[med-svn] [iqtree] 04/04: Update + deactivate patches
Andreas Tille
tille at debian.org
Fri Sep 9 09:31:33 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository iqtree.
commit b5cfc5fae884889ef2cd69985632a99b4f452339
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 9 11:20:05 2016 +0200
Update + deactivate patches
---
debian/changelog | 1 +
debian/patches/32bit_name.patch | 2 +-
debian/patches/series | 3 +-
debian/patches/spelling.patch | 91 -----------------------------------------
debian/patches/sse.patch | 32 +++------------
5 files changed, 8 insertions(+), 121 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index ab336b1..d4511f1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
iqtree (1.4.4+dfsg-1) unstable; urgency=medium
* New upstream version
+ * Disable sse patch
-- Andreas Tille <tille at debian.org> Fri, 09 Sep 2016 11:07:13 +0200
diff --git a/debian/patches/32bit_name.patch b/debian/patches/32bit_name.patch
index f6c78a9..6db8167 100644
--- a/debian/patches/32bit_name.patch
+++ b/debian/patches/32bit_name.patch
@@ -12,5 +12,5 @@ Last-Update: Tue, 02 Feb 2016 08:41:45 +0100
- SET(EXE_SUFFIX "${EXE_SUFFIX}32")
+ SET(EXE_SUFFIX "${EXE_SUFFIX}")
if (GCC OR CLANG)
- set(COMBINED_FLAGS "${COMBINED_FLAGS}")
+ set(COMBINED_FLAGS "${COMBINED_FLAGS} -m32")
endif()
diff --git a/debian/patches/series b/debian/patches/series
index 6a10a76..3e9cfa5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-spelling.patch
-sse.patch
+#sse.patch
32bit_name.patch
#avoid_mavx.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
deleted file mode 100644
index 9b942b6..0000000
--- a/debian/patches/spelling.patch
+++ /dev/null
@@ -1,91 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 17 Dec 2015 17:13:25 +0100
-Description: Fix spelling
-
---- a/mpdablock.cpp
-+++ b/mpdablock.cpp
-@@ -56,7 +56,7 @@ void MPdaBlock::Read(NxsToken &token)
-
- int ntax = sgraph->getNTaxa();
- if (ntax <= 0) {
-- errormsg = "PDA Block should be preceeded by Splits Block";
-+ errormsg = "PDA Block should be preceded by Splits Block";
- throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
-
- }
---- a/mtreeset.cpp
-+++ b/mtreeset.cpp
-@@ -677,11 +677,11 @@ void MTreeSet::computeRFDist(int *rfdist
-
- if (info_file) {
- oinfo.close();
-- cout << "Detailed split occurences printed to " << info_file << endl;
-+ cout << "Detailed split occurrences printed to " << info_file << endl;
- }
- if (tree_file) {
- otree.close();
-- cout << "Detailed split occurences on tree printed to " << tree_file << endl;
-+ cout << "Detailed split occurrences on tree printed to " << tree_file << endl;
- }
- }
-
---- a/tools.h
-+++ b/tools.h
-@@ -1863,7 +1863,7 @@ const char ERR_WRITE_OUTPUT[] = "Cannot
- const char ERR_NO_K[] = "You must specify the number of taxa in the PD set.";
- const char ERR_TOO_SMALL_K[] = "Size of PD-set must be at least the size of initial set.";
- const char ERR_NO_BUDGET[] = "Total budget is not specified or less than zero.";
--const char ERR_TOO_SMALL_BUDGET[] = "Not enough budget to conserve the inital set of taxa.";
-+const char ERR_TOO_SMALL_BUDGET[] = "Not enough budget to conserve the initial set of taxa.";
-
- const char ERR_INTERNAL[] = "Internal error, pls contact authors!";
-
---- a/pruning.h
-+++ b/pruning.h
-@@ -87,7 +87,7 @@ public:
- LeafSet::iterator nearestLeaf();
-
- /**
-- mark the node in the inital set to be not PRUNABLE
-+ mark the node in the initial set to be not PRUNABLE
- */
- void doInitialSet();
-
---- a/phyloanalysis.cpp
-+++ b/phyloanalysis.cpp
-@@ -455,7 +455,7 @@ void reportTree(ofstream &out, Params &p
- }
- }
- if (is_codon)
-- out << endl << "NOTE: Branch lengths are intepreted as number of nucleotide substitutions per codon site!"
-+ out << endl << "NOTE: Branch lengths are interpreted as number of nucleotide substitutions per codon site!"
- << endl << " Rescale them by 1/3 if you want to have #nt substitutions per nt site" << endl;
- if (main_tree)
- if (params.aLRT_replicates > 0 || params.gbo_replicates || (params.num_bootstrap_samples && params.compute_ml_tree)) {
-@@ -548,7 +548,7 @@ void reportPhyloAnalysis(Params ¶ms,
- }
- for (IntVector::iterator i2 = counts.begin(); i2 != counts.end(); i2++) {
- if (*i2 != 0) {
-- cout << "#Trees occuring " << (i2-counts.begin()) << " times: " << *i2 << endl;
-+ cout << "#Trees occurring " << (i2-counts.begin()) << " times: " << *i2 << endl;
- }
- }
- }
---- a/iqtree.h
-+++ b/iqtree.h
-@@ -684,13 +684,13 @@ public:
- /** corresponding log-likelihood on original alignment */
- DoubleVector boot_orig_logl;
-
-- /** Set of splits occuring in bootstrap trees */
-+ /** Set of splits occurring in bootstrap trees */
- vector<SplitGraph*> boot_splits;
-
- /** log-likelihood of bootstrap consensus tree */
- double boot_consense_logl;
-
-- /** Corresponding map for set of splits occuring in bootstrap trees */
-+ /** Corresponding map for set of splits occurring in bootstrap trees */
- //SplitIntMap boot_splits_map;
-
- /** summarize all bootstrap trees */
diff --git a/debian/patches/sse.patch b/debian/patches/sse.patch
index db87c83..4848fa6 100644
--- a/debian/patches/sse.patch
+++ b/debian/patches/sse.patch
@@ -23,37 +23,15 @@ Last-Update: Tue, 02 Feb 2016 08:41:45 +0100
elseif (ICC)
if (WIN32)
set(SSE_FLAGS "/arch:SSE3")
-@@ -273,8 +273,7 @@ elseif (IQTREE_FLAGS MATCHES "avx") # AV
-
+@@ -272,8 +272,9 @@ elseif (IQTREE_FLAGS MATCHES "avx") # AV
+ set(COMBINED_FLAGS "${COMBINED_FLAGS} ${AVX_FLAGS}")
SET(EXE_SUFFIX "${EXE_SUFFIX}-avx")
else() #SSE intruction set
- message("Vectorization : SSE3")
- add_definitions(-D__SSE3)
++ #message("Vectorization : SSE3")
++ #add_definitions(-D__SSE3)
+ message("Vectorization : SSE2")
-
endif()
---- a/phylokernel.h
-+++ b/phylokernel.h
-@@ -15,6 +15,10 @@
- inline Vec2d horizontal_add(Vec2d x[2]) {
- #if INSTRSET >= 3 // SSE3
- return _mm_hadd_pd(x[0],x[1]);
-+#elif INSTRSET >= 2 // SSE3
-+ Vec2d help0 = _mm_shuffle_pd(x[0], x[1], _MM_SHUFFLE2(0,0));
-+ Vec2d help1 = _mm_shuffle_pd(x[0], x[1], _MM_SHUFFLE2(1,1));
-+ return _mm_add_pd(help0, help1);
- #else
- #error "You must compile with SSE3 enabled!"
- #endif
---- a/pll/pll.h
-+++ b/pll/pll.h
-@@ -82,7 +82,7 @@ extern "C" {
- #define PLL_VECTOR_WIDTH 2
-
- #else
--#define PLL_BYTE_ALIGNMENT 1
-+#define PLL_BYTE_ALIGNMENT 8
- #define PLL_VECTOR_WIDTH 1
- #endif
-
+
--
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