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Old 03-30-2016, 08:00 AM   #1
sydghyyh14
Junior Member
 
Location: Beijng, China

Join Date: Mar 2010
Posts: 7
Default breakdancer install error

I want to install BreakDancer-1.3.6.
After make, I got error as following, who can tell me how to fix it?
[ 1%] Creating directories for 'boost-libs'
[ 3%] Performing download step (verify and extract) for 'boost-libs'
-- verifying file...
file='/data/home/suyao/tools/BreakDancer/breakdancer-master/vendor/boost-1.54-breakdancer.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
src='/data/home/suyao/tools/BreakDancer/breakdancer-master/vendor/boost-1.54-breakdancer.tar.gz'
dst='/data/home/suyao/tools/BreakDancer/breakdancer-master/build/vendor/boost/boost-src'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 4%] No patch step for 'boost-libs'
[ 6%] No update step for 'boost-libs'
[ 7%] Performing configure step for 'boost-libs'
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Detecting Python version... 2.6
Detecting Python root... /usr
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

./b2

To adjust configuration, edit 'project-config.jam'.
Further information:

- Command line help:
./b2 --help

- Getting started guide:
http://www.boost.org/more/getting_st...-variants.html

- Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html

[ 9%] Performing build step for 'boost-libs'
[ 10%] No install step for 'boost-libs'
[ 12%] Completed 'boost-libs'
[ 12%] Built target boost-libs
[ 14%] Creating directories for 'samtools-lib'
[ 15%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
file='/data/home/suyao/tools/BreakDancer/breakdancer-master/vendor/samtools-0.1.19.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
src='/data/home/suyao/tools/BreakDancer/breakdancer-master/vendor/samtools-0.1.19.tar.gz'
dst='/data/home/suyao/tools/BreakDancer/breakdancer-master/build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 17%] No patch step for 'samtools-lib'
[ 18%] No update step for 'samtools-lib'
[ 20%] Performing configure step for 'samtools-lib'
Building samtools, build log at /data/home/suyao/tools/BreakDancer/breakdancer-master/build/vendor/samtools/build.log
[ 21%] Performing build step for 'samtools-lib'
[ 23%] No install step for 'samtools-lib'
[ 25%] Completed 'samtools-lib'
[ 25%] Built target samtools-lib
[ 25%] Built target deps
[ 26%] Creating directories for 'gtest160'
[ 28%] Performing download step (verify and extract) for 'gtest160'
-- verifying file...
file='/data/home/suyao/tools/BreakDancer/breakdancer-master/build-common/vendor/gtest-1.6.0.tar.gz'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
src='/data/home/suyao/tools/BreakDancer/breakdancer-master/build-common/vendor/gtest-1.6.0.tar.gz'
dst='/data/home/suyao/tools/BreakDancer/breakdancer-master/build/vendor/src/gtest160'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 29%] No patch step for 'gtest160'
[ 31%] No update step for 'gtest160'
[ 32%] Performing configure step for 'gtest160'
-- Configuring done
-- Generating done
-- Build files have been written to: /data/home/suyao/tools/BreakDancer/breakdancer-master/build/vendor/gtest160-build
[ 34%] Performing build step for 'gtest160'
make[3]: Warning: File `Makefile' has modification time 25 s in the future
make[4]: Warning: File `CMakeFiles/Makefile2' has modification time 25 s in the future
make[5]: Warning: File `CMakeFiles/gtest.dir/progress.make' has modification time 25 s in the future
make[5]: Warning: File `CMakeFiles/gtest.dir/progress.make' has modification time 25 s in the future
[ 50%] Built target gtest
make[5]: Warning: File `CMakeFiles/gtest_main.dir/progress.make' has modification time 25 s in the future
make[5]: Warning: File `CMakeFiles/gtest_main.dir/progress.make' has modification time 25 s in the future
[100%] Built target gtest_main
[ 35%] No install step for 'gtest160'
[ 37%] Completed 'gtest160'
[ 37%] Built target gtest160
[ 39%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BedWriter.cpp.o
[ 40%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BreakDancer.cpp.o
[ 42%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/ReadRegionData.cpp.o
[ 43%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/SvBuilder.cpp.o
[ 45%] Linking CXX static library libbreakdancer.a
[ 45%] Built target breakdancer
[ 46%] Building CXX object build/src/lib/common/CMakeFiles/common.dir/Options.cpp.o
[ 48%] Building CXX object build/src/lib/common/CMakeFiles/common.dir/ReadFlags.cpp.o
[ 50%] Linking CXX static library libcommon.a
[ 50%] Built target common
[ 51%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/Alignment.cpp.o
[ 53%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/BamConfig.cpp.o
[ 54%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/BamConfigEntry.cpp.o
[ 56%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/BamIo.cpp.o
[ 57%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/BamMerger.cpp.o
[ 59%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/BamSummary.cpp.o
[ 60%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/BamWriter.cpp.o
[ 62%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/ConfigLoader.cpp.o
[ 64%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/FastqWriter.cpp.o
[ 65%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/IlluminaPEReadClassifier.cpp.o
[ 67%] Building CXX object build/src/lib/io/CMakeFiles/io.dir/LibraryFlagDistribution.cpp.o
[ 68%] Linking CXX static library libio.a
[ 68%] Built target io
[ 70%] Building CXX object build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir/BreakDancerMax.cpp.o
make[2]: Warning: File `build/src/lib/io/libio.a' has modification time 22 s in the future
[ 71%] Linking CXX executable ../../../../bin/breakdancer-max
../../../../vendor/samtools/libbam.a(bam_import.o): In function `__bam_get_lines':
/data/home/suyao/tools/BreakDancer/breakdancer-master/build/vendor/samtools/bam_import.c:76: undefined reference to `gzopen64'
../../../../vendor/samtools/libbam.a(bam_import.o): In function `sam_open':
/data/home/suyao/tools/BreakDancer/breakdancer-master/build/vendor/samtools/bam_import.c:472: undefined reference to `gzopen64'
../../../../vendor/samtools/libbam.a(bam_import.o): In function `sam_header_read2':
/data/home/suyao/tools/BreakDancer/breakdancer-master/build/vendor/samtools/bam_import.c:126: undefined reference to `gzopen64'
collect2: ld 杩.. 1
make[2]: *** [bin/breakdancer-max] ?.. 1
make[1]: *** [build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir/all] ?.. 2
make: *** [all] ?.. 2
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Old 03-30-2016, 08:35 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,143
Default

What OS are you using? Find zlib and zlib-devel packages and install those for your OS.
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Old 03-30-2016, 08:59 AM   #3
sydghyyh14
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Location: Beijng, China

Join Date: Mar 2010
Posts: 7
Default

My OS is Red Hat 4.4.5-6
zlib-1.2.3-27.el6.x86_64
zlib-devel-1.2.3-27.el6.x86_64
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Old 03-30-2016, 09:24 AM   #4
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,143
Default

Post #9 here shows a change you can make to the Makefile to indicate the location where your zlib is installed. You may need to find the right place to do the modification in Breakdancer source.
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Old 03-30-2016, 07:28 PM   #5
sydghyyh14
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Location: Beijng, China

Join Date: Mar 2010
Posts: 7
Default

I do not know how to modify Breakdancer source.

And I found "Performing Test CXX11_FLAG0 - Failed" after cmake as following:
Score floating point type: double
-- Performing Test CXX11_FLAG0
-- Performing Test CXX11_FLAG0 - Failed
-- Performing Test CXX11_FLAG1
-- Performing Test CXX11_FLAG1 - Success
-- C++11 support enabled via -std=c++0x
-- Performing Test CXX11_STDLIB_FLAG0
-- Performing Test CXX11_STDLIB_FLAG0 - Success
-- Sufficient C++11 library support found with flag ' '
-- Configuring done
-- Generating done
-- Build files have been written to: /data/home/suyao/tools/BreakDancer/breakdancer-master/build

who can give me more suggestion?
Thank you!
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