Your message dated Fri, 06 Nov 2015 09:22:21 +0000
with message-id <e1zuddx-0003rk...@franck.debian.org>
and subject line Bug#803479: fixed in r-bioc-genomicalignments 1.6.1-1
has caused the Debian Bug report #803479,
regarding r-bioc-genomicalignments: FTBFS: cigar_utils.c:179:33: error: request
for member 'elts' in something not a structure or union
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.)
--
803479: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=803479
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: r-bioc-genomicalignments
Version: 1.4.1-1
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org
Dear Maintainer,
r-bioc-genomicalignments fails to build from source in unstable/amd64:
[..]
cigar_utils.c: In function 'drop_or_append_or_merge_range':
cigar_utils.c:179:33: error: request for member 'elts' in something
not a structure or union
prev_end_plus_1 = range_buf->a.elts[buf_nelt_minus_1] +
^
cigar_utils.c:180:19: error: request for member 'elts' in something
not a structure or union
range_buf->b.elts[buf_nelt_minus_1];
^
cigar_utils.c:183:16: error: request for member 'elts' in something
not a structure or union
range_buf->b.elts[buf_nelt_minus_1] += width;
^
cigar_utils.c:185:21: warning: assignment from incompatible pointer
type [-Wincompatible-pointer-types]
OP_buf_prev_elt = OP_buf->elts +
^
cigar_utils.c:196:18: error: incompatible types when assigning to type
'CharAE {aka struct char_ae}' from type 'CharAE * {aka struct char_ae
*}'
OP_buf_new_elt = new_CharAE(1);
^
cigar_utils.c: In function 'explode_cigar_ops':
cigar_utils.c:361:8: error: incompatible types when assigning to type
'CharAE {aka struct char_ae}' from type 'CharAE * {aka struct char_ae
*}'
OPbuf = new_CharAE(0);
^
cigar_utils.c: In function 'explode_cigar_op_lengths':
cigar_utils.c:403:9: error: incompatible types when assigning to type
'IntAE {aka struct int_ae}' from type 'IntAE * {aka struct int_ae *}'
OPLbuf = new_IntAE(0, 0, 0);
^
cigar_utils.c: In function 'cigar_ranges':
cigar_utils.c:607:14: error: incompatible types when assigning to type
'IntPairAE {aka struct intpair_ae}' from type 'IntPairAE * {aka struct
intpair_ae *}'
range_buf1 = new_IntPairAE(ans_len, 0);
^
cigar_utils.c:614:14: error: incompatible types when assigning to type
'IntPairAEAE {aka struct intpair_aeae}' from type 'IntPairAEAE * {aka
struct intpair_aeae *}'
range_buf2 = new_IntPairAEAE(ans_len, ans_len);
^
cigar_utils.c:621:10: error: incompatible types when assigning to type
'CharAEAE {aka struct char_aeae}' from type 'CharAEAE * {aka struct
char_aeae *}'
OP_buf = new_CharAEAE(cigar_len, 0);
^
cigar_utils.c:660:16: warning: assignment from incompatible pointer
type [-Wincompatible-pointer-types]
range_buf_p = range_buf2.elts + *f_elt - 1;
^
/usr/lib/R/etc/Makeconf:134: recipe for target 'cigar_utils.o' failed
make[1]: *** [cigar_utils.o] Error 1
make[1]: Leaving directory '/build/r-bioc-genomicalignments-1.4.1/src'
make[1]: Entering directory
'/build/r-bioc-genomicalignments-1.4.1/src'
make[1]: Leaving directory '/build/r-bioc-genomicalignments-1.4.1/src'
ERROR: compilation failed for package 'GenomicAlignments'
* removing
'/build/r-bioc-genomicalignments-1.4.1/debian/r-bioc-genomicalignments/usr/lib/R/site-library/GenomicAlignments'
/usr/share/R/debian/r-cran.mk:98: recipe for target 'R_any_arch'
failed
make: *** [R_any_arch] Error 1
dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit
status 2
[..]
The full build log is attached or (an alternate build) can be viewed
here:
https://reproducible.debian.net/logs/unstable/amd64/r-bioc-genomicalignments_1.4.1-1.build1.log.gz
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` la...@debian.org / chris-lamb.co.uk
`-
r-bioc-genomicalignments.1.4.1-1.unstable.amd64.log.txt.gz
Description: application/gzip
--- End Message ---
--- Begin Message ---
Source: r-bioc-genomicalignments
Source-Version: 1.6.1-1
We believe that the bug you reported is fixed in the latest version of
r-bioc-genomicalignments, 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 803...@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-genomicalignments
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: Sat, 31 Oct 2015 19:33:11 +0100
Source: r-bioc-genomicalignments
Binary: r-bioc-genomicalignments
Architecture: source amd64
Version: 1.6.1-1
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-genomicalignments - BioConductor representation and manipulation of
short genomic ali
Closes: 803479
Changes:
r-bioc-genomicalignments (1.6.1-1) unstable; urgency=medium
.
* New upstream version
Closes: #803479
* Add new (Build-)Depends: r-bioc-summarizedexperiment
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