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(adapted patches) - TODO: Does not build - perhaps further adaptation to seqan-1.4 is needed + * Do not use copy of outdated gcc header file which destroys portability + to other architectures - -- Andreas Tille <[email protected]> Wed, 13 Aug 2014 08:27:09 +0200 + -- Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 <[email protected]> -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 \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
