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#352 error when Bowtie2 installation

v0.9.0
open
nobody
None
5
2017-04-07
2017-03-21
Mao Wansi
No

Hello there;

I got some errors while install Bowtie2, following is the error section.
as I didn't download TBB, I used 'make NO_TBB=1' for installation.

make NO_TBB=1
g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"cat VERSION\"" -DBUILD_HOST="\"hostname\"" -DBUILD_TIME="\"date\"" -DCOMPILER_VERSION="\"g++ -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-I third_party \
-o bowtie2-align-s bt2_search.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 limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
-lreadline -ltermcap -lz -lpthread
pat.cpp: In member function ‘void CFilePatternSource::open()’:
pat.cpp:467: error: ‘gzbuffer’ was not declared in this scope
bowtie_main.cpp: In function ‘int createfifo(std::vector<char*, std::allocator\<char*=""> >&)’:
bowtie_main.cpp:158: warning: ignoring return value of ‘char mktemp(char)’, declared with attribute warn_unused_result
make: *** [bowtie2-align-s] Error 1</char*,>

Thanks in advance.

Discussion

  • Alan Harris

    Alan Harris - 2017-04-07

    I am encountering the same error when trying to make bowtie2-2.3 from source. Any assistance would be appreciated.

     

    • Mao Wansi

      Mao Wansi - 2017-04-07

      it seems you need to load one c++ lib named 'zlib'

      From: Alan Harris ralanharris@users.sf.net
      Sent: Friday, April 07, 2017 3:33 AM
      To: [bowtie-bio:bugs]
      Subject: [bowtie-bio:bugs] #352 error when Bowtie2 installation

      I am encountering the same error when trying to make bowtie2-2.3 from source. Any assistance would be appreciated.

      [bugs:#352]https://sourceforge.net/p/bowtie-bio/bugs/352/ error when Bowtie2 installation

      Status: open
      Group: v0.9.0
      Created: Tue Mar 21, 2017 06:05 AM UTC by Mao Wansi
      Last Updated: Tue Mar 21, 2017 06:05 AM UTC
      Owner: nobody

      Hello there;

      I got some errors while install Bowtie2, following is the error section.
      as I didn't download TBB, I used 'make NO_TBB=1' for installation.

      make NO_TBB=1
      g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"cat VERSION\"" -DBUILD_HOST="\"hostname\"" -DBUILD_TIME="\"date\"" -DCOMPILER_VERSION="\"g++ -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-align-s bt2_search.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 limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -lreadline -ltermcap -lz -lpthread
      pat.cpp: In member function ‘void CFilePatternSource::open()’:
      pat.cpp:467: error: ‘gzbuffer’ was not declared in this scope
      bowtie_main.cpp: In function ‘int createfifo(std::vector<char*, std::allocator\<char*=""> >&)’:
      bowtie_main.cpp:158: warning: ignoring return value of ‘char mktemp(char)’, declared with attribute warn_unused_result
      make: *** [bowtie2-align-s] Error 1</char*,>

      Thanks in advance.

      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/bowtie-bio/bugs/352/

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