Your message dated Wed, 09 May 2012 15:02:39 +0000
with message-id <e1ss8px-00033z...@franck.debian.org>
and subject line Bug#672090: fixed in bowtie2 2.0.0-beta5-2
has caused the Debian Bug report #672090,
regarding bowtie2: FTBFS: word_io.h:86:27: error: 'read' was not declared in
this scope
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
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--
672090: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=672090
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: bowtie2
Source-Version: 2.0.0-beta5-2
We believe that the bug you reported is fixed in the latest version of
bowtie2, which is due to be installed in the Debian FTP archive:
bowtie2-examples_2.0.0-beta5-2_all.deb
to main/b/bowtie2/bowtie2-examples_2.0.0-beta5-2_all.deb
bowtie2_2.0.0-beta5-2.debian.tar.gz
to main/b/bowtie2/bowtie2_2.0.0-beta5-2.debian.tar.gz
bowtie2_2.0.0-beta5-2.dsc
to main/b/bowtie2/bowtie2_2.0.0-beta5-2.dsc
bowtie2_2.0.0-beta5-2_amd64.deb
to main/b/bowtie2/bowtie2_2.0.0-beta5-2_amd64.deb
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 672...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated bowtie2 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...@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Thu, 26 Apr 2012 13:59:54 +0200
Source: bowtie2
Binary: bowtie2 bowtie2-examples
Architecture: source amd64 all
Version: 2.0.0-beta5-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
bowtie2 - ultrafast memory-efficient short read aligner
bowtie2-examples - Examples for bowtie2,
Closes: 672090
Changes:
bowtie2 (2.0.0-beta5-2) unstable; urgency=low
.
[ Alexandre Mestiashvili ]
* file sse_util.h has missing copyright header.
The Author (Benjamin Langmead) has
confirmed that the file is distributed under GPL3 license.
.
[ Andreas Tille ]
* debian/upstream: Added publication
* debian/patches/fix_makefile_machine_detection.patch + debian/rules:
prevent -mXX and -msse2 switches for non Intel architectures
.
[ Alexandre Mestiashvili ]
* debian/patches/bowtie2_gcc4.7.patch Closes: #672090
* updated DEP3 headers
* bumperd Standards-Version to 3.9.3
* uname -m doesn't detect 32 bit chroot env - updated patcH
Checksums-Sha1:
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609d7f7687311846e7446c0177064940ee22e01d 4191
bowtie2_2.0.0-beta5-2.debian.tar.gz
5ec5f546fc99ff041ed415cd51838e18dc2bbf28 897834 bowtie2_2.0.0-beta5-2_amd64.deb
b761eff24ee62d3749d4c3c2b57c5af77189dbe6 4877066
bowtie2-examples_2.0.0-beta5-2_all.deb
Checksums-Sha256:
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bowtie2_2.0.0-beta5-2.dsc
7c4e956b36a23c8ecafd89a6a38f0d4aa63c2e10e1d935473d3e05cd48388ad2 4191
bowtie2_2.0.0-beta5-2.debian.tar.gz
9930e6cdf2b23bcf68bea8c2bb1f88d28346a1848eb3b315402dbaa5fdad8977 897834
bowtie2_2.0.0-beta5-2_amd64.deb
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bowtie2-examples_2.0.0-beta5-2_all.deb
Files:
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b9626cb229dd8b731df244007f31d28a 4191 science extra
bowtie2_2.0.0-beta5-2.debian.tar.gz
b83e5869cbc37ad6ffdf1a16523005ca 897834 science extra
bowtie2_2.0.0-beta5-2_amd64.deb
5245de5a027175647ce741d5efdc9835 4877066 science extra
bowtie2-examples_2.0.0-beta5-2_all.deb
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--- End Message ---
