* [gentoo-commits] proj/sci:master commit in: profiles/, sci-chemistry/camshift/, sci-chemistry/camshift/files/
@ 2021-01-18 12:21 Andrew Ammerlaan
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From: Andrew Ammerlaan @ 2021-01-18 12:21 UTC (permalink / raw
To: gentoo-commits
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-chemistry@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
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