[med-svn] r17931 - in trunk/packages/bowtie/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Sep 3 07:53:20 UTC 2014
Author: tille
Date: 2014-09-03 07:53:19 +0000 (Wed, 03 Sep 2014)
New Revision: 17931
Added:
trunk/packages/bowtie/trunk/debian/patches/do_not_use_outdated_copy_of_cpuid_h.patch
Modified:
trunk/packages/bowtie/trunk/debian/changelog
trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch
trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch
trunk/packages/bowtie/trunk/debian/patches/series
trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch
trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch
Log:
Revert changes to old version to fix build issue on all arches except amd64
Modified: trunk/packages/bowtie/trunk/debian/changelog
===================================================================
--- trunk/packages/bowtie/trunk/debian/changelog 2014-09-03 06:17:33 UTC (rev 17930)
+++ trunk/packages/bowtie/trunk/debian/changelog 2014-09-03 07:53:19 UTC (rev 17931)
@@ -1,9 +1,9 @@
-bowtie (1.1.0-1) UNRELEASED; urgency=medium
+bowtie (1.0.1-2) UNRELEASED; urgency=medium
- * New upstream version (adapted patches)
- TODO: Does not build - perhaps further adaptation to seqan-1.4 is needed
+ * Do not use copy of outdated gcc header file which destroys portability
+ to other architectures
- -- Andreas Tille <tille at debian.org> Wed, 13 Aug 2014 08:27:09 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 03 Sep 2014 09:50:22 +0200
bowtie (1.0.1-1) unstable; urgency=medium
Modified: trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2014-09-03 06:17:33 UTC (rev 17930)
+++ trunk/packages/bowtie/trunk/debian/patches/disable_bits_flag.patch 2014-09-03 07:53:19 UTC (rev 17931)
@@ -3,18 +3,18 @@
to run.
Author: Ognyan Kulev <ogi at debian.org>
Forwarded: not-needed
-Last-Update: 2014-08-13
-
+Last-Update: 2013-04-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/Makefile
+++ b/Makefile
-@@ -120,8 +120,8 @@ ifeq (32,$(BITS))
- $(error bowtie2 compilation requires a 64-bit platform )
+@@ -133,6 +133,9 @@ ifeq (64,$(BITS))
+ BITS_FLAG = -m64
endif
--DEBUG_FLAGS = -O0 -g3 -m64
--RELEASE_FLAGS = -O3 -m64
-+DEBUG_FLAGS = -O0 -g3
-+RELEASE_FLAGS = -O3
++# Debian: Disable selection of 32/64-bits. Use multiarch instead.
++BITS_FLAG =
++
+ DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG)
+ RELEASE_FLAGS = -O3 $(BITS_FLAG)
NOASSERT_FLAGS = -DNDEBUG
- FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-
Added: trunk/packages/bowtie/trunk/debian/patches/do_not_use_outdated_copy_of_cpuid_h.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/do_not_use_outdated_copy_of_cpuid_h.patch (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/do_not_use_outdated_copy_of_cpuid_h.patch 2014-09-03 07:53:19 UTC (rev 17931)
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 03 Sep 2014 09:50:22 +0200
+Description: Do not use copy of outdated gcc header file which destroys
+ portability to other architectures.
+
+--- a/Makefile
++++ b/Makefile
+@@ -4,7 +4,7 @@
+
+ SEQAN_DIR = /usr/include/seqan
+ SEQAN_INC = -I $(SEQAN_DIR)
+-INC = $(SEQAN_INC) -I third_party
++INC = $(SEQAN_INC)
+ CPP = g++
+ CXX = $(CPP)
+ CC = gcc
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch 2014-09-03 06:17:33 UTC (rev 17930)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-popcount.patch 2014-09-03 07:53:19 UTC (rev 17931)
@@ -5,7 +5,7 @@
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/diff_sample.h
+++ b/diff_sample.h
-@@ -476,6 +476,8 @@ static String<T> getDeltaMap(T v, const
+@@ -475,6 +475,8 @@ static String<T> getDeltaMap(T v, const
return amap;
}
@@ -14,7 +14,7 @@
/**
* Return population count (count of all bits set to 1) of i.
*/
-@@ -488,6 +490,7 @@ static unsigned int popCount(T i) {
+@@ -487,6 +489,7 @@ static unsigned int popCount(T i) {
}
return cnt;
}
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2014-09-03 06:17:33 UTC (rev 17930)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-rename-ChunkPool.patch 2014-09-03 07:53:19 UTC (rev 17931)
@@ -223,7 +223,7 @@
static bool chunkVerbose; // have chunk allocator output status messages?
static bool recal;
static int recalMaxCycle;
-@@ -222,7 +222,7 @@ static void resetOptions() {
+@@ -221,7 +221,7 @@ static void resetOptions() {
randomizeQuals = false; // randomize quality values
stats = false; // print performance stats
chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread
@@ -232,7 +232,7 @@
chunkVerbose = false; // have chunk allocator output status messages?
recal = false;
recalMaxCycle = 64;
-@@ -1192,7 +1192,7 @@ static void exactSearchWorkerStateful(vo
+@@ -1202,7 +1202,7 @@ static void exactSearchWorkerStateful(vo
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
@@ -241,7 +241,7 @@
UnpairedExactAlignerV1Factory alSEfact(
ebwt,
NULL,
-@@ -1361,7 +1361,7 @@ static void mismatchSearchWorkerFullStat
+@@ -1371,7 +1371,7 @@ static void mismatchSearchWorkerFullStat
// Global initialization
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
@@ -250,7 +250,7 @@
Unpaired1mmAlignerV1Factory alSEfact(
ebwtFw,
-@@ -1658,7 +1658,7 @@ static void twoOrThreeMismatchSearchWork
+@@ -1668,7 +1668,7 @@ static void twoOrThreeMismatchSearchWork
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
@@ -259,7 +259,7 @@
Unpaired23mmAlignerV1Factory alSEfact(
ebwtFw,
&ebwtBw,
-@@ -2091,7 +2091,7 @@ static void seededQualSearchWorkerFullSt
+@@ -2101,7 +2101,7 @@ static void seededQualSearchWorkerFullSt
// Global initialization
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink);
Modified: trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch 2014-09-03 06:17:33 UTC (rev 17930)
+++ trunk/packages/bowtie/trunk/debian/patches/seqan-rename-fill-to-resize.patch 2014-09-03 07:53:19 UTC (rev 17931)
@@ -3,22 +3,22 @@
SeqAn ticket: http://trac.seqan.de/ticket/77
Forwarded: no
Author: Ognyan Kulev <ogi at debian.org>
-Last-Update: 2014-08-13
+Last-Update: 2013-04-18
--- a/blockwise_sa.h
+++ b/blockwise_sa.h
-@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS
+@@ -448,8 +448,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS
try {
// Allocate and initialize containers for holding bucket
// sizes and representatives.
- fill(bucketSzs, numBuckets, 0, Exact());
-- fill(bucketReps, numBuckets, OFF_MASK, Exact());
+- fill(bucketReps, numBuckets, 0xffffffff, Exact());
+ resize(bucketSzs, numBuckets, 0, Exact());
-+ resize(bucketReps, numBuckets, OFF_MASK, Exact());
++ resize(bucketReps, numBuckets, 0xffffffff, Exact());
} catch(bad_alloc &e) {
if(this->_passMemExc) {
throw e; // rethrow immediately
-@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
+@@ -806,7 +806,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
// Not the last bucket
assert_lt(_cur, length(_sampleSuffs));
hi = _sampleSuffs[_cur];
@@ -27,7 +27,7 @@
assert_eq(zHi[0], 0);
calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
}
-@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
+@@ -815,7 +815,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
assert_gt(_cur, 0);
assert_leq(_cur, length(_sampleSuffs));
lo = _sampleSuffs[_cur-1];
@@ -38,7 +38,7 @@
calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
--- a/diff_sample.h
+++ b/diff_sample.h
-@@ -452,7 +452,7 @@ static String<T> getDeltaMap(T v, const
+@@ -451,7 +451,7 @@ static String<T> getDeltaMap(T v, const
// Declare anchor-map-related items
String<T> amap;
size_t amapEnts = 1;
@@ -47,39 +47,39 @@
amap[0] = 0;
// Print out difference cover (and optionally calculate
// anchor map)
-@@ -532,7 +532,7 @@ public:
+@@ -531,7 +531,7 @@ public:
assert_gt(_d, 0);
assert_eq(1, popCount(_v)); // must be power of 2
// Build map from d's to idx's
- fill(_dInv, _v, 0xffffffff, Exact());
+ resize(_dInv, _v, 0xffffffff, Exact());
- uint32_t lim = (uint32_t)length(_ds);
- for(uint32_t i = 0; i < lim; i++) {
- _dInv[_ds[i]] = i;
-@@ -656,7 +656,7 @@ void DifferenceCoverSample<TStr>::doBuil
+ for(size_t i = 0; i < length(_ds); i++) _dInv[_ds[i]] = i;
+ }
+
+@@ -652,7 +652,7 @@ void DifferenceCoverSample<TStr>::doBuil
VMSG_NL(" Doing sanity check");
- TIndexOffU added = 0;
- String<TIndexOffU> sorted;
-- fill(sorted, length(_isaPrime), OFF_MASK, Exact());
-+ resize(sorted, length(_isaPrime), OFF_MASK, Exact());
+ uint32_t added = 0;
+ String<uint32_t> sorted;
+- fill(sorted, length(_isaPrime), 0xffffffff, Exact());
++ resize(sorted, length(_isaPrime), 0xffffffff, Exact());
for(size_t di = 0; di < this->d(); di++) {
uint32_t d = _ds[di];
size_t i = 0;
-@@ -717,7 +717,7 @@ void DifferenceCoverSample<TStr>::buildS
+@@ -713,7 +713,7 @@ void DifferenceCoverSample<TStr>::buildS
assert_eq(length(_doffs), d+1);
// Size sPrime appropriately
reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS
-- fill(sPrime, sPrimeSz, OFF_MASK, Exact());
-+ resize(sPrime, sPrimeSz, OFF_MASK, Exact());
+- fill(sPrime, sPrimeSz, 0xffffffff, Exact());
++ resize(sPrime, sPrimeSz, 0xffffffff, Exact());
// Slot suffixes from text into sPrime according to the mu
// mapping; where the mapping would leave a blank, insert a 0
- TIndexOffU added = 0;
-@@ -823,7 +823,7 @@ void DifferenceCoverSample<TStr>::build(
+ uint32_t added = 0;
+@@ -818,7 +818,7 @@ void DifferenceCoverSample<TStr>::build(
// arrays back into sPrime.
VMSG_NL(" Allocating rank array");
reserve(_isaPrime, length(sPrime)+1, Exact());
-- fill(_isaPrime, length(sPrime), OFF_MASK, Exact());
-+ resize(_isaPrime, length(sPrime), OFF_MASK, Exact());
+- fill(_isaPrime, length(sPrime), 0xffffffff, Exact());
++ resize(_isaPrime, length(sPrime), 0xffffffff, Exact());
assert_gt(length(_isaPrime), 0);
{
Timer timer(cout, " Ranking v-sort output time: ", this->verbose());
Modified: trunk/packages/bowtie/trunk/debian/patches/series
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/series 2014-09-03 06:17:33 UTC (rev 17930)
+++ trunk/packages/bowtie/trunk/debian/patches/series 2014-09-03 07:53:19 UTC (rev 17931)
@@ -6,3 +6,4 @@
disable_bits_flag.patch
no_hash_style_both_for_mips.patch
seqan-popcount.patch
+do_not_use_outdated_copy_of_cpuid_h.patch
Modified: trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2014-09-03 06:17:33 UTC (rev 17930)
+++ trunk/packages/bowtie/trunk/debian/patches/use-dpkg-buildflags.patch 2014-09-03 07:53:19 UTC (rev 17931)
@@ -6,7 +6,7 @@
--- a/Makefile
+++ b/Makefile
-@@ -192,7 +192,7 @@ DEFS=-fno-strict-aliasing \
+@@ -195,7 +195,7 @@ DEFS=-fno-strict-aliasing \
$(MM_DEF) \
$(SHMEM_DEF)
Modified: trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2014-09-03 06:17:33 UTC (rev 17930)
+++ trunk/packages/bowtie/trunk/debian/patches/use_debian_seqan.patch 2014-09-03 07:53:19 UTC (rev 17931)
@@ -15,11 +15,11 @@
SEQAN_INC = -I $(SEQAN_DIR)
INC = $(SEQAN_INC) -I third_party
CPP = g++
-@@ -145,7 +145,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh)
+@@ -151,7 +151,6 @@ GENERAL_LIST = $(wildcard scripts/*.sh)
$(wildcard genomes/NC_008253.fna) \
$(wildcard reads/e_coli_1000.*) \
$(wildcard reads/e_coli_1000_*) \
- SeqAn-1.1 \
- bowtie \
- bowtie-build \
- bowtie-inspect \
+ doc/manual.html \
+ doc/README \
+ doc/style.css \
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