Question: breakdancer build error
0
gravatar for phhz1113
3.6 years ago by
phhz11130
phhz11130 wrote:

I want to build break dancer. I got "Performing Test CXX11_FLAG0 - Failed" after cmake and got error after make. as following. Who can tell me how to fix it?

After cmake:

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

After make: [ 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:

[ 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: FileCMakeFiles/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: FileCMakeFiles/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: FileCMakeFiles/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 functionsam_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 functionsam_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

genome • 1.5k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by phhz11130

how can I install zlib-devel? I can not find it on http://zlib.net/

ADD REPLYlink written 3.6 years ago by phhz11130
0
gravatar for Pierre Lindenbaum
3.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

you need to install the zlib-devel package.

ADD COMMENTlink written 3.6 years ago by Pierre Lindenbaum124k
0
gravatar for Philipp Bayer
3.6 years ago by
Philipp Bayer6.5k
Australia/Perth/UWA
Philipp Bayer6.5k wrote:

Many errors like this one - see for example here

Solution: Install zlib-devel and/or zlib, depending on which your system has

ADD COMMENTlink written 3.6 years ago by Philipp Bayer6.5k
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