[Debian-med-packaging] Bug#848751: blasr: FTBFS: DNASequence.hpp:15:29: fatal error: pbbam/BamRecord.h: No such file or directory

[Lucas Nussbaum]

Source: blasr
Version: 5.3-1
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20161219 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):
> g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer  -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial  -c -o SDPMatcher.o SDPMatcher.cpp
> In file included from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13:0,
>                  from SAWriter.cpp:3:
> /usr/include/pbseq/alignment/suffixarray/../../pbdata/DNASequence.hpp:15:29: fatal error: pbbam/BamRecord.h: No such file or directory
>  #include <pbbam/BamRecord.h>
>                              ^
> compilation terminated.
> <builtin>: recipe for target 'SAWriter.o' failed
> make[2]: *** [SAWriter.o] Error 1

The full build log is available from:
   http://aws-logs.debian.net/2016/12/19/blasr_5.3-1_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.