[Debian-med-packaging] Bug#803479: r-bioc-genomicalignments: FTBFS: cigar_utils.c:179:33: error: request for member 'elts' in something not a structure or union

[Andreas Tille]

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-builds at lists.alioth.debian.org
> Usertags: ftbfs
> X-Debbugs-Cc: reproducible-builds at 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
>      `. `'`      lamby at debian.org / chris-lamb.co.uk
>        `-


> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging


-- 
http://fam-tille.de