Your message dated Sat, 08 Mar 2014 15:20:23 +0000 with message-id <e1wmj31-0000rh...@franck.debian.org> and subject line Bug#733398: fixed in bowtie 1.0.0-6 has caused the Debian Bug report #733398, regarding bowtie: FTBFS: diff_sample.h:532:27: error: call of overloaded 'popCount(uint32_t&)' is ambiguous to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 733398: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=733398 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: bowtie Version: 1.0.0-5 Severity: serious Tags: jessie sid User: debian...@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.
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--- Begin Message ---Source: bowtie Source-Version: 1.0.0-6 We believe that the bug you reported is fixed in the latest version of bowtie, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 733...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Ognyan Kulev <o...@debian.org> (supplier of updated bowtie package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Format: 1.8 Date: Sat, 08 Mar 2014 15:13:16 +0200 Source: bowtie Binary: bowtie bowtie-examples Architecture: source amd64 all Version: 1.0.0-6 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Ognyan Kulev <o...@debian.org> Description: bowtie - Ultrafast memory-efficient short read aligner bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short read al Closes: 733398 Changes: bowtie (1.0.0-6) unstable; urgency=low . * debian/patches/seqan-popcount.patch: New patch. (Closes: #733398) * Version 1.4 of seqan-dev is required now. * Standards-Version: 3.9.5 (no changes needed). * Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy. Checksums-Sha1: 16d0ded9ea36dd3779c521c5358db0839631c51b 2125 bowtie_1.0.0-6.dsc 1790123c4393e17031c908fa66cafb6d266ac2ac 10742 bowtie_1.0.0-6.debian.tar.gz 16462084da4e297c495e789ca1ab2171dcb2d885 1318596 bowtie_1.0.0-6_amd64.deb 73631ded0e50bf7933e4becf52f727b1d990df7c 6546686 bowtie-examples_1.0.0-6_all.deb Checksums-Sha256: 92b48c638bbb8b9c230511e3dbad1934bd72cb0929d1f39dd2454e8850c009ff 2125 bowtie_1.0.0-6.dsc 204485cdd68ca240283f857a4d6dd11164d7ea04ab45d772dda9b2f28a54f032 10742 bowtie_1.0.0-6.debian.tar.gz dfa1d59bb421ffa7986b5f87de6fe7c412094e489358becbfdda49a2f7a89444 1318596 bowtie_1.0.0-6_amd64.deb f51f22f5262488141f9d940910e9197091a3777d4b7f85bb7289050a94f65d0e 6546686 bowtie-examples_1.0.0-6_all.deb Files: 681f6bbabdc00fd235e71e34f8ddc1c4 2125 science extra bowtie_1.0.0-6.dsc a3ceb471131732ba426aea5d1de3ea31 10742 science extra bowtie_1.0.0-6.debian.tar.gz 47cd4b61081d9c10f5d55dbca90c8f1c 1318596 science extra bowtie_1.0.0-6_amd64.deb d897e6c0daa4bfbd3e4b39b9cd9cd30b 6546686 science extra bowtie-examples_1.0.0-6_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) iQIcBAEBAgAGBQJTGyjLAAoJEKuYKI420z0Hw9wP/iHuodyL/sdRNvB7BB+WCEck c66HM0dGEfRO0YV6pQgLA//aqy4OM4pU1WOx20pkafxN/pNK8MoS1pRo2cR4KxGH KL1FC8P42kmhlxYMygg8I4FmxV8GntidErhEwrpc9QvvLr/EBz9wp89uxIZ2nHGk ipXOWwTtupWBHqlVUdOGh13KeDbN2q0RNNOglIoMvhkUiag3RPD/ntlva2AJokiF 2nQm1JURuHk23qYuQcQJi8pILS0osjMPpfvfsULhvyg/ArEOyTtMDHQh9n5sSQHF fxiErnmrfQg6dmXQ2QEKqlYHKu3iho63GgKUCXnMEV5P3sUfuKqtR3YDA+XbsPZ1 Q2vzvyOf7i2Y/RtijrpZwlqAN6UdQ073La34+s1Z1c+SGULSdw2/J+YXxNISOQsN x3wB0kdpKX+sXr1LVluMKf0MjitswoTmN8CLNodZHrd2wfdvMemlEyFlOoDt2W1Z hEJUgXryHRygctQeFuKwm/8Yw9dZdw3i6J7DErXQTEDkKvLOVsobsUA/ucnq/HPn 3pHxpPPu9TPGfA7lTuprB+dGEv5CZB1nlIYFvVYBa4uQbxTr2K0wOugWYYiB/Ku1 aMQLReHs6rS7Q6fT+8Y0FcdVxsPfw0glOnPurY5j7gMVzXOOPSSpqSv3Q9uAoG0T AKVLzIyd4kdHniKEv0tG =Yvyw -----END PGP SIGNATURE-----
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