[med-svn] [relion] 12/36: Add patches: Properly build GUI + one upstream fix

Roland Fehrenbacher rfehren-guest at moszumanska.debian.org
Mon Oct 13 20:41:10 UTC 2014 

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rfehren-guest pushed a commit to branch master
in repository relion.

commit 215beaec4e14863da8e5567c2416d725b19c3534
Author: Roland Fehrenbacher <rf at q-leap.de>
Date:   Fri Oct 10 22:29:02 2014 +0000

    Add patches: Properly build GUI + one upstream fix
---
 .../0001-Fix-fltk-config-path-in-configure.patch   | 21 ++++++
 .../0002-Fix-autopicking-buffer-overflow.patch     | 22 ++++++
 .../0003-Add-enable-gui-flag-to-configure.patch    | 40 +++++++++++
 debian/patches/0004-Fix-fltk-header-includes.patch | 79 ++++++++++++++++++++++
 debian/patches/series                              |  4 ++
 5 files changed, 166 insertions(+)

diff --git a/debian/patches/0001-Fix-fltk-config-path-in-configure.patch b/debian/patches/0001-Fix-fltk-config-path-in-configure.patch
new file mode 100644
index 0000000..5f5f0a1
--- /dev/null
+++ b/debian/patches/0001-Fix-fltk-config-path-in-configure.patch
@@ -0,0 +1,21 @@
+From: Roland Fehrenbacher <rf at q-leap.de>
+Date: Wed, 30 Jul 2014 10:28:43 +0200
+Subject: Fix fltk-config path in configure
+
+---
+ configure.ac | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/configure.ac b/configure.ac
+index 57cbba9..5e83df3 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -55,7 +55,7 @@ AC_MSG_ERROR([Cannot find the FFTW3 library. Please install it (with threads ena
+ #Check for FLTK
+ # as g++ seems needed and not gcc for compilation, 
+ #just check for presence of fltk-config program 
+-[fltkfile=`pwd`/bin/fltk-config]
++[fltkfile=/usr/bin/fltk-config]
+ AC_CHECK_FILE($fltkfile, 
+ [
+ enable_fltk=yes
diff --git a/debian/patches/0002-Fix-autopicking-buffer-overflow.patch b/debian/patches/0002-Fix-autopicking-buffer-overflow.patch
new file mode 100644
index 0000000..1439236
--- /dev/null
+++ b/debian/patches/0002-Fix-autopicking-buffer-overflow.patch
@@ -0,0 +1,22 @@
+From: Roland Fehrenbacher <rf at q-leap.de>
+Date: Wed, 30 Jul 2014 10:35:10 +0200
+Subject: Fix autopicking buffer overflow
+
+Fix taken from http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Known_issue
+---
+ src/rwSPIDER.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/rwSPIDER.h b/src/rwSPIDER.h
+index 07db268..837ef52 100644
+--- a/src/rwSPIDER.h
++++ b/src/rwSPIDER.h
+@@ -96,7 +96,7 @@ struct SPIDERhead
+     char fNada2[576]; // empty 700-76-40=624-40-8= 576 bytes
+ 
+     char cdat[12];   // 211-213   creation date
+-    char ctim[8];  // 214-215   creation time
++    char ctim[9];  // 214-215   creation time
+     char ctit[160];  // 216-255   title
+ } ;
+ 
diff --git a/debian/patches/0003-Add-enable-gui-flag-to-configure.patch b/debian/patches/0003-Add-enable-gui-flag-to-configure.patch
new file mode 100644
index 0000000..048394c
--- /dev/null
+++ b/debian/patches/0003-Add-enable-gui-flag-to-configure.patch
@@ -0,0 +1,40 @@
+From: Roland Fehrenbacher <rf at q-leap.de>
+Date: Wed, 30 Jul 2014 11:10:07 +0200
+Subject: Add --enable-gui flag to configure
+
+---
+ configure.ac | 21 +++++++++++++--------
+ 1 file changed, 13 insertions(+), 8 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 5e83df3..1a47e43 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -56,14 +56,19 @@ AC_MSG_ERROR([Cannot find the FFTW3 library. Please install it (with threads ena
+ # as g++ seems needed and not gcc for compilation, 
+ #just check for presence of fltk-config program 
+ [fltkfile=/usr/bin/fltk-config]
+-AC_CHECK_FILE($fltkfile, 
+-[
+-enable_fltk=yes
+-], 
+-[
+-AC_MSG_RESULT(warning: bin/fltk-config was not found, so GUI will not be built)
+-enable_fltk=no
+-])
++AC_ARG_ENABLE([gui],
++    AC_HELP_STRING([--enable-gui], [compile GUI]),
++    if test x$enableval = "xyes"; then
++        AC_CHECK_FILE($fltkfile,
++        [
++        enable_fltk=yes
++        ],
++        [
++        AC_MSG_RESULT(warning: bin/fltk-config was not found, so GUI will not be built)
++        enable_fltk=no
++        ])
++    fi,
++    [enable_fltk=no])
+ AM_CONDITIONAL(HAVE_FLTK, test "$enable_fltk" = yes)
+ 
+ # If no --prefix is passed to the configure script, relion programs and
diff --git a/debian/patches/0004-Fix-fltk-header-includes.patch b/debian/patches/0004-Fix-fltk-header-includes.patch
new file mode 100644
index 0000000..33c91a3
--- /dev/null
+++ b/debian/patches/0004-Fix-fltk-header-includes.patch
@@ -0,0 +1,79 @@
+From: Roland Fehrenbacher <rf at q-leap.de>
+Date: Wed, 30 Jul 2014 10:28:02 +0200
+Subject: Fix fltk header includes
+
+---
+ src/displayer.h    | 24 ++++++++++++------------
+ src/manualpicker.h | 24 ++++++++++++------------
+ 2 files changed, 24 insertions(+), 24 deletions(-)
+
+diff --git a/src/displayer.h b/src/displayer.h
+index bdaa4ff..eeb1a6d 100644
+--- a/src/displayer.h
++++ b/src/displayer.h
+@@ -29,18 +29,18 @@
+ #include <src/time.h>
+ #include <src/args.h>
+ 
+-#include <external/fltk-1.3.0/FL/Fl.H>
+-#include <external/fltk-1.3.0/FL/Fl_Shared_Image.H>
+-#include <external/fltk-1.3.0/FL/Fl_Double_Window.H>
+-#include <external/fltk-1.3.0/FL/Fl_Scroll.H>
+-#include <external/fltk-1.3.0/FL/Fl_Image.H>
+-#include <external/fltk-1.3.0/FL/Fl_JPEG_Image.H>
+-#include <external/fltk-1.3.0/FL/Fl_Box.H>
+-#include <external/fltk-1.3.0/FL/fl_draw.H>
+-#include <external/fltk-1.3.0/FL/Fl_Menu_Bar.H>
+-#include <external/fltk-1.3.0/FL/Fl_File_Chooser.H>
+-#include <external/fltk-1.3.0/FL/Fl_Float_Input.H>
+-#include <external/fltk-1.3.0/FL/Fl_Text_Display.H>
++#include <Fl/Fl.H>
++#include <Fl/Fl_Shared_Image.H>
++#include <Fl/Fl_Double_Window.H>
++#include <Fl/Fl_Scroll.H>
++#include <Fl/Fl_Image.H>
++#include <Fl/Fl_JPEG_Image.H>
++#include <Fl/Fl_Box.H>
++#include <Fl/fl_draw.H>
++#include <Fl/Fl_Menu_Bar.H>
++#include <Fl/Fl_File_Chooser.H>
++#include <Fl/Fl_Float_Input.H>
++#include <Fl/Fl_Text_Display.H>
+ 
+ #define GUI_BACKGROUND_COLOR (fl_rgb_color(240,240,240))
+ #define GUI_INPUT_COLOR (fl_rgb_color(255,255,230))
+diff --git a/src/manualpicker.h b/src/manualpicker.h
+index 31a33cb..8daf975 100644
+--- a/src/manualpicker.h
++++ b/src/manualpicker.h
+@@ -24,18 +24,18 @@
+ #include "src/args.h"
+ #include "src/filename.h"
+ #include "src/gui_entries.h"
+-#include <external/fltk-1.3.0/FL/Fl.H>
+-#include <external/fltk-1.3.0/FL/Fl_Shared_Image.H>
+-#include <external/fltk-1.3.0/FL/Fl_Double_Window.H>
+-#include <external/fltk-1.3.0/FL/Fl_Scroll.H>
+-#include <external/fltk-1.3.0/FL/Fl_Image.H>
+-#include <external/fltk-1.3.0/FL/Fl_JPEG_Image.H>
+-#include <external/fltk-1.3.0/FL/Fl_Box.H>
+-#include <external/fltk-1.3.0/FL/fl_draw.H>
+-#include <external/fltk-1.3.0/FL/Fl_Menu_Bar.H>
+-#include <external/fltk-1.3.0/FL/Fl_File_Chooser.H>
+-#include <external/fltk-1.3.0/FL/Fl_Float_Input.H>
+-#include <external/fltk-1.3.0/FL/Fl_Text_Display.H>
++#include <Fl/Fl.H>
++#include <Fl/Fl_Shared_Image.H>
++#include <Fl/Fl_Double_Window.H>
++#include <Fl/Fl_Scroll.H>
++#include <Fl/Fl_Image.H>
++#include <Fl/Fl_JPEG_Image.H>
++#include <Fl/Fl_Box.H>
++#include <Fl/fl_draw.H>
++#include <Fl/Fl_Menu_Bar.H>
++#include <Fl/Fl_File_Chooser.H>
++#include <Fl/Fl_Float_Input.H>
++#include <Fl/Fl_Text_Display.H>
+ 
+ #define MWCOL1 300
+ #define MWCOL2 60
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..9c6461d
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,4 @@
+0001-Fix-fltk-config-path-in-configure.patch
+0002-Fix-autopicking-buffer-overflow.patch
+0003-Add-enable-gui-flag-to-configure.patch
+0004-Fix-fltk-header-includes.patch

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