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  • Kristina_A
    replied
    Tried, same error :/
    Any other ideas .. ?

    Thank you

    Leave a comment:


  • KaiYe
    replied
    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

    Leave a comment:


  • Kristina_A
    replied
    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

    Leave a comment:


  • KaiYe
    replied
    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.

    Leave a comment:


  • Robby
    started a topic problems with installing Pindel

    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

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