commit: 2bbfb53c3bb28a361b7b35048cca664eb0861351 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Mon Jan 18 12:21:24 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Mon Jan 18 12:21:24 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2bbfb53c
sci-chemistry/camshift: remove pack, upstream is gone Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 1 - sci-chemistry/camshift/camshift-1.35.0.ebuild | 51 -------- sci-chemistry/camshift/files/1.35.0-gcc47.patch | 148 ----------------------- sci-chemistry/camshift/files/1.35.0-gentoo.patch | 85 ------------- sci-chemistry/camshift/metadata.xml | 8 -- 5 files changed, 293 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index f94c862e6..829de8c5b 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -118,4 +118,3 @@ sci-biology/vague-bin sci-biology/VelvetOptimiser sci-biology/wcd sci-biology/wgs_tools -sci-chemistry/camshift diff --git a/sci-chemistry/camshift/camshift-1.35.0.ebuild b/sci-chemistry/camshift/camshift-1.35.0.ebuild deleted file mode 100644 index 3964d0400..000000000 --- a/sci-chemistry/camshift/camshift-1.35.0.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils flag-o-matic - -DESCRIPTION="Structure based prediction of protein chemical shifts" -HOMEPAGE="http://www-vendruscolo.ch.cam.ac.uk/camshift/camshift.php"; -SRC_URI="http://www-vendruscolo.ch.cam.ac.uk/${PN}/${P}.tar.gz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cpu_flags_x86_sse" - -RDEPEND=" - virtual/blas - virtual/lapack" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}"/${PV}-gcc47.patch - "${FILESDIR}"/${PV}-gentoo.patch ) - -src_configure(){ - local myeconfargs=( - --with-lapack - --with-external-blas - $(use_enable cpu_flags_x86_sse mkasm) - ) - autotools-utils_src_configure -} - -src_compile() { - autotools-utils_src_compile \ - CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dobin "${BUILD_DIR}"/bin/${PN} - - insinto /usr/share/${PN} - doins -r data - dodoc README NEWS ChangeLog AUTHORS -} diff --git a/sci-chemistry/camshift/files/1.35.0-gcc47.patch b/sci-chemistry/camshift/files/1.35.0-gcc47.patch deleted file mode 100644 index 7e9d4b973..000000000 --- a/sci-chemistry/camshift/files/1.35.0-gcc47.patch +++ /dev/null @@ -1,148 +0,0 @@ - include/almost/forcefield/intern/angleenergy.h | 14 ++++----- - include/almost/forcefield/intern/bondenergy.h | 2 +- - include/almost/kernel/molecule.h | 2 +- - include/almost/kernel/rmsd.h | 42 +++++++++++++------------- - src/lib/io/formostream.cpp | 4 +-- - 5 files changed, 32 insertions(+), 32 deletions(-) - -diff --git a/include/almost/forcefield/intern/angleenergy.h b/include/almost/forcefield/intern/angleenergy.h -index 75308ca..a9bc70c 100644 ---- a/include/almost/forcefield/intern/angleenergy.h -+++ b/include/almost/forcefield/intern/angleenergy.h -@@ -419,7 +419,7 @@ namespace Almost { - int f = Coor<float_type>::DIM*this->first_[i]; - int m = Coor<float_type>::DIM*this->middle_[i]; - int l = Coor<float_type>::DIM*this->last_[i]; -- dangle = angle(coor,f,m,l); -+ dangle = this->angle(coor,f,m,l); - ene += this->ka_[i]*(dangle-this->a0_[i])*(dangle-this->a0_[i]); - } - return ene; -@@ -444,9 +444,9 @@ namespace Almost { - vkj[2] = coor.coor[l+2]-coor.coor[m+2]; - - -- float_type nij = norm(vij); -- float_type nkj = norm(vkj); -- float_type n = scal(vij,vkj); -+ float_type nij = this->norm(vij); -+ float_type nkj = this->norm(vkj); -+ float_type n = this->scal(vij,vkj); - float_type cosd = n/(nij*nkj);; - float_type dangle = acos(cosd); - float_type sind = sqrt(1-cosd*cosd); -@@ -513,9 +513,9 @@ namespace Almost { - vkj[2] = coor.coor[l+2]-coor.coor[m+2]; - - -- float_type nij = norm(vij); -- float_type nkj = norm(vkj); -- float_type n = scal(vij,vkj); -+ float_type nij = this->norm(vij); -+ float_type nkj = this->norm(vkj); -+ float_type n = this->scal(vij,vkj); - float_type cosd = n/(nij*nkj);; - float_type dangle = acos(cosd); - float_type sind = sqrt(1-cosd*cosd); -diff --git a/include/almost/forcefield/intern/bondenergy.h b/include/almost/forcefield/intern/bondenergy.h -index f60d99c..d6977f2 100644 ---- a/include/almost/forcefield/intern/bondenergy.h -+++ b/include/almost/forcefield/intern/bondenergy.h -@@ -242,7 +242,7 @@ namespace Almost { - float_type d; - int f = this->first_[i]; - int s = this->second_[i]; -- d = sqrt(distanceP2(coor.coor+Coor<float_type>::DIM*f, -+ d = sqrt(this->distanceP2(coor.coor+Coor<float_type>::DIM*f, - coor.coor+Coor<float_type>::DIM*s)); - e +=this->kb_[i]*(d-this->b0_[i])*(d-this->b0_[i]); - } -diff --git a/include/almost/kernel/molecule.h b/include/almost/kernel/molecule.h -index e399d8d..0ea1d28 100644 ---- a/include/almost/kernel/molecule.h -+++ b/include/almost/kernel/molecule.h -@@ -1100,7 +1100,7 @@ namespace Kernel { - if(this->fragment_atoms_[i][j]>=gpos) ++this->fragment_atoms_[i][j]; - - -- return add_atom_(fd,atom,pos); -+ return this->add_atom_(fd,atom,pos); - } - - -diff --git a/include/almost/kernel/rmsd.h b/include/almost/kernel/rmsd.h -index 0947666..210f53e 100644 ---- a/include/almost/kernel/rmsd.h -+++ b/include/almost/kernel/rmsd.h -@@ -172,6 +172,27 @@ namespace Almost { - /*====================================================================*/ - - template <typename float_type> -+ float_type EPpythag(float_type a,float_type b) -+ { -+ /* finds sqrt(a*a+b*b) without overflow or destructive underflow */ -+ -+ float_type p,r,s,t,u; -+ -+ p=(abs(a) > abs(b) ? abs(a) : abs(b)); -+ if (p>0) { -+ r=(abs(a)<abs(b)?abs(a):abs(b))/p; -+ r=r*r; -+ for (t=4.0+r;t!=4.0;t=4.0+r) { -+ s=r/t; -+ u=1.0+2.0*s; -+ p=u*p; -+ r=(s/u)*(s/u)*r; -+ } -+ } -+ return(p); -+ } -+ -+ template <typename float_type> - int EPimtql2(int n,float_type *d,float_type *e,float_type **z) - { - int i,j,k,l,m,ii,mml; -@@ -316,27 +337,6 @@ namespace Almost { - - /*====================================================================*/ - -- template <typename float_type> -- float_type EPpythag(float_type a,float_type b) -- { -- /* finds sqrt(a*a+b*b) without overflow or destructive underflow */ -- -- float_type p,r,s,t,u; -- -- p=(abs(a) > abs(b) ? abs(a) : abs(b)); -- if (p>0) { -- r=(abs(a)<abs(b)?abs(a):abs(b))/p; -- r=r*r; -- for (t=4.0+r;t!=4.0;t=4.0+r) { -- s=r/t; -- u=1.0+2.0*s; -- p=u*p; -- r=(s/u)*(s/u)*r; -- } -- } -- return(p); -- } -- - template<typename float_type> - inline float_type rmsd_dist(const Almost::Coor<float_type> & ref, - const Almost::Coor<float_type> & to_move, -diff --git a/src/lib/io/formostream.cpp b/src/lib/io/formostream.cpp -index 9a98154..1469b8a 100644 ---- a/src/lib/io/formostream.cpp -+++ b/src/lib/io/formostream.cpp -@@ -1572,9 +1572,9 @@ PDBOStream & operator<<(PDBOStream & pdb, const Molecules & molecules){ - - for(int i=0;i<molecules.solvent_size();i++){ - pdb<<molecules.solvent(i); -- int i = molecules.solvent_size()-1; -+ int j = molecules.solvent_size()-1; - sprintf(buff, -- "%-6s%5i\n","TER",molecules.solvent(i).atom_size() -+ "%-6s%5j\n","TER",molecules.solvent(i).atom_size() - +molecules.solvent(i).atom_offset()); - pdb.stream()<<buff; - diff --git a/sci-chemistry/camshift/files/1.35.0-gentoo.patch b/sci-chemistry/camshift/files/1.35.0-gentoo.patch deleted file mode 100644 index 845325713..000000000 --- a/sci-chemistry/camshift/files/1.35.0-gentoo.patch +++ /dev/null @@ -1,85 +0,0 @@ - bin/Makefile.am | 2 +- - configure.in | 18 +++--------------- - src/forcefield/Makefile.am | 4 ++-- - src/lib/Makefile.am | 2 +- - 4 files changed, 7 insertions(+), 19 deletions(-) - -diff --git a/bin/Makefile.am b/bin/Makefile.am -index c9f5f40..0f1d790 100644 ---- a/bin/Makefile.am -+++ b/bin/Makefile.am -@@ -1,4 +1,4 @@ --INCLUDES = -I../.. -I../include/almost -+INCLUDES = -I$(top_srcdir) -I$(top_srcdir)/include/almost - bin_PROGRAMS=camshift - - if LIBBZ2 -diff --git a/configure.in b/configure.in -index e0d186d..9b15335 100644 ---- a/configure.in -+++ b/configure.in -@@ -167,9 +167,6 @@ echo Constraint disabled value $ - fi - - --#C and CPPFLAFS --CFLAGS="-O9 -ffast-math -fomit-frame-pointer" --CXXFLAGS="-O9 -ffast-math" - - #alm_sse - mkasm=false -@@ -231,11 +228,6 @@ else - echo OS ${host-os} - fi - --if test x$darwin = xtrue; then --CFLAGS=$CFLAGS" -fast" --CXXFLAGS=$CXXFLAGS" -fast" --fi -- - if test x$powerpc = xtrue; then - AC_DEFINE([POWERPC],[],"PowerPC CPU") - fi -@@ -250,17 +242,13 @@ AM_CONDITIONAL(IX86, test x$ix86 = xtrue) - - if test x$darwin = xtrue; then - if test x$ix86 = xtrue; then --CXXFLAGS=$CXXFLAGS" -msse -msse2 -mmmx" --CFLAGS=$CFLAGS" -msse -msse2 -mmmx" --fi --fi -- --if test x$darwin = xtrue; then --if test x$ix86 = xtrue; then - CCAS=$PWD/darwinas - fi - fi - -+PKG_CHECK_MODULES(BLAS, blas) -+PKG_CHECK_MODULES(LAPACK, lapack) -+ - echo ${host} ${host-cpu} ${host-vendor} ${host-os} $ix86 $powerpc - AC_OUTPUT( - almost.h -diff --git a/src/forcefield/Makefile.am b/src/forcefield/Makefile.am -index 8d143ab..4b72814 100644 ---- a/src/forcefield/Makefile.am -+++ b/src/forcefield/Makefile.am -@@ -1,4 +1,4 @@ --INCLUDES = -I../../include/almost -+INCLUDES = -I$(top_srcdir)/include/almost - - lib_LIBRARIES= libnbimpl.a --libnbimpl_a_SOURCES=enefunc.c enefuncvdw.c pbcenefunc.c forcefunc.c forcefuncvdw.c pbcforcefunc.c sasaenefunc.c pbcsasaenefunc.c sasaforcefunc.c pbcsasaforcefunc.c eneforcefunc.c enefunchs.c forcefunchs.c enefuncsoft.c forcefuncsoft.c qvdwfunc.c $(ASMF) -\ No newline at end of file -+libnbimpl_a_SOURCES=enefunc.c enefuncvdw.c pbcenefunc.c forcefunc.c forcefuncvdw.c pbcforcefunc.c sasaenefunc.c pbcsasaenefunc.c sasaforcefunc.c pbcsasaforcefunc.c eneforcefunc.c enefunchs.c forcefunchs.c enefuncsoft.c forcefuncsoft.c qvdwfunc.c $(ASMF) -diff --git a/src/lib/Makefile.am b/src/lib/Makefile.am -index 02ee6ee..0e9001f 100644 ---- a/src/lib/Makefile.am -+++ b/src/lib/Makefile.am -@@ -1,4 +1,4 @@ --INCLUDES=-I../../include/almost -+INCLUDES=-I$(top_srcdir)/include/almost - lib_LIBRARIES=libAlm.a - PBDSOURCES = pdb/pdbatomline.cpp \ - pdb/pdbauthorline.cpp \ diff --git a/sci-chemistry/camshift/metadata.xml b/sci-chemistry/camshift/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/camshift/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemis...@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata>
