From 3b08f674e3f771b49370edb144dab0958c8cf721 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Tue, 31 Aug 2021 08:59:54 +0100 Subject: gentoo resync : 31.08.2021 --- .../files/rosetta-fragments-3.1-nnmake.patch | 153 --------------------- 1 file changed, 153 deletions(-) delete mode 100644 sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch (limited to 'sci-libs/rosetta-fragments/files/rosetta-fragments-3.1-nnmake.patch') 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} -- cgit v1.2.3