commit: 4ccc9f448c6fef32e56e05502a2ab45a441865c3
Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 30 17:14:06 2021 +0000
Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
CommitDate: Mon Aug 30 17:38:47 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4ccc9f44
sci-libs/rosetta-fragments: Remove last-rited package
Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org>
profiles/package.mask | 1 -
sci-libs/rosetta-fragments/Manifest | 1 -
.../files/rosetta-fragments-3.1-chemshift.patch | 62 ---------
.../files/rosetta-fragments-3.1-nnmake.patch | 153 ---------------------
sci-libs/rosetta-fragments/metadata.xml | 8 --
.../rosetta-fragments-3.1-r1.ebuild | 62 ---------
6 files changed, 287 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 2cb9476c1f4..2d85a7f8cfd 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -288,7 +288,6 @@ sci-biology/ncbi-tools
sci-biology/njplot
sci-biology/psipred
sci-chemistry/mars
-sci-libs/rosetta-fragments
# Andreas K. Hüttel <dilfri...@gentoo.org> (2021-07-31)
# Obsolete; all versions in current Perl core distributions
diff --git a/sci-libs/rosetta-fragments/Manifest
b/sci-libs/rosetta-fragments/Manifest
deleted file mode 100644
index 838f4129d74..00000000000
--- a/sci-libs/rosetta-fragments/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST rosetta3.1_fragments.tgz 221931894 BLAKE2B
0fb5764f24f3386cdbce9afce7da3f81cce91a6a0a57a265e5dbe0bf06146e4ab057c02961ed0dd8074f86309257bcf5b42ca0d1c6adf92c9f8ebf36b3f25f5d
SHA512
a2b2646c916ea1b98e2c7267c1eadb1fd6cb76d015c24bd4e8318ce127cb5d96ca56bfdd76821e1dd884e03d59631f544e221b9f541ad4063a99e96dbb029da1
diff --git
a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch
b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch
deleted file mode 100644
index cb8fd9197d1..00000000000
--- a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch
+++ /dev/null
@@ -1,62 +0,0 @@
- chemshift/make.system | 24 ++++++++++++------------
- chemshift/makefile | 2 +-
- 2 files changed, 13 insertions(+), 13 deletions(-)
-
-diff --git a/chemshift/make.system b/chemshift/make.system
-index 53bbd38..d105802 100644
---- a/chemshift/make.system
-+++ b/chemshift/make.system
-@@ -60,18 +60,18 @@ endif
- ########## once COMPILER is set, here are the options
-
- # defaults
--F77=f77
--FFLAGS=
--FOPTIMFLAGS=-O
--FDEBUGFLAGS=-g
-+F77?=f77
-+FFLAGS?=
-+FOPTIMFLAGS?=
-+FDEBUGFLAGS?=
- FPROFILEFLAGS=-P
-
- ifeq ($(COMPILER),gnu)
-- F77 = g77
-- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132
-Wimplicit
-- FOPTIMFLAGS = -O -ffast-math -malign-double
-- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W
-- FPROFILEFLAGS = -pg
-+ F77 ?= g77
-+ FFLAGS += -W -ffixed-line-length-132 -Wimplicit
-+ FOPTIMFLAGS += -malign-double
-+ FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W
-+ FPROFILEFLAGS =
- endif
-
- ifeq ($(COMPILER),pgi) # on mary, good bounds checking
-@@ -108,9 +108,9 @@ endif
-
- # Suse ppc gnu
- ifeq ($(COMPILER),ppc)
-- F77 = g77
-- FFLAGS = -Wall -finline-functions -funroll-loops -W
-ffixed-line-length-132
-- FDEBUGFLAGS = -g -C -Mbounds
-+ F77 ?= g77
-+ FFLAGS += -Wall -W -ffixed-line-length-132
-+ FDEBUGFLAGS += -C -Mbounds
- FOPTIMFLAGS =
- endif
-
-diff --git a/chemshift/makefile b/chemshift/makefile
-index 712e98f..05d3b64 100644
---- a/chemshift/makefile
-+++ b/chemshift/makefile
-@@ -64,7 +64,7 @@ regular: compile
- # rule to compile executable
- compile: $(BASE_NAME).$(COMPILER)
- $(BASE_NAME).$(COMPILER) : print ${OBJS}
-- $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
-+ $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
-
- # rule to compile object files:
- .$(COMPILER).%.o: %.f
diff --git
a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch
b/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch
deleted file mode 100644
index 91da48017ef..00000000000
--- a/sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch
+++ /dev/null
@@ -1,153 +0,0 @@
- nnmake/dipolar_nn.f | 2 +-
- nnmake/make.system | 33 ++++++++++++++++-----------------
- nnmake/make_fragments.pl | 36 ++++++++++++++++++------------------
- nnmake/makefile | 2 +-
- 4 files changed, 36 insertions(+), 37 deletions(-)
-
-diff --git a/nnmake/dipolar_nn.f b/nnmake/dipolar_nn.f
-index c159888..4412a20 100644
---- a/nnmake/dipolar_nn.f
-+++ b/nnmake/dipolar_nn.f
-@@ -1396,7 +1396,7 @@ car pairDipolar(1,i) .le. pairDipolar(1,i+1)
- write(0,*)'rejected'
- write(0,*)x(1,iset),x(2,iset),x(3,iset),x(4,iset),x(5,iset)
- do i=1,maplength(iset)
-- write(0,'(i,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5),
-+ write(0,'(i6,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5),
- # b(i)
- enddo
- goto 300
-diff --git a/nnmake/make.system b/nnmake/make.system
-index 34bea8f..2fbfabf 100644
---- a/nnmake/make.system
-+++ b/nnmake/make.system
-@@ -55,18 +55,17 @@ endif
- ########## once COMPILER is set, here are the options
-
- # defaults
--F77=f77
--FFLAGS=
--FOPTIMFLAGS=-O
--FDEBUGFLAGS=-g
--FPROFILEFLAGS=-P
-+F77?=f77
-+FOPTIMFLAGS=
-+FDEBUGFLAGS=
-+FPROFILEFLAGS=
-
- ifeq ($(COMPILER),gnu)
-- F77 = g77
-- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132
-Wimplicit
-- FOPTIMFLAGS = -O -ffast-math -malign-double
-- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W
-- FPROFILEFLAGS = -pg
-+ F77 ?= g77
-+ FFLAGS += -W -ffixed-line-length-132 -Wimplicit
-+ FOPTIMFLAGS += -malign-double
-+ FDEBUGFLAGS += -Wall -Wimplicit -Wsurprising -Wformat -W
-+ FPROFILEFLAGS =
- endif
-
- ifeq ($(COMPILER),pgi) # on mary, good bounds checking
-@@ -82,9 +81,9 @@ ifeq ($(COMPILER),pgi) # on mary, good bounds checking
- endif
-
- ifeq ($(COMPILER),absoft) # on mary, fast
-- F77 = f77
-- FFLAGS = -N109 -s -W
-- LINKFLAGS = -lU77
-+ F77 ?= f77
-+ FFLAGS ?= -N109 -s -W
-+ LINKFLAGS += -lU77
- FDEBUGFLAGS = -C -g
- FOPTIMFLAGS = -O -N18
- FPROFILEFLAGS = -P -O
-@@ -103,10 +102,10 @@ endif
-
- # Suse ppc gnu
- ifeq ($(COMPILER),ppc)
-- F77 = g77
-- FFLAGS = -Wall -finline-functions -funroll-loops -W
-ffixed-line-length-132
-- FDEBUGFLAGS = -g -C -Mbounds
-- FOPTIMFLAGS =
-+ F77 ?= g77
-+ FFLAGS += -Wall -W -ffixed-line-length-132
-+ FDEBUGFLAGS += -C -Mbounds
-+ FOPTIMFLAGS +=
- endif
-
- # alpha flags
-diff --git a/nnmake/make_fragments.pl b/nnmake/make_fragments.pl
-index 5273685..29619a2 100755
---- a/nnmake/make_fragments.pl
-+++ b/nnmake/make_fragments.pl
-@@ -19,38 +19,38 @@
-
- my $TAIL = "_v1_3";
-
--$src_dir = '/work/chu/rosetta/rosetta_C++/rosetta-2.2.0/rosetta_fragments';
--$shareware_dir = '/work/chu/src/shareware';
--$scratch = "/scratch/shared";
-+$src_dir = '@GENTOO_PORTAGE_EPREFIX@/';
-+$shareware_dir = '$src_dir/usr/share';
-+$scratch = "$src_dir/scratch/shared";
-
- # psi-blast
- #my $BLAST_BIN_DIR = "$shareware_dir/new_blast/blast-2.2.12/bin";
--my $PSIBLAST = "$shareware_dir/blast/bin/blastpgp"; # PSI-BLAST (duh.)
--my $NR = "/$scratch/genomes/nr"; # nr blast database filename
--my $VALL_BLAST_DB = "/$scratch/nnmake_database/vall.blast.2006-05-05";
# vall blast database filename (cvs respository 'nnmake_database')
--my $BLOSUM = "$scratch/nnmake_database/"; # BLOSUM score matrices
directory (cvs repository 'nnmake_database')
-+my $PSIBLAST = "$src_dir/usr/bin/blastpgp"; # PSI-BLAST (duh.)
-+my $NR = "$shareware_dir/nr"; # nr blast database filename
-+my $VALL_BLAST_DB =
"$shareware_dir/rosetta-fragments/nnmake_database/vall.blast.2006-05-05";
# vall blast database filename (cvs respository 'nnmake_database')
-+my $BLOSUM = "$shareware_dir/rosetta-fragments/nnmake_database/"; #
BLOSUM score matrices directory (cvs repository 'nnmake_database')
-
- # psipred
--my $FILTNR = "$scratch/genomes/filtnr"; # filtnr blast database
filename
--my $MAKEMAT = "$shareware_dir/blast/bin/makemat"; # makemat utility
(part of NCBI tools)
--my $PSIPRED = "$shareware_dir/psipred/bin/psipred"; # psipred
--my $PSIPASS2 = "$shareware_dir/psipred/bin/psipass2"; # psipass2 (part of
psipred pkg)
-+my $FILTNR = "$src_dir/tmp/filtnr"; # filtnr blast database filename
-+my $MAKEMAT = "$src_dir/usr/bin/makemat"; # makemat utility (part of
NCBI tools)
-+my $PSIPRED = "$src_dir/usr/bin/psipred"; # psipred
-+my $PSIPASS2 = "$src_dir/usr/bin/psipass2"; # psipass2 (part of psipred
pkg)
- my $PSIPRED_DATA = "$shareware_dir/psipred/data"; # dir containing
psipred data files.
-
- # prof
- #my $PROF = "$shareware_dir/prof/run_prof.py";
--my $PROF = "$src_dir/nnmake/run_prof.py"; # remember to change prof
executable location in run_prof.py
-+my $PROF = "$src_dir/usr/bin/run_prof.py"; # remember to change prof
executable location in run_prof.py
-
- # nnmake
--my $VALL = "$scratch/nnmake_database"; # dir containing vall
database (cvs repository 'nnmake_database')
--my $VALL2 = "$scratch/nnmake_database"; # alt dir containing vall
database (cvs repository 'nnmake_database')
-+my $VALL = "$shareware_dir/rosetta-fragments/nnmake_database"; # dir
containing vall database (cvs repository 'nnmake_database')
-+my $VALL2 = "$shareware_dir/rosetta-fragments/nnmake_database"; #
alt dir containing vall database (cvs repository 'nnmake_database')
- my $VALL_NAME = "vall.dat.2006-05-05"; # filename of vall
(vall.dat.<id> and vall_cst_coord.dat.<id> must exist)
--my $NNMAKE = "$src_dir/nnmake/pNNMAKE.gnu"; # nnmake
binary (cvs respository 'nnmake')
--my $TRIMLOOPS = "$src_dir/nnmake/trimLoopLibrary.pl"; #
trimLoopLibrary.pl (cvs respository 'nnmake')
-+my $NNMAKE = "$src_dir/usr/bin/pNNMAKE"; # nnmake
binary (cvs respository 'nnmake')
-+my $TRIMLOOPS = "$src_dir/usr/bin/trimLoopLibrary.pl"; #
trimLoopLibrary.pl (cvs respository 'nnmake')
-
- # chemshift
--my $CHEMSHIFT = "$src_dir/chemshift/pCHEMSHIFT.gnu"; # chemshift binary
(cvs repository 'chemshift')
--my $TALOS_DB = "$scratch/chemshift_database"; #
TALOS databases directory (cvs respository 'chemshift_database')
-+my $CHEMSHIFT = "$src_dir/usr/bin/pCHEMSHIFT"; # chemshift binary (cvs
repository 'chemshift')
-+my $TALOS_DB = "$shareware_dir/rosetta-fragments/chemshift_database";
# TALOS databases directory (cvs respository
'chemshift_database')
-
- # jufo (secondary structure prediction software)
- my $JUFO = "$shareware_dir/jufo/molecule.exe"; #
jufo executable
-diff --git a/nnmake/makefile b/nnmake/makefile
-index c09ac1c..ebfde68 100644
---- a/nnmake/makefile
-+++ b/nnmake/makefile
-@@ -102,7 +102,7 @@ VallCoord: coord_compile
- # rule to compile executable
- compile: print $(BASE_NAME).$(COMPILER)
- $(BASE_NAME).$(COMPILER) : ${OBJS}
-- $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
-+ $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS)
-
- coord_compile: print $(COORD_BASE_NAME).$(COMPILER)
- $(COORD_BASE_NAME).$(COMPILER) : ${COORD_OBJS}
diff --git a/sci-libs/rosetta-fragments/metadata.xml
b/sci-libs/rosetta-fragments/metadata.xml
deleted file mode 100644
index 8937bad0b17..00000000000
--- a/sci-libs/rosetta-fragments/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-chemis...@gentoo.org</email>
- <name>Gentoo Chemistry Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
deleted file mode 100644
index bc262a212a4..00000000000
--- a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic prefix toolchain-funcs vcs-clean
-
-DESCRIPTION="Fragment library for rosetta"
-HOMEPAGE="http://www.rosettacommons.org";
-SRC_URI="rosetta3.1_fragments.tgz"
-
-LICENSE="rosetta"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
- sci-biology/ncbi-tools
- sci-biology/update-blastdb
- sci-biology/psipred"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}"/${PN/-/_}
-
-PATCHES=(
- "${FILESDIR}"/${P}-nnmake.patch
- "${FILESDIR}"/${P}-chemshift.patch
-)
-
-pkg_nofetch() {
- einfo "Go to ${HOMEPAGE} and get ${PN}.tgz and rename it to ${A}"
- einfo "which must be placed into your DISTDIR directory."
-}
-
-src_prepare() {
- default
- tc-export F77
- eprefixify nnmake/*.pl
-}
-
-src_compile() {
- emake -C nnmake
- emake -C chemshift
-}
-
-src_install() {
- esvn_clean .
-
- newbin nnmake/pNNMAKE.gnu pNNMAKE
- newbin chemshift/pCHEMSHIFT.gnu pCHEMSHIFT
-
- dobin nnmake/*.pl
-
- insinto /usr/share/${PN}
- doins -r *_database
- dodoc \
- fragments.README \
- nnmake/{nnmake.README,vall/*.pl} \
- chemshift/chemshift.README
-}
