[Debian-med-packaging] Bug#733398: bowtie: FTBFS: diff_sample.h:532:27: error: call of overloaded 'popCount(uint32_t&)' is ambiguous

[David Suárez]

Source: bowtie
Version: 1.0.0-5
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20131226 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++ -O3  \
> 		-DCOMPILER_OPTIONS="\"-O3   -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security  -Wl,-z,relro\""  -Wl,--hash-style=both -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security  -Wl,-z,relro \
> 		-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
> 		-I /usr/include/seqan -I . \
> 		-o bowtie-inspect bowtie_inspect.cpp \
> 		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
> 		-lpthread
> In file included from bowtie_inspect.cpp:8:0:
> diff_sample.h: In constructor 'DifferenceCoverSample<T>::DifferenceCoverSample(const TStr&, uint32_t, bool, bool, std::ostream&)':
> diff_sample.h:532:27: error: call of overloaded 'popCount(uint32_t&)' is ambiguous
>    assert_eq(1, popCount(_v)); // must be power of 2
>                            ^
> assert_helpers.h:52:16: note: in definition of macro 'assert_eq'
>   if(!((ex) == (ac))) { \
>                 ^
> diff_sample.h:532:27: note: candidates are:
>    assert_eq(1, popCount(_v)); // must be power of 2
>                            ^
> assert_helpers.h:52:16: note: in definition of macro 'assert_eq'
>   if(!((ex) == (ac))) { \
>                 ^
> In file included from blockwise_sa.h:13:0,
>                  from ebwt.h:27,
>                  from bowtie_inspect.cpp:10:
> diff_sample.h:482:21: note: unsigned int popCount(T) [with T = unsigned int]
>  static unsigned int popCount(T i) {
>                      ^
> In file included from /usr/include/seqan/index/index_fm_rank_support_bit_string.h:40:0,
>                  from /usr/include/seqan/index.h:167,
>                  from ebwt.h:16,
>                  from bowtie_inspect.cpp:10:
> /usr/include/seqan/misc/misc_bit_twiddling.h:358:1: note: unsigned int seqan::popCount(TWord) [with TWord = unsigned int]
>  popCount(TWord word)
>  ^
> In file included from bowtie_inspect.cpp:8:0:
> diff_sample.h:532:27: error: call of overloaded 'popCount(uint32_t&)' is ambiguous
>    assert_eq(1, popCount(_v)); // must be power of 2
>                            ^
> assert_helpers.h:53:107: note: in definition of macro 'assert_eq'
>    std::cout << "assert_eq: expected (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
>                                                                                                            ^
> diff_sample.h:532:27: note: candidates are:
>    assert_eq(1, popCount(_v)); // must be power of 2
>                            ^
> assert_helpers.h:53:107: note: in definition of macro 'assert_eq'
>    std::cout << "assert_eq: expected (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
>                                                                                                            ^
> In file included from blockwise_sa.h:13:0,
>                  from ebwt.h:27,
>                  from bowtie_inspect.cpp:10:
> diff_sample.h:482:21: note: unsigned int popCount(T) [with T = unsigned int]
>  static unsigned int popCount(T i) {
>                      ^
> In file included from /usr/include/seqan/index/index_fm_rank_support_bit_string.h:40:0,
>                  from /usr/include/seqan/index.h:167,
>                  from ebwt.h:16,
>                  from bowtie_inspect.cpp:10:
> /usr/include/seqan/misc/misc_bit_twiddling.h:358:1: note: unsigned int seqan::popCount(TWord) [with TWord = unsigned int]
>  popCount(TWord word)
>  ^
> In file included from bowtie_inspect.cpp:8:0:
> diff_sample.h:532:27: error: call of overloaded 'popCount(uint32_t&)' is ambiguous
>    assert_eq(1, popCount(_v)); // must be power of 2
>                            ^
> assert_helpers.h:53:137: note: in definition of macro 'assert_eq'
>    std::cout << "assert_eq: expected (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
>                                                                                                                                          ^
> diff_sample.h:532:27: note: candidates are:
>    assert_eq(1, popCount(_v)); // must be power of 2
>                            ^
> assert_helpers.h:53:137: note: in definition of macro 'assert_eq'
>    std::cout << "assert_eq: expected (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
>                                                                                                                                          ^
> In file included from blockwise_sa.h:13:0,
>                  from ebwt.h:27,
>                  from bowtie_inspect.cpp:10:
> diff_sample.h:482:21: note: unsigned int popCount(T) [with T = unsigned int]
>  static unsigned int popCount(T i) {
>                      ^
> In file included from /usr/include/seqan/index/index_fm_rank_support_bit_string.h:40:0,
>                  from /usr/include/seqan/index.h:167,
>                  from ebwt.h:16,
>                  from bowtie_inspect.cpp:10:
> /usr/include/seqan/misc/misc_bit_twiddling.h:358:1: note: unsigned int seqan::popCount(TWord) [with TWord = unsigned int]
>  popCount(TWord word)
>  ^
> make[2]: *** [bowtie-inspect] Error 1

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2013/12/26/bowtie_1.0.0-5_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.