diff --git a/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/bsdiff-4.3-r5.ebuild b/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/bsdiff-4.3-r6.ebuild similarity index 86% rename from sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/bsdiff-4.3-r5.ebuild rename to sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/bsdiff-4.3-r6.ebuild index 617b6c068e..2418efc22c 100644 --- a/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/bsdiff-4.3-r5.ebuild +++ b/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/bsdiff-4.3-r6.ebuild @@ -16,13 +16,12 @@ SLOT="0" LICENSE="BSD-2" KEYWORDS="alpha amd64 arm arm64 hppa ia64 mips ppc sparc x86 ~x86-fbsd ~x86-freebsd ~amd64-linux ~x86-linux ~ppc-macos" -RDEPEND="app-arch/bzip2 - dev-libs/libdivsufsort" +RDEPEND="app-arch/bzip2" DEPEND="${RDEPEND}" src_prepare() { epatch ${FILESDIR}/4.3_bspatch-support-input-output-positioning.patch || die - epatch ${FILESDIR}/4.3_bsdiff-divsufsort.patch || die + epatch ${FILESDIR}/4.3_bsdiff-convert-to-sais-lite-suffix-sort.patch || die } doecho() { @@ -32,7 +31,7 @@ doecho() { src_compile() { append-lfs-flags - doecho $(tc-getCC) ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o bsdiff bsdiff.c -lbz2 -ldivsufsort64 || die "failed compiling bsdiff" + doecho $(tc-getCC) ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o bsdiff bsdiff.c sais.c -lbz2 || die "failed compiling bsdiff" doecho $(tc-getCC) ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} -o bspatch bspatch.c -lbz2 || die "failed compiling bspatch" } diff --git a/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/files/4.3_bsdiff-convert-to-sais-lite-suffix-sort.patch b/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/files/4.3_bsdiff-convert-to-sais-lite-suffix-sort.patch new file mode 100644 index 0000000000..589ecad248 --- /dev/null +++ b/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/files/4.3_bsdiff-convert-to-sais-lite-suffix-sort.patch @@ -0,0 +1,754 @@ +From f220517e188924e67040c6171ca7e0dede16c6b4 Mon Sep 17 00:00:00 2001 +From: Geoff Levand +Date: Tue, 14 Jul 2015 14:29:21 -0700 +Subject: [PATCH 2/2] bsdiff: Convert to sais-lite suffix sort + +Convert the bsdiff suffix sort algorithm from its own qsufsort implementation to +the sais-lite suffix sort algorithm from [1]. Fixes problems with slow +operation and program hangs as reported in [2] through [4]. + + [1] https://sites.google.com/site/yuta256/sais + [2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=409664 + [3] https://github.com/sparkle-project/Sparkle/pull/515 + [4] https://chromium.googlesource.com/chromiumos/third_party/bsdiff/+/e2b85ce4ea246ca804ee2a9e18005c44e193d868 + +Signed-off-by: Geoff Levand +--- + bsdiff.c | 104 +------------ + sais.c | 534 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + sais.h | 59 +++++++ + 3 files changed, 597 insertions(+), 100 deletions(-) + create mode 100644 sais.c + create mode 100644 sais.h + +diff --git a/bsdiff.c b/bsdiff.c +index 150a7f7..5c6c94f 100644 +--- a/bsdiff.c ++++ b/bsdiff.c +@@ -38,106 +38,9 @@ __FBSDID("$FreeBSD: src/usr.bin/bsdiff/bsdiff/bsdiff.c,v 1.1 2005/08/06 01:59:05 + #include + #include + +-#define MIN(x,y) (((x)<(y)) ? (x) : (y)) +- +-static void split(off_t *I,off_t *V,off_t start,off_t len,off_t h) +-{ +- off_t i,j,k,x,tmp,jj,kk; +- +- if(len<16) { +- for(k=start;kstart) split(I,V,start,jj-start,h); +- +- for(i=0;ikk) split(I,V,kk,start+len-kk,h); +-} ++#include "sais.h" + +-static void qsufsort(off_t *I,off_t *V,u_char *old,off_t oldsize) +-{ +- off_t buckets[256]; +- off_t i,h,len; +- +- for(i=0;i<256;i++) buckets[i]=0; +- for(i=0;i0;i--) buckets[i]=buckets[i-1]; +- buckets[0]=0; +- +- for(i=0;i ++#include ++#include "sais.h" ++ ++#ifndef UCHAR_SIZE ++# define UCHAR_SIZE 256 ++#endif ++#ifndef MINBUCKETSIZE ++# define MINBUCKETSIZE 256 ++#endif ++ ++#define sais_bool_type int ++#define SAIS_LMSSORT2_LIMIT 0x3fffffff ++ ++#define SAIS_MYMALLOC(_num, _type) ((_type *)malloc((_num) * sizeof(_type))) ++#define SAIS_MYFREE(_ptr, _num, _type) free((_ptr)) ++#define chr(_a) (cs == sizeof(sais_index_type) ? ((sais_index_type *)T)[(_a)] : ((unsigned char *)T)[(_a)]) ++ ++/* find the start or end of each bucket */ ++static ++void ++getCounts(const void *T, sais_index_type *C, sais_index_type n, sais_index_type k, int cs) { ++ sais_index_type i; ++ for(i = 0; i < k; ++i) { C[i] = 0; } ++ for(i = 0; i < n; ++i) { ++C[chr(i)]; } ++} ++static ++void ++getBuckets(const sais_index_type *C, sais_index_type *B, sais_index_type k, sais_bool_type end) { ++ sais_index_type i, sum = 0; ++ if(end) { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum; } } ++ else { for(i = 0; i < k; ++i) { sum += C[i]; B[i] = sum - C[i]; } } ++} ++ ++/* sort all type LMS suffixes */ ++static ++void ++LMSsort1(const void *T, sais_index_type *SA, ++ sais_index_type *C, sais_index_type *B, ++ sais_index_type n, sais_index_type k, int cs) { ++ sais_index_type *b, i, j; ++ sais_index_type c0, c1; ++ ++ /* compute SAl */ ++ if(C == B) { getCounts(T, C, n, k, cs); } ++ getBuckets(C, B, k, 0); /* find starts of buckets */ ++ j = n - 1; ++ b = SA + B[c1 = chr(j)]; ++ --j; ++ *b++ = (chr(j) < c1) ? ~j : j; ++ for(i = 0; i < n; ++i) { ++ if(0 < (j = SA[i])) { ++ assert(chr(j) >= chr(j + 1)); ++ if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } ++ assert(i < (b - SA)); ++ --j; ++ *b++ = (chr(j) < c1) ? ~j : j; ++ SA[i] = 0; ++ } else if(j < 0) { ++ SA[i] = ~j; ++ } ++ } ++ /* compute SAs */ ++ if(C == B) { getCounts(T, C, n, k, cs); } ++ getBuckets(C, B, k, 1); /* find ends of buckets */ ++ for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) { ++ if(0 < (j = SA[i])) { ++ assert(chr(j) <= chr(j + 1)); ++ if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } ++ assert((b - SA) <= i); ++ --j; ++ *--b = (chr(j) > c1) ? ~(j + 1) : j; ++ SA[i] = 0; ++ } ++ } ++} ++static ++sais_index_type ++LMSpostproc1(const void *T, sais_index_type *SA, ++ sais_index_type n, sais_index_type m, int cs) { ++ sais_index_type i, j, p, q, plen, qlen, name; ++ sais_index_type c0, c1; ++ sais_bool_type diff; ++ ++ /* compact all the sorted substrings into the first m items of SA ++ 2*m must be not larger than n (proveable) */ ++ assert(0 < n); ++ for(i = 0; (p = SA[i]) < 0; ++i) { SA[i] = ~p; assert((i + 1) < n); } ++ if(i < m) { ++ for(j = i, ++i;; ++i) { ++ assert(i < n); ++ if((p = SA[i]) < 0) { ++ SA[j++] = ~p; SA[i] = 0; ++ if(j == m) { break; } ++ } ++ } ++ } ++ ++ /* store the length of all substrings */ ++ i = n - 1; j = n - 1; c0 = chr(n - 1); ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1)); ++ for(; 0 <= i;) { ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) <= c1)); ++ if(0 <= i) { ++ SA[m + ((i + 1) >> 1)] = j - i; j = i + 1; ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1)); ++ } ++ } ++ ++ /* find the lexicographic names of all substrings */ ++ for(i = 0, name = 0, q = n, qlen = 0; i < m; ++i) { ++ p = SA[i], plen = SA[m + (p >> 1)], diff = 1; ++ if((plen == qlen) && ((q + plen) < n)) { ++ for(j = 0; (j < plen) && (chr(p + j) == chr(q + j)); ++j) { } ++ if(j == plen) { diff = 0; } ++ } ++ if(diff != 0) { ++name, q = p, qlen = plen; } ++ SA[m + (p >> 1)] = name; ++ } ++ ++ return name; ++} ++static ++void ++LMSsort2(const void *T, sais_index_type *SA, ++ sais_index_type *C, sais_index_type *B, sais_index_type *D, ++ sais_index_type n, sais_index_type k, int cs) { ++ sais_index_type *b, i, j, t, d; ++ sais_index_type c0, c1; ++ assert(C != B); ++ ++ /* compute SAl */ ++ getBuckets(C, B, k, 0); /* find starts of buckets */ ++ j = n - 1; ++ b = SA + B[c1 = chr(j)]; ++ --j; ++ t = (chr(j) < c1); ++ j += n; ++ *b++ = (t & 1) ? ~j : j; ++ for(i = 0, d = 0; i < n; ++i) { ++ if(0 < (j = SA[i])) { ++ if(n <= j) { d += 1; j -= n; } ++ assert(chr(j) >= chr(j + 1)); ++ if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } ++ assert(i < (b - SA)); ++ --j; ++ t = c0; t = (t << 1) | (chr(j) < c1); ++ if(D[t] != d) { j += n; D[t] = d; } ++ *b++ = (t & 1) ? ~j : j; ++ SA[i] = 0; ++ } else if(j < 0) { ++ SA[i] = ~j; ++ } ++ } ++ for(i = n - 1; 0 <= i; --i) { ++ if(0 < SA[i]) { ++ if(SA[i] < n) { ++ SA[i] += n; ++ for(j = i - 1; SA[j] < n; --j) { } ++ SA[j] -= n; ++ i = j; ++ } ++ } ++ } ++ ++ /* compute SAs */ ++ getBuckets(C, B, k, 1); /* find ends of buckets */ ++ for(i = n - 1, d += 1, b = SA + B[c1 = 0]; 0 <= i; --i) { ++ if(0 < (j = SA[i])) { ++ if(n <= j) { d += 1; j -= n; } ++ assert(chr(j) <= chr(j + 1)); ++ if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } ++ assert((b - SA) <= i); ++ --j; ++ t = c0; t = (t << 1) | (chr(j) > c1); ++ if(D[t] != d) { j += n; D[t] = d; } ++ *--b = (t & 1) ? ~(j + 1) : j; ++ SA[i] = 0; ++ } ++ } ++} ++static ++sais_index_type ++LMSpostproc2(sais_index_type *SA, sais_index_type n, sais_index_type m) { ++ sais_index_type i, j, d, name; ++ ++ /* compact all the sorted LMS substrings into the first m items of SA */ ++ assert(0 < n); ++ for(i = 0, name = 0; (j = SA[i]) < 0; ++i) { ++ j = ~j; ++ if(n <= j) { name += 1; } ++ SA[i] = j; ++ assert((i + 1) < n); ++ } ++ if(i < m) { ++ for(d = i, ++i;; ++i) { ++ assert(i < n); ++ if((j = SA[i]) < 0) { ++ j = ~j; ++ if(n <= j) { name += 1; } ++ SA[d++] = j; SA[i] = 0; ++ if(d == m) { break; } ++ } ++ } ++ } ++ if(name < m) { ++ /* store the lexicographic names */ ++ for(i = m - 1, d = name + 1; 0 <= i; --i) { ++ if(n <= (j = SA[i])) { j -= n; --d; } ++ SA[m + (j >> 1)] = d; ++ } ++ } else { ++ /* unset flags */ ++ for(i = 0; i < m; ++i) { ++ if(n <= (j = SA[i])) { j -= n; SA[i] = j; } ++ } ++ } ++ ++ return name; ++} ++ ++/* compute SA and BWT */ ++static ++void ++induceSA(const void *T, sais_index_type *SA, ++ sais_index_type *C, sais_index_type *B, ++ sais_index_type n, sais_index_type k, int cs) { ++ sais_index_type *b, i, j; ++ sais_index_type c0, c1; ++ /* compute SAl */ ++ if(C == B) { getCounts(T, C, n, k, cs); } ++ getBuckets(C, B, k, 0); /* find starts of buckets */ ++ j = n - 1; ++ b = SA + B[c1 = chr(j)]; ++ *b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j; ++ for(i = 0; i < n; ++i) { ++ j = SA[i], SA[i] = ~j; ++ if(0 < j) { ++ --j; ++ assert(chr(j) >= chr(j + 1)); ++ if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } ++ assert(i < (b - SA)); ++ *b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j; ++ } ++ } ++ /* compute SAs */ ++ if(C == B) { getCounts(T, C, n, k, cs); } ++ getBuckets(C, B, k, 1); /* find ends of buckets */ ++ for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) { ++ if(0 < (j = SA[i])) { ++ --j; ++ assert(chr(j) <= chr(j + 1)); ++ if((c0 = chr(j)) != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } ++ assert((b - SA) <= i); ++ *--b = ((j == 0) || (chr(j - 1) > c1)) ? ~j : j; ++ } else { ++ SA[i] = ~j; ++ } ++ } ++} ++static ++sais_index_type ++computeBWT(const void *T, sais_index_type *SA, ++ sais_index_type *C, sais_index_type *B, ++ sais_index_type n, sais_index_type k, int cs) { ++ sais_index_type *b, i, j, pidx = -1; ++ sais_index_type c0, c1; ++ /* compute SAl */ ++ if(C == B) { getCounts(T, C, n, k, cs); } ++ getBuckets(C, B, k, 0); /* find starts of buckets */ ++ j = n - 1; ++ b = SA + B[c1 = chr(j)]; ++ *b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j; ++ for(i = 0; i < n; ++i) { ++ if(0 < (j = SA[i])) { ++ --j; ++ assert(chr(j) >= chr(j + 1)); ++ SA[i] = ~((sais_index_type)(c0 = chr(j))); ++ if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } ++ assert(i < (b - SA)); ++ *b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j; ++ } else if(j != 0) { ++ SA[i] = ~j; ++ } ++ } ++ /* compute SAs */ ++ if(C == B) { getCounts(T, C, n, k, cs); } ++ getBuckets(C, B, k, 1); /* find ends of buckets */ ++ for(i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) { ++ if(0 < (j = SA[i])) { ++ --j; ++ assert(chr(j) <= chr(j + 1)); ++ SA[i] = (c0 = chr(j)); ++ if(c0 != c1) { B[c1] = b - SA; b = SA + B[c1 = c0]; } ++ assert((b - SA) <= i); ++ *--b = ((0 < j) && (chr(j - 1) > c1)) ? ~((sais_index_type)chr(j - 1)) : j; ++ } else if(j != 0) { ++ SA[i] = ~j; ++ } else { ++ pidx = i; ++ } ++ } ++ return pidx; ++} ++ ++/* find the suffix array SA of T[0..n-1] in {0..255}^n */ ++static ++sais_index_type ++sais_main(const void *T, sais_index_type *SA, ++ sais_index_type fs, sais_index_type n, sais_index_type k, int cs, ++ sais_bool_type isbwt) { ++ sais_index_type *C, *B, *D, *RA, *b; ++ sais_index_type i, j, m, p, q, t, name, pidx = 0, newfs; ++ sais_index_type c0, c1; ++ unsigned int flags; ++ ++ assert((T != NULL) && (SA != NULL)); ++ assert((0 <= fs) && (0 < n) && (1 <= k)); ++ ++ if(k <= MINBUCKETSIZE) { ++ if((C = SAIS_MYMALLOC((size_t)k, sais_index_type)) == NULL) { return -2; } ++ if(k <= fs) { ++ B = SA + (n + fs - k); ++ flags = 1; ++ } else { ++ if((B = SAIS_MYMALLOC((size_t)k, sais_index_type)) == NULL) { SAIS_MYFREE(C, k, sais_index_type); return -2; } ++ flags = 3; ++ } ++ } else if(k <= fs) { ++ C = SA + (n + fs - k); ++ if(k <= (fs - k)) { ++ B = C - k; ++ flags = 0; ++ } else if(k <= (MINBUCKETSIZE * 4)) { ++ if((B = SAIS_MYMALLOC((size_t)k, sais_index_type)) == NULL) { return -2; } ++ flags = 2; ++ } else { ++ B = C; ++ flags = 8; ++ } ++ } else { ++ if((C = B = SAIS_MYMALLOC((size_t)k, sais_index_type)) == NULL) { return -2; } ++ flags = 4 | 8; ++ } ++ if((n <= SAIS_LMSSORT2_LIMIT) && (2 <= (n / k))) { ++ if(flags & 1) { flags |= ((k * 2) <= (fs - k)) ? 32 : 16; } ++ else if((flags == 0) && ((k * 2) <= (fs - k * 2))) { flags |= 32; } ++ } ++ ++ /* stage 1: reduce the problem by at least 1/2 ++ sort all the LMS-substrings */ ++ getCounts(T, C, n, k, cs); getBuckets(C, B, k, 1); /* find ends of buckets */ ++ for(i = 0; i < n; ++i) { SA[i] = 0; } ++ b = &t; i = n - 1; j = n; m = 0; c0 = chr(n - 1); ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1)); ++ for(; 0 <= i;) { ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) <= c1)); ++ if(0 <= i) { ++ *b = j; b = SA + --B[c1]; j = i; ++m; ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1)); ++ } ++ } ++ ++ if(1 < m) { ++ if(flags & (16 | 32)) { ++ if(flags & 16) { ++ if((D = SAIS_MYMALLOC((size_t)k * 2, sais_index_type)) == NULL) { ++ if(flags & (1 | 4)) { SAIS_MYFREE(C, k, sais_index_type); } ++ if(flags & 2) { SAIS_MYFREE(B, k, sais_index_type); } ++ return -2; ++ } ++ } else { ++ D = B - k * 2; ++ } ++ assert((j + 1) < n); ++ ++B[chr(j + 1)]; ++ for(i = 0, j = 0; i < k; ++i) { ++ j += C[i]; ++ if(B[i] != j) { assert(SA[B[i]] != 0); SA[B[i]] += n; } ++ D[i] = D[i + k] = 0; ++ } ++ LMSsort2(T, SA, C, B, D, n, k, cs); ++ name = LMSpostproc2(SA, n, m); ++ if(flags & 16) { SAIS_MYFREE(D, k * 2, sais_index_type); } ++ } else { ++ LMSsort1(T, SA, C, B, n, k, cs); ++ name = LMSpostproc1(T, SA, n, m, cs); ++ } ++ } else if(m == 1) { ++ *b = j + 1; ++ name = 1; ++ } else { ++ name = 0; ++ } ++ ++ /* stage 2: solve the reduced problem ++ recurse if names are not yet unique */ ++ if(name < m) { ++ if(flags & 4) { SAIS_MYFREE(C, k, sais_index_type); } ++ if(flags & 2) { SAIS_MYFREE(B, k, sais_index_type); } ++ newfs = (n + fs) - (m * 2); ++ if((flags & (1 | 4 | 8)) == 0) { ++ if((k + name) <= newfs) { newfs -= k; } ++ else { flags |= 8; } ++ } ++ assert((n >> 1) <= (newfs + m)); ++ RA = SA + m + newfs; ++ for(i = m + (n >> 1) - 1, j = m - 1; m <= i; --i) { ++ if(SA[i] != 0) { ++ RA[j--] = SA[i] - 1; ++ } ++ } ++ if(sais_main(RA, SA, newfs, m, name, sizeof(sais_index_type), 0) != 0) { ++ if(flags & 1) { SAIS_MYFREE(C, k, sais_index_type); } ++ return -2; ++ } ++ ++ i = n - 1; j = m - 1; c0 = chr(n - 1); ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1)); ++ for(; 0 <= i;) { ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) <= c1)); ++ if(0 <= i) { ++ RA[j--] = i + 1; ++ do { c1 = c0; } while((0 <= --i) && ((c0 = chr(i)) >= c1)); ++ } ++ } ++ for(i = 0; i < m; ++i) { SA[i] = RA[SA[i]]; } ++ if(flags & 4) { ++ if((C = B = SAIS_MYMALLOC((size_t)k, sais_index_type)) == NULL) { return -2; } ++ } ++ if(flags & 2) { ++ if((B = SAIS_MYMALLOC((size_t)k, sais_index_type)) == NULL) { ++ if(flags & 1) { SAIS_MYFREE(C, k, sais_index_type); } ++ return -2; ++ } ++ } ++ } ++ ++ /* stage 3: induce the result for the original problem */ ++ if(flags & 8) { getCounts(T, C, n, k, cs); } ++ /* put all left-most S characters into their buckets */ ++ if(1 < m) { ++ getBuckets(C, B, k, 1); /* find ends of buckets */ ++ i = m - 1, j = n, p = SA[m - 1], c1 = chr(p); ++ do { ++ q = B[c0 = c1]; ++ while(q < j) { SA[--j] = 0; } ++ do { ++ SA[--j] = p; ++ if(--i < 0) { break; } ++ p = SA[i]; ++ } while((c1 = chr(p)) == c0); ++ } while(0 <= i); ++ while(0 < j) { SA[--j] = 0; } ++ } ++ if(isbwt == 0) { induceSA(T, SA, C, B, n, k, cs); } ++ else { pidx = computeBWT(T, SA, C, B, n, k, cs); } ++ if(flags & (1 | 4)) { SAIS_MYFREE(C, k, sais_index_type); } ++ if(flags & 2) { SAIS_MYFREE(B, k, sais_index_type); } ++ ++ return pidx; ++} ++ ++/*---------------------------------------------------------------------------*/ ++ ++sais_index_type ++sais(const unsigned char *T, sais_index_type *SA, int n) { ++ if((T == NULL) || (SA == NULL) || (n < 0)) { return -1; } ++ if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; } ++ return sais_main(T, SA, 0, n, UCHAR_SIZE, sizeof(unsigned char), 0); ++} ++ ++sais_index_type ++sais_int(const int *T, sais_index_type *SA, int n, int k) { ++ if((T == NULL) || (SA == NULL) || (n < 0) || (k <= 0)) { return -1; } ++ if(n <= 1) { if(n == 1) { SA[0] = 0; } return 0; } ++ return sais_main(T, SA, 0, n, k, sizeof(int), 0); ++} ++ ++sais_index_type ++sais_bwt(const unsigned char *T, unsigned char *U, sais_index_type *A, int n) { ++ int i; ++ sais_index_type pidx; ++ if((T == NULL) || (U == NULL) || (A == NULL) || (n < 0)) { return -1; } ++ if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; } ++ pidx = sais_main(T, A, 0, n, UCHAR_SIZE, sizeof(unsigned char), 1); ++ if(pidx < 0) { return pidx; } ++ U[0] = T[n - 1]; ++ for(i = 0; i < pidx; ++i) { U[i + 1] = (unsigned char)A[i]; } ++ for(i += 1; i < n; ++i) { U[i] = (unsigned char)A[i]; } ++ pidx += 1; ++ return pidx; ++} ++ ++sais_index_type ++sais_int_bwt(const sais_index_type *T, sais_index_type *U, sais_index_type *A, int n, int k) { ++ int i; ++ sais_index_type pidx; ++ if((T == NULL) || (U == NULL) || (A == NULL) || (n < 0) || (k <= 0)) { return -1; } ++ if(n <= 1) { if(n == 1) { U[0] = T[0]; } return n; } ++ pidx = sais_main(T, A, 0, n, k, sizeof(int), 1); ++ if(pidx < 0) { return pidx; } ++ U[0] = T[n - 1]; ++ for(i = 0; i < pidx; ++i) { U[i + 1] = A[i]; } ++ for(i += 1; i < n; ++i) { U[i] = A[i]; } ++ pidx += 1; ++ return pidx; ++} +diff --git a/sais.h b/sais.h +new file mode 100644 +index 0000000..1abd0af +--- /dev/null ++++ b/sais.h +@@ -0,0 +1,59 @@ ++/* ++ * sais.h for sais-lite ++ * Copyright (c) 2008-2010 Yuta Mori All Rights Reserved. ++ * ++ * Permission is hereby granted, free of charge, to any person ++ * obtaining a copy of this software and associated documentation ++ * files (the "Software"), to deal in the Software without ++ * restriction, including without limitation the rights to use, ++ * copy, modify, merge, publish, distribute, sublicense, and/or sell ++ * copies of the Software, and to permit persons to whom the ++ * Software is furnished to do so, subject to the following ++ * conditions: ++ * ++ * The above copyright notice and this permission notice shall be ++ * included in all copies or substantial portions of the Software. ++ * ++ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, ++ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES ++ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND ++ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT ++ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, ++ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING ++ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR ++ * OTHER DEALINGS IN THE SOFTWARE. ++ */ ++ ++#ifndef _SAIS_H ++#define _SAIS_H 1 ++ ++#ifdef __cplusplus ++extern "C" { ++#endif /* __cplusplus */ ++ ++#include ++ ++#define sais_index_type off_t ++ ++/* find the suffix array SA of T[0..n-1] ++ use a working space (excluding T and SA) of at most 2n+O(lg n) */ ++sais_index_type ++sais(const unsigned char *T, sais_index_type *SA, int n); ++ ++/* find the suffix array SA of T[0..n-1] in {0..k-1}^n ++ use a working space (excluding T and SA) of at most MAX(4k,2n) */ ++sais_index_type ++sais_int(const int *T, sais_index_type *SA, int n, int k); ++ ++/* burrows-wheeler transform */ ++sais_index_type ++sais_bwt(const unsigned char *T, unsigned char *U, sais_index_type *A, int n); ++sais_index_type ++sais_int_bwt(const sais_index_type *T, sais_index_type *U, sais_index_type *A, int n, int k); ++ ++ ++#ifdef __cplusplus ++} /* extern "C" */ ++#endif /* __cplusplus */ ++ ++#endif /* _SAIS_H */ +-- +2.1.0 + diff --git a/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/files/4.3_bsdiff-divsufsort.patch b/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/files/4.3_bsdiff-divsufsort.patch deleted file mode 100644 index 48bc8c30f2..0000000000 --- a/sdk_container/src/third_party/coreos-overlay/dev-util/bsdiff/files/4.3_bsdiff-divsufsort.patch +++ /dev/null @@ -1,187 +0,0 @@ -diff -urN bsdiff-4.3/bsdiff.c bsdiff-4.3-new/bsdiff.c ---- bsdiff-4.3/bsdiff.c 2005-08-16 15:13:52.000000000 -0700 -+++ bsdiff-4.3-new/bsdiff.c 2012-03-28 17:17:04.000000000 -0700 -@@ -38,106 +38,15 @@ - #include - #include - --#define MIN(x,y) (((x)<(y)) ? (x) : (y)) -- --static void split(off_t *I,off_t *V,off_t start,off_t len,off_t h) --{ -- off_t i,j,k,x,tmp,jj,kk; -- -- if(len<16) { -- for(k=start;kstart) split(I,V,start,jj-start,h); -- -- for(i=0;ikk) split(I,V,kk,start+len-kk,h); --} -- --static void qsufsort(off_t *I,off_t *V,u_char *old,off_t oldsize) --{ -- off_t buckets[256]; -- off_t i,h,len; -+#if _FILE_OFFSET_BITS == 64 -+#include "divsufsort64.h" -+#define saidx_t saidx64_t -+#define divsufsort divsufsort64 -+#else -+#include "divsufsort.h" -+#endif - -- for(i=0;i<256;i++) buckets[i]=0; -- for(i=0;i0;i--) buckets[i]=buckets[i-1]; -- buckets[0]=0; -- -- for(i=0;i 100) break; - }; - - if((len!=oldscore) || (scan==newsize)) {