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authorMichael Mair-Keimberger (asterix) <m.mairkeimberger@gmail.com>2017-01-29 09:44:12 +0100
committerDavid Seifert <soap@gentoo.org>2017-01-29 21:09:14 +0100
commit141b4f1e62b2f729dd0d7c27bdee231458ba3704 (patch)
tree17744cc127150b5e9fda35254545cc978897265d /sci-biology/psipred/files
parentsci-biology/primer3: remove unused patch (diff)
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sci-biology/psipred: remove unused patches
Closes: https://github.com/gentoo/gentoo/pull/3708
Diffstat (limited to 'sci-biology/psipred/files')
-rw-r--r--sci-biology/psipred/files/2.6.1-Makefile.patch42
-rw-r--r--sci-biology/psipred/files/2.6.1-path.patch34
-rw-r--r--sci-biology/psipred/files/3.0-path.patch38
3 files changed, 0 insertions, 114 deletions
diff --git a/sci-biology/psipred/files/2.6.1-Makefile.patch b/sci-biology/psipred/files/2.6.1-Makefile.patch
deleted file mode 100644
index 0a6df743ec83..000000000000
--- a/sci-biology/psipred/files/2.6.1-Makefile.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- src/Makefile 2008-03-09 22:59:51.000000000 +0100
-+++ src/Makefile.new 2009-04-09 12:31:38.669457918 +0200
-@@ -6,9 +6,7 @@
- #### CFLAGS Flags to pass to C compiler.
-
- INCDIR = .
--CC = cc
-
--CFLAGS = -O
- LIBS = -lm
-
- all: psipred psipass2 seq2mtx pfilt
-@@ -20,13 +18,13 @@
- /bin/rm -f psipred psipass2 seq2mtx pfilt
-
- psipred: sspred_avpred.c ssdefs.h sspred_net.h
-- $(CC) $(CFLAGS) sspred_avpred.c $(LIBS) -o psipred
-+ $(CC) $(CFLAGS) $(LDFLAGS) sspred_avpred.c $(LIBS) -o psipred
-
- psipass2: sspred_hmulti.c ssdefs.h sspred_net2.h
-- $(CC) $(CFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
-+ $(CC) $(CFLAGS) $(LDFLAGS) sspred_hmulti.c $(LIBS) -o psipass2
-
- seq2mtx: seq2mtx.c
-- $(CC) $(CFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
-+ $(CC) $(CFLAGS) $(LDFLAGS) seq2mtx.c $(LIBS) -o seq2mtx
-
- pfilt: pfilt.c
-- $(CC) $(CFLAGS) pfilt.c $(LIBS) -o pfilt
-+ $(CC) $(CFLAGS) $(LDFLAGS) pfilt.c $(LIBS) -o pfilt
---- src/Makefile 2009-04-09 12:34:41.636939862 +0200
-+++ src/Makefile.new 2009-04-09 12:36:03.796098341 +0200
-@@ -12,7 +12,8 @@
- all: psipred psipass2 seq2mtx pfilt
-
- install:
-- /bin/cp psipred psipass2 seq2mtx pfilt ../bin
-+ /bin/mkdir -p $(DESTDIR)/usr/bin
-+ /bin/cp psipred psipass2 seq2mtx pfilt $(DESTDIR)/usr/bin
-
- clean:
- /bin/rm -f psipred psipass2 seq2mtx pfilt
diff --git a/sci-biology/psipred/files/2.6.1-path.patch b/sci-biology/psipred/files/2.6.1-path.patch
deleted file mode 100644
index 9b8d6b9fecfa..000000000000
--- a/sci-biology/psipred/files/2.6.1-path.patch
+++ /dev/null
@@ -1,34 +0,0 @@
---- runpsipred 2008-04-05 00:14:36.000000000 +0200
-+++ runpsipred.new 2009-04-09 12:40:46.376203036 +0200
-@@ -14,13 +14,13 @@
- set dbname = nr
-
- # Where the NCBI programs have been installed
--set ncbidir = /usr/local/bin
-+set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V2 programs have been installed
--set execdir = ./bin
-+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V2 data files have been installed
--set datadir = ./data
-+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
-
- set basename = $1:r
- set rootname = $basename:t
---- runpsipred_single 2008-04-05 00:14:38.000000000 +0200
-+++ runpsipred_single.new 2009-04-09 12:41:10.086067082 +0200
-@@ -10,10 +10,10 @@
- # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
-
- # Where the PSIPRED V2 programs have been installed
--set execdir = ./bin
-+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V2 data files have been installed
--set datadir = ./data
-+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
-
- set basename = $1:r
- set rootname = $basename:t
diff --git a/sci-biology/psipred/files/3.0-path.patch b/sci-biology/psipred/files/3.0-path.patch
deleted file mode 100644
index ebf9b2a61f4e..000000000000
--- a/sci-biology/psipred/files/3.0-path.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-diff --git a/runpsipred b/runpsipred
-index e133686..6ad57cc 100755
---- a/runpsipred
-+++ b/runpsipred
-@@ -14,13 +14,13 @@
- set dbname = uniref90
-
- # Where the NCBI programs have been installed
--set ncbidir = /usr/local/bin
-+set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V3 programs have been installed
--set execdir = ./bin
-+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V3 data files have been installed
--set datadir = ./data
-+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
-
- set basename = $1:r
- set rootname = $basename:t
-diff --git a/runpsipred_single b/runpsipred_single
-index 1f7680b..7bd5bc3 100755
---- a/runpsipred_single
-+++ b/runpsipred_single
-@@ -10,10 +10,10 @@
- # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
-
- # Where the PSIPRED V3 programs have been installed
--set execdir = ./bin
-+set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
-
- # Where the PSIPRED V3 data files have been installed
--set datadir = ./data
-+set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
-
- set basename = $1:r
- set rootname = $basename:t