[Debian-med-packaging] Bug#672090: Bug#672090: bowtie2: FTBFS: word_io.h:86:27: error: 'read' was not declared in this scope
Alex Mestiashvili
alex at biotec.tu-dresden.de
Wed May 9 13:08:03 UTC 2012
On 05/08/2012 01:36 PM, Lucas Nussbaum wrote:
> Source: bowtie2
> Version: 2.0.0-beta5-1
> Severity: serious
> Tags: wheezy sid
> User: debian-qa at 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.
>
>
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
Hello,
Thank you for reporting.
The problem was related to gcc4.7 - missing unistd.h include.
The fix is available in git repository.
http://anonscm.debian.org/gitweb/?p=debian-med/bowtie2.git
Will try to upload it after a review.
Best regards,
Alex
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