[Debian-med-packaging] Bug#753217: Bug#753233: r-bioc-rsamtools: FTBFS: utilities.c:99:5: error: unknown type name 'cachedXVectorList'

[Andreas Tille]

Hi,

just a quick note:  I'm in the process of upgrading all BioConductor
packages (r-bioc-*).  Unfortunately some of them are needing new
(Build-)Dependencies.  Since this takes a bit longer than expected due
to a complex chain of dependencies these build problems are caused by
incompatibilities between just upgraded and not yet upgraded
BioConductor components.

It will be dealt with in the next 1-2 weeks (hopefully).

Kind regards and thanks for your QA qork to autobuild the archive

      Andreas.

On Sun, Jun 29, 2014 at 06:49:14PM +0200, David Suárez wrote:
> 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.
> 
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