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  • #1

    problems with installing Pindel

    Hello everyone,
    I have problems installing Pindel.

    First I downloaded the binary version, but I received the following error message:
    pindel_x86_64: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by pindel_x86_64)
    Because of that I tried the source code version, but I receive the following error message, when I try to install it:
    path is now: /path/samtools/
    make -C src pindel
    make[1]: Entering directory `/path/pindel/src'
    g++ -Wall -Werror -g -c -O3 -fopenmp -I/path/samtools/ pindel.cpp -o pindel.o
    cc1plus: warnings being treated as errors
    parameter.h:25: Warnung: »class Parameter« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    parameter.h:118: Warnung: »class IntParameter« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    parameter.h:135: Warnung: »class UIntParameter« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    parameter.h:152: Warnung: »class BoolParameter« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    parameter.h:174: Warnung: »class FloatParameter« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    parameter.h:191: Warnung: »class StringParameter« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    search_variant.h:4: Warnung: »class SearchVariant« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    searchshortinsertions.h:4: Warnung: »class SearchShortInsertions« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    searchdeletions.h:4: Warnung: »class SearchDeletions« hat virtuelle Funktionen aber nicht-virtuellen Destruktor
    pindel.cpp: In function »int init(int, char**, ControlState&)«:
    pindel.cpp:742: Warnung: Umwandlung in »int« von »double«
    make[1]: *** [pindel.o] Fehler 1
    make[1]: Leaving directory `/path/pindel/src'
    make: *** [pindel] Fehler 2
    Creating pindel2vcf utility...
    pindel2vcf created.
    mv: Aufruf von stat für „src/pindel“ nicht möglich: Datei oder Verzeichnis nicht gefunden

    Pindel successfully compiled. The pindel executable can be found in this directory.

    You can test pindel with the example files in the demo directory; example commands are given in the RUNME in that directory.

    For help and background information, see the pindel wiki and its FAQ on https://trac.nbic.nl/pindel/wiki/PindelFaq
    Or contact us on [email protected]
    What is missing? What is wrong? Who can help me?

    Best regards
    Robby
    Tags: None
  • #2
    Originally posted by Robby View Post
    Hello everyone,
    I have problems installing Pindel.

    First I downloaded the binary version, but I received the following error message:
    pindel_x86_64: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by pindel_x86_64)
    Because of that I tried the source code version, but I receive the following error message, when I try to install it:


    What is missing? What is wrong? Who can help me?

    Best regards
    Robby
    Please remove -Werror in the makefile.

    Comment

    • #3
      I'm also having issues installing Pindel

      pindel.h:35:17: error: sam.h: No such file or directory
      g++ -g -c -O3 -fopenmp -I/home/kaluzaite/downloads/pindel/ pindel.cpp -o pindel.o
      In file included from pindel.cpp:35:
      pindel.h:34:19: error: khash.h: No such file or directory
      pindel.h:35:17: error: sam.h: No such file or directory
      pindel.h:452: error: expected ‘,’ or ‘...’ before ‘*’ token
      pindel.h:452: error: ISO C++ forbids declaration of ‘bam1_t’ with no type
      pindel.h:453: error: expected ‘,’ or ‘...’ before ‘*’ token
      pindel.h:453: error: ISO C++ forbids declaration of ‘bam1_core_t’ with no type
      pindel.h:454: error: expected ‘,’ or ‘...’ before ‘*’ token
      pindel.h:454: error: ISO C++ forbids declaration of ‘bam1_t’ with no type
      pindel.h:458: error: expected ‘,’ or ‘...’ before ‘*’ token
      pindel.h:458: error: ISO C++ forbids declaration of ‘bam_header_t’ with no type
      pindel.h:460: error: variable or field ‘bam_init_header_hash’ declared void
      pindel.h:460: error: ‘bam_header_t’ was not declared in this scope
      pindel.h:460: error: ‘header’ was not declared in this scope
      reader.h:57: error: expected ‘,’ or ‘...’ before ‘*’ token
      reader.h:57: error: ISO C++ forbids declaration of ‘bam1_t’ with no type
      search_MEI.h:102: error: expected ‘,’ or ‘...’ before ‘*’ token
      search_MEI.h:102: error: ISO C++ forbids declaration of ‘bam1_t’ with no type
      gz_line_reader.h:22: error: ‘gzFile’ does not name a type
      make[1]: *** [pindel.o] Error 1
      make[1]: Leaving directory `/clusterapp/clusterhome/kaluzaite/downloads/pindel/src'
      make: *** [pindel] Error 2

      mv: cannot stat `src/pindel': No such file or directory
      mv: cannot stat `src/pindel2vcf': No such file or directory
      mv: cannot stat `src/sam2pindel': No such file or directory

      Pindel successfully compiled. The pindel executable can be found in this directory.


      Samtools are in place, and I tried removing -Wall and -Werror.
      It says it has successfully installed, but pindel executable file does not appear anywhere.

      help?

      Thank you in advance,
      Kristina

      Comment

      • #4
        Originally posted by Kristina_A View Post
        pindel.h:35:17: error: sam.h: No such file or directory
        g++ -g -c -O3 -fopenmp -I/home/kaluzaite/downloads/pindel/ pindel.cpp -o pindel.o
        In file included from pindel.cpp:35:
        pindel.h:34:19: error: khash.h: No such file or directory
        pindel.h:35:17: error: sam.h: No such file or directory
        pindel.h:452: error: expected ‘,’ or ‘...’ before ‘*’ token
        pindel.h:452: error: ISO C++ forbids declaration of ‘bam1_t’ with no type
        pindel.h:453: error: expected ‘,’ or ‘...’ before ‘*’ token
        pindel.h:453: error: ISO C++ forbids declaration of ‘bam1_core_t’ with no type
        pindel.h:454: error: expected ‘,’ or ‘...’ before ‘*’ token
        pindel.h:454: error: ISO C++ forbids declaration of ‘bam1_t’ with no type
        pindel.h:458: error: expected ‘,’ or ‘...’ before ‘*’ token
        pindel.h:458: error: ISO C++ forbids declaration of ‘bam_header_t’ with no type
        pindel.h:460: error: variable or field ‘bam_init_header_hash’ declared void
        pindel.h:460: error: ‘bam_header_t’ was not declared in this scope
        pindel.h:460: error: ‘header’ was not declared in this scope
        reader.h:57: error: expected ‘,’ or ‘...’ before ‘*’ token
        reader.h:57: error: ISO C++ forbids declaration of ‘bam1_t’ with no type
        search_MEI.h:102: error: expected ‘,’ or ‘...’ before ‘*’ token
        search_MEI.h:102: error: ISO C++ forbids declaration of ‘bam1_t’ with no type
        gz_line_reader.h:22: error: ‘gzFile’ does not name a type
        make[1]: *** [pindel.o] Error 1
        make[1]: Leaving directory `/clusterapp/clusterhome/kaluzaite/downloads/pindel/src'
        make: *** [pindel] Error 2

        mv: cannot stat `src/pindel': No such file or directory
        mv: cannot stat `src/pindel2vcf': No such file or directory
        mv: cannot stat `src/sam2pindel': No such file or directory

        Pindel successfully compiled. The pindel executable can be found in this directory.


        Samtools are in place, and I tried removing -Wall and -Werror.
        It says it has successfully installed, but pindel executable file does not appear anywhere.

        help?

        Thank you in advance,
        Kristina
        use samtools 0.1.18

        Comment

        • #5
          Tried, same error :/
          Any other ideas .. ?

          Thank you

          Comment

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