[med-svn] [staden] 05/08: Adapt patches to new upstream version
Andreas Tille
tille at debian.org
Thu Jul 14 18:29:35 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository staden.
commit 2a1e9197c8d05ef3ae82f74b430f496051030bad
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 14 20:22:34 2016 +0200
Adapt patches to new upstream version
---
.../patches/cope_with_modern_windowmanager.patch | 26 ---------
debian/patches/delete_rpath_from_configure.patch | 25 --------
debian/patches/fix_undefined_min.patch | 11 ----
debian/patches/hardening.patch | 15 -----
debian/patches/hardening_format-security.patch | 45 --------------
debian/patches/include_xalloc.patch | 8 +--
debian/patches/make_help_menus_work.patch | 28 ---------
debian/patches/remove_svnversion_dep.patch | 21 -------
debian/patches/series | 7 ---
debian/patches/spelling.patch | 68 ----------------------
10 files changed, 2 insertions(+), 252 deletions(-)
diff --git a/debian/patches/cope_with_modern_windowmanager.patch b/debian/patches/cope_with_modern_windowmanager.patch
deleted file mode 100644
index 84c3ed3..0000000
--- a/debian/patches/cope_with_modern_windowmanager.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Author: James Bonfield <jkb at sanger.ac.uk>
-Last-Update: Mon, 22 Feb 2016 09:56:12 +0000
-Upstream: Upstream explained problem at https://bugs.debian.org/815176#30 and provided the solution later in the bug report
-Bug-Debian: https://bugs.debian.org/815176
-Description: Deal with modern window managers
-
---- a/gap4/contig_editor.tcl
-+++ b/gap4/contig_editor.tcl
-@@ -108,7 +108,7 @@ proc create_editor {w edname join reveal
- xtoplevel $w
- fix_maxsize $w
- }
-- wm resizable $w 1 0
-+ # wm resizable $w 1 0
-
- catch {set $w.Grab [grab current]}
- frame $w.grab
-@@ -450,7 +450,7 @@ proc create_editor {w edname join reveal
- #
- bind $w <Any-Configure> {
- if {[winfo toplevel %W] == "%W"} {
-- after 1000 {if {[winfo exists %W]} {wm geometry %W {}}}
-+ wm geometry %W {}
- }
- }
- SetDefaultTags CONTIG_EDITOR.TAGS $editor
diff --git a/debian/patches/delete_rpath_from_configure.patch b/debian/patches/delete_rpath_from_configure.patch
deleted file mode 100644
index 03136cc..0000000
--- a/debian/patches/delete_rpath_from_configure.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 20 Jan 2014 11:21:17 +0100
-Description: UNUSED
- The intention was to fix multi-arch build but this failed
-
---- a/configure
-+++ b/configure
-@@ -11477,15 +11477,8 @@ fi
-
-
- # Step 0.d: Disable -rpath support?
--
-- { echo "$as_me:$LINENO: checking if rpath support is requested" >&5
--echo $ECHO_N "checking if rpath support is requested... $ECHO_C" >&6; }
-- # Check whether --enable-rpath was given.
--if test "${enable_rpath+set}" = set; then
-- enableval=$enable_rpath; doRpath=$enableval
--else
-- doRpath=yes
--fi
-+ # Force disabling rpath
-+ doRpath=no
-
- { echo "$as_me:$LINENO: result: $doRpath" >&5
- echo "${ECHO_T}$doRpath" >&6; }
diff --git a/debian/patches/fix_undefined_min.patch b/debian/patches/fix_undefined_min.patch
deleted file mode 100644
index 8145bb9..0000000
--- a/debian/patches/fix_undefined_min.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/eba/conf.c
-+++ b/eba/conf.c
-@@ -385,7 +385,7 @@ float max_cosa(TRACE *tx, TRACE *ty, TRA
-
- char probFromQual(float qual)
- {
-- return (char)(100.0*(1.0 - min(qual,1.0)));
-+ return (char)(100.0*(1.0 - MIN(qual,1.0)));
- }
-
-
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
deleted file mode 100644
index 8ace069..0000000
--- a/debian/patches/hardening.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 21 Apr 2014 22:34:28 +0200
-Description: Hardening requires propagation of LDFLAGS into all build targets
-
---- a/system.mk.in
-+++ b/system.mk.in
-@@ -73,7 +73,7 @@ CPP = @CPP@
- CPPFLAGS = @CPPFLAGS@
- LDFLAGS = -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@
- #CLDFLAGS = -L$(L) -Wl,-rpath-link,$(L) $(subst -L,-Wl$(comma)-rpath-link$(comma),$(filter -L%,$(IOLIB_LIB)))
--CLDFLAGS = -L$(L) @CC_SEARCH_FLAGS@
-+CLDFLAGS = -L$(L) @LDFLAGS@ @CC_SEARCH_FLAGS@
- CXXLDFLAGS = $(CLDFLAGS)
- F77 = @F77@
- FFLAGS = @FFLAGS@
diff --git a/debian/patches/hardening_format-security.patch b/debian/patches/hardening_format-security.patch
deleted file mode 100644
index 5118c0d..0000000
--- a/debian/patches/hardening_format-security.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-LastChanged: Tue, 29 Oct 2013 22:26:41 +0100
-Description: Build using Debian hardening options
- When using -Werror=format-security the following patches are needed
-
---- a/gap4/gap-error.c
-+++ b/gap4/gap-error.c
-@@ -89,7 +89,7 @@ void error_sig(int sig) {
- }
-
- static void xperror_out_func(char *name, char *str) {
-- verror(ERR_FATAL, name, str);
-+ verror(ERR_FATAL, name, "%s", str);
- }
-
- /* NOT FATAL */
---- a/gap4/show_relationships.c
-+++ b/gap4/show_relationships.c
-@@ -34,7 +34,7 @@ int show_relationships(GapIO *io,
- cright = io_crnbr(io, contigs[i].contig);
-
- /* print contig information */
-- vmessage(contig_line);
-+ vmessage("%s", contig_line);
- vmessage("%25d %8d %15d %8d\n", contigs[i].contig,
- clen, cleft, cright);
-
-@@ -66,7 +66,7 @@ int show_relationships(GapIO *io,
- } else if (ordered == 0) {
-
- /* print contig information */
-- vmessage(contig_line);
-+ vmessage("%s", contig_line);
-
- for (i = 0; i < num_contigs; i++){
- clen = io_clength(io, contigs[i].contig);
-@@ -106,7 +106,7 @@ int show_relationships(GapIO *io,
- cright = io_crnbr(io, contigs[i].contig);
-
- /* print contig information */
-- vmessage(contig_line);
-+ vmessage("%s", contig_line);
- vmessage("%25d %8d %15d %8d\n",contigs[i].contig,
- clen, cleft, cright);
-
diff --git a/debian/patches/include_xalloc.patch b/debian/patches/include_xalloc.patch
index 44935c3..5a6c0b2 100644
--- a/debian/patches/include_xalloc.patch
+++ b/debian/patches/include_xalloc.patch
@@ -3,21 +3,17 @@ Author: Colin Watson <cjwatson at ubuntu.com>
Forwarded: no
Last-Update: 2016-01-05
-Index: b/hetins/hetins.c
-===================================================================
--- a/hetins/hetins.c
+++ b/hetins/hetins.c
-@@ -9,6 +9,8 @@
- #include <io_lib/Read.h>
+@@ -10,6 +10,8 @@
#include <io_lib/traceType.h>
+ #include <io_lib/xalloc.h>
+#include "xalloc.h"
+
#define FULL_TEST 2
#define TEST 1
-Index: b/stops/stops.c
-===================================================================
--- a/stops/stops.c
+++ b/stops/stops.c
@@ -13,6 +13,8 @@
diff --git a/debian/patches/make_help_menus_work.patch b/debian/patches/make_help_menus_work.patch
index 6146a0b..105fb8e 100644
--- a/debian/patches/make_help_menus_work.patch
+++ b/debian/patches/make_help_menus_work.patch
@@ -2,34 +2,6 @@ Author: Tim Booth <tbooth at ceh.ac.uk>
Last-Update: Wed, 12 Jun 2013 17:47:51 +0100
Description: Fix help menus
---- a/gap5/gap5rc_menu_full
-+++ b/gap5/gap5rc_menu_full
-@@ -212,12 +212,12 @@ add_command {Assembly.Map Reads.Bwa bwas
-
-
- add_command {Help.Contents} 1 0 {show_help gap5 Contents}
--add_command {Help.Introduction} 1 0 {show_help gap5 Gap4-Introduction}
-+# add_command {Help.Introduction} 1 0 {show_help gap5 Gap4-Introduction}
- add_command {Help.Output Window} 1 0 {show_help interface {UI-Output}}
- add_separator {Help.S1}
- add_command {Help.Index} 1 0 {show_help gap5 Index}
- add_separator {Help.S2}
--add_command {Help.Show Licence} 1 0 {ShowLicence}
-+add_command {Help.Show Licence} 1 0 {show_help gap5 Copyright}
-
- #For testing busy mode
- #add_command {File.Busy On} 1 2 {SetBusy}
---- a/gap4/gaprc_menu_full
-+++ b/gap4/gaprc_menu_full
-@@ -200,7 +200,7 @@ add_command {Help.Output Window} 1 0 {sh
- add_separator {Help.S1}
- add_command {Help.Index} 1 0 {show_help gap4 Index}
- add_separator {Help.S2}
--add_command {Help.Show Licence} 1 0 {ShowLicence}
-+add_command {Help.Show Licence} 1 0 {show_help gap4 Copyright}
-
- #For testing busy mode
- #add_command {File.Busy On} 1 2 {SetBusy}
--- a/gap4/gaprc_menu_mito
+++ b/gap4/gaprc_menu_mito
@@ -176,7 +176,7 @@ add_command {Help.Output Window} 1 0 {sh
diff --git a/debian/patches/remove_svnversion_dep.patch b/debian/patches/remove_svnversion_dep.patch
deleted file mode 100644
index fe2cadf..0000000
--- a/debian/patches/remove_svnversion_dep.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Jan says:
-(1) In system.mk.in, replaced "SVNVERS := $(shell @SVNVERSION@ $(SRCROOT))"
-with "SVNVERS := sourceforge-2.0.0b9-src" (svnversion prints
-"Unversioned directory" as the .svn directories aren't included in the
-archive, and the whitespace in that messes up the -D flag generated from
-SVNVERS).
-
-I think I need to set this from the Debian version, as it appears in title
-bars of applications. I don't want to set it manually.
---- a/system.mk.in
-+++ b/system.mk.in
-@@ -61,7 +61,8 @@
- # How else do we get commas in a subst text or pattern?
- comma = ,
-
--SVNVERS := $(shell @SVNVERSION@ $(SRCROOT))
-+#Use package version rather than SVN version
-+SVNVERS := $(shell dpkg-parsechangelog -l at PWD@/debian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- )
-
- LIB_RUNTIME_DIR = ${prefix}/lib/staden
- CC = @CC@
diff --git a/debian/patches/series b/debian/patches/series
index d8f28db..ef6dc90 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,14 +1,7 @@
-# remove_svnversion_dep.patch
make_help_menus_work.patch
-hardening_format-security.patch
-hardening.patch
fix_tcl_path.patch
fix_awk.patch
-# delete_rpath_from_configure.patch
enable_setting_stadenroot.patch
-spelling.patch
-cope_with_modern_windowmanager.patch
include_xalloc.patch
use_mkstemp_instead_of_tmpnam.patch
fix_implicit_declaration.patch
-fix_undefined_min.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index 91793a3..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,68 +0,0 @@
-Description: fix some spelling issues
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 20 Feb 2016 20:06:23 +0100
-
---- a/gap5/tg_index.c
-+++ b/gap5/tg_index.c
-@@ -49,7 +49,7 @@
-
- void usage(void) {
- fprintf(stderr, "Usage: g_index [options] data_file ...\n");
-- fprintf(stderr, " -o output Specify ouput filename (g_db)\n");
-+ fprintf(stderr, " -o output Specify output filename (g_db)\n");
- fprintf(stderr, "\n");
- fprintf(stderr, " -m Input is MAQ format\n");
- fprintf(stderr, " -M Input is MAQ-long format\n");
---- a/copy_reads/copy_reads.c
-+++ b/copy_reads/copy_reads.c
-@@ -478,7 +478,7 @@ int check_cons_match(char *seq1,
-
- if (mism > max_mismatch) {
-
-- vmessage("\nLocal mismatch of %f found at postion %d over a window length of %d\n",
-+ vmessage("\nLocal mismatch of %f found at position %d over a window length of %d\n",
- (float)mism / win_len * 100, i-win_len+1, win_len);
- vmessage("Aborting this match\n\n");
- return -1;
-@@ -490,7 +490,7 @@ int check_cons_match(char *seq1,
- mism += !same_char(seq1[i], seq2[j]);
- }
- if (mism > max_mismatch) {
-- vmessage("\nLocal mismatch of %f found at postion %d over a window length of %d\n",
-+ vmessage("\nLocal mismatch of %f found at position %d over a window length of %d\n",
- (float)mism / win_len * 100, i-win_len, win_len);
- vmessage("Aborting this match\n\n");
- return -1;
---- a/primer3/src/ntdpal_main.c
-+++ b/primer3/src/ntdpal_main.c
-@@ -33,7 +33,7 @@ main(argc, argv)
- " creating or widening a gap respectively (<gval> and <lval> are\n"
- " subtracted from the output score).\n"
- "-a causes the scoring matrix to be modified by dpal_set_ambiguity_codes.\n"
-- "-e causes the end postion of the alignment in both sequences to\n"
-+ "-e causes the end position of the alignment in both sequences to\n"
- " be printed. Do not confuse with the 'e' <mode>\n"
- "-h use a different scoring matrix: G and C matches = 3, A and T = 2\n"
- "-p causes the alignment to be displayed.\n"
---- a/primer3/src/primer3_lib.c
-+++ b/primer3/src/primer3_lib.c
-@@ -2888,7 +2888,7 @@ const primer_args *pa;
- *
- * Note: we don't insist that the start codon be ATG, since in some
- * cases the caller will not have the full sequence in 's', nor even
-- * know the postion of the start codon relative to s.
-+ * know the position of the start codon relative to s.
- */
- static int
- find_stop_codon(const char *s, int start, int direction)
---- a/gap5/do_fij.c
-+++ b/gap5/do_fij.c
-@@ -892,7 +892,7 @@ int do_it_fij(fij_arg *fij_args, char *s
- h->filter_words = 0;
- }
- if (h->filter_words)
-- vmessage("Filtering words occuring more than %d times.\n",
-+ vmessage("Filtering words occurring more than %d times.\n",
- h->filter_words);
-
- for (contig2_num = (contig1_num < first_shared1
--
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