[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

[Chris Lamb]

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
       `-
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