commit: 818302cf458db807d47ab01c43d99271a5b9a8d4 Author: Michael Mair-Keimberger (asterix) <m.mairkeimberger <AT> gmail <DOT> com> AuthorDate: Mon Jan 30 18:01:14 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Tue Jan 31 08:42:00 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=818302cf
sci-libs/rosetta-fragments: remove unused patches Closes: https://github.com/gentoo/gentoo/pull/3730 .../rosetta-fragments/files/3.1-chemshift.patch | 33 ------- sci-libs/rosetta-fragments/files/3.1-nnmake.patch | 107 --------------------- 2 files changed, 140 deletions(-) diff --git a/sci-libs/rosetta-fragments/files/3.1-chemshift.patch b/sci-libs/rosetta-fragments/files/3.1-chemshift.patch deleted file mode 100644 index 6ea69b2..00000000 --- a/sci-libs/rosetta-fragments/files/3.1-chemshift.patch +++ /dev/null @@ -1,33 +0,0 @@ ---- chemshift/makefile 2009-01-09 16:08:00.000000000 +0100 -+++ chemshift/makefile.new 2009-04-09 11:30:34.179824057 +0200 -@@ -64,7 +64,7 @@ - # 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 ---- chemshift/make.system 2009-01-09 16:08:00.000000000 +0100 -+++ chemshift/make.system.new 2009-04-09 11:35:16.126466293 +0200 -@@ -61,16 +61,14 @@ - - # defaults - F77=f77 --FFLAGS= - FOPTIMFLAGS=-O - FDEBUGFLAGS=-g - 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 -+ F77 = $(FORTRANC) -+ FOPTIMFLAGS = -+ FDEBUGFLAGS = - FPROFILEFLAGS = -pg - endif - diff --git a/sci-libs/rosetta-fragments/files/3.1-nnmake.patch b/sci-libs/rosetta-fragments/files/3.1-nnmake.patch deleted file mode 100644 index 35568bb..00000000 --- a/sci-libs/rosetta-fragments/files/3.1-nnmake.patch +++ /dev/null @@ -1,107 +0,0 @@ ---- nnmake/make.system 2009-01-09 16:07:59.000000000 +0100 -+++ nnmake/make.system.new 2009-04-09 10:54:50.000000000 +0200 -@@ -62,10 +62,9 @@ - FPROFILEFLAGS=-P - - ifeq ($(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 -+ F77 = $(FORTRANC) -+ FOPTIMFLAGS = -+ FDEBUGFLAGS = - FPROFILEFLAGS = -pg - endif - ---- nnmake/dipolar_nn.f 2009-01-09 16:08:00.000000000 +0100 -+++ nnmake/dipolar_nn.f.new 2009-04-09 11:06:24.923302302 +0200 -@@ -1396,7 +1396,7 @@ - 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 ---- nnmake/make.system 2009-04-09 11:10:34.399945087 +0200 -+++ nnmake/make.system.new 2009-04-09 11:19:41.287390259 +0200 -@@ -55,7 +55,6 @@ - - # defaults - F77=f77 --FFLAGS= - FOPTIMFLAGS=-O - FDEBUGFLAGS=-g - FPROFILEFLAGS=-P ---- nnmake/makefile 2009-01-09 16:08:00.000000000 +0100 -+++ nnmake/makefile.new 2009-04-09 11:22:43.454037887 +0200 -@@ -102,7 +102,7 @@ - # 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} ---- nnmake/make_fragments.pl 2009-01-09 15:53:33.000000000 +0100 -+++ nnmake/make_fragments.pl.new 2009-04-09 13:01:52.987174602 +0200 -@@ -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"; -+$src_dir = '/'; -+$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/blast-db/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
