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commit: 818302cf458db807d47ab01c43d99271a5b9a8d4 |
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Author: Michael Mair-Keimberger (asterix) <m.mairkeimberger <AT> gmail <DOT> com> |
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AuthorDate: Mon Jan 30 18:01:14 2017 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Tue Jan 31 08:42:00 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=818302cf |
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|
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sci-libs/rosetta-fragments: remove unused patches |
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|
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Closes: https://github.com/gentoo/gentoo/pull/3730 |
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|
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.../rosetta-fragments/files/3.1-chemshift.patch | 33 ------- |
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sci-libs/rosetta-fragments/files/3.1-nnmake.patch | 107 --------------------- |
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2 files changed, 140 deletions(-) |
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|
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diff --git a/sci-libs/rosetta-fragments/files/3.1-chemshift.patch b/sci-libs/rosetta-fragments/files/3.1-chemshift.patch |
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deleted file mode 100644 |
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index 6ea69b2..00000000 |
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--- a/sci-libs/rosetta-fragments/files/3.1-chemshift.patch |
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+++ /dev/null |
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@@ -1,33 +0,0 @@ |
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---- chemshift/makefile 2009-01-09 16:08:00.000000000 +0100 |
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-+++ chemshift/makefile.new 2009-04-09 11:30:34.179824057 +0200 |
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-@@ -64,7 +64,7 @@ |
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- # rule to compile executable |
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- compile: $(BASE_NAME).$(COMPILER) |
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- $(BASE_NAME).$(COMPILER) : print ${OBJS} |
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-- $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS) |
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-+ $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS) |
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- |
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- # rule to compile object files: |
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- .$(COMPILER).%.o: %.f |
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---- chemshift/make.system 2009-01-09 16:08:00.000000000 +0100 |
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-+++ chemshift/make.system.new 2009-04-09 11:35:16.126466293 +0200 |
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-@@ -61,16 +61,14 @@ |
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- |
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- # defaults |
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- F77=f77 |
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--FFLAGS= |
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- FOPTIMFLAGS=-O |
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- FDEBUGFLAGS=-g |
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- FPROFILEFLAGS=-P |
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- |
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- ifeq ($(COMPILER),gnu) |
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-- F77 = g77 |
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-- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit |
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-- FOPTIMFLAGS = -O -ffast-math -malign-double |
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-- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W |
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-+ F77 = $(FORTRANC) |
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-+ FOPTIMFLAGS = |
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-+ FDEBUGFLAGS = |
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- FPROFILEFLAGS = -pg |
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- endif |
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- |
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|
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diff --git a/sci-libs/rosetta-fragments/files/3.1-nnmake.patch b/sci-libs/rosetta-fragments/files/3.1-nnmake.patch |
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deleted file mode 100644 |
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index 35568bb..00000000 |
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--- a/sci-libs/rosetta-fragments/files/3.1-nnmake.patch |
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+++ /dev/null |
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@@ -1,107 +0,0 @@ |
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---- nnmake/make.system 2009-01-09 16:07:59.000000000 +0100 |
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-+++ nnmake/make.system.new 2009-04-09 10:54:50.000000000 +0200 |
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-@@ -62,10 +62,9 @@ |
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- FPROFILEFLAGS=-P |
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- |
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- ifeq ($(COMPILER),gnu) |
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-- F77 = g77 |
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-- FFLAGS = -finline-functions -funroll-loops -W -ffixed-line-length-132 -Wimplicit |
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-- FOPTIMFLAGS = -O -ffast-math -malign-double |
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-- FDEBUGFLAGS = -g -Wall -Wimplicit -Wsurprising -Wformat -W |
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-+ F77 = $(FORTRANC) |
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-+ FOPTIMFLAGS = |
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-+ FDEBUGFLAGS = |
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- FPROFILEFLAGS = -pg |
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- endif |
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- |
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---- nnmake/dipolar_nn.f 2009-01-09 16:08:00.000000000 +0100 |
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-+++ nnmake/dipolar_nn.f.new 2009-04-09 11:06:24.923302302 +0200 |
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-@@ -1396,7 +1396,7 @@ |
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- write(0,*)'rejected' |
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- write(0,*)x(1,iset),x(2,iset),x(3,iset),x(4,iset),x(5,iset) |
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- do i=1,maplength(iset) |
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-- write(0,'(i,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5), |
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-+ write(0,'(i6,6f6.3)')i,A(i,1),A(i,2),A(i,3),A(i,4),A(i,5), |
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- # b(i) |
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- enddo |
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- goto 300 |
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---- nnmake/make.system 2009-04-09 11:10:34.399945087 +0200 |
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-+++ nnmake/make.system.new 2009-04-09 11:19:41.287390259 +0200 |
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-@@ -55,7 +55,6 @@ |
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- |
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- # defaults |
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- F77=f77 |
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--FFLAGS= |
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- FOPTIMFLAGS=-O |
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- FDEBUGFLAGS=-g |
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- FPROFILEFLAGS=-P |
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---- nnmake/makefile 2009-01-09 16:08:00.000000000 +0100 |
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-+++ nnmake/makefile.new 2009-04-09 11:22:43.454037887 +0200 |
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-@@ -102,7 +102,7 @@ |
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- # rule to compile executable |
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- compile: print $(BASE_NAME).$(COMPILER) |
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- $(BASE_NAME).$(COMPILER) : ${OBJS} |
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-- $(F77) $(FFLAGS) -o $@ $(OBJS) $(LINKFLAGS) |
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-+ $(F77) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(LINKFLAGS) |
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- |
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- coord_compile: print $(COORD_BASE_NAME).$(COMPILER) |
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- $(COORD_BASE_NAME).$(COMPILER) : ${COORD_OBJS} |
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---- nnmake/make_fragments.pl 2009-01-09 15:53:33.000000000 +0100 |
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-+++ nnmake/make_fragments.pl.new 2009-04-09 13:01:52.987174602 +0200 |
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-@@ -19,38 +19,38 @@ |
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- |
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- my $TAIL = "_v1_3"; |
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- |
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--$src_dir = '/work/chu/rosetta/rosetta_C++/rosetta-2.2.0/rosetta_fragments'; |
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--$shareware_dir = '/work/chu/src/shareware'; |
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--$scratch = "/scratch/shared"; |
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-+$src_dir = '/'; |
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-+$shareware_dir = '$src_dir/usr/share'; |
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-+$scratch = "$src_dir/scratch/shared"; |
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- |
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- # psi-blast |
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- #my $BLAST_BIN_DIR = "$shareware_dir/new_blast/blast-2.2.12/bin"; |
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--my $PSIBLAST = "$shareware_dir/blast/bin/blastpgp"; # PSI-BLAST (duh.) |
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--my $NR = "/$scratch/genomes/nr"; # nr blast database filename |
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--my $VALL_BLAST_DB = "/$scratch/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database') |
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--my $BLOSUM = "$scratch/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database') |
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-+my $PSIBLAST = "$src_dir/usr/bin/blastpgp"; # PSI-BLAST (duh.) |
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-+my $NR = "$shareware_dir/blast-db/nr"; # nr blast database filename |
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-+my $VALL_BLAST_DB = "$shareware_dir/rosetta-fragments/nnmake_database/vall.blast.2006-05-05"; # vall blast database filename (cvs respository 'nnmake_database') |
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-+my $BLOSUM = "$shareware_dir/rosetta-fragments/nnmake_database/"; # BLOSUM score matrices directory (cvs repository 'nnmake_database') |
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- |
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- # psipred |
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--my $FILTNR = "$scratch/genomes/filtnr"; # filtnr blast database filename |
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--my $MAKEMAT = "$shareware_dir/blast/bin/makemat"; # makemat utility (part of NCBI tools) |
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--my $PSIPRED = "$shareware_dir/psipred/bin/psipred"; # psipred |
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--my $PSIPASS2 = "$shareware_dir/psipred/bin/psipass2"; # psipass2 (part of psipred pkg) |
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-+my $FILTNR = "$src_dir/tmp/filtnr"; # filtnr blast database filename |
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-+my $MAKEMAT = "$src_dir/usr/bin/makemat"; # makemat utility (part of NCBI tools) |
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-+my $PSIPRED = "$src_dir/usr/bin/psipred"; # psipred |
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-+my $PSIPASS2 = "$src_dir/usr/bin/psipass2"; # psipass2 (part of psipred pkg) |
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- my $PSIPRED_DATA = "$shareware_dir/psipred/data"; # dir containing psipred data files. |
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- |
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- # prof |
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- #my $PROF = "$shareware_dir/prof/run_prof.py"; |
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--my $PROF = "$src_dir/nnmake/run_prof.py"; # remember to change prof executable location in run_prof.py |
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-+my $PROF = "$src_dir/usr/bin/run_prof.py"; # remember to change prof executable location in run_prof.py |
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- |
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- # nnmake |
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--my $VALL = "$scratch/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database') |
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--my $VALL2 = "$scratch/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database') |
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-+my $VALL = "$shareware_dir/rosetta-fragments/nnmake_database"; # dir containing vall database (cvs repository 'nnmake_database') |
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-+my $VALL2 = "$shareware_dir/rosetta-fragments/nnmake_database"; # alt dir containing vall database (cvs repository 'nnmake_database') |
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- my $VALL_NAME = "vall.dat.2006-05-05"; # filename of vall (vall.dat.<id> and vall_cst_coord.dat.<id> must exist) |
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--my $NNMAKE = "$src_dir/nnmake/pNNMAKE.gnu"; # nnmake binary (cvs respository 'nnmake') |
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--my $TRIMLOOPS = "$src_dir/nnmake/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake') |
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-+my $NNMAKE = "$src_dir/usr/bin/pNNMAKE"; # nnmake binary (cvs respository 'nnmake') |
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-+my $TRIMLOOPS = "$src_dir/usr/bin/trimLoopLibrary.pl"; # trimLoopLibrary.pl (cvs respository 'nnmake') |
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- |
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- # chemshift |
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--my $CHEMSHIFT = "$src_dir/chemshift/pCHEMSHIFT.gnu"; # chemshift binary (cvs repository 'chemshift') |
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--my $TALOS_DB = "$scratch/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database') |
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-+my $CHEMSHIFT = "$src_dir/usr/bin/pCHEMSHIFT"; # chemshift binary (cvs repository 'chemshift') |
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-+my $TALOS_DB = "$shareware_dir/rosetta-fragments/chemshift_database"; # TALOS databases directory (cvs respository 'chemshift_database') |
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- |
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- # jufo (secondary structure prediction software) |
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- my $JUFO = "$shareware_dir/jufo/molecule.exe"; # jufo executable |
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