problems with installing Pindel

[Robby]

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

[KaiYe]

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.

[Kristina_A]

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

[KaiYe]

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

[Kristina_A]

Tried, same error :/
Any other ideas .. ?

Thank you