Installation Error 127

[Poorva Sethi]

Hi
Can you please help me with errors I got I tried to install
BEDTools-Version-2.9.0 on Ubuntu 10.04.1.
(This is my first time with Bedtools)

Thanks
-Poorva.

- Building in src/utils/lineFileUtilities
* compiling lineFileUtilities.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//lineFileUtilities.o] Error 127

- Building in src/utils/bedFile
* compiling bedFile.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//bedFile.o] Error 127

- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//bedGraphFile.o] Error 127

- Building in src/utils/tabFile
* compiling tabFile.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//tabFile.o] Error 127

- Building in src/utils/genomeFile
* compiling genomeFile.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//genomeFile.o] Error 127

- Building in src/utils/gzstream
g++ -I. -O -Wall -c -o ../../../obj//gzstream.o gzstream.C
make[1]: g++: Command not found
make[1]: *** [../../../obj//gzstream.o] Error 127

- Building in src/utils/fileType
* compiling fileType.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//fileType.o] Error 127

- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//bedFilePE.o] Error 127

- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//sequenceUtils.o] Error 127

- Building in src/utils/BamTools
* compiling BamReader.cpp
make[1]: g++: Command not found
make[1]: *** [../../../obj//BamReader.o] Error 127

- Building in src/bamToBed
* compiling bamToBed.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//bamToBed.o] Error 127

- Building in src/bedToBam
* compiling bedToBam.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//bedToBam.o] Error 127

- Building in src/bedToIgv
* compiling bedToIgv.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//bedToIgv.o] Error 127

- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//bed12ToBed6.o] Error 127

- Building in src/closestBed
* compiling closestMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//closestMain.o] Error 127

- Building in src/complementBed
* compiling complementMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//complementMain.o] Error 127

- Building in src/coverageBed
* compiling coverageMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//coverageMain.o] Error 127

- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//fastaFromBedMain.o] Error 127

- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//genomeCoverageMain.o] Error 127

- Building in src/groupBy
* compiling groupBy.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//groupBy.o] Error 127

- Building in src/intersectBed
* compiling intersectMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//intersectMain.o] Error 127

- Building in src/linksBed
* compiling linksMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//linksMain.o] Error 127

- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//maskFastaFromBedMain.o] Error 127

- Building in src/mergeBed
* compiling mergeMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//mergeMain.o] Error 127

- Building in src/overlap
* compiling overlap.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//overlap.o] Error 127

- Building in src/pairToBed
* compiling pairToBedMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//pairToBedMain.o] Error 127

- Building in src/pairToPair
* compiling pairToPairMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//pairToPairMain.o] Error 127

- Building in src/shuffleBed
* compiling shuffleBedMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//shuffleBedMain.o] Error 127

- Building in src/slopBed
* compiling slopBedMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//slopBedMain.o] Error 127

- Building in src/sortBed
* compiling sortMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//sortMain.o] Error 127

- Building in src/subtractBed
* compiling subtractMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//subtractMain.o] Error 127

- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//unionBedGraphs.o] Error 127

- Building in src/windowBed
* compiling windowMain.cpp
make[1]: g++: Command not found
make[1]: *** [../../obj//windowMain.o] Error 127

[Aaron Quinlan]

You system seems to lack the gcc compiler. One must install the "build tools" for Ubuntu. If you have sudo priveleges, you could try:

$ sudo apt-get install build-essential

Otherwise, contact a system administrator.

[Poorva Sethi]

Thanks Aaron,
I installed gcc compiler using :$ sudo apt-get install build-
essential
but when I again did make all it gave me errors as shown below,
Can you please help me solve this problem and install Bedtools.

Thanks again,
Poorva.

Building BEDTools:
=========================================================

- Building in src/utils/lineFileUtilities
* compiling lineFileUtilities.cpp

- Building in src/utils/bedFile
* compiling bedFile.cpp

In file included from bedFile.h:16,
from bedFile.cpp:12:
../../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from bedFile.h:16,
from bedFile.cpp:12:
../../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a
type

make[1]: *** [../../../obj//bedFile.o] Error 1

- Building in src/utils/bedGraphFile
* compiling bedGraphFile.cpp

In file included from bedGraphFile.h:15,
from bedGraphFile.cpp:12:
../../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from bedGraphFile.h:15,
from bedGraphFile.cpp:12:
../../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a
type

make[1]: *** [../../../obj//bedGraphFile.o] Error 1

- Building in src/utils/tabFile
* compiling tabFile.cpp

In file included from tabFile.h:15,
from tabFile.cpp:13:
../../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from tabFile.h:15,
from tabFile.cpp:13:
../../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a
type

make[1]: *** [../../../obj//tabFile.o] Error 1

- Building in src/utils/genomeFile
* compiling genomeFile.cpp

- Building in src/utils/gzstream
g++ -I. -O -Wall -c -o ../../../obj//gzstream.o gzstream.C

In file included from gzstream.C:29:
./gzstream.h:35:18: error: zlib.h: No such file or directory
In file included from gzstream.C:29:
./gzstream.h:50: error: ‘gzFile’ does not name a type
gzstream.C: In member function ‘gzstreambuf* gzstreambuf::open(const
char*, int)’:
gzstream.C:61: error: ‘file’ was not declared in this scope
gzstream.C:61: error: ‘gzopen’ was not declared in this scope
gzstream.C: In member function ‘gzstreambuf* gzstreambuf::close()’:
gzstream.C:72: error: ‘file’ was not declared in this scope
gzstream.C:72: error: ‘gzclose’ was not declared in this scope
gzstream.C:72: error: ‘Z_OK’ was not declared in this scope
gzstream.C: In member function ‘virtual int gzstreambuf::underflow()’:
gzstream.C:90: error: ‘file’ was not declared in this scope
gzstream.C:90: error: ‘gzread’ was not declared in this scope
gzstream.C: In member function ‘int gzstreambuf::flush_buffer()’:
gzstream.C:107: error: ‘file’ was not declared in this scope
gzstream.C:107: error: ‘gzwrite’ was not declared in this scope

make[1]: *** [../../../obj//gzstream.o] Error 1

- Building in src/utils/fileType
* compiling fileType.cpp

- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp

In file included from ../../utils//bedFile/bedFile.h:16,
from bedFilePE.h:12,
from bedFilePE.cpp:15:
../../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../../utils//bedFile/bedFile.h:16,
from bedFilePE.h:12,
from bedFilePE.cpp:15:
../../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a
type

make[1]: *** [../../../obj//bedFilePE.o] Error 1

- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp

- Building in src/utils/BamTools
* compiling BamReader.cpp

In file included from BamReader.cpp:22:
BGZF.h:26:18: error: zlib.h: No such file or directory
In file included from BamReader.cpp:22:
BGZF.h: In static member function ‘static bool
BamTools::BgzfData::CheckBlockHeader(char*)’:
BGZF.h:165: error: ‘Z_DEFLATED’ was not declared in this scope

make[1]: *** [../../../obj//BamReader.o] Error 1

- Building in src/bamToBed
* compiling bamToBed.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from ../utils//BamTools/BamAncillary.h:12,
from bamToBed.cpp:14:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from ../utils//BamTools/BamAncillary.h:12,
from bamToBed.cpp:14:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//bamToBed.o] Error 1

- Building in src/bedToBam
* compiling bedToBam.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from bedToBam.cpp:13:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from bedToBam.cpp:13:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//bedToBam.o] Error 1

- Building in src/bedToIgv
* compiling bedToIgv.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from bedToIgv.cpp:13:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from bedToIgv.cpp:13:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//bedToIgv.o] Error 1

- Building in src/bed12ToBed6
* compiling bed12ToBed6.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from bed12ToBed6.cpp:13:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from bed12ToBed6.cpp:13:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//bed12ToBed6.o] Error 1

- Building in src/closestBed
* compiling closestMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from closestBed.h:15,
from closestMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from closestBed.h:15,
from closestMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//closestMain.o] Error 1

- Building in src/complementBed
* compiling complementMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from complementBed.h:12,
from complementMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from complementBed.h:12,
from complementMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//complementMain.o] Error 1

- Building in src/coverageBed
* compiling coverageMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from coverageBed.h:15,
from coverageMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from coverageBed.h:15,
from coverageMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//coverageMain.o] Error 1

- Building in src/fastaFromBed
* compiling fastaFromBedMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from fastaFromBed.h:15,
from fastaFromBedMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from fastaFromBed.h:15,
from fastaFromBedMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//fastaFromBedMain.o] Error 1

- Building in src/genomeCoverageBed
* compiling genomeCoverageMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from genomeCoverageBed.h:12,
from genomeCoverageMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from genomeCoverageBed.h:12,
from genomeCoverageMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//genomeCoverageMain.o] Error 1

- Building in src/groupBy
* compiling groupBy.cpp

In file included from ../utils//tabFile/tabFile.h:15,
from groupBy.cpp:29:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//tabFile/tabFile.h:15,
from groupBy.cpp:29:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//groupBy.o] Error 1

- Building in src/intersectBed
* compiling intersectMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from intersectBed.h:15,
from intersectMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from intersectBed.h:15,
from intersectMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//intersectMain.o] Error 1

- Building in src/linksBed
* compiling linksMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from linksBed.h:12,
from linksMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from linksBed.h:12,
from linksMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//linksMain.o] Error 1

- Building in src/maskFastaFromBed
* compiling maskFastaFromBedMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from maskFastaFromBed.h:14,
from maskFastaFromBedMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from maskFastaFromBed.h:14,
from maskFastaFromBedMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//maskFastaFromBedMain.o] Error 1

- Building in src/mergeBed
* compiling mergeMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from mergeBed.h:12,
from mergeMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from mergeBed.h:12,
from mergeMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//mergeMain.o] Error 1

- Building in src/overlap
* compiling overlap.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from overlap.cpp:19:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from overlap.cpp:19:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//overlap.o] Error 1

- Building in src/pairToBed
* compiling pairToBedMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from pairToBed.h:20,
from pairToBedMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from pairToBed.h:20,
from pairToBedMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//pairToBedMain.o] Error 1

- Building in src/pairToPair
* compiling pairToPairMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from pairToPair.h:15,
from pairToPairMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from pairToPair.h:15,
from pairToPairMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//pairToPairMain.o] Error 1

- Building in src/shuffleBed
* compiling shuffleBedMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from shuffleBed.h:12,
from shuffleBedMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from shuffleBed.h:12,
from shuffleBedMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//shuffleBedMain.o] Error 1

- Building in src/slopBed
* compiling slopBedMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from slopBed.h:13,
from slopBedMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from slopBed.h:13,
from slopBedMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//slopBedMain.o] Error 1

- Building in src/sortBed
* compiling sortMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from sortBed.h:12,
from sortMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from sortBed.h:12,
from sortMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//sortMain.o] Error 1

- Building in src/subtractBed
* compiling subtractMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from subtractBed.h:15,
from subtractMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from subtractBed.h:15,
from subtractMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//subtractMain.o] Error 1

- Building in src/unionBedGraphs
* compiling unionBedGraphs.cpp

In file included from ../utils//bedGraphFile/bedGraphFile.h:15,
from unionBedGraphs.cpp:19:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedGraphFile/bedGraphFile.h:15,
from unionBedGraphs.cpp:19:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//unionBedGraphs.o] Error 1

- Building in src/windowBed
* compiling windowMain.cpp

In file included from ../utils//bedFile/bedFile.h:16,
from windowBed.h:20,
from windowMain.cpp:12:
../utils//gzstream/gzstream.h:35:18: error: zlib.h: No such file or
directory
In file included from ../utils//bedFile/bedFile.h:16,
from windowBed.h:20,
from windowMain.cpp:12:
../utils//gzstream/gzstream.h:50: error: ‘gzFile’ does not name a type

make[1]: *** [../../obj//windowMain.o] Error 1

[Aaron Quinlan]

Your system also lacks the zlib (this is the library behind gzip) development tools.

Try:

$ sudo apt-get install zlib1g-dev

Best,

Aaron

[Poorva Sethi]

Hi Aaron
I've installed Zlib; it works fine now.
Thank you for your help.

Best,
Poorva.

> ...
>
> read more »

[Aaron Quinlan]

Great. Sorry for the difficulty --- I hope to soon have a configuration script that will notify people of what libraries are missing. On the "to do" list.

Best,
Aaron