[med-svn] [exonerate] 04/05: Adapt patches
Andreas Tille
tille at debian.org
Sun Mar 20 11:46:08 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository exonerate.
commit 622a99704a8b38da3af70ccecb5557d0e1e32ea8
Author: Andreas Tille <tille at debian.org>
Date: Sun Mar 20 12:24:18 2016 +0100
Adapt patches
---
debian/patches/fix_build-as-needed.patch | 25 +++++++++++++------------
debian/patches/manpages.patch | 24 ++++++++++++------------
debian/patches/manpagesyntax.patch | 8 ++++----
debian/patches/spelling.patch | 4 ++--
4 files changed, 31 insertions(+), 30 deletions(-)
diff --git a/debian/patches/fix_build-as-needed.patch b/debian/patches/fix_build-as-needed.patch
index 148395b..82ab22b 100644
--- a/debian/patches/fix_build-as-needed.patch
+++ b/debian/patches/fix_build-as-needed.patch
@@ -1,14 +1,15 @@
Author: Micah Gersten <micahg at ubuntu.com>
-Date: Mon, 12 Dec 2011 09:15:02 UTC
-Closes: #651802
---- exonerate-2.2.0.orig/configure.in
-+++ exonerate-2.2.0/configure.in
-@@ -289,7 +289,7 @@
- if test "$enable_pthreads" = yes; then
- echo "Using PTHREADS"
- CFLAGS="$CFLAGS -DUSE_PTHREADS"
-- LDFLAGS="$LDFLAGS -lpthread"
-+ LIBS="$LIBS -lpthread"
- elif test "$enable_pthreads" = no; then
- echo "Not using pthreads"
+Last-Update: Andreas Tille <tille at debian.org> Sun, 20 Mar 2016 12:17:12 +0100
+Bug-Debian: https://bugs.debian.org/651802
+
+--- a/configure.in
++++ b/configure.in
+@@ -196,7 +196,7 @@ if test "$enable_gprof" = yes; then
+ echo " Run: <program> then run: gprof <program> gmon.out"
+ CFLAGS="$CFLAGS -O0 -static -pg"
+ LDFLAGS="$LDFLAGS -g -pg -nodefaultlibs"
+- LIBS="$LIBS -lc_p -lgcc -lm"
++ LIBS="$LIBS -lc_p -lgcc -lm -lpthread"
+ elif test "$enable_gprof" = no; then
+ echo "Not using options for profiling with gprof"
else
diff --git a/debian/patches/manpages.patch b/debian/patches/manpages.patch
index 758c099..06216a5 100644
--- a/debian/patches/manpages.patch
+++ b/debian/patches/manpages.patch
@@ -3,9 +3,9 @@ Date: Mon, 12 Dec 2011 13:13:02 +0100
Description: Fix some errors in manpages. More errors can be
found using
LC_ALL=en_US.UTF-8 MANWIDTH=80 man --warnings -E UTF-8 -l <file> >/dev/null
---- exonerate-2.2.0.orig/doc/man/man1/exonerate.1
-+++ exonerate-2.2.0/doc/man/man1/exonerate.1
-@@ -33,7 +33,6 @@
+--- a/doc/man/man1/exonerate.1
++++ b/doc/man/man1/exonerate.1
+@@ -33,7 +33,6 @@ the results are not guaranteed to be opt
.RE
.SH CONVENTIONS
@@ -13,9 +13,9 @@ Description: Fix some errors in manpages. More errors can be
A number of conventions (and idiosyncracies) are used within
exonerate. An understanding of them facilitates interpretation
of the output.
---- exonerate-2.2.0.orig/doc/man/man1/exonerate-server.1
-+++ exonerate-2.2.0/doc/man/man1/exonerate-server.1
-@@ -19,7 +19,6 @@
+--- a/doc/man/man1/exonerate-server.1
++++ b/doc/man/man1/exonerate-server.1
+@@ -19,7 +19,6 @@ to allow fast of large datasets.
.RE
.SH OVERVIEW
@@ -23,9 +23,9 @@ Description: Fix some errors in manpages. More errors can be
.\"
Firstly, an
.B .esd
---- exonerate-2.2.0.orig/doc/man/man1/fastautils.1
-+++ exonerate-2.2.0/doc/man/man1/fastautils.1
-@@ -55,9 +55,6 @@
+--- a/doc/man/man1/fastautils.1
++++ b/doc/man/man1/fastautils.1
+@@ -55,9 +55,6 @@ These are utilities for the manipulation
databases which are distributed with the exonerate sequence alignment
program.
.P
@@ -35,9 +35,9 @@ Description: Fix some errors in manpages. More errors can be
.RE
.\"
.SH ENVIRONMENT
---- exonerate-2.2.0.orig/doc/man/man1/ipcress.1
-+++ exonerate-2.2.0/doc/man/man1/ipcress.1
-@@ -35,7 +35,6 @@
+--- a/doc/man/man1/ipcress.1
++++ b/doc/man/man1/ipcress.1
+@@ -35,7 +35,6 @@ sequence comparison tool.
.\"
.RE
.SH INPUT FORMAT
diff --git a/debian/patches/manpagesyntax.patch b/debian/patches/manpagesyntax.patch
index 800f7cc..90efdd8 100644
--- a/debian/patches/manpagesyntax.patch
+++ b/debian/patches/manpagesyntax.patch
@@ -76,7 +76,7 @@ Description: Fix manpage syntax
Most arguments have short and long forms. The long forms
are more likely to be stable over time, and hence should
be used in scripts which call exonerate.
-@@ -1194,7 +1194,7 @@ show the observed relative frequencies o
+@@ -1229,7 +1229,7 @@ show the observed relative frequencies o
the splice sites in the chosen organism (in ACGT order).
.B Example 5' splice data file:
@@ -85,7 +85,7 @@ Description: Fix manpage syntax
.nf
# start of example 5' splice data
-@@ -1210,11 +1210,11 @@ the splice sites in the chosen organism
+@@ -1245,11 +1245,11 @@ the splice sites in the chosen organism
5 6 85 4
16 18 21 45
# end of test 5' splice data
@@ -99,7 +99,7 @@ Description: Fix manpage syntax
.nf
# start of example 3' splice data
-@@ -1236,7 +1236,7 @@ the splice sites in the chosen organism
+@@ -1271,7 +1271,7 @@ the splice sites in the chosen organism
splice
28 14 47 11
# end of example 3' splice data
@@ -108,7 +108,7 @@ Description: Fix manpage syntax
.fi
.TP
-@@ -1338,7 +1338,7 @@ This documentation accompanies version 2
+@@ -1373,7 +1373,7 @@ This documentation accompanies version 2
.\"
.SH AUTHOR
Guy St.C. Slater. <guy at ebi.ac.uk>.
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index a616457..8ed1de4 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -26,7 +26,7 @@ Description: Fix spelling
.TP 10
--- a/doc/man/man1/exonerate.1
+++ b/doc/man/man1/exonerate.1
-@@ -357,7 +357,7 @@ It is currently only available when usin
+@@ -378,7 +378,7 @@ It is currently only available when usin
This model allows alignment of a protein sequence to genomic
DNA. This is similar to the protein2dna model,
with the addition of modelling of introns and intron phases.
@@ -35,7 +35,7 @@ Description: Fix spelling
.\"
.TP
.B protein2genome:bestfit
-@@ -737,7 +737,7 @@ subject to alignment during refinement b
+@@ -760,7 +760,7 @@ subject to alignment during refinement b
.\"
.RE
--
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