[Debian-med-packaging] Bug#753224: r-bioc-shortread: FTBFS: alphabet.c:53:5: error: unknown type name 'cachedXStringSet'
David Suárez
david.sephirot at gmail.com
Sun Jun 29 16:49:56 UTC 2014
Source: r-bioc-shortread
Version: 1.20.0-1
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20140628 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c alphabet.c -o alphabet.o
> alphabet.c: In function 'alphabet_by_cycle':
> alphabet.c:53:5: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache = cache_XStringSet(stringSet);
> ^
> alphabet.c:53:5: warning: implicit declaration of function 'cache_XStringSet' [-Wimplicit-function-declaration]
> alphabet.c:56:9: error: unknown type name 'cachedCharSeq'
> cachedCharSeq seq = get_cachedXStringSet_elt(&cache, i);
> ^
> alphabet.c:56:9: warning: implicit declaration of function 'get_cachedXStringSet_elt' [-Wimplicit-function-declaration]
> alphabet.c:57:28: error: request for member 'length' in something not a structure or union
> for (j = 0; j < seq.length; ++j) {
> ^
> alphabet.c:58:37: error: request for member 'seq' in something not a structure or union
> int idx = map[decode(seq.seq[j])];
> ^
> alphabet.c: In function 'alphabet_pair_by_cycle':
> alphabet.c:126:5: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache1 = cache_XStringSet(stringSet1);
> ^
> alphabet.c:127:5: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache2 = cache_XStringSet(stringSet2);
> ^
> alphabet.c:130:9: error: unknown type name 'cachedCharSeq'
> cachedCharSeq seq1 = get_cachedXStringSet_elt(&cache1, i);
> ^
> alphabet.c:131:9: error: unknown type name 'cachedCharSeq'
> cachedCharSeq seq2 = get_cachedXStringSet_elt(&cache2, i);
> ^
> alphabet.c:132:29: error: request for member 'length' in something not a structure or union
> for (j = 0; j < seq1.length; ++j) {
> ^
> alphabet.c:133:41: error: request for member 'seq' in something not a structure or union
> int idx1 = map1[decode1(seq1.seq[j])];
> ^
> alphabet.c:134:41: error: request for member 'seq' in something not a structure or union
> int idx2 = map2[decode2(seq2.seq[j])];
> ^
> alphabet.c: In function 'alphabet_score':
> alphabet.c:162:5: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache = cache_XStringSet(stringSet);
> ^
> alphabet.c:164:9: error: unknown type name 'cachedCharSeq'
> cachedCharSeq seq = get_cachedXStringSet_elt(&cache, i);
> ^
> alphabet.c:166:28: error: request for member 'length' in something not a structure or union
> for (j = 0; j < seq.length; ++j)
> ^
> alphabet.c:167:41: error: request for member 'seq' in something not a structure or union
> dans[i] += dscore[decode(seq.seq[j])];
> ^
> alphabet.c: In function 'alphabet_as_int':
> alphabet.c:187:5: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache = cache_XStringSet(stringSet);
> ^
> alphabet.c:190:5: error: unknown type name 'cachedCharSeq'
> cachedCharSeq seq = get_cachedXStringSet_elt(&cache, 0);
> ^
> alphabet.c:191:20: error: request for member 'length' in something not a structure or union
> int width = seq.length;
> ^
> alphabet.c:196:16: error: request for member 'length' in something not a structure or union
> if (seq.length > width)
> ^
> alphabet.c:197:24: error: request for member 'length' in something not a structure or union
> width = seq.length;
> ^
> alphabet.c:208:21: error: request for member 'length' in something not a structure or union
> for (j = 0; j < seq.length; ++j)
> ^
> alphabet.c:209:43: error: request for member 'seq' in something not a structure or union
> ians[len * j + i] = iscore[decode(seq.seq[j])];
> ^
> alphabet.c: At top level:
> alphabet.c:220:5: error: unknown type name 'cachedCharSeq'
> cachedCharSeq ref;
> ^
> alphabet.c: In function 'compare_cachedCharSeq':
> alphabet.c:230:11: error: unknown type name 'cachedCharSeq'
> const cachedCharSeq ra = ((const XSort *) a)->ref;
> ^
> alphabet.c:231:11: error: unknown type name 'cachedCharSeq'
> const cachedCharSeq rb = ((const XSort *) b)->ref;
> ^
> alphabet.c:233:24: error: request for member 'length' in something not a structure or union
> const int diff = ra.length - rb.length;
> ^
> alphabet.c:233:36: error: request for member 'length' in something not a structure or union
> const int diff = ra.length - rb.length;
> ^
> alphabet.c:234:31: error: request for member 'length' in something not a structure or union
> size_t len = diff < 0 ? ra.length : rb.length;
> ^
> alphabet.c:234:43: error: request for member 'length' in something not a structure or union
> size_t len = diff < 0 ? ra.length : rb.length;
> ^
> alphabet.c:235:24: error: request for member 'seq' in something not a structure or union
> int res = memcmp(ra.seq, rb.seq, len);
> ^
> alphabet.c:235:32: error: request for member 'seq' in something not a structure or union
> int res = memcmp(ra.seq, rb.seq, len);
> ^
> alphabet.c: In function 'stable_compare_cachedCharSeq':
> alphabet.c:241:11: error: unknown type name 'cachedCharSeq'
> const cachedCharSeq ra = ((const XSort *) a)->ref;
> ^
> alphabet.c:242:11: error: unknown type name 'cachedCharSeq'
> const cachedCharSeq rb = ((const XSort *) b)->ref;
> ^
> alphabet.c:244:24: error: request for member 'length' in something not a structure or union
> const int diff = ra.length - rb.length;
> ^
> alphabet.c:244:36: error: request for member 'length' in something not a structure or union
> const int diff = ra.length - rb.length;
> ^
> alphabet.c:245:31: error: request for member 'length' in something not a structure or union
> size_t len = diff < 0 ? ra.length : rb.length;
> ^
> alphabet.c:245:43: error: request for member 'length' in something not a structure or union
> size_t len = diff < 0 ? ra.length : rb.length;
> ^
> alphabet.c:246:24: error: request for member 'seq' in something not a structure or union
> int res = memcmp(ra.seq, rb.seq, len);
> ^
> alphabet.c:246:32: error: request for member 'seq' in something not a structure or union
> int res = memcmp(ra.seq, rb.seq, len);
> ^
> alphabet.c: At top level:
> alphabet.c:252:22: error: unknown type name 'cachedXStringSet'
> void _alphabet_order(cachedXStringSet cache, XSort * xptr, const int len)
> ^
> alphabet.c: In function 'alphabet_order':
> alphabet.c:269:5: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache = cache_XStringSet(stringSet);
> ^
> alphabet.c:271:5: warning: implicit declaration of function '_alphabet_order' [-Wimplicit-function-declaration]
> _alphabet_order(cache, xptr, len);
> ^
> alphabet.c: In function 'alphabet_duplicated':
> alphabet.c:289:5: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache = cache_XStringSet(stringSet);
> ^
> alphabet.c: In function 'alphabet_rank':
> alphabet.c:312:5: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache = cache_XStringSet(stringSet);
> ^
> alphabet.c: In function 'aligned_read_rank':
> alphabet.c:348:9: error: unknown type name 'cachedXStringSet'
> cachedXStringSet cache = cache_XStringSet(sread);
> ^
> make[1]: *** [alphabet.o] Error 1
The full build log is available from:
http://aws-logs.debian.net/ftbfs-logs/2014/06/28/r-bioc-shortread_1.20.0-1_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
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