Source: bowtie2 Version: 2.0.0-beta5-1 Severity: serious Tags: wheezy sid User: debian...@lists.debian.org Usertags: qa-ftbfs-20120508 qa-ftbfs Justification: FTBFS on amd64
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part: > /usr/bin/g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 > -m64 -msse2 -funroll-loops -g3 \"" \ > -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" > -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" > -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE > -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 > -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ > \ > -o bowtie2-build bt2_build.cpp \ > ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp > bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp > diff_sample.cpp bowtie_build_main.cpp \ > > In file included from bt2_idx.h:45:0, > from bt2_build.cpp:27: > word_io.h: In function 'uint32_t readU32(int, bool)': > word_io.h:86:27: error: 'read' was not declared in this scope > word_io.h: In function 'uint32_t readI32(int, bool)': > word_io.h:134:27: error: 'read' was not declared in this scope > In file included from bt2_idx.h:47:0, > from bt2_build.cpp:27: > ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': > ref_read.h:69:21: error: 'read' was not declared in this scope > In file included from bt2_build.cpp:27:0: > bt2_idx.h: In destructor 'Ebwt::~Ebwt()': > bt2_idx.h:927:3: error: 'close' was not declared in this scope > bt2_idx.h:928:3: error: 'close' was not declared in this scope > In file included from ref_read.h:32:0, > from ref_read.cpp:20: > word_io.h: In function 'uint32_t readU32(int, bool)': > word_io.h:86:27: error: 'read' was not declared in this scope > word_io.h: In function 'uint32_t readI32(int, bool)': > word_io.h:134:27: error: 'read' was not declared in this scope > In file included from ref_read.cpp:20:0: > ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': > ref_read.h:69:21: error: 'read' was not declared in this scope > edit.cpp: In static member function 'static void > Edit::printQAlign(std::ostream&, const char*, const BTDnaString&, const > EList<Edit>&)': > edit.cpp:100:8: warning: variable 'ins' set but not used > [-Wunused-but-set-variable] > edit.cpp:124:8: warning: variable 'ins' set but not used > [-Wunused-but-set-variable] > edit.cpp:146:8: warning: variable 'ins' set but not used > [-Wunused-but-set-variable] > edit.cpp: In static member function 'static void > Edit::printQAlignNoCheck(std::ostream&, const char*, const BTDnaString&, > const EList<Edit>&)': > edit.cpp:180:8: warning: variable 'ins' set but not used > [-Wunused-but-set-variable] > edit.cpp:201:8: warning: variable 'ins' set but not used > [-Wunused-but-set-variable] > edit.cpp:222:8: warning: variable 'ins' set but not used > [-Wunused-but-set-variable] > edit.cpp: In static member function 'static void Edit::toRef(const > BTDnaString&, const EList<Edit>&, BTDnaString&, bool, size_t, size_t)': > edit.cpp:277:8: warning: variable 'ins' set but not used > [-Wunused-but-set-variable] > edit.cpp: In static member function 'static bool Edit::repOk(const > EList<Edit>&, const BTDnaString&, bool, size_t, size_t)': > edit.cpp:358:8: warning: variable 'del' set but not used > [-Wunused-but-set-variable] > edit.cpp:358:21: warning: variable 'ins' set but not used > [-Wunused-but-set-variable] > edit.cpp:358:34: warning: variable 'mm' set but not used > [-Wunused-but-set-variable] > In file included from bt2_idx.h:45:0, > from bt2_idx.cpp:25: > word_io.h: In function 'uint32_t readU32(int, bool)': > word_io.h:86:27: error: 'read' was not declared in this scope > word_io.h: In function 'uint32_t readI32(int, bool)': > word_io.h:134:27: error: 'read' was not declared in this scope > In file included from bt2_idx.h:47:0, > from bt2_idx.cpp:25: > ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': > ref_read.h:69:21: error: 'read' was not declared in this scope > In file included from bt2_idx.cpp:25:0: > bt2_idx.h: In destructor 'Ebwt::~Ebwt()': > bt2_idx.h:927:3: error: 'close' was not declared in this scope > bt2_idx.h:928:3: error: 'close' was not declared in this scope > In file included from bt2_idx.h:45:0, > from bt2_io.cpp:25: > word_io.h: In function 'uint32_t readU32(int, bool)': > word_io.h:86:27: error: 'read' was not declared in this scope > word_io.h: In function 'uint32_t readI32(int, bool)': > word_io.h:134:27: error: 'read' was not declared in this scope > In file included from bt2_idx.h:47:0, > from bt2_io.cpp:25: > ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': > ref_read.h:69:21: error: 'read' was not declared in this scope > In file included from bt2_io.cpp:25:0: > bt2_idx.h: In destructor 'Ebwt::~Ebwt()': > bt2_idx.h:927:3: error: 'close' was not declared in this scope > bt2_idx.h:928:3: error: 'close' was not declared in this scope > bt2_io.cpp: In member function 'void Ebwt::readIntoMemory(int, int, bool, > bool, bool, bool, EbwtParams*, bool, bool, bool)': > bt2_io.cpp:61:28: error: 'close' was not declared in this scope > bt2_io.cpp:69:29: error: 'close' was not declared in this scope > bt2_io.cpp:268:34: error: 'lseek' was not declared in this scope > bt2_io.cpp:282:59: error: 'read' was not declared in this scope > bt2_io.cpp:316:44: error: 'lseek' was not declared in this scope > bt2_io.cpp:329:70: error: 'read' was not declared in this scope > bt2_io.cpp:340:43: error: 'lseek' was not declared in this scope > bt2_io.cpp:348:42: error: 'lseek' was not declared in this scope > bt2_io.cpp:378:71: error: 'read' was not declared in this scope > bt2_io.cpp:397:43: error: 'lseek' was not declared in this scope > bt2_io.cpp:417:31: error: 'lseek' was not declared in this scope > bt2_io.cpp:443:43: error: 'lseek' was not declared in this scope > bt2_io.cpp:451:66: error: 'read' was not declared in this scope > bt2_io.cpp:473:44: error: 'lseek' was not declared in this scope > bt2_io.cpp:481:74: error: 'read' was not declared in this scope > bt2_io.cpp:500:42: error: 'lseek' was not declared in this scope > bt2_io.cpp:516:44: error: 'read' was not declared in this scope > bt2_io.cpp:575:60: error: 'read' was not declared in this scope > bt2_io.cpp:596:45: error: 'lseek' was not declared in this scope > bt2_io.cpp:608:59: error: 'read' was not declared in this scope > bt2_io.cpp:617:71: error: 'read' was not declared in this scope > bt2_io.cpp:640:45: error: 'lseek' was not declared in this scope > bt2_io.cpp:660:27: error: 'lseek' was not declared in this scope > In file included from bt2_idx.h:45:0, > from bt2_util.cpp:26: > word_io.h: In function 'uint32_t readU32(int, bool)': > word_io.h:86:27: error: 'read' was not declared in this scope > word_io.h: In function 'uint32_t readI32(int, bool)': > word_io.h:134:27: error: 'read' was not declared in this scope > In file included from bt2_idx.h:47:0, > from bt2_util.cpp:26: > ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': > ref_read.h:69:21: error: 'read' was not declared in this scope > In file included from bt2_util.cpp:26:0: > bt2_idx.h: In destructor 'Ebwt::~Ebwt()': > bt2_idx.h:927:3: error: 'close' was not declared in this scope > bt2_idx.h:928:3: error: 'close' was not declared in this scope > In file included from ref_read.h:32:0, > from reference.h:32, > from reference.cpp:21: > word_io.h: In function 'uint32_t readU32(int, bool)': > word_io.h:86:27: error: 'read' was not declared in this scope > word_io.h: In function 'uint32_t readI32(int, bool)': > word_io.h:134:27: error: 'read' was not declared in this scope > In file included from reference.h:32:0, > from reference.cpp:21: > ref_read.h: In constructor 'RefRecord::RefRecord(int, bool)': > ref_read.h:69:21: error: 'read' was not declared in this scope > reference.cpp: In constructor 'BitPairReference::BitPairReference(const > string&, bool, bool, EList<std::basic_string<char> >*, EList<SString<char> > >*, bool, bool, bool, bool, bool, bool)': > reference.cpp:181:2: error: 'close' was not declared in this scope > make[1]: *** [bowtie2-build] Error 1 The full build log is available from: http://people.debian.org/~lucas/logs/2012/05/08/bowtie2_2.0.0-beta5-1_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 about 50 AMD64 nodes of the Grid'5000 platform, using a clean chroot. Internet was not accessible from the build systems. -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
