HI Chris,
thanks for your reproducible builds effort.
I assume this is an effect of the current upgrade of all BioC modules
(packages r-bioc-*). I'm doing the migration right into unstable which
is strictly speaking not correct but considering the user number and the
quite closed set of packages involved not a real problem. I guess this
bug can be closed with a simple upgrade I plan to do over the weekend.
I'd recommend to stay tuned with further bug reports affecting r-bioc-*
packages in the next couple of days to save your own time.
Kind regards
Andreas.
On Fri, Oct 30, 2015 at 01:24:52PM +0000, Chris Lamb wrote:
> 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
> `-
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