From: Samuli Suominen Date: Sun, 23 Oct 2011 20:07:55 +0000 (+0000) Subject: old X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=03d9c69df84de555dd1db97df5712d3d2f1462f5;p=gentoo.git old Package-Manager: portage-2.2.0_alpha70/cvs/Linux x86_64 --- diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog index c2e894f70230..76d80d4a687d 100644 --- a/sci-chemistry/coot/ChangeLog +++ b/sci-chemistry/coot/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-chemistry/coot # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.49 2011/10/08 16:22:59 phajdan.jr Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.50 2011/10/23 20:07:55 ssuominen Exp $ + + 23 Oct 2011; Samuli Suominen + -files/0.6.1-libpng14.patch, -coot-0.6.1.ebuild: + old 08 Oct 2011; Pawel Hajdan jr coot-0.6.2.ebuild: x86 stable wrt bug #385759 diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest index d25a674f29d7..76ab9533ee3b 100644 --- a/sci-chemistry/coot/Manifest +++ b/sci-chemistry/coot/Manifest @@ -1,26 +1,26 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA512 +Hash: SHA1 -AUX 0.6.1-libpng14.patch 950 RMD160 c2d1c298ada419272d79d49972b13e414a234cd3 SHA1 bfd4828ab8e05863ce197c59865901ce3186fb66 SHA256 7b121a0bccd49da0c459003512a2c61368eeab41b33a6726525ace501eb03559 AUX 0.6.2-clipper-config.patch 431 RMD160 7a00939760bc4c062bbde1a65f53b9556b93c3bc SHA1 0d72c4c898fd29802c74d237b54f715444922956 SHA256 9ae9129e733d845ad2e4dd505bc5e0987147fc3a5e5dd2457b5857643809db2f AUX 0.6.2-gl.patch 383 RMD160 6460e87e4da57ff845f96f072dec1354ed117bee SHA1 00bc0bbfc7d4fb00ebc8477941469bef2ed6b670 SHA256 9d47a6cf2d0c7644b945f88acdc7af146df4f9a5a8f883a0e72e1bc8ccf8b380 AUX 0.6.2-libpng15.patch 1396 RMD160 a7295bf9b312df0f19f82aec3f9458b4d7881606 SHA1 dfa904f324398cc4c7169ec223fb1cec9e72f482 SHA256 e1a1a172f92702aab5921943201baeba36643f9c5bbf1aa40151c4d4dd9dfee6 AUX 0.6.2-mmdb-config.patch 432 RMD160 8418198b08d15af9ee5d80b15ea46bb9efd2b973 SHA1 3e6f5c888b476d8d37da4effa67a8053784a7a3c SHA256 41484424f2f7f61b0555c893a51884d02f7bd471e70c4c0903c8740dcc273f77 AUX 0.6.2-ssm.patch 1276 RMD160 8c7eef0034efc2c57bd774fe8ebb1bd0ba9c7aa2 SHA1 8812f35fba16a45b21ecce5243fd26d6105e29e3 SHA256 42f1098b0d56f85125293ca24410061e7a9bee10c94ba6e9fd3496439368bf75 AUX 0.6.2-test.patch 457 RMD160 1a3e0956d8b7f051fdd964524c0ba9eabf8c2aca SHA1 a8f9584be09cc58e7cb55801115e9649b05aa910 SHA256 494ef09e407c3047145c250c70b90c7679a1c5b9f84c57a680e40580bd980397 -DIST coot-0.6.1.tar.gz 12229005 RMD160 76cbf28320ff52f02b40164eea00e7ec8a6b6c2c SHA1 cdd74e394e07dc17b99f56fce7cf180a177d53d7 SHA256 7897eb62e1add5f8deddd16d24ffd9b4c763e784714cd47fa9777beb79f56066 DIST coot-0.6.2.tar.gz 13597123 RMD160 707eb3df47681a011f42874210b940329a748bc7 SHA1 46b663125cef4c01387330d144e49acb0b0b5709 SHA256 d2f55db4f75c721d120ea33a4ca42c1abf246dff29a75b7f189e604e32709e78 -DIST greg-data-0.6.1.tar.gz 7930213 RMD160 e9a17d1ef2d3f15b3792ea5c7204901e0105b76b SHA1 f4158fa440406b88d0bb72880cdee9a3653c4233 SHA256 658a557b85ee6b90fc446cb3c605556586a2a5a0575ddd11b42265e019eb74a0 DIST greg-data-0.6.2.tar.gz 8044588 RMD160 065acee98384540d0c2ffaf2511dfd1aa400b11c SHA1 92cec24dab594d8024f41047af2bf6760e9e7d00 SHA256 c9fedf6e1fa60fda178753bbfb539671c274f64d4daca2b63ab49c59bd4c5856 -EBUILD coot-0.6.1.ebuild 3934 RMD160 6376495fce52056acbaaf0df862fbb502b8a7600 SHA1 0ecc3bfa5760bb663d62c67c98c6146f3f77e707 SHA256 7ac1bd7397140da0386b360ef613067a2932d381d0a85e9ad97218fac20f944d EBUILD coot-0.6.2-r1.ebuild 4219 RMD160 8b72c7448aae3040e560cd3844c720648e33801b SHA1 8beb6b3d74975b883c65492e9fb72636f4c5e3a6 SHA256 061496180fb395bf803af9e40dc86e8142870337d4a0913226e0082135307101 EBUILD coot-0.6.2.ebuild 4137 RMD160 9db72443a58fc996cc93870578beabec20364e78 SHA1 04ea15f0b045f8cb8d158fed84600b2ec6c2bb89 SHA256 7e1b4547c5c8eedb081991b30c3dbc2fc1abd29e73a193fcc3027f2b93445319 -MISC ChangeLog 7242 RMD160 c0a3ce3df2d1ea1ec429c517bf5467fea3c0b590 SHA1 40672b91d84c03ab93d63c42b2ac3b29f535b8bc SHA256 2ee6bf7059ffd2555bcf99ecba722b3734a8decfbc5aadfd906dfafe4c3a165e +MISC ChangeLog 7353 RMD160 d9f936a6a603356d1318babcdc10fa1963f5dabf SHA1 98107221517c4423c0d0530b92b2bd7c8ee8b141 SHA256 4d5b54ecb95d9e0f1c44980176197b42e5eca09f3af6ce35f9ac39159569e93c MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8 -----BEGIN PGP SIGNATURE----- -Version: GnuPG v2.0.17 (GNU/Linux) +Version: GnuPG v2.0.18 (GNU/Linux) -iEYEAREKAAYFAk6QeOoACgkQuUQtlDBCeQJ5jACaAqnVjWLGtd3uMndYGN4aUtlt -H8EAniRn9HIt3d+wDsymoMDInwhOeXgp -=XdT0 +iQEcBAEBAgAGBQJOpHPtAAoJEEdUh39IaPFNdPMH/3Oc633XaBvgGQhMegu+frrF +PQzGw2upzLnBLEUC2+7nwPmvK/WWM21qa6vXIvJxW8hVJwVDPJmb/mX7k5nyqfQi +NmyyCl9kWZ0FCa9eoJhZcnQThui7VcIO6K2flarNatmYf9m+3lpAy2T6g8JdN5kY +Oe6CucfdWnTzc/p/eyVOkSzdZ2V6FS52rPzai1OuEep5CQXSr0aYB871EL/E3Qcl +CBNfvmKVnZgyLjaHUNAEHw4BSvloVu5K1EYPf5PO3owd71OTFudaNGXniKgChGdS +mvMJjIElTQT7xf8JmgGzE2l2QnvELIhSLJKmwaVm0Ezcb+YlCFErmonD8ZOrByI= +=Jj4L -----END PGP SIGNATURE----- diff --git a/sci-chemistry/coot/coot-0.6.1.ebuild b/sci-chemistry/coot/coot-0.6.1.ebuild deleted file mode 100644 index 9274fc43c921..000000000000 --- a/sci-chemistry/coot/coot-0.6.1.ebuild +++ /dev/null @@ -1,154 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.6.1.ebuild,v 1.13 2011/06/28 17:01:28 jlec Exp $ - -EAPI=3 - -PYTHON_DEPEND="2" - -inherit autotools base eutils python versionator - -MY_S2_PV=$(replace_version_separator 2 - ${PV}) -MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} -MY_S_P=${MY_S2_P}-${PR/r/revision-} -MY_PV=${PV} -MY_P=${PN}-${MY_PV} - -DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" -HOMEPAGE="http://www.biop.ox.ac.uk/coot/" -SRC_URI=" - http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz - test? ( mirror://gentoo/greg-data-${PV}.tar.gz )" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="test" - -SCIDEPS=" - >=sci-libs/ccp4-libs-6.1 - >=sci-libs/clipper-20090520 - >=sci-libs/coot-data-2 - >=sci-libs/gsl-1.3 - sci-libs/mmdb - sci-chemistry/reduce - sci-chemistry/refmac - sci-chemistry/probe" - -XDEPS=" - gnome-base/libgnomecanvas - gnome-base/librsvg:2 - media-libs/libpng - media-libs/freeglut - x11-libs/gtk+:2 - x11-libs/gtkglext" - -SCHEMEDEPS=" - dev-scheme/net-http - dev-scheme/guile-gui - >=dev-scheme/guile-lib-0.1.6 - dev-scheme/guile-www - ~x11-libs/guile-gtk-2.1" - -RDEPEND=" - ${SCIDEPS} - ${XDEPS} - ${SCHEMEDEPS} - dev-python/pygtk:2 - >=dev-libs/gmp-4.2.2-r2 - >=net-misc/curl-7.19.6 - net-dns/libidn" -DEPEND="${RDEPEND} - dev-lang/swig - sys-devel/bc - test? ( dev-scheme/greg )" - -S="${WORKDIR}/${MY_P}" -#S="${WORKDIR}/${MY_S2_P}" - -pkg_setup() { - python_set_active_version 2 -} - -src_prepare() { - base_src_prepare - - # Link against single-precision fftw - sed -i \ - -e "s:lfftw:lsfftw:g" \ - -e "s:lrfftw:lsrfftw:g" \ - "${S}"/macros/clipper.m4 - - epatch "${FILESDIR}"/${PV}-libpng14.patch - - eautoreconf -} - -src_configure() { - # All the --with's are used to activate various parts. - # Yes, this is broken behavior. - econf \ - --includedir='${prefix}/include/coot' \ - --with-gtkcanvas-prefix="${EPREFIX}/usr" \ - --with-clipper-prefix="${EPREFIX}/usr" \ - --with-mmdb-prefix="${EPREFIX}/usr" \ - --with-ssmlib-prefix="${EPREFIX}/usr" \ - --with-gtkgl-prefix="${EPREFIX}/usr" \ - --with-guile \ - --with-python="${EPREFIX}/usr" \ - --with-guile-gtk \ - --with-gtk2 \ - --with-pygtk -} - -src_compile() { - emake || die "emake failed" - python_convert_shebangs $(python_get_version) src/coot_gtk2.py - cp "${S}"/src/coot_gtk2.py python/coot.py || die -} - -src_test() { - source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" - mkdir "${T}"/coot_test - - export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" - export COOT_SCHEME_DIR="${S}/scheme/" - export COOT_RESOURCES_FILE="${S}/cootrc" - export COOT_PIXMAPS_DIR="${S}/pixmaps" - export COOT_DATA_DIR="${S}" - export COOT_PYTHON_DIR="${S}/python" - export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" - export PYTHONHOME="${EPREFIX}"/usr - export CCP4_SCR="${T}"/coot_test - export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" - export SYMINFO="${S}/syminfo.lib" - - export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data - - cat > command-line-greg.scm <<- EOF - (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 - - einfo "Running test with following paths ..." - einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" - einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" - einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" - einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" - einfo "COOT_DATA_DIR $COOT_DATA_DIR" - einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" - einfo "PYTHONPATH $PYTHONPATH" - einfo "PYTHONHOME $PYTHONHOME" - einfo "CCP4_SCR ${CCP4_SCR}" - einfo "CLIBD_MON ${CLIBD_MON}" - einfo "SYMINFO ${SYMINFO}" - - "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die - "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die -} diff --git a/sci-chemistry/coot/files/0.6.1-libpng14.patch b/sci-chemistry/coot/files/0.6.1-libpng14.patch deleted file mode 100644 index cb09759ed1a2..000000000000 --- a/sci-chemistry/coot/files/0.6.1-libpng14.patch +++ /dev/null @@ -1,17 +0,0 @@ -http://code.google.com/p/coot/source/diff?spec=svn2956&old=2307&r=2907&format=unidiff&path=%2Ftrunk%2Fccp4mg-utils%2Fppmutil.cc -diff --git a/ccp4mg-utils/ppmutil.cc b/ccp4mg-utils/ppmutil.cc -index 4f0fb5e..20b1d0d 100644 ---- a/ccp4mg-utils/ppmutil.cc -+++ b/ccp4mg-utils/ppmutil.cc -@@ -2501,7 +2501,11 @@ void image_info::readpng(const char *filename){ - pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green; - pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue; - if(row_pointers[i][j]num_trans){ -+#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4 -+ pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]]; -+#else - pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]]; -+#endif - }else - pixels[i*width*colourspace+j*colourspace+3] = 255; - }