Source: bowtie
Version: 1.0.0-5
Severity: serious
Tags: jessie sid
User: [email protected]
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.
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