[med-svn] [lamarc] 02/06: Refresh patches
Andreas Tille
tille at debian.org
Fri Jan 19 12:18:36 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository lamarc.
commit bae7444e3ee9132c3ff90b018a690a05a7fceffc
Author: Andreas Tille <tille at debian.org>
Date: Thu Jan 4 22:28:57 2018 +0100
Refresh patches
---
debian/patches/fix_install_target.patch | 18 +---
debian/patches/gcc-7.patch | 127 -----------------------
debian/patches/limits.patch | 14 +--
debian/patches/series | 1 -
debian/patches/use_debian_packaged_boost.patch | 12 +--
debian/patches/use_debian_packaged_tinyxml.patch | 55 ++++------
6 files changed, 35 insertions(+), 192 deletions(-)
diff --git a/debian/patches/fix_install_target.patch b/debian/patches/fix_install_target.patch
index 7eca266..a522a7f 100644
--- a/debian/patches/fix_install_target.patch
+++ b/debian/patches/fix_install_target.patch
@@ -5,7 +5,7 @@ Description: Drop duplicate from list of files to install,
--- a/Makefile.am
+++ b/Makefile.am
-@@ -1005,7 +1005,7 @@ lamarc.app: lamarc
+@@ -1013,7 +1013,7 @@ lamarc.app$(EXEEXT): lamarc
## html documentation
## ############################################################
@@ -14,15 +14,7 @@ Description: Drop duplicate from list of files to install,
html_DATA = \
doc/html/bayes.html \
-@@ -1026,7 +1026,6 @@ html_DATA = \
- doc/html/genotype.html \
- doc/html/glossary.html \
- doc/html/growthmenu.html \
-- doc/html/forces.html \
- doc/html/index.html \
- doc/html/insumfile.2reg3rep.html \
- doc/html/insumfile.2reg3rep.xml \
-@@ -1056,7 +1055,7 @@ html_DATA = \
+@@ -1063,7 +1063,7 @@ html_DATA = \
doc/html/viral_data.html \
doc/html/xmlinput.html
@@ -31,7 +23,7 @@ Description: Drop duplicate from list of files to install,
htmlimg_DATA = \
doc/html/images/LamarcAnalysisScreen.png \
-@@ -1081,7 +1080,7 @@ htmlimg_DATA = \
+@@ -1088,7 +1088,7 @@ htmlimg_DATA = \
doc/html/images/uncorrelated.gif \
doc/html/images/variably_correlated.gif
@@ -40,7 +32,7 @@ Description: Drop duplicate from list of files to install,
htmlbconv_DATA = \
doc/html/batch_converter/README.txt \
-@@ -1098,7 +1097,7 @@ htmlbconv_DATA = \
+@@ -1105,7 +1105,7 @@ htmlbconv_DATA = \
doc/html/batch_converter/sample-conv-cmd.html \
doc/html/batch_converter/sample-conv-cmd.xml
@@ -49,7 +41,7 @@ Description: Drop duplicate from list of files to install,
htmlbconvimg_DATA = \
doc/html/batch_converter/images/CombinedPanels.png \
-@@ -1131,7 +1130,7 @@ htmlbconvimg_DATA = \
+@@ -1138,7 +1138,7 @@ htmlbconvimg_DATA = \
doc/html/batch_converter/images/lam_conv_export_file_mac_expanded.png
diff --git a/debian/patches/gcc-7.patch b/debian/patches/gcc-7.patch
deleted file mode 100644
index 9ae6f91..0000000
--- a/debian/patches/gcc-7.patch
+++ /dev/null
@@ -1,127 +0,0 @@
-Author: Gert Wollny <gw.fossdev at gmail.com>
-Last-Update: Mon, 04 Dec 2017 19:32:42 +0100
-Description: make_pair doesn't require the explicite type specification
-
---- a/src/tools/mathx.cpp
-+++ b/src/tools/mathx.cpp
-@@ -778,7 +778,7 @@
- {
- eigvals[i] = a[i][i];
- }
-- return make_pair<DoubleVec1d, DoubleVec2d>(eigvals, eigvecs);
-+ return make_pair(eigvals, eigvecs);
- } // Eigen
-
- //------------------------------------------------------------------------------------
---- a/src/tree/argtree.cpp
-+++ b/src/tree/argtree.cpp
-@@ -371,7 +371,7 @@
- if (forcefound)
- {
- // add to target map array
-- Branch_ptr nullptr;
-+ Branch_ptr null_ptr;
- if (recfound)
- {
- // recombination case - returns a pair of branches
-@@ -388,7 +388,7 @@
- else
- {
- // everything else
-- targetpair p = make_pair(recbranches.first, nullptr);
-+ targetpair p = make_pair(recbranches.first, null_ptr);
- targetmap.insert(make_pair(argedges[edge].GetSource(), p));
- }
-
-@@ -404,7 +404,7 @@
- else
- {
- // everything else
-- targetpair q = make_pair(recbranches.second, nullptr);
-+ targetpair q = make_pair(recbranches.second, null_ptr);
- targetmap.insert(make_pair(argedges[edge+1].GetSource(), q));
- }
- }
-@@ -421,7 +421,7 @@
- else
- {
- // everything else
-- targetpair p = make_pair(newbranch, nullptr);
-+ targetpair p = make_pair(newbranch, null_ptr);
- targetmap.insert(make_pair(argedges[edge].GetSource(), p));
- }
- }
---- a/src/tree/arrangervec.cpp
-+++ b/src/tree/arrangervec.cpp
-@@ -122,7 +122,7 @@
- for(it = cp.arrangers.begin(); it != cp.arrangers.end(); it++)
- {
- Arranger* arr = it->second->Clone();
-- arrangers.insert(std::make_pair<string, Arranger*>(arr->GetName(), arr));
-+ arrangers.insert(std::make_pair(arr->GetName(), arr));
- }
- }
- }
---- a/src/tree/collector.cpp
-+++ b/src/tree/collector.cpp
-@@ -205,7 +205,7 @@
-
- void ParamCollector::AddParamSummary(ForceParameters fp, long ncopy)
- {
-- m_paramsum.push_back(make_pair<ForceParameters, long>(fp, ncopy));
-+ m_paramsum.push_back(make_pair(fp, ncopy));
- }
-
- //------------------------------------------------------------------------------------
---- a/src/tree/prior.cpp
-+++ b/src/tree/prior.cpp
-@@ -85,12 +85,12 @@
- case LINEAR:
- newparam = rnd.Float() * (m_upperbound - m_lowerbound) + m_lowerbound;
- newlnparam = log(newparam);
-- return std::make_pair<double, double>(newparam, newlnparam);
-+ return std::make_pair(newparam, newlnparam);
- break;
- case LOGARITHMIC:
- newlnparam = rnd.Float() * (m_lnupper - m_lnlower) + m_lnlower;
- newparam = exp(newlnparam);
-- return std::make_pair<double, double>(newparam, newlnparam);
-+ return std::make_pair(newparam, newlnparam);
- break;
- }
- string e = "Unknown prior type " + ToString(m_priortype) +
-@@ -117,7 +117,7 @@
- {
- newparam = 2.0 * m_upperbound - newparam;
- }
-- return std::make_pair<double,double>(newparam, log(newparam));
-+ return std::make_pair(newparam, log(newparam));
- break;
- case LOGARITHMIC:
- string e = "Cannot use prior type " + ToString(m_priortype) +
-@@ -135,7 +135,7 @@
- std::pair<double, double> Prior::RandomDrawWithinBounds(double lower, double upper) const
- {
- Random& rnd = registry.GetRandom();
-- double newparam, newlnparam;
-+ double newparam = 0, newlnparam = 0;
- double lowbound = std::max(m_lowerbound, lower);
- double upbound = std::min(m_upperbound, upper);
- switch (m_priortype)
-@@ -143,15 +143,14 @@
- case LINEAR:
- newparam = rnd.Float() * (upbound - lowbound) + lowbound;
- newlnparam = log(newparam);
-- return std::make_pair<double, double>(newparam, newlnparam);
- break;
- case LOGARITHMIC:
- lowbound = log(lowbound);
- upbound = log(upbound);
- newlnparam = rnd.Float() * (upbound - lowbound) + lowbound;
- newparam = exp(newlnparam);
-- return std::make_pair<double, double>(newparam, newlnparam);
- break;
- }
-+ return std::make_pair(newparam, newlnparam);
-
- } // RandomDrawWithinBounds
diff --git a/debian/patches/limits.patch b/debian/patches/limits.patch
index ca9ae2a..8799ea6 100644
--- a/debian/patches/limits.patch
+++ b/debian/patches/limits.patch
@@ -2,21 +2,11 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Fri, 01 Dec 2017 19:42:59 +0100
Description: Add missing climits
---- a/src/tools/stringx.cpp
-+++ b/src/tools/stringx.cpp
-@@ -15,6 +15,7 @@
- #include <string>
- #include <cstring>
- #include <cstdio>
-+#include <climits>
-
- // NOTE: older versions required including <direct.h> here and
- // using _getcwd() below for MSWINDOWS compiles
--- a/src/xml/tixml_base.cpp
+++ b/src/xml/tixml_base.cpp
-@@ -13,6 +13,8 @@
- #include "tinyxml.h"
+@@ -26,6 +26,8 @@ limitations under the License.
#include "tixml_base.h"
+ #include <climits>
+#include <climits>
+
diff --git a/debian/patches/series b/debian/patches/series
index 1c7458c..3209b61 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,4 @@
use_debian_packaged_tinyxml.patch
use_debian_packaged_boost.patch
-gcc-7.patch
limits.patch
fix_install_target.patch
diff --git a/debian/patches/use_debian_packaged_boost.patch b/debian/patches/use_debian_packaged_boost.patch
index e7de208..cb63d47 100644
--- a/debian/patches/use_debian_packaged_boost.patch
+++ b/debian/patches/use_debian_packaged_boost.patch
@@ -4,7 +4,7 @@ Description: Use Debian packaged boost
--- a/Makefile.am
+++ b/Makefile.am
-@@ -98,7 +98,7 @@ lamarc_includes = \
+@@ -101,7 +101,7 @@ lamarc_includes = \
-I $(lamarc_srcdir)/ui_util \
-I $(lamarc_srcdir)/ui_vars \
-I $(lamarc_srcdir)/xml \
@@ -13,7 +13,7 @@ Description: Use Debian packaged boost
-I $(top_srcdir)/resources
-@@ -1146,7 +1146,6 @@ htmltrait_DATA = \
+@@ -1153,7 +1153,6 @@ htmltrait_DATA = \
license_info = \
COPYING \
@@ -21,20 +21,20 @@ Description: Use Debian packaged boost
doc/licenses/gpl.txt \
doc/licenses/lamarc.txt \
doc/licenses/lgpl.txt \
-@@ -1167,7 +1166,6 @@ wx_stuff = \
+@@ -1174,7 +1173,6 @@ wx_stuff = \
EXTRA_DIST = \
Makefile.am \
configure.ac \
- boost \
+ tinyxml \
$(license_info) \
$(wx_curr) \
- $(scripts_to_dist) \
-@@ -1192,7 +1190,7 @@ EXTRA_DIST = \
+@@ -1200,7 +1198,7 @@ EXTRA_DIST = \
# $(vcprojdir)/lamarc.vcproj
dist-hook:
- rm -rf `find $(distdir)/boost -name CVS`
+ rm -rf `find . -name CVS`
+ rm -rf `find $(distdir)/tinyxml -name CVS`
## ############################################################
- ## support for sanity checks
diff --git a/debian/patches/use_debian_packaged_tinyxml.patch b/debian/patches/use_debian_packaged_tinyxml.patch
index e45ae14..59a44b2 100644
--- a/debian/patches/use_debian_packaged_tinyxml.patch
+++ b/debian/patches/use_debian_packaged_tinyxml.patch
@@ -4,13 +4,16 @@ Description: Use Debian packaged tinyxml
--- a/Makefile.am
+++ b/Makefile.am
-@@ -69,18 +69,6 @@ lam_conv_rc.o : $(top_srcdir)/re
+@@ -72,21 +72,6 @@ lam_conv_rc.o : $(top_srcdir)/re
## to this list
LDADD =
-noinst_LIBRARIES = libtinyxml.a
-
--libtinyxml_a_CXXFLAGS = -DTIXML_USE_STL
+-libtinyxml_a_CXXFLAGS = -DTIXML_USE_STL
+-if LAMARC_APP_OSX
+- libtinyxml_a_CXXFLAGS += -mmacosx-version-min=10.7
+-endif
-
-libtinyxml_a_SOURCES = \
- tinyxml/tinyxml.h \
@@ -23,7 +26,7 @@ Description: Use Debian packaged tinyxml
## ############################################################
## setting up compiler flags
## ############################################################
-@@ -111,8 +99,7 @@ lamarc_includes = \
+@@ -117,8 +102,7 @@ lamarc_includes = \
-I $(lamarc_srcdir)/ui_vars \
-I $(lamarc_srcdir)/xml \
-I $(top_srcdir)/boost \
@@ -33,7 +36,7 @@ Description: Use Debian packaged tinyxml
## include resource file if needed
-@@ -604,14 +591,6 @@ xml_sources = \
+@@ -610,14 +594,6 @@ xml_sources = \
src/xml/toxml.cpp \
$(xml_core_sources)
@@ -48,51 +51,37 @@ Description: Use Debian packaged tinyxml
config_sources = \
config/conf.h
-@@ -634,7 +613,7 @@ lamarc_SOURCES = $(lamarcgcov_sources
+@@ -640,7 +616,7 @@ lamarc_SOURCES = $(lamarcgcov_sources
$(lamarc_resources) \
$(config_sources)
-lamarc_LDADD = libtinyxml.a
-+lamarc_LDADD = -ltinyxml
++lamarc_LDADD = ltinyxml
old_lam_conv_core = \
src/conversion/ConverterIf.cpp \
-@@ -942,9 +921,9 @@ lam_conv_SOURCES = \
- $(lam_conv_core) \
- $(lam_conv_resources)
+@@ -950,12 +926,12 @@ lam_conv_SOURCES = \
--lam_conv_LDADD = @WX_LIBS@ -lX11 libtinyxml.a
-+lam_conv_LDADD = @WX_LIBS@ -lX11 -ltinyxml
+ lam_conv_LDADD = @WX_LIBS@
+ if LAMARC_APP_OSX
+- lam_conv_LDADD += libtinyxml.a
++ lam_conv_LDADD += linyxml
+ else
+- lam_conv_LDADD += -lX11 libtinyxml.a
++ lam_conv_LDADD += -lX11 ltinyxml
+ endif
-EXTRA_lam_conv_SOURCES = $(tinyxml_suite) $(lam_conv_icons)
+EXTRA_lam_conv_SOURCES = $(lam_conv_icons)
batch_lam_conv_core = \
src/guiconv/batchconverter.h \
-@@ -961,9 +940,7 @@ batch_lam_conv_testable = \
- batch_lam_conv_SOURCES = \
- $(batch_lam_conv_testable)
+@@ -974,8 +950,6 @@ batch_lam_conv_SOURCES = \
--batch_lam_conv_LDADD = @WX_LIBS@ -lX11 libtinyxml.a
--
--EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)
-+batch_lam_conv_LDADD = @WX_LIBS@ -lX11 -ltinyxml
+ batch_lam_conv_LDADD = lam_conv_LDADD
+-EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)
+-
## ############################################################
## To make OSX executables for wxWindows stuff
-@@ -1191,7 +1168,6 @@ EXTRA_DIST = \
- Makefile.am \
- configure.ac \
- boost \
-- tinyxml \
- $(license_info) \
- $(wx_curr) \
- $(scripts_to_dist) \
-@@ -1217,7 +1193,6 @@ EXTRA_DIST = \
-
- dist-hook:
- rm -rf `find $(distdir)/boost -name CVS`
-- rm -rf `find $(distdir)/tinyxml -name CVS`
-
## ############################################################
- ## support for sanity checks
--
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