[Debian-med-packaging] Bug#753233: r-bioc-rsamtools: FTBFS: utilities.c:99:5: error: unknown type name 'cachedXVectorList'

[David Suárez]

Source: r-bioc-rsamtools
Version: 1.14.2-1
Severity: serious
Tags: jessie sid
User: debian-qa at 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c utilities.c -o utilities.o
> utilities.c: In function '_as_XStringSet':
> utilities.c:99:5: error: unknown type name 'cachedXVectorList'
>      cachedXVectorList cache;
>      ^
> utilities.c:100:5: error: unknown type name 'cachedCharSeq'
>      cachedCharSeq dest;
>      ^
> utilities.c:101:5: warning: implicit declaration of function 'cache_XVectorList' [-Wimplicit-function-declaration]
>      cache = cache_XVectorList(ans);
>      ^
> utilities.c:104:9: warning: implicit declaration of function 'get_cachedXRawList_elt' [-Wimplicit-function-declaration]
>          dest = get_cachedXRawList_elt(&cache, i);
>          ^
> utilities.c:105:46: error: request for member 'length' in something not a structure or union
>          Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, (char *) dest.seq,
>                                               ^
> utilities.c:105:72: error: request for member 'seq' in something not a structure or union
>          Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, (char *) dest.seq,
>                                                                         ^
> utilities.c:106:43: error: request for member 'length' in something not a structure or union
>                                        dest.length, seq, strlen(seq), lkup0,
>                                            ^
> make[1]: *** [utilities.o] Error 1

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2014/06/28/r-bioc-rsamtools_1.14.2-1_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.