From 4ccc9f448c6fef32e56e05502a2ab45a441865c3 Mon Sep 17 00:00:00 2001 From: Jakov Smolić Date: Mon, 30 Aug 2021 19:14:06 +0200 Subject: sci-libs/rosetta-fragments: Remove last-rited package MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jakov Smolić --- 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 --------- 5 files changed, 286 deletions(-) delete mode 100644 sci-libs/rosetta-fragments/Manifest delete mode 100644 sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-chemshift.patch delete mode 100644 sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch delete mode 100644 sci-libs/rosetta-fragments/metadata.xml delete mode 100644 sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild (limited to 'sci-libs') diff --git a/sci-libs/rosetta-fragments/Manifest b/sci-libs/rosetta-fragments/Manifest deleted file mode 100644 index 838f4129d740..000000000000 --- 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 cb8fd9197d1b..000000000000 --- 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 91da48017eff..000000000000 --- 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. and vall_cst_coord.dat. 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) : ${COORD_OBJS} diff --git a/sci-libs/rosetta-fragments/metadata.xml b/sci-libs/rosetta-fragments/metadata.xml deleted file mode 100644 index 8937bad0b175..000000000000 --- a/sci-libs/rosetta-fragments/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - diff --git a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild b/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild deleted file mode 100644 index bc262a212a42..000000000000 --- a/sci-libs/rosetta-fragments/rosetta-fragments-3.1-r1.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic prefix toolchain-funcs vcs-clean - -DESCRIPTION="Fragment library for rosetta" -HOMEPAGE="http://www.rosettacommons.org" -SRC_URI="rosetta3.1_fragments.tgz" - -LICENSE="rosetta" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND="" -RDEPEND=" - sci-biology/ncbi-tools - sci-biology/update-blastdb - sci-biology/psipred" - -RESTRICT="fetch" - -S="${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 -} -- cgit v1.2.3-65-gdbad