Your message dated Thu, 24 Jul 2014 10:05:05 +0000
with message-id <e1xaftz-000061...@franck.debian.org>
and subject line Bug#753224: fixed in r-bioc-shortread 1.22.0-1
has caused the Debian Bug report #753224,
regarding r-bioc-shortread: FTBFS: alphabet.c:53:5: error: unknown type name
'cachedXStringSet'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
753224: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=753224
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: r-bioc-shortread
Version: 1.20.0-1
Severity: serious
Tags: jessie sid
User: debian...@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.
--- End Message ---
--- Begin Message ---
Source: r-bioc-shortread
Source-Version: 1.22.0-1
We believe that the bug you reported is fixed in the latest version of
r-bioc-shortread, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 753...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated r-bioc-shortread package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 24 Jul 2014 11:38:30 +0200
Source: r-bioc-shortread
Binary: r-bioc-shortread
Architecture: source amd64
Version: 1.22.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
r-bioc-shortread - GNU R classes and methods for high-throughput short-read
sequenci
Closes: 753224
Changes:
r-bioc-shortread (1.22.0-1) unstable; urgency=medium
.
* New upstream version
* Moved debian/upstream to debian/upstream/metadata
* Add autopkgtest
* (Build-)Depends: r-bioc-genomicalignments
Closes: #753224
Checksums-Sha1:
eaaef94af7ebe45a878442aa022deaf9b4bc4dba 2330 r-bioc-shortread_1.22.0-1.dsc
e9de0a6a0f0e204c18268bd92286f6048bea7dc3 5151983
r-bioc-shortread_1.22.0.orig.tar.gz
6d823da035c0c92fab6e78c55a45be4cf46e0c5b 4860
r-bioc-shortread_1.22.0-1.debian.tar.xz
50287ad9761aa8b7c741cc34cbfb70dc78a16f9e 4163460
r-bioc-shortread_1.22.0-1_amd64.deb
Checksums-Sha256:
863ff3f26da7039fd3c7860c22315d6925afab635968b70559d83312f43d4bc3 2330
r-bioc-shortread_1.22.0-1.dsc
d36db1e54832705be8ad5947eeea99fdbfd5deea9cc1d85698c353573c71a78f 5151983
r-bioc-shortread_1.22.0.orig.tar.gz
e091f29a12c6e14f4409859fd5e9b17558401a82e68732329abbb4cf1daed6ba 4860
r-bioc-shortread_1.22.0-1.debian.tar.xz
efd706d226c6a412e1ef43522370fdd2b2693af1f92b99d736c37286986d598b 4163460
r-bioc-shortread_1.22.0-1_amd64.deb
Files:
cf68f9c2ec7cf2869c3c7fb9ee9ef0dc 4163460 gnu-r optional
r-bioc-shortread_1.22.0-1_amd64.deb
cbb0443b39d088cad116638c167f7027 2330 gnu-r optional
r-bioc-shortread_1.22.0-1.dsc
5730295ed8e5c433e52316ac94336dda 5151983 gnu-r optional
r-bioc-shortread_1.22.0.orig.tar.gz
d07632a850fede5b2ce5339ae6e11226 4860 gnu-r optional
r-bioc-shortread_1.22.0-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1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=oqyu
-----END PGP SIGNATURE-----
--- End Message ---
