# libccp4mg-utils.so* is LGPLv2+ -# libcoot-surface.so* is a mix of LGPLv2+ and GPLv3+ -# all others are GPLv3+ -%{_libdir}/*.so.* -%{_datadir}/coot/ -%{_datadir}/applications/%{name}.desktop -%{_datadir}/appdata/%{name}.appdata.xml -%{_datadir}/icons/hicolor/ -%{python_sitelib}/coot/ - -%files devel -%defattr(-,root,root,-) -%{_libdir}/*.so -%{_includedir}/coot/ - -%files doc -%defattr(-,root,root,-) -%doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf - -%changelog -* Mon Feb 22 2016 Orion Poplawski - 0.8.2-3 -- Rebuild for gsl 2.1 - -* Wed Feb 03 2016 Fedora Release Engineering - 0.8.2-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild - -* Mon Sep 7 2015 Tim Fenn - 0.8.2-1 -- update to 0.8.2 -- add patch for coot-utils - -* Sun Jun 28 2015 Tim Fenn - 0.8.1-3 -- fix to appdata.xml -- add all icon pixmaps, edit desktop file to match - -* Wed Jun 17 2015 Fedora Release Engineering - 0.8.1-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild - -* Sat Jan 31 2015 Tim Fenn - 0.8.1-1 -- update to 0.8.1 -- update URL -- no sxml support in guile 1.8 (remove AM_GUILE_LIB check) -- add gtk update icon cache scriptlets -- add appdata xml file and additional app-data-validate scripts - -* Sat Aug 16 2014 Fedora Release Engineering - 0.7.2-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild - -* Sat Jun 07 2014 Fedora Release Engineering - 0.7.2-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild - -* Fri Dec 27 2013 Tim Fenn - 0.7.2-1 -- update to 0.7.2 -- update upstream URLs, no longer using vcs - -* Sun Aug 11 2013 Tim Fenn - 0.7-5.20120929svn4458 -- add ghostscript to buildrequires - -* Fri Aug 09 2013 Tim Fenn - 0.7-4.20120929svn4458 -- use xz instead of gz (BZ 982385) -- update for soname bump in deps (BZ 989141) -- use guile1.8-compat, add guile requires - -* Sat Aug 03 2013 Fedora Release Engineering - 0.7-3.20120929svn4458 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild - -* Wed Feb 13 2013 Fedora Release Engineering - 0.7-2.20120929svn4458 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild - -* Sat Sep 29 2012 Tim Fenn - 0.7-1.20120929svn4458 -- update to 0.7 - -* Wed Jul 18 2012 Fedora Release Engineering - 0.6.2-14.20110715svn3566 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild - -* Tue Feb 28 2012 Fedora Release Engineering - 0.6.2-13.20110715svn3566 -- Rebuilt for c++ ABI breakage - -* Sat Jan 14 2012 Tim Fenn - 0.6.2-12.20110715svn3566 -- patches to fix unistd.h issue and compilation errors - -* Thu Jan 12 2012 Fedora Release Engineering - 0.6.2-11.20110715svn3566 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild - -* Sat Dec 10 2011 Tim Fenn - 0.6.2-10.20110715svn3566 -- patch for new libpng - -* Tue Dec 06 2011 Adam Jackson - 0.6.2-9.20110715svn3566 -- Rebuild for new libpng - -* Fri Jul 15 2011 Tim Fenn - 0.6.2-8.20110715svn3566 -- update to SVN 3566 (0.6.2 final) - -* Tue Apr 26 2011 Tim Fenn - 0.6.2-7.20110421svn3461 -- add reference structures source file - -* Tue Apr 26 2011 Tim Fenn - 0.6.2-6.20110421svn3461 -- add missing source - -* Thu Apr 21 2011 Tim Fenn - 0.6.2-5.20110421svn3461 -- update to SVN 3461 -- fix missing Requires: guile-lib - -* Tue Mar 29 2011 Tim Fenn - 0.6.2-4.20110328svn3442 -- update to SVN 3442 (should remove guile-gtk broken dependencies) - -* Fri Feb 25 2011 Tim Fenn - 0.6.2-3.20110225svn3399 -- update to SVN 3399 - -* Tue Feb 08 2011 Fedora Release Engineering - 0.6.2-2.20101012svn3213 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild - -* Tue Oct 12 2010 Tim Fenn - 0.6.2-1.20101012svn3213 -- update to 0.6.2 - -* Thu Aug 05 2010 Tim Fenn - 0.6.1-3.20100127svn2740 -- fix file attr -- add comment to make check error - -* Tue Jul 20 2010 Tim Fenn - 0.6.1-2.20100127svn2740 -- move some documentation to subpackage -- add check section - -* Wed Jan 27 2010 Tim Fenn - 0.6.1-1.20100127svn2740 -- update to SVN 2740, 0.6.1 release -- add curl buildrequires - -* Thu Dec 03 2009 Tim Fenn - 0.6-6.20091203svn2545 -- update to SVN 2545, 0.6 release - -* Mon Nov 30 2009 Tim Fenn - 0.6-5.20091130svn2528 -- fix texi, include user-manual -- update to SVN 2528 -- remove net-http, guile-goosh and guile-gui - -* Wed Oct 07 2009 Tim Fenn - 0.6-4.20091007svn2404 -- update buildrequires -- use tetex-latex on EL builds -- update to SVN 2404 (fixes some licensing issues) - -* Mon Oct 05 2009 Tim Fenn - 0.6-3.20091005svn2400 -- update to SVN 2400 - -* Wed Sep 23 2009 Tim Fenn - 0.6-2.20090920svn2334 -- edit summary -- update upstream URL -- make create_server.py non-executable -- chmod src to 644 - -* Sun Sep 20 2009 Tim Fenn - 0.6-1.20090920svn2334 -- update to 0.6 -- get source from VCS system - -* Wed Mar 25 2009 Tim Fenn - 0.5.2-3 -- fix summary -- add additional licensing information -- split guile-extras into original tarballs - -* Sat Mar 14 2009 Tim Fenn - 0.5.2-2 -- fix for desktop-file-install -- gcc 4.4 patch - -* Mon Dec 15 2008 Tim Fenn - 0.5.2-1 -- update to 0.5.2 - -* Thu Nov 27 2008 Tim Fenn - 0.5-3 -- use consistent buildroot -- include gtkglext-devel, guile-lib, desktop-file-utils in buildrequires -- remove pyobject2 in buildrequires - -* Tue Nov 18 2008 Tim Fenn - 0.5-2 -- enable guile -- include extra guile modules - -* Mon Nov 17 2008 Tim Fenn - 0.5-1 -- initial build diff --git a/dead.package b/dead.package new file mode 100644 index 0000000..67bbcda --- /dev/null +++ b/dead.package @@ -0,0 +1,3 @@ +2016-05-31: Retired because of broken deps in preparation of Fedora 24 +Reference: https://fedorahosted.org/rel-eng/ticket/6416 + diff --git a/sources b/sources deleted file mode 100644 index 6037d9b..0000000 --- a/sources +++ /dev/null @@ -1,2 +0,0 @@ -71a6653bedff7c764dea38289ef0e65c coot-0.8.2.tar.gz -257ab90d44f1c877ada96720dbb87c13 reference-structures.tar.gz From 35fb0231e53748d9829c4183276a4cbeb750dc1e Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 9 Feb 2017 09:04:24 -0500 Subject: [PATCH 2/7] add missing patch --- coot-guile.patch | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 coot-guile.patch diff --git a/coot-guile.patch b/coot-guile.patch new file mode 100644 index 0000000..e79a6a9 --- /dev/null +++ b/coot-guile.patch @@ -0,0 +1,27 @@ +--- macros/guile_orig.m4 2013-07-31 00:25:19.715073145 -0700 ++++ macros/guile.m4 2013-07-31 00:27:01.763927099 -0700 +@@ -72,21 +72,21 @@ + # The variables are marked for substitution, as by @code{AC_SUBST}. + # + AC_DEFUN([GUILE_PROGS], +- [AC_PATH_PROG(GUILE,guile) ++ [AC_PATH_PROG(GUILE,guile1.8) + if test x$with_guile = xyes ; then + if test "$GUILE" = "" ; then + AC_MSG_ERROR([guile required but not found]) + fi + fi + AC_SUBST(GUILE) +- AC_PATH_PROG(GUILE_CONFIG,guile-config) ++ AC_PATH_PROG(GUILE_CONFIG,guile1.8-config) + if test x$with_guile = xyes ; then + if test "$GUILE_CONFIG" = "" ; then + AC_MSG_ERROR([guile-config required but not found]) + fi + fi + AC_SUBST(GUILE_CONFIG) +- AC_PATH_PROG(GUILE_TOOLS,guile-tools) ++ AC_PATH_PROG(GUILE_TOOLS,guile1.8-tools) + AC_SUBST(GUILE_TOOLS) + ]) + From f702dbc7a1e320354c2a57e150f6c5dd53b7263c Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 9 Feb 2017 09:07:02 -0500 Subject: [PATCH 3/7] add missing patch --- __init__.py | 1 + coot.desktop | 10 +++++++++ coot.in | 62 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 73 insertions(+) create mode 100644 __init__.py create mode 100644 coot.desktop create mode 100755 coot.in diff --git a/__init__.py b/__init__.py new file mode 100644 index 0000000..83d04e7 --- /dev/null +++ b/__init__.py @@ -0,0 +1 @@ +# File to allow this directory to be treated as a python package. diff --git a/coot.desktop b/coot.desktop new file mode 100644 index 0000000..79a76c6 --- /dev/null +++ b/coot.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Encoding=UTF-8 +Name=coot +GenericName=coot +Comment=macromolecular model builder +Exec=coot +Icon=coot +Terminal=false +Type=Application +Categories=Graphics;Science diff --git a/coot.in b/coot.in new file mode 100755 index 0000000..7c2b35f --- /dev/null +++ b/coot.in @@ -0,0 +1,62 @@ +#!/bin/sh +# -*-shell-script-*- +# coot wrapper script +# Copyright 2004, 2005, 2006, 2007 University of York +# written by Paul Emsley + +COOT_PREFIX="@prefix@" +current_exe_dir="@libexecdir@" + +coot_real=$current_exe_dir/coot-bin +# echo coot-real is at $coot_real + +# ---------------------------------------------------------------------------- +# ---------------------------------------------------------------------------- +# If the COOT_PREFIX is correct, then these should not need modification +# i.e. nothing below here need be changed. +# ---------------------------------------------------------------------------- +# ---------------------------------------------------------------------------- +# +prefix=$COOT_PREFIX + +SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib +COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme +COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb +COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps +COOT_DATA_DIR=$COOT_PREFIX/share/coot +COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc +COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures +COOT_PYTHON_DIR= +COOT_REFMAC_LIB_DIR= + +PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR + +GUILE_WARN_DEPRECATED=no + +if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then + GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH + export GUILE_LOAD_PATH +fi + +# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH + +export SYMINFO +export COOT_PREFIX +export COOT_STANDARD_RESIDUES +export COOT_REFMAC_LIB_DIR +export COOT_PYTHON_DIR +export PYTHONPATH +export COOT_SCHEME_DIR +export COOT_REF_STRUCTS +export COOT_RESOURCES_FILE +export COOT_PIXMAPS_DIR +export COOT_DATA_DIR + +echo $coot_real $* +$coot_real $* +status=$? + +if [ $status != 0 ] ; then + @bindir@/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real +fi + From 072e89cc6560409949d2f19c41d7c9252400727a Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Mon, 15 May 2017 20:35:26 +0000 Subject: [PATCH 4/7] - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 0aaef5b..dba3168 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.8 -Release: 1%{?dist} +Release: 2%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Mon May 15 2017 Fedora Release Engineering - 0.8.8-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild + * Sat Mar 18 2017 Tim Fenn - 0.8.8-1 - update to 0.8.8 From cc804d9af5f7546334f18b6b2e07009a274427cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Esser?= Date: Mon, 24 Jul 2017 14:20:40 +0200 Subject: [PATCH 5/7] Rebuilt for Boost 1.64 --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index dba3168..f31afb3 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.8 -Release: 2%{?dist} +Release: 3%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Mon Jul 24 2017 Björn Esser - 0.8.8-3 +- Rebuilt for Boost 1.64 + * Mon May 15 2017 Fedora Release Engineering - 0.8.8-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild From aae6b2b7f698d9ad14a92cfc7dbdbf021b2da35e Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 26 Jul 2017 05:28:31 +0000 Subject: [PATCH 6/7] - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index f31afb3..735e6be 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.8 -Release: 3%{?dist} +Release: 4%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Wed Jul 26 2017 Fedora Release Engineering - 0.8.8-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild + * Mon Jul 24 2017 Björn Esser - 0.8.8-3 - Rebuilt for Boost 1.64 From d01dc8c1911996529c43483575dcd3b289d5b22d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 2 Aug 2017 19:10:04 +0000 Subject: [PATCH 7/7] - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 735e6be..b45849b 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.8 -Release: 4%{?dist} +Release: 5%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Wed Aug 02 2017 Fedora Release Engineering - 0.8.8-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild + * Wed Jul 26 2017 Fedora Release Engineering - 0.8.8-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild