1 |
commit: dd0d369425cbd225ec9c58a76456c4f539bda386 |
2 |
Author: Michał Górny <mgorny <AT> gentoo <DOT> org> |
3 |
AuthorDate: Sat Dec 9 23:24:48 2017 +0000 |
4 |
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> |
5 |
CommitDate: Sun Dec 10 00:05:29 2017 +0000 |
6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dd0d3694 |
7 |
|
8 |
sci-biology/vaal: [QA] Move the patch to a distfile |
9 |
|
10 |
Closes: https://bugs.gentoo.org/620620 |
11 |
|
12 |
sci-biology/vaal/Manifest | 5 +- |
13 |
.../files/vaal-46233_remove-namespace-std.patch | 911 --------------------- |
14 |
sci-biology/vaal/vaal-46233-r2.ebuild | 5 +- |
15 |
3 files changed, 6 insertions(+), 915 deletions(-) |
16 |
|
17 |
diff --git a/sci-biology/vaal/Manifest b/sci-biology/vaal/Manifest |
18 |
index 8276750cfdc..59235379245 100644 |
19 |
--- a/sci-biology/vaal/Manifest |
20 |
+++ b/sci-biology/vaal/Manifest |
21 |
@@ -1,2 +1,3 @@ |
22 |
-DIST VAAL_manual.doc 48128 SHA256 08b662105e8db41b33ea5d6626b58d5a5d793b1dd40fdc663a7068d9abacdc83 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171 WHIRLPOOL 3a7432974921946e28cd037e47b79fd31631f7a7915a96589a8485b84a3296e1e7d8768e84f4f9086b2648e270f9f84f1e73261bb0b492b3fa7a6cc6fe36f175 |
23 |
-DIST vaal-46233.tar.gz 1148052 SHA256 a1c27ae25583c1333c5169bb33a37cf461bc93b1c18c7e49f585c1cdc9e5a131 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321 WHIRLPOOL e848bcd6b2dd0c0c52142a3d55acef6a98b816e37355d22386bf3a2fac21e1318a821a394ebd5851cd530aa9afb0d178debc3f74638ee0d0820209a0f432f59f |
24 |
+DIST VAAL_manual.doc 48128 BLAKE2B cc31bcdfd4d6faa8c247a9d23a6254ac8a8f8f5de20f8d188c7ed57b9f8231920b4fc7e246394b1bb48ebf457a777d82e704b51b91feb6191e5da331e5765aa9 SHA512 4da21b6559659764e108c118773bd8ed365b67e3a22de52c7c13429979bb765e7f5d05955ce746a7a55e8d3a6baa752ad575289e71dfd7fb5b8b7207f5cff171 |
25 |
+DIST vaal-46233.tar.gz 1148052 BLAKE2B c3fa8ebd722e41bfa1e821d988316900a07d502b6a6b2be394b7227f269ae60a47645b45b6616a782189dcef8a1ea341265e40f257d2ee3f005e8d023273e0b6 SHA512 7a6927d06e1788411063d38e446b7e3c93192e4322a33ea652855f72e550f35debcdb970b895f1fb8504411a54d9096f3dcf506faebd33d50eb033937e15a321 |
26 |
+DIST vaal-46233_remove-namespace-std.patch.bz2 5879 BLAKE2B eb10f5cec8c65c12461346b151dc2c6d60a6f980cdfda78bd97bf0cc33451f808481763e5766b76a78d3d8ef6d5f2f8798bf7b8a7b605e0d32867fdaa9073e3a SHA512 4141094b68b4f9c643abf15d2c5e1486525a69b9d8762cd8034abd3e6f85726ed50d7f25edfcf88fc429ab90db288a583f14b2b5d8e6605cdbfab515f295979c |
27 |
|
28 |
diff --git a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch b/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch |
29 |
deleted file mode 100644 |
30 |
index c3c3ec03248..00000000000 |
31 |
--- a/sci-biology/vaal/files/vaal-46233_remove-namespace-std.patch |
32 |
+++ /dev/null |
33 |
@@ -1,911 +0,0 @@ |
34 |
-Remove 'using namespace std' causing massive havoc with newly |
35 |
-introduced std::align in GCC-5. Fix bug |
36 |
-https://bugs.gentoo.org/show_bug.cgi?id=568438 |
37 |
- |
38 |
---- vaal-46233/src/efasta/EfastaTools.cc |
39 |
-+++ vaal-46233/src/efasta/EfastaTools.cc |
40 |
-@@ -18,6 +18,8 @@ |
41 |
- #include "math/Functions.h" |
42 |
- #include "math/Array.h" |
43 |
- |
44 |
-+using std::set; |
45 |
-+ |
46 |
- #define Err(message) \ |
47 |
- { cout << message << endl << "\nInvalid.\n" << endl; \ |
48 |
- TracebackThisProcess( ); } |
49 |
---- vaal-46233/src/Equiv.cc |
50 |
-+++ vaal-46233/src/Equiv.cc |
51 |
-@@ -9,6 +9,8 @@ |
52 |
- #include "Equiv.h" |
53 |
- #include "Vec.h" |
54 |
- |
55 |
-+using std::swap; |
56 |
-+ |
57 |
- bool equivalence_relation::equiv(int a, int b) const |
58 |
- { if ( a == b ) return true; |
59 |
- int c = a; |
60 |
---- vaal-46233/src/FastaFilestream.cc |
61 |
-+++ vaal-46233/src/FastaFilestream.cc |
62 |
-@@ -13,6 +13,8 @@ |
63 |
- |
64 |
- #include <strstream> |
65 |
- |
66 |
-+using std::string; |
67 |
-+ |
68 |
- template <typename vecT, typename seqT, typename convT, typename verifT> |
69 |
- FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename, |
70 |
- FastaNameParser* name_parser ) |
71 |
---- vaal-46233/src/FastaFilestreamPreview.cc |
72 |
-+++ vaal-46233/src/FastaFilestreamPreview.cc |
73 |
-@@ -11,6 +11,8 @@ |
74 |
- |
75 |
- #include <algorithm> |
76 |
- |
77 |
-+using std::streamoff; |
78 |
-+ |
79 |
- FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream) |
80 |
- : max_sequence_size_(0), start_offset_(0) |
81 |
- { |
82 |
---- vaal-46233/src/FastaFilestreamPreview.h |
83 |
-+++ vaal-46233/src/FastaFilestreamPreview.h |
84 |
-@@ -12,6 +12,8 @@ |
85 |
- |
86 |
- #include "Vec.h" |
87 |
- |
88 |
-+using std::streampos; |
89 |
-+ |
90 |
- // FastaFilestreamPreview understands just enough about the fasta |
91 |
- // format to be able to count the number of sequences in the specified |
92 |
- // filestream and to know where each sequence starts in that filestream. |
93 |
---- vaal-46233/src/Fastavector.cc |
94 |
-+++ vaal-46233/src/Fastavector.cc |
95 |
-@@ -14,6 +14,8 @@ |
96 |
- #include <istream> |
97 |
- #include <string> |
98 |
- |
99 |
-+using std::max; |
100 |
-+ |
101 |
- // Split this into chunks, separated by gaps ('n'), and return each chunk as a |
102 |
- // gapless fastavector. |
103 |
- // TODO: generalize this into a templatized STL algorithm. |
104 |
---- vaal-46233/src/Fastavector.h |
105 |
-+++ vaal-46233/src/Fastavector.h |
106 |
-@@ -24,6 +24,9 @@ |
107 |
- #include <iostream> |
108 |
- #include <unistd.h> |
109 |
- |
110 |
-+using std::string; |
111 |
-+using std::istringstream; |
112 |
-+ |
113 |
- typedef std::tuple<String, int, int> FastaRegion; |
114 |
- |
115 |
- class fastaindex { |
116 |
---- vaal-46233/src/FetchReads.cc |
117 |
-+++ vaal-46233/src/FetchReads.cc |
118 |
-@@ -36,6 +36,8 @@ |
119 |
- #include "Qualvector.h" |
120 |
- #include "random/Random.h" |
121 |
- |
122 |
-+using std::istringstream; |
123 |
-+ |
124 |
- // Heuristic constants: |
125 |
- |
126 |
- namespace |
127 |
---- vaal-46233/src/feudal/BaseVec.cc |
128 |
-+++ vaal-46233/src/feudal/BaseVec.cc |
129 |
-@@ -21,6 +21,7 @@ |
130 |
- using std::ostream; |
131 |
- using std::cout; |
132 |
- using std::endl; |
133 |
-+using std::max_element; |
134 |
- |
135 |
- // Cap: in a given basevector, replace any sequence of N > n identical |
136 |
- // bases by n of the same base. |
137 |
---- vaal-46233/src/graph/Digraph.cc |
138 |
-+++ vaal-46233/src/graph/Digraph.cc |
139 |
-@@ -16,6 +16,8 @@ |
140 |
- #include "graph/Digraph.h" |
141 |
- #include "math/Functions.h" |
142 |
- |
143 |
-+using std::make_pair; |
144 |
-+ |
145 |
- Bool digraph::HasEdge( int v, int w ) const { |
146 |
- return find( from_[v].begin(), from_[v].end(), w ) != from_[v].end(); |
147 |
- } |
148 |
---- vaal-46233/src/graph/DigraphTemplate.h |
149 |
-+++ vaal-46233/src/graph/DigraphTemplate.h |
150 |
-@@ -34,6 +34,8 @@ |
151 |
- #include "graph/Digraph.h" |
152 |
- #include <cstddef> |
153 |
- |
154 |
-+using std::make_pair; |
155 |
-+ |
156 |
- template<class E> vec<int> digraphE<E>::EdgesConnectedTo( const vec<int>& v ) const |
157 |
- { vec<int> G = VerticesConnectedTo(v), e; |
158 |
- for ( int x = 0; x < G.isize( ); x++ ) |
159 |
---- vaal-46233/src/IndexedAlignmentPlusVector.cc |
160 |
-+++ vaal-46233/src/IndexedAlignmentPlusVector.cc |
161 |
-@@ -9,6 +9,8 @@ |
162 |
- #include "IndexedAlignmentPlusVector.h" |
163 |
- #include "VecAlignmentPlus.h" |
164 |
- |
165 |
-+using std::streamoff; |
166 |
-+ |
167 |
- // These strings are at the head of the vector and index files for verification purposes. |
168 |
- |
169 |
- const String VecAlignmentPlusHeaderIO::mStrVectorHeader( "alignment_plus vector V.2\n" ); |
170 |
---- vaal-46233/src/IndexedAlignmentPlusVector.h |
171 |
-+++ vaal-46233/src/IndexedAlignmentPlusVector.h |
172 |
-@@ -15,6 +15,7 @@ |
173 |
- |
174 |
- #include "Alignment.h" |
175 |
- |
176 |
-+using std::streampos; |
177 |
- |
178 |
- // This class encapsulates the header information for both vectors and indices. |
179 |
- |
180 |
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc |
181 |
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsBuilder.cc |
182 |
-@@ -10,6 +10,7 @@ |
183 |
- #include "kmers/KmerParcels.h" |
184 |
- #include "system/WorklistN.h" |
185 |
- |
186 |
-+using std::fixed; |
187 |
- |
188 |
- inline String Tag(String S = "KPs") { return Date() + " (" + S + "): "; } |
189 |
- |
190 |
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h |
191 |
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsClasses.h |
192 |
-@@ -6,6 +6,9 @@ |
193 |
- // Institute is not responsible for its use, misuse, or functionality. // |
194 |
- /////////////////////////////////////////////////////////////////////////////// |
195 |
- |
196 |
-+using std::hex; |
197 |
-+using std::dec; |
198 |
-+ |
199 |
- // --------------------------------- |
200 |
- // NaifTimer |
201 |
- // --------------------------------- |
202 |
---- vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h |
203 |
-+++ vaal-46233/src/kmers/kmer_parcels/KmerParcelsStatistics.h |
204 |
-@@ -10,7 +10,7 @@ |
205 |
- #ifndef KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H |
206 |
- #define KMERS__KMER_PARCELS__KMER_PARCELS_STATISTICS_H |
207 |
- |
208 |
-- |
209 |
-+using std::map; |
210 |
- |
211 |
- // -------------------------------------- |
212 |
- // MapOfCounters |
213 |
---- vaal-46233/src/layout/ContigActualloc.h |
214 |
-+++ vaal-46233/src/layout/ContigActualloc.h |
215 |
-@@ -17,6 +17,8 @@ |
216 |
- #include "system/Crash.h" |
217 |
- #include "Misc.h" |
218 |
- |
219 |
-+using std::set; |
220 |
-+using std::map; |
221 |
- |
222 |
- // |
223 |
- // Class contig_actualloc |
224 |
---- vaal-46233/src/lookup/ImperfectLookup.h |
225 |
-+++ vaal-46233/src/lookup/ImperfectLookup.h |
226 |
-@@ -52,6 +52,8 @@ |
227 |
- #include "lookup/AlignCollector.h" |
228 |
- #include "solid/Solid.h" |
229 |
- |
230 |
-+using std::unique_ptr; |
231 |
-+ |
232 |
- class TaskTimer; |
233 |
- |
234 |
- |
235 |
-@@ -534,7 +536,7 @@ |
236 |
- aligns.resize( nqueries ); |
237 |
- } |
238 |
- |
239 |
-- auto_ptr<TaskTimer> t1, t2; |
240 |
-+ unique_ptr<TaskTimer> t1, t2; |
241 |
- |
242 |
- if ( m_instr_level & IO_TIMER != 0 ) t1.reset( new TaskTimer() ); |
243 |
- if ( m_instr_level & CPU_TIMER != 0 ) t2.reset( new TaskTimer() ); |
244 |
---- vaal-46233/src/lookup/LookAlign.cc |
245 |
-+++ vaal-46233/src/lookup/LookAlign.cc |
246 |
-@@ -29,6 +29,8 @@ |
247 |
- #include "random/Random.h" |
248 |
- #include "system/ParsedArgs.h" |
249 |
- |
250 |
-+using std::istrstream; |
251 |
-+ |
252 |
- String QUERY("QUERY"); |
253 |
- |
254 |
- void look_align::ResetFromAlign(const align & al, const basevector & b1, |
255 |
---- vaal-46233/src/lookup/LookAlignFinder.h |
256 |
-+++ vaal-46233/src/lookup/LookAlignFinder.h |
257 |
-@@ -12,6 +12,8 @@ |
258 |
- #include "lookup/LookAlign.h" |
259 |
- #include "Vec.h" |
260 |
- |
261 |
-+using std::set; |
262 |
-+ |
263 |
- /** |
264 |
- Class: LookAlignFinder |
265 |
- |
266 |
---- vaal-46233/src/lookup/LookAlignSort.h |
267 |
-+++ vaal-46233/src/lookup/LookAlignSort.h |
268 |
-@@ -15,6 +15,8 @@ |
269 |
- |
270 |
- #include <functional> |
271 |
- |
272 |
-+using std::set; |
273 |
-+ |
274 |
- /// Read in look_aligns from file, sort, and load into vecs |
275 |
- /// \param fname name of look_align text file |
276 |
- /// \param aligns vector into which to put the alignments |
277 |
---- vaal-46233/src/lookup/LookupTable.h |
278 |
-+++ vaal-46233/src/lookup/LookupTable.h |
279 |
-@@ -18,6 +18,8 @@ |
280 |
- |
281 |
- #include <set> |
282 |
- |
283 |
-+using std::set; |
284 |
-+ |
285 |
- typedef pair<unsigned int, unsigned int> LocSeq; |
286 |
- |
287 |
- /// |
288 |
---- vaal-46233/src/lookup/QueryLookupTableCore.cc |
289 |
-+++ vaal-46233/src/lookup/QueryLookupTableCore.cc |
290 |
-@@ -456,6 +456,9 @@ |
291 |
- #include "system/ParsedArgs.h" |
292 |
- #include "system/file/FileReader.h" |
293 |
- |
294 |
-+using std::istrstream; |
295 |
-+using std::less_equal; |
296 |
-+ |
297 |
- #define ABORT(MSG) \ |
298 |
- { out << MSG << " Abort." << endl << endl; \ |
299 |
- exit(1); } |
300 |
---- vaal-46233/src/lookup/ShortQueryLookup.cc |
301 |
-+++ vaal-46233/src/lookup/ShortQueryLookup.cc |
302 |
-@@ -32,6 +32,8 @@ |
303 |
- #include "lookup/AlignCollector.h" |
304 |
- #include "lookup/ImperfectLookup.h" |
305 |
- |
306 |
-+using std::ios_base; |
307 |
-+ |
308 |
- // Run an alignment processing chain: seqs -> look -> receiver -> aligns |
309 |
- // That is, look turns seqs into hits, which receiver accepts |
310 |
- // and turns into alignments which are passed to aligns. The |
311 |
---- vaal-46233/src/Map.h |
312 |
-+++ vaal-46233/src/Map.h |
313 |
-@@ -21,7 +21,7 @@ |
314 |
- #include <map> |
315 |
- #include <ext/hash_map> |
316 |
- using namespace __gnu_cxx; |
317 |
-- |
318 |
-+using std::map; |
319 |
- |
320 |
- ///Return true if k is a key in map m |
321 |
- template<class Key, class Value, typename Cmp> |
322 |
---- vaal-46233/src/math/Array.h |
323 |
-+++ vaal-46233/src/math/Array.h |
324 |
-@@ -12,6 +12,9 @@ |
325 |
- #include "CoreTools.h" |
326 |
- #include "Vec.h" |
327 |
- |
328 |
-+using std::map; |
329 |
-+using std::fill; |
330 |
-+ |
331 |
- // ============================================================================== |
332 |
- // A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> > |
333 |
- // The elements are uninitialized. |
334 |
---- vaal-46233/src/math/Functions.cc |
335 |
-+++ vaal-46233/src/math/Functions.cc |
336 |
-@@ -10,8 +10,8 @@ |
337 |
- #include "STLExtensions.h" |
338 |
- #include "math/Functions.h" |
339 |
- |
340 |
-- |
341 |
-- |
342 |
-+using std::isfinite; |
343 |
-+using std::make_pair; |
344 |
- |
345 |
- /* CombineNormalDistribution Filipe Ribeiro 2009-06-22 |
346 |
- * |
347 |
---- vaal-46233/src/math/Functions.h |
348 |
-+++ vaal-46233/src/math/Functions.h |
349 |
-@@ -14,6 +14,10 @@ |
350 |
- #include <cmath> |
351 |
- #include <numeric> |
352 |
- |
353 |
-+using std::min; |
354 |
-+using std::cerr; |
355 |
-+using std::swap; |
356 |
-+ |
357 |
- // =========================================================================== |
358 |
- // |
359 |
- // Min functions |
360 |
---- vaal-46233/src/math/HoInterval.cc |
361 |
-+++ vaal-46233/src/math/HoInterval.cc |
362 |
-@@ -10,6 +10,8 @@ |
363 |
- #include "math/HoInterval.h" |
364 |
- #include "STLExtensions.h" |
365 |
- |
366 |
-+using std::make_pair; |
367 |
-+ |
368 |
- bool ho_interval::Merge(const ho_interval & o) { |
369 |
- if (!Meets(*this,o)) return false; |
370 |
- *this = Span(*this, o); |
371 |
---- vaal-46233/src/math/HoInterval.h |
372 |
-+++ vaal-46233/src/math/HoInterval.h |
373 |
-@@ -14,6 +14,8 @@ |
374 |
- #include "feudal/MasterVec.h" |
375 |
- #include "feudal/SerfVec.h" |
376 |
- |
377 |
-+using std::max; |
378 |
-+ |
379 |
- /// Class: ho_interval |
380 |
- /// A half-open interval [a, b). |
381 |
- class ho_interval { |
382 |
---- vaal-46233/src/PackAlign.h |
383 |
-+++ vaal-46233/src/PackAlign.h |
384 |
-@@ -133,6 +133,8 @@ |
385 |
- #include "pairwise_aligners/Mutmer.h" |
386 |
- #include "feudal/BinaryStream.h" |
387 |
- |
388 |
-+using std::make_pair; |
389 |
-+ |
390 |
- const int Bits2 = 3, Bits3 = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095, |
391 |
- Bits16 = 65535; |
392 |
- |
393 |
---- vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc |
394 |
-+++ vaal-46233/src/pairwise_aligners/MakeAlignsMethod.cc |
395 |
-@@ -19,6 +19,9 @@ |
396 |
- #include "pairwise_aligners/AlignFromMutmers.h" |
397 |
- #include "pairwise_aligners/SmithWatBandedA.h" |
398 |
- |
399 |
-+using std::map; |
400 |
-+using std::set; |
401 |
-+ |
402 |
- // If there's a perfect match of length at least perf but we produced no proper |
403 |
- // alignment, use banded Smith-Waterman to create one. |
404 |
- |
405 |
---- vaal-46233/src/pairwise_aligners/MatchList.cc |
406 |
-+++ vaal-46233/src/pairwise_aligners/MatchList.cc |
407 |
-@@ -9,6 +9,8 @@ |
408 |
- |
409 |
- #include "pairwise_aligners/MatchList.h" |
410 |
- |
411 |
-+using std::max; |
412 |
-+ |
413 |
- bool MatchList::FindMatchInSorted( const int id1, const Match& newMatch ) const |
414 |
- { |
415 |
- const vec<Match>& sortedMatches = m_sortedMatches[id1]; |
416 |
---- vaal-46233/src/pairwise_aligners/SuffixTree.h |
417 |
-+++ vaal-46233/src/pairwise_aligners/SuffixTree.h |
418 |
-@@ -23,6 +23,8 @@ |
419 |
- #include <list> |
420 |
- #include <string> |
421 |
- |
422 |
-+using std::list; |
423 |
-+ |
424 |
- /** |
425 |
- * Implementation of a suffix tree for basevectors. |
426 |
- * This is a data structure for exact (sub)string matching. |
427 |
---- vaal-46233/src/paths/AlignHyperKmerPath.cc |
428 |
-+++ vaal-46233/src/paths/AlignHyperKmerPath.cc |
429 |
-@@ -23,6 +23,9 @@ |
430 |
- #include "paths/KmerBaseBroker.h" |
431 |
- #include "paths/KmerPath.h" |
432 |
- |
433 |
-+using std::ostringstream; |
434 |
-+using std::set; |
435 |
-+ |
436 |
- // Function: AlignHyperKmerPath |
437 |
- // |
438 |
- // AlignHyperKmerPath takes a HyperKmerPath h, whose KmerPath edges are assumed |
439 |
---- vaal-46233/src/paths/AlignSeqsToHyper.cc |
440 |
-+++ vaal-46233/src/paths/AlignSeqsToHyper.cc |
441 |
-@@ -26,6 +26,7 @@ |
442 |
- #include "paths/ReadsToPathsCoreX.h" |
443 |
- #include "paths/SeqOnHyper.h" |
444 |
- |
445 |
-+using std::multimap; |
446 |
- |
447 |
- // Local class: simple_align |
448 |
- // |
449 |
---- vaal-46233/src/paths/HyperKmerPath.cc |
450 |
-+++ vaal-46233/src/paths/HyperKmerPath.cc |
451 |
-@@ -19,6 +19,8 @@ |
452 |
- #include "paths/HyperKmerPath.h" |
453 |
- #include "paths/KmerBaseBroker.h" |
454 |
- |
455 |
-+using std::ostrstream; |
456 |
-+using std::ends; |
457 |
- |
458 |
- void HyperKmerPath::ReduceLoops( ) |
459 |
- { for ( int v = 0; v < N( ); v++ ) |
460 |
---- vaal-46233/src/paths/KmerBaseBroker.h |
461 |
-+++ vaal-46233/src/paths/KmerBaseBroker.h |
462 |
-@@ -20,6 +20,8 @@ |
463 |
- #include <algorithm> // for set_union |
464 |
- #include <map> |
465 |
- |
466 |
-+using std::map; |
467 |
-+ |
468 |
- /** |
469 |
- Class: KmerBaseBrokerTemplate |
470 |
- |
471 |
---- vaal-46233/src/paths/KmerPath.h |
472 |
-+++ vaal-46233/src/paths/KmerPath.h |
473 |
-@@ -22,6 +22,8 @@ |
474 |
- #include "HashSimple.h" |
475 |
- #include "graph/Digraph.h" |
476 |
- |
477 |
-+using std::make_pair; |
478 |
-+ |
479 |
- class KmerPathLoc; // forward declaration |
480 |
- |
481 |
- /** |
482 |
---- vaal-46233/src/paths/KmerPathInterval.h |
483 |
-+++ vaal-46233/src/paths/KmerPathInterval.h |
484 |
-@@ -8,6 +8,8 @@ |
485 |
- #include "CommonSemanticTypes.h" |
486 |
- #include "feudal/BinaryStreamTraits.h" |
487 |
- |
488 |
-+using std::max; |
489 |
-+ |
490 |
- // Portability note: endianness |
491 |
- // The implementations here would need to be changed for big endian architectures. |
492 |
- |
493 |
-@@ -285,6 +287,12 @@ |
494 |
- Models <tagged read path interval>. |
495 |
- */ |
496 |
- // TODO: potentially dangerous truncation of index by PathId, ReadId |
497 |
-+template<class TAG> |
498 |
-+void Contains( const vec<TAG>& segs, kmer_id_t index, vec<longlong>& answer, bool append = false, int cap = -1 ); |
499 |
-+ |
500 |
-+template<class TAG> |
501 |
-+void Contains( const vec<TAG>& segs, KmerPathInterval rpi, vec<longlong>& answer, bool append = false, int cap = -1 ); |
502 |
-+ |
503 |
- class tagged_rpint { |
504 |
- |
505 |
- public: /* PUBLIC METHODS */ |
506 |
-@@ -362,11 +370,11 @@ |
507 |
- |
508 |
- template<class TAG> |
509 |
- friend void Contains( const vec<TAG>& segs, kmer_id_t index, |
510 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
511 |
-+ vec<longlong>& answer, bool append, int cap ); |
512 |
- |
513 |
- template<class TAG> |
514 |
- friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, |
515 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
516 |
-+ vec<longlong>& answer, bool append, int cap ); |
517 |
- |
518 |
- template<class TAG> |
519 |
- friend longlong Instance( const vec<TAG>& segs, kmer_id_t k ); |
520 |
-@@ -489,11 +497,11 @@ |
521 |
- |
522 |
- template<class TAG> |
523 |
- friend void Contains( const vec<TAG>& segs, kmer_id_t index, |
524 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
525 |
-+ vec<longlong>& answer, bool append, int cap ); |
526 |
- |
527 |
- template<class TAG> |
528 |
- friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, |
529 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
530 |
-+ vec<longlong>& answer, bool append, int cap ); |
531 |
- |
532 |
- template<class TAG> |
533 |
- friend longlong Instance( const vec<TAG>& segs, kmer_id_t k ); |
534 |
-@@ -620,11 +628,11 @@ |
535 |
- |
536 |
- template<class TAG> |
537 |
- friend void Contains( const vec<TAG>& segs, kmer_id_t index, |
538 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
539 |
-+ vec<longlong>& answer, bool append, int cap ); |
540 |
- |
541 |
- template<class TAG> |
542 |
- friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, |
543 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
544 |
-+ vec<longlong>& answer, bool append, int cap ); |
545 |
- |
546 |
- template<class TAG> |
547 |
- friend kmer_id_t Instance( const vec<TAG>& segs, kmer_id_t k ); |
548 |
---- vaal-46233/src/paths/ReadsToPathsCoreX.cc |
549 |
-+++ vaal-46233/src/paths/ReadsToPathsCoreX.cc |
550 |
-@@ -20,6 +20,8 @@ |
551 |
- #include "paths/MakeAlignsPathsParallelX.h" |
552 |
- #include "paths/ReadsToPathsCoreX.h" |
553 |
- |
554 |
-+using std::map; |
555 |
-+ |
556 |
- static inline |
557 |
- String Tag(String S = "RTPCX") { return Date() + " (" + S + "): "; } |
558 |
- |
559 |
---- vaal-46233/src/paths/SuperBaseVector.h |
560 |
-+++ vaal-46233/src/paths/SuperBaseVector.h |
561 |
-@@ -10,6 +10,8 @@ |
562 |
- #include <numeric> |
563 |
- #include <functional> |
564 |
- |
565 |
-+using std::mem_fun_ref; |
566 |
-+ |
567 |
- /// A simple class which holds a series of basevectors with |
568 |
- /// (possibly negative) gaps between them. This is what a |
569 |
- /// KmerPath logically maps to in sequence space. The function |
570 |
---- vaal-46233/src/polymorphism/VAAL2.cc |
571 |
-+++ vaal-46233/src/polymorphism/VAAL2.cc |
572 |
-@@ -42,7 +42,7 @@ |
573 |
- #include "feudal/BinaryStream.h" |
574 |
- #include "feudal/VirtualMasterVec.h" |
575 |
- |
576 |
--using namespace std; |
577 |
-+ |
578 |
- |
579 |
- // Trim reads so that they contain only kmers in the unipaths. |
580 |
- |
581 |
---- vaal-46233/src/polymorphism/VAAL3.cc |
582 |
-+++ vaal-46233/src/polymorphism/VAAL3.cc |
583 |
-@@ -29,6 +29,8 @@ |
584 |
- #include "polymorphism/VAALTools.h" |
585 |
- #include "solexa/SolexaTools.h" |
586 |
- |
587 |
-+using std::ostringstream; |
588 |
-+ |
589 |
- int main( int argc, char *argv[] ) |
590 |
- { |
591 |
- RunTime( ); |
592 |
---- vaal-46233/src/PrintAlignment.h |
593 |
-+++ vaal-46233/src/PrintAlignment.h |
594 |
-@@ -14,6 +14,8 @@ |
595 |
- #include "CoreTools.h" |
596 |
- #include "Qualvector.h" |
597 |
- |
598 |
-+using std::ostringstream; |
599 |
-+ |
600 |
- void PrintBlanks( ostream& out, int n ); |
601 |
- |
602 |
- template<class BASEVEC> |
603 |
---- vaal-46233/src/Qualvector.cc |
604 |
-+++ vaal-46233/src/Qualvector.cc |
605 |
-@@ -10,6 +10,8 @@ |
606 |
- #include "FastIfstream.h" |
607 |
- #include "Qualvector.h" |
608 |
- |
609 |
-+using std::istrstream; |
610 |
-+ |
611 |
- /// \file |
612 |
- /// \ingroup grp_quals |
613 |
- /// \copydoc Qualvector.h |
614 |
---- vaal-46233/src/SeqInterval.cc |
615 |
-+++ vaal-46233/src/SeqInterval.cc |
616 |
-@@ -9,6 +9,8 @@ |
617 |
- #include "SeqInterval.h" |
618 |
- #include "Vec.h" |
619 |
- |
620 |
-+using std::max; |
621 |
-+using std::min; |
622 |
- |
623 |
- /* |
624 |
- * seq_interval |
625 |
---- vaal-46233/src/SeqInterval.h |
626 |
-+++ vaal-46233/src/SeqInterval.h |
627 |
-@@ -14,7 +14,9 @@ |
628 |
- #include <algorithm> |
629 |
- #include <iostream> |
630 |
- |
631 |
--using namespace std; |
632 |
-+using std::binary_function; |
633 |
-+using std::ostream; |
634 |
-+using std::istream; |
635 |
- |
636 |
- /* |
637 |
- * class seq_interval |
638 |
---- vaal-46233/src/Set.h |
639 |
-+++ vaal-46233/src/Set.h |
640 |
-@@ -16,7 +16,7 @@ |
641 |
- #include <set> |
642 |
- #include "CoreTools.h" |
643 |
- |
644 |
--using namespace std; |
645 |
-+using std::set; |
646 |
- |
647 |
- template<class T> bool Member( const set<T>& the_set, const T& value ) |
648 |
- { return the_set.find(value) != the_set.end( ); } // Breaks cxx |
649 |
---- vaal-46233/src/ShortVector.h |
650 |
-+++ vaal-46233/src/ShortVector.h |
651 |
-@@ -14,6 +14,8 @@ |
652 |
- #include "system/Types.h" |
653 |
- #include "feudal/BinaryStream.h" |
654 |
- |
655 |
-+using std::uninitialized_fill_n; |
656 |
-+ |
657 |
- // ================================================================================ |
658 |
- // |
659 |
- // A shortvector holds a list of up to 255 things of any type T. |
660 |
---- vaal-46233/src/solexa/FourBase2.h |
661 |
-+++ vaal-46233/src/solexa/FourBase2.h |
662 |
-@@ -15,6 +15,10 @@ |
663 |
- #include "feudal/MasterVec.h" |
664 |
- #include "feudal/SerfVec.h" |
665 |
- |
666 |
-+using std::max_element; |
667 |
-+using std::min_element; |
668 |
-+using std::accumulate; |
669 |
-+ |
670 |
- class four_base2 { |
671 |
- |
672 |
- public: |
673 |
---- vaal-46233/src/solexa/FourBase.cc |
674 |
-+++ vaal-46233/src/solexa/FourBase.cc |
675 |
-@@ -9,6 +9,9 @@ |
676 |
- |
677 |
- #include "solexa/FourBase.h" |
678 |
- |
679 |
-+using std::string; |
680 |
-+using std::istringstream; |
681 |
-+ |
682 |
- int four_base::Call( ) const |
683 |
- { |
684 |
- int result = 0; |
685 |
---- vaal-46233/src/solexa/FourBase.h |
686 |
-+++ vaal-46233/src/solexa/FourBase.h |
687 |
-@@ -16,6 +16,8 @@ |
688 |
- #include "feudal/MasterVec.h" |
689 |
- #include "feudal/SerfVec.h" |
690 |
- |
691 |
-+using std::max; |
692 |
-+ |
693 |
- /* |
694 |
- Class: four_base |
695 |
- |
696 |
---- vaal-46233/src/solexa/SolexaMetrics.h |
697 |
-+++ vaal-46233/src/solexa/SolexaMetrics.h |
698 |
-@@ -42,6 +42,8 @@ |
699 |
- #include "CommonSemanticTypes.h" |
700 |
- #include <map> |
701 |
- |
702 |
-+using std::map; |
703 |
-+ |
704 |
- /// Definition of general macros. |
705 |
- |
706 |
- class solexa_metric_db { |
707 |
---- vaal-46233/src/solexa/SolexaTools.cc |
708 |
-+++ vaal-46233/src/solexa/SolexaTools.cc |
709 |
-@@ -20,6 +20,8 @@ |
710 |
- #include "FastaFileset.h" |
711 |
- #include "util/BaitMap.h" |
712 |
- |
713 |
-+using std::ostringstream; |
714 |
-+ |
715 |
- void SolexaPredictorParameters::SetFromFile(const String & fname) { |
716 |
- Ifstream(is, fname); |
717 |
- String params = Slurp(is); |
718 |
---- vaal-46233/src/STLExtensions.h |
719 |
-+++ vaal-46233/src/STLExtensions.h |
720 |
-@@ -9,7 +9,7 @@ |
721 |
- #ifndef STLEXTENSIONS_H |
722 |
- #define STLEXTENSIONS_H |
723 |
- |
724 |
--using namespace std; |
725 |
-+ |
726 |
- |
727 |
- #include <functional> |
728 |
- #include <vector> |
729 |
-@@ -21,6 +21,13 @@ |
730 |
- #include "feudal/BinaryStream.h" |
731 |
- #include "system/StaticAssert.h" |
732 |
- |
733 |
-+using std::binary_function; |
734 |
-+using std::unary_function; |
735 |
-+using std::pair; |
736 |
-+using std::bitset; |
737 |
-+using std::vector; |
738 |
-+using std::ostream; |
739 |
-+ |
740 |
- /// minimum<T> is a function object. |
741 |
- /// |
742 |
- /// If f is an object of class minimum<T> and x and y are objects of |
743 |
---- vaal-46233/src/system/ParsedArgs.cc |
744 |
-+++ vaal-46233/src/system/ParsedArgs.cc |
745 |
-@@ -26,6 +26,9 @@ |
746 |
- #include "system/HostName.h" |
747 |
- #include "system/UseGDB.h" |
748 |
- |
749 |
-+using std::istrstream; |
750 |
-+using std::mem_fun_ref; |
751 |
-+ |
752 |
- #ifndef FatalErr |
753 |
- #define FatalErr(message) { cout << message << endl << endl; exit(-1); } |
754 |
- #endif |
755 |
---- vaal-46233/src/system/ParsedArgs.h |
756 |
-+++ vaal-46233/src/system/ParsedArgs.h |
757 |
-@@ -97,6 +97,8 @@ |
758 |
- #include "TokenizeString.h" |
759 |
- #include "ParseSet.h" |
760 |
- |
761 |
-+using std::stringstream; |
762 |
-+ |
763 |
- class parsed_arg_help { |
764 |
- |
765 |
- public: |
766 |
---- vaal-46233/src/system/ProcBuf.cc |
767 |
-+++ vaal-46233/src/system/ProcBuf.cc |
768 |
-@@ -15,6 +15,8 @@ |
769 |
- #include <sys/wait.h> |
770 |
- #include <unistd.h> |
771 |
- |
772 |
-+using std::ios_base; |
773 |
-+ |
774 |
- namespace |
775 |
- { |
776 |
- size_t const BUFFER_SIZE = 8192; |
777 |
---- vaal-46233/src/system/RunTime.cc |
778 |
-+++ vaal-46233/src/system/RunTime.cc |
779 |
-@@ -41,6 +41,10 @@ |
780 |
- #include <unwind.h> |
781 |
- #endif |
782 |
- |
783 |
-+using std::strstream; |
784 |
-+using std::hex; |
785 |
-+using std::setw; |
786 |
-+ |
787 |
- /// =========================================================================== |
788 |
- /// |
789 |
- /// ReturnAddress(i), where 0 <= i <= 100: get the return address. The |
790 |
---- vaal-46233/src/system/RunTime.h |
791 |
-+++ vaal-46233/src/system/RunTime.h |
792 |
-@@ -14,6 +14,8 @@ |
793 |
- #include "system/Exit.h" |
794 |
- #include "system/Types.h" |
795 |
- |
796 |
-+using std::ostream; |
797 |
-+ |
798 |
- typedef void ArachneSignalHandler(int, siginfo_t*, void*); |
799 |
- |
800 |
- void arachne_signal_handler( int signal_number, siginfo_t* info, void* context, |
801 |
---- vaal-46233/src/system/System.cc |
802 |
-+++ vaal-46233/src/system/System.cc |
803 |
-@@ -35,6 +35,11 @@ |
804 |
- |
805 |
- #include <dirent.h> |
806 |
- |
807 |
-+using std::istringstream; |
808 |
-+using std::istream_iterator; |
809 |
-+using std::ostrstream; |
810 |
-+using std::ends; |
811 |
-+ |
812 |
- int SystemInternal( String command, const char *shell ) |
813 |
- { |
814 |
- flush(cout); |
815 |
---- vaal-46233/src/system/System.h |
816 |
-+++ vaal-46233/src/system/System.h |
817 |
-@@ -21,6 +21,17 @@ |
818 |
- #include "system/Exit.h" |
819 |
- #include "system/file/TempFile.h" |
820 |
- |
821 |
-+using std::vector; |
822 |
-+using std::ostream; |
823 |
-+using std::ofstream; |
824 |
-+using std::cout; |
825 |
-+using std::flush; |
826 |
-+using std::endl; |
827 |
-+using std::istream; |
828 |
-+using std::ifstream; |
829 |
-+using std::ios; |
830 |
-+using std::setprecision; |
831 |
-+ |
832 |
- #ifndef InputErr |
833 |
- #define InputErr(message) \ |
834 |
- { cout << "\nFatal error at " << Date( ) << ": " << message << endl; \ |
835 |
---- vaal-46233/src/system/TraceVal.h |
836 |
-+++ vaal-46233/src/system/TraceVal.h |
837 |
-@@ -24,6 +24,9 @@ |
838 |
- #include "system/Types.h" |
839 |
- #include "system/Assert.h" |
840 |
- |
841 |
-+using std::cout; |
842 |
-+using std::endl; |
843 |
-+ |
844 |
- // Macros: Tracing macros |
845 |
- // TRACEVAL_ON - undefine if you're not doing tracing |
846 |
- // TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles |
847 |
---- vaal-46233/src/system/Types.h |
848 |
-+++ vaal-46233/src/system/Types.h |
849 |
-@@ -14,7 +14,7 @@ |
850 |
- #include <cstdlib> |
851 |
- #include <netinet/in.h> |
852 |
- |
853 |
--using namespace std; |
854 |
-+ |
855 |
- |
856 |
- // This assumes that all suns run Solaris... |
857 |
- #if __sun == 1 |
858 |
---- vaal-46233/src/util/BaitMap.cc |
859 |
-+++ vaal-46233/src/util/BaitMap.cc |
860 |
-@@ -236,7 +236,7 @@ |
861 |
- bool BaitMap::write(String file_name) |
862 |
- { |
863 |
- std::ofstream out(file_name.c_str()); |
864 |
-- ForceAssert(out); |
865 |
-+ ForceAssert(static_cast<bool>(out)); |
866 |
- |
867 |
- for (unsigned int i = 0; i < this->size(); i++) |
868 |
- { |
869 |
-@@ -250,7 +250,7 @@ |
870 |
- } |
871 |
- |
872 |
- out.close(); |
873 |
-- ForceAssert(out); |
874 |
-+ ForceAssert(static_cast<bool>(out)); |
875 |
- |
876 |
- return true; |
877 |
- } |
878 |
-@@ -260,7 +260,7 @@ |
879 |
- bool BaitMap::write_names(String file_name) |
880 |
- { |
881 |
- std::ofstream out(file_name.c_str()); |
882 |
-- ForceAssert(out); |
883 |
-+ ForceAssert(static_cast<bool>(out)); |
884 |
- |
885 |
- for (unsigned int i = 0; i < this->size(); i++) |
886 |
- { |
887 |
-@@ -268,7 +268,7 @@ |
888 |
- } |
889 |
- |
890 |
- out.close(); |
891 |
-- ForceAssert(out); |
892 |
-+ ForceAssert(static_cast<bool>(out)); |
893 |
- |
894 |
- return true; |
895 |
- } |
896 |
---- vaal-46233/src/util/BaitMap.h |
897 |
-+++ vaal-46233/src/util/BaitMap.h |
898 |
-@@ -20,6 +20,8 @@ |
899 |
- |
900 |
- #include <map> |
901 |
- |
902 |
-+using std::map; |
903 |
-+ |
904 |
- class BaitMap |
905 |
- { |
906 |
- public: |
907 |
---- vaal-46233/src/util/Qualb.cc |
908 |
-+++ vaal-46233/src/util/Qualb.cc |
909 |
-@@ -10,6 +10,8 @@ |
910 |
- #include "FastIfstream.h" |
911 |
- #include "Qualvector.h" |
912 |
- |
913 |
-+using std::istrstream; |
914 |
-+ |
915 |
- int main( int argc, char *argv[] ) |
916 |
- { |
917 |
- RunTime( ); |
918 |
---- vaal-46233/src/Vec.h |
919 |
-+++ vaal-46233/src/Vec.h |
920 |
-@@ -48,6 +48,14 @@ |
921 |
- #include "Compare.h" |
922 |
- #include "system/file/FileReader.h" |
923 |
- |
924 |
-+using std::initializer_list; |
925 |
-+using std::numeric_limits; |
926 |
-+using std::ostream_iterator; |
927 |
-+using std::less; |
928 |
-+using std::equal_to; |
929 |
-+using std::setfill; |
930 |
-+using std::setw; |
931 |
-+ |
932 |
- ///////////////////////////////////////////////////////////////////////////// |
933 |
- // |
934 |
- // vec Class Declaration and Template Definitions |
935 |
---- vaal-46233/src/VecUtilities.h |
936 |
-+++ vaal-46233/src/VecUtilities.h |
937 |
-@@ -37,6 +37,7 @@ |
938 |
- #include "Vec.h" |
939 |
- #include <cstddef> |
940 |
- |
941 |
-+using std::greater; |
942 |
- |
943 |
- ///////////////////////////////////////////////////////////////////////////// |
944 |
- // |
945 |
|
946 |
diff --git a/sci-biology/vaal/vaal-46233-r2.ebuild b/sci-biology/vaal/vaal-46233-r2.ebuild |
947 |
index 7185fc1c24d..85076f33057 100644 |
948 |
--- a/sci-biology/vaal/vaal-46233-r2.ebuild |
949 |
+++ b/sci-biology/vaal/vaal-46233-r2.ebuild |
950 |
@@ -9,7 +9,8 @@ DESCRIPTION="Algorithm for detecting SNPs, indels, and other polymorphisms" |
951 |
HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/" |
952 |
SRC_URI=" |
953 |
ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz |
954 |
- ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc" |
955 |
+ ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc |
956 |
+ https://dev.gentoo.org/~mgorny/dist/${P}_remove-namespace-std.patch.bz2" |
957 |
|
958 |
LICENSE="Whitehead-MIT" |
959 |
SLOT="0" |
960 |
@@ -25,7 +26,7 @@ DEPEND=" |
961 |
|
962 |
DOCS=( "${DISTDIR}/VAAL_manual.doc" ) |
963 |
PATCHES=( |
964 |
- "${FILESDIR}/${P}_remove-namespace-std.patch" |
965 |
+ "${WORKDIR}/${P}_remove-namespace-std.patch" |
966 |
) |
967 |
|
968 |
src_prepare() { |