[med-svn] r7019 - in trunk/packages/rostlab/profnet/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Tue Jun 14 17:14:10 UTC 2011
Author: lkajan-guest
Date: 2011-06-14 17:14:10 +0000 (Tue, 14 Jun 2011)
New Revision: 7019
Removed:
trunk/packages/rostlab/profnet/trunk/debian/patches/patches.patch
Modified:
trunk/packages/rostlab/profnet/trunk/debian/README.Debian
trunk/packages/rostlab/profnet/trunk/debian/changelog
trunk/packages/rostlab/profnet/trunk/debian/copyright
trunk/packages/rostlab/profnet/trunk/debian/patches/series
Log:
1.0.20-1 UNRELEASED: New upstream release; Removed -Werror patch - upstream does not need it any more; Explained the reason for the many binary packages in README.Debian
Modified: trunk/packages/rostlab/profnet/trunk/debian/README.Debian
===================================================================
--- trunk/packages/rostlab/profnet/trunk/debian/README.Debian 2011-06-14 16:50:45 UTC (rev 7018)
+++ trunk/packages/rostlab/profnet/trunk/debian/README.Debian 2011-06-14 17:14:10 UTC (rev 7019)
@@ -1,6 +1,9 @@
-profnet for Debian
-------------------
+profnet
+=======
+profnet_* binaries are neural network implementations in Fortran. Due to the original design of the code, a specific binary is compiled for each particular network architecture, changing certain constants in the source code. Therefore, there is a binary for every network architecture used. Note: certain array structures are intentionally indexed out of bounds in some of the binaries.
-This package presents `profnet'.
+Q: Why so many binary packages?
+-------------------------------
+There are a handful of prediction methods built around each of the binary profnet packages. Each depends on the mathching profnet binary package. Each prediction method requires a different neural network architecture and therefore - due to the design of the code - a different binary. Binaries are compiled with constants set to the architecture of the network and are therefore not reusable for other architectures. Improving this code is not planned. A reimplementation of these networks with a neural network library is underway.
- -- Guy Yachdav <gyachdav at rostlab.org> Mon, 30 Nov 2009 14:56:34 +0100
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 14 Jun 2011 18:50:52 +0200
Modified: trunk/packages/rostlab/profnet/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/profnet/trunk/debian/changelog 2011-06-14 16:50:45 UTC (rev 7018)
+++ trunk/packages/rostlab/profnet/trunk/debian/changelog 2011-06-14 17:14:10 UTC (rev 7019)
@@ -1,3 +1,11 @@
+profnet (1.0.20-1) unstable; urgency=low
+
+ * New upstream release
+ * Removed -Werror patch - upstream does not need it any more
+ * Explained the reason for the many binary packages in README.Debian
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 14 Jun 2011 18:50:52 +0200
+
profnet (1.0.19-4) stable; urgency=low
* build for Debian unstable
Modified: trunk/packages/rostlab/profnet/trunk/debian/copyright
===================================================================
--- trunk/packages/rostlab/profnet/trunk/debian/copyright 2011-06-14 16:50:45 UTC (rev 7018)
+++ trunk/packages/rostlab/profnet/trunk/debian/copyright 2011-06-14 17:14:10 UTC (rev 7019)
@@ -1,4 +1,4 @@
-This package was debianized by Guy Yachdav <gyachdav at rostlab.org> on
+This package was debianized by Guy Yachdav <gyachdav at rostlab.org> on
Mon, 30 Nov 2009 14:53:52 +0100
Upstream Author:
Deleted: trunk/packages/rostlab/profnet/trunk/debian/patches/patches.patch
===================================================================
--- trunk/packages/rostlab/profnet/trunk/debian/patches/patches.patch 2011-06-14 16:50:45 UTC (rev 7018)
+++ trunk/packages/rostlab/profnet/trunk/debian/patches/patches.patch 2011-06-14 17:14:10 UTC (rev 7019)
@@ -1,224 +0,0 @@
-Index: profnet-1.0.19/src-phd/Makefile
-===================================================================
---- profnet-1.0.19.orig/src-phd/Makefile 2010-01-05 11:53:20.000000000 +0100
-+++ profnet-1.0.19/src-phd/Makefile 2011-06-12 19:23:16.193205641 +0200
-@@ -95,8 +95,8 @@
- #
- # -finit-local-zero - initializing variables - solves all of the above but not all compilers support it. Solution: initialize all variables properly.
-
--FFLAGS := -O3 -fbounds-check
--FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-+FFLAGS := -O3
-+FFLAGS := $(FFLAGS) -Wall
-
- profphd_net : phd.f lib-phd.f phdParameter.f
- $(F77) $(FFLAGS) -o $@ phd.f lib-phd.f
-Index: profnet-1.0.19/bval.patch
-===================================================================
---- profnet-1.0.19.orig/bval.patch 2010-02-23 10:42:49.000000000 +0100
-+++ profnet-1.0.19/bval.patch 2011-06-12 19:05:29.463916012 +0200
-@@ -9,8 +9,9 @@
- #=====================================================================
- ARCH = LINUX
- -FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
- +FFLAGS := -O3 -Wuninitialized
-- FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-++FFLAGS := $(FFLAGS) -Wall
- #=====================================================================
- NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/prof.f bval_dir/prof.f
-Index: profnet-1.0.19/chop.patch
-===================================================================
---- profnet-1.0.19.orig/chop.patch 2010-05-12 20:05:27.000000000 +0200
-+++ profnet-1.0.19/chop.patch 2011-06-12 19:05:29.467916030 +0200
-@@ -1,11 +1,16 @@
--diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile chop_dir/Makefile
----- src/Makefile 2010-02-10 17:55:33.923514458 +0100
--+++ chop_dir/Makefile 2010-05-12 20:05:09.819459484 +0200
--@@ -1,6 +1,6 @@
-+--- src/Makefile 2010-02-10 17:55:33.000000000 +0100
-++++ chop_dir/Makefile 2011-06-12 18:32:32.874114630 +0200
-+@@ -1,10 +1,10 @@
- #=====================================================================
- F77 = gfortran
- -BIN = profnet_prof
- +BIN = profnet_chop
- #=====================================================================
- ARCH = LINUX
-- FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-++FFLAGS := -O3 -fbounds-check
-++FFLAGS := $(FFLAGS) -Wall
-+ #=====================================================================
-+ NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f
-+ SOURCES := $(NN_OBJS) profPar.f
-Index: profnet-1.0.19/con.patch
-===================================================================
---- profnet-1.0.19.orig/con.patch 2010-02-23 10:48:52.000000000 +0100
-+++ profnet-1.0.19/con.patch 2011-06-12 19:05:29.467916030 +0200
-@@ -1,14 +1,20 @@
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile con_dir/Makefile
----- src/Makefile 2010-02-10 17:55:33.923514458 +0100
--+++ con_dir/Makefile 2010-02-23 10:48:22.263658539 +0100
--@@ -1,6 +1,6 @@
-+--- src/Makefile 2010-02-10 17:55:33.000000000 +0100
-++++ con_dir/Makefile 2011-06-12 18:34:50.926799202 +0200
-+@@ -1,10 +1,10 @@
- #=====================================================================
- F77 = gfortran
- -BIN = profnet_prof
- +BIN = profnet_con
- #=====================================================================
- ARCH = LINUX
-- FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-++FFLAGS := -O3 -fbounds-check
-++FFLAGS := $(FFLAGS) -Wall
-+ #=====================================================================
-+ NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f
-+ SOURCES := $(NN_OBJS) profPar.f
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f con_dir/profPar.f
- --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100
- +++ con_dir/profPar.f 2010-02-23 10:47:35.907691244 +0100
-Index: profnet-1.0.19/isis.patch
-===================================================================
---- profnet-1.0.19.orig/isis.patch 2010-04-23 15:28:30.000000000 +0200
-+++ profnet-1.0.19/isis.patch 2011-06-12 19:05:29.467916030 +0200
-@@ -1,14 +1,20 @@
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile isis_dir/Makefile
----- src/Makefile 2010-02-10 17:55:33.923514458 +0100
--+++ isis_dir/Makefile 2010-02-26 11:22:10.199787414 +0100
--@@ -1,6 +1,6 @@
-+--- src/Makefile 2010-02-10 17:55:33.000000000 +0100
-++++ isis_dir/Makefile 2011-06-12 18:37:59.599734777 +0200
-+@@ -1,10 +1,10 @@
- #=====================================================================
- F77 = gfortran
- -BIN = profnet_prof
- +BIN = profnet_isis
- #=====================================================================
- ARCH = LINUX
-- FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-++FFLAGS := -O3 -fbounds-check
-++FFLAGS := $(FFLAGS) -Wall
-+ #=====================================================================
-+ NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f
-+ SOURCES := $(NN_OBJS) profPar.f
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f isis_dir/profPar.f
- --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100
- +++ isis_dir/profPar.f 2010-02-26 11:20:32.863648133 +0100
-Index: profnet-1.0.19/md.patch
-===================================================================
---- profnet-1.0.19.orig/md.patch 2010-03-17 16:18:21.000000000 +0100
-+++ profnet-1.0.19/md.patch 2011-06-12 19:05:29.467916030 +0200
-@@ -9,8 +9,9 @@
- #=====================================================================
- ARCH = LINUX
- -FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
- +FFLAGS := -O3 -Wuninitialized
-- FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-++FFLAGS := $(FFLAGS) -Wall
- #=====================================================================
- NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/prof.f md_dir/prof.f
-Index: profnet-1.0.19/norsnet.patch
-===================================================================
---- profnet-1.0.19.orig/norsnet.patch 2010-03-16 18:31:11.000000000 +0100
-+++ profnet-1.0.19/norsnet.patch 2011-06-12 19:05:29.467916030 +0200
-@@ -9,8 +9,9 @@
- #=====================================================================
- ARCH = LINUX
- -FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
- +FFLAGS := -O3 -Wuninitialized
-- FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-++FFLAGS := $(FFLAGS) -Wall
- #=====================================================================
- NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/prof.f norsnet_dir/prof.f
-Index: profnet-1.0.19/prof.patch
-===================================================================
---- /dev/null 1970-01-01 00:00:00.000000000 +0000
-+++ profnet-1.0.19/prof.patch 2011-06-12 19:05:29.467916030 +0200
-@@ -0,0 +1,13 @@
-+--- src/Makefile 2010-02-10 17:55:33.000000000 +0100
-++++ prof_dir/Makefile 2011-06-12 18:43:25.449350577 +0200
-+@@ -3,8 +3,8 @@
-+ BIN = profnet_prof
-+ #=====================================================================
-+ ARCH = LINUX
-+-FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-++FFLAGS := -O3 -fbounds-check
-++FFLAGS := $(FFLAGS) -Wall
-+ #=====================================================================
-+ NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f
-+ SOURCES := $(NN_OBJS) profPar.f
-Index: profnet-1.0.19/snapfun.patch
-===================================================================
---- profnet-1.0.19.orig/snapfun.patch 2010-02-23 10:42:49.000000000 +0100
-+++ profnet-1.0.19/snapfun.patch 2011-06-12 19:05:29.467916030 +0200
-@@ -1,47 +1,20 @@
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile snapfun_dir/Makefile
----- src/Makefile 2010-02-10 17:55:33.923514458 +0100
--+++ snapfun_dir/Makefile 2010-02-23 10:38:31.391656287 +0100
--@@ -1,6 +1,6 @@
-+--- src/Makefile 2010-02-10 17:55:33.000000000 +0100
-++++ snapfun_dir/Makefile 2011-06-12 18:45:30.297969668 +0200
-+@@ -1,10 +1,10 @@
- #=====================================================================
- F77 = gfortran
- -BIN = profnet_prof
- +BIN = profnet_snapfun
- #=====================================================================
- ARCH = LINUX
-- FFLAGS := -O3 -fbounds-check -Wuninitialized
--diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/Makefile.orig snapfun_dir/Makefile.orig
----- src/Makefile.orig 1970-01-01 01:00:00.000000000 +0100
--+++ snapfun_dir/Makefile.orig 2010-02-23 10:38:31.395653152 +0100
--@@ -0,0 +1,29 @@
--+#=====================================================================
--+F77 = gfortran
--+BIN = profnet_prof
--+#=====================================================================
--+ARCH = LINUX
--+FFLAGS := -O3 -fbounds-check -Wuninitialized
--+FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
--+#=====================================================================
--+all: $(BIN)
--+
--+#=====================================================================
--+# Make Neural Network
--+#=====================================================================
--+
--+NN_OBJS=prof.f lib-prof.f lib-sys-$(ARCH).f
--+
--+$(BIN): $(NN_OBJS)
--+ @echo --- making $(BIN)
--+ $(F77) -o $@ $(FFLAGS) $(NN_OBJS)
--+
--+clean:
--+ rm -f *.o $(BIN)
--+
--+install:
--+ mkdir -p $(DESTDIR)$(prefix)/usr/bin && \
--+ cp $(BIN) $(DESTDIR)$(prefix)/usr/bin/
--+
--+.PHONY: all clean install
--+
-+-FFLAGS := -O3 -fbounds-check -Wuninitialized
-+-FFLAGS := $(FFLAGS) -Wall -Wno-unused -Werror
-++FFLAGS := -O3 -fbounds-check
-++FFLAGS := $(FFLAGS) -Wall
-+ #=====================================================================
-+ NN_OBJS := prof.f lib-prof.f lib-sys-$(ARCH).f
-+ SOURCES := $(NN_OBJS) profPar.f
- diff -ruN -x '.*.swp' -x 'profnet*' -x .svn src/profPar.f snapfun_dir/profPar.f
- --- src/profPar.f 2010-02-23 10:17:25.315661972 +0100
- +++ snapfun_dir/profPar.f 2010-02-23 10:38:31.399648899 +0100
Modified: trunk/packages/rostlab/profnet/trunk/debian/patches/series
===================================================================
--- trunk/packages/rostlab/profnet/trunk/debian/patches/series 2011-06-14 16:50:45 UTC (rev 7018)
+++ trunk/packages/rostlab/profnet/trunk/debian/patches/series 2011-06-14 17:14:10 UTC (rev 7019)
@@ -1 +0,0 @@
-patches.patch
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