Hi all, I am trying to set up bedtools2 and it fails at the "make" step.
The errors generated are as follows:
Building BEDTools:
DETECTED_VERSION = v2.25.0
CURRENT_VERSION =
Updating version file.
Creating BamTools API
Building in src/utils/bedFile
compiling bedFile.cpp
Building in src/utils/BinTree
compiling BinTree.cpp
In file included from BinTree.cpp:1:
In file included from ./BinTree.h:18:
In file included from ../../utils//Contexts/ContextIntersect.h:11:
In file included from ../../utils//Contexts/ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
In file included from BinTree.cpp:1:
./BinTree.h:69:13: warning: private field '_maxBinNumFound' is not used
[-Wunused-private-field]
binNumType _maxBinNumFound;
^
3 warnings generated.
Building in src/utils/version
compiling version.cpp
Building in src/utils/bedGraphFile
compiling bedGraphFile.cpp
Building in src/utils/chromsweep
compiling chromsweep.cpp
Building in src/utils/Contexts
compiling ContextBase.cpp
In file included from ContextBase.cpp:8:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextIntersect.cpp
In file included from ContextIntersect.cpp:8:
In file included from ./ContextIntersect.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextFisher.cpp
In file included from ContextFisher.cpp:6:
In file included from ./ContextFisher.h:11:
In file included from ./ContextJaccard.h:11:
In file included from ./ContextIntersect.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextMap.cpp
In file included from ContextMap.cpp:8:
In file included from ./ContextMap.h:11:
In file included from ./ContextIntersect.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextSample.cpp
In file included from ContextSample.cpp:7:
In file included from ./ContextSample.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextSpacing.cpp
In file included from ContextSpacing.cpp:7:
In file included from ./ContextSpacing.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextMerge.cpp
In file included from ContextMerge.cpp:9:
In file included from ./ContextMerge.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextJaccard.cpp
In file included from ContextJaccard.cpp:8:
In file included from ./ContextJaccard.h:11:
In file included from ./ContextIntersect.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextClosest.cpp
In file included from ContextClosest.cpp:8:
In file included from ./ContextClosest.h:12:
In file included from ./ContextIntersect.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextSubtract.cpp
In file included from ContextSubtract.cpp:8:
In file included from ./ContextSubtract.h:12:
In file included from ./ContextIntersect.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextCoverage.cpp
In file included from ContextCoverage.cpp:8:
In file included from ./ContextCoverage.h:12:
In file included from ./ContextIntersect.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextComplement.cpp
In file included from ContextComplement.cpp:8:
In file included from ./ContextComplement.h:12:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling ContextGroupBy.cpp
In file included from ContextGroupBy.cpp:9:
In file included from ./ContextGroupBy.h:11:
In file included from ./ContextBase.h:23:
In file included from ../../utils//FileRecordTools/FileRecordMergeMgr.h:11:
In file included from ../../utils//FileRecordTools/FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
Building in src/utils/FileRecordTools
compiling FileRecordMgr.cpp
In file included from FileRecordMgr.cpp:2:
In file included from ./FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling FileRecordMergeMgr.cpp
In file included from FileRecordMergeMgr.cpp:9:
In file included from ./FileRecordMergeMgr.h:11:
In file included from ./FileRecordMgr.h:17:
In file included from ../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../utils//BamTools/include/api/BamAlignment.h:15:
../../utils//BamTools/include/api/BamConstants.h:129:25: warning: implicit
conversion from 'int' to 'const char' changes value from 139 to -117
[-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../utils//BamTools/include/api/BamConstants.h:132:25: warning: implicit
conversion from 'int' to 'const char' changes value from 255 to -1
[-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
Building in FileReaders
compiling FileReader.cpp
In file included from FileReader.cpp:3:
In file included from ./FileReader.h:10:
In file included from ./BufferedStreamMgr.h:14:
In file included from ./InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling SingleLineDelimTextFileReader.cpp
In file included from SingleLineDelimTextFileReader.cpp:1:
In file included from ./SingleLineDelimTextFileReader.h:11:
In file included from ./FileReader.h:10:
In file included from ./BufferedStreamMgr.h:14:
In file included from ./InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling BamFileReader.cpp
In file included from BamFileReader.cpp:1:
In file included from ./BamFileReader.h:11:
In file included from ./FileReader.h:10:
In file included from ./BufferedStreamMgr.h:14:
In file included from ./InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling BufferedStreamMgr.cpp
In file included from BufferedStreamMgr.cpp:8:
In file included from ./BufferedStreamMgr.h:14:
In file included from ./InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling InputStreamMgr.cpp
In file included from InputStreamMgr.cpp:8:
In file included from ./InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
Building in Records
compiling Record.cpp
compiling EmptyRecord.cpp
In file included from EmptyRecord.cpp:10:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling Bed3Interval.cpp
In file included from Bed3Interval.cpp:3:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling Bed4Interval.cpp
In file included from Bed4Interval.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling BedGraphInterval.cpp
In file included from BedGraphInterval.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling Bed5Interval.cpp
In file included from Bed5Interval.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling Bed6Interval.cpp
In file included from Bed6Interval.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling PlusFields.cpp
In file included from PlusFields.cpp:1:
./PlusFields.h:11:17: warning: using directive refers to implicitly-defined
namespace 'std'
using namespace std;
^
In file included from PlusFields.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
3 warnings generated.
compiling BedPlusInterval.cpp
In file included from BedPlusInterval.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling Bed12Interval.cpp
In file included from Bed12Interval.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling BamRecord.cpp
In file included from BamRecord.cpp:8:
In file included from ./BamRecord.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling GffRecord.cpp
In file included from GffRecord.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling GffPlusRecord.cpp
In file included from GffPlusRecord.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling VcfRecord.cpp
In file included from VcfRecord.cpp:9:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling NoPosPlusRecord.cpp
In file included from NoPosPlusRecord.cpp:2:
In file included from ../../../utils//FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:11:
In file included from ../../../utils//FileRecordTools/FileReaders/FileReader.h:10:
In file included from ../../../utils//FileRecordTools/FileReaders/BufferedStreamMgr.h:14:
In file included from ../../../utils//FileRecordTools/FileReaders/InputStreamMgr.h:14:
In file included from ../../../utils//BamTools/include/api/BamReader.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling BlockMgr.cpp
In file included from BlockMgr.cpp:9:
In file included from ./RecordMgr.h:21:
In file included from ./BamRecord.h:14:
In file included from ../../../utils//BamTools/include/api/BamAlignment.h:15:
../../../utils//BamTools/include/api/BamConstants.h:129:25: warning:
implicit conversion from 'int' to 'const char' changes value from 139
to -117 [-Wconstant-conversion]
const char GZIP_ID2 = 139;
../../../utils//BamTools/include/api/BamConstants.h:132:25: warning:
implicit conversion from 'int' to 'const char' changes value from 255
to -1 [-Wconstant-conversion]
const char OS_UNKNOWN = 255;
~~~~~~~~~~ ^~~
2 warnings generated.
compiling StrandQueue.cpp
In file included from StrandQueue.cpp:8:
In file included from ./StrandQueue.h:11:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/queue:401:5: error:
static_assert failed due to requirement 'is_same<Record *,
value_type>::value' ""
static_assert((is_same<_Tp, value_type>::value), "" );
^ ~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:805:36: note:
expanded from macro 'static_assert'
define static_assert(b, m) _Static_assert(b, m)
^ ~~~
StrandQueue.cpp:13:26: note: in instantiation of template class
'std::1::priority_queue<Record , std::__1::vector<const Record ,
std::1::allocator<const Record > >, RecordPtrSortDescFunctor>'
requested here
queueType queue = new queueType();
^
StrandQueue.cpp:32:47: error: no member named 'top' in
'std::1::priority_queue<Record *, std::1::vector<const Record ,
std::__1::allocator<const Record > >, RecordPtrSortDescFunctor>'
return const_cast<Record *>(_queues[minIdx]->top());
StrandQueue.cpp:38:19: error: no member named 'pop' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[minIdx]->pop();
~~~~~~~~~~~~~~~ ^
StrandQueue.cpp:45:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[0]->empty()) return NULL;
~~~~~~~~~~ ^
StrandQueue.cpp:46:24: error: no member named 'top' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
record = _queues[0]->top();
~~~~~~~~~~ ^
StrandQueue.cpp:49:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[1]->empty()) return NULL;
~~~~~~~~~~ ^
StrandQueue.cpp:51:24: error: no member named 'top' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
record = _queues[1]->top();
~~~~~~~~~~ ^
StrandQueue.cpp:54:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[0]->empty()) return NULL;
~~~~~~~~~~ ^
StrandQueue.cpp:55:24: error: no member named 'top' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
record = _queues[2]->top();
~~~~~~~~~~ ^
StrandQueue.cpp:66:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[0]->empty()) return;
~~~~~~~~~~ ^
StrandQueue.cpp:67:15: error: no member named 'pop' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[0]->pop();
~~~~~~~~~~ ^
StrandQueue.cpp:70:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[1]->empty()) return;
~~~~~~~~~~ ^
StrandQueue.cpp:71:15: error: no member named 'pop' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[1]->pop();
~~~~~~~~~~ ^
StrandQueue.cpp:74:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[2]->empty()) return;
~~~~~~~~~~ ^
StrandQueue.cpp:75:15: error: no member named 'pop' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[2]->pop();
~~~~~~~~~~ ^
StrandQueue.cpp:85:15: error: no member named 'push' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[0]->push(record);
~~~~~~~~~~ ^
StrandQueue.cpp:88:15: error: no member named 'push' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[1]->push(record);
~~~~~~~~~~ ^
StrandQueue.cpp:91:15: error: no member named 'push' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[2]->push(record);
~~~~~~~~~~ ^
StrandQueue.cpp:101:26: error: no member named 'size' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
sumSize += _queues[i]->size();
~~~~~~~~~~ ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [../../../../obj//StrandQueue.o] Error 1
make[1]: *** [Records] Error 2
make: *** [src/utils/FileRecordTools] Error 2
Violaui-MacBook-Pro:bedtools2 violakyoungalee$ bedtools
-bash: bedtools: command not found
Violaui-MacBook-Pro:bedtools2 violakyoungalee$ make
Building BEDTools:
=========================================================
DETECTED_VERSION = v2.25.0
CURRENT_VERSION = v2.25.0
Creating BamTools API
Building in src/utils/bedFile
make[1]: `../../../obj//bedFile.o' is up to date.
Building in src/utils/BinTree
make[1]: `../../../obj//BinTree.o' is up to date.
Building in src/utils/version
make[1]: Nothing to be done for `all'.
Building in src/utils/bedGraphFile
make[1]: `../../../obj//bedGraphFile.o' is up to date.
Building in src/utils/chromsweep
make[1]: `../../../obj//chromsweep.o' is up to date.
Building in src/utils/Contexts
make[1]: Nothing to be done for `all'.
Building in src/utils/FileRecordTools
Building in FileReaders
make[2]: Nothing to be done for `all'.
Building in Records
compiling StrandQueue.cpp
In file included from StrandQueue.cpp:8:
In file included from ./StrandQueue.h:11:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/queue:401:5: error:
static_assert failed due to requirement 'is_same<Record *,
value_type>::value' ""
static_assert((is_same<_Tp, value_type>::value), "" );
^ ~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:805:36: note:
expanded from macro 'static_assert'
define static_assert(b, m) _Static_assert(b, m)
^ ~~~
StrandQueue.cpp:13:26: note: in instantiation of template class
'std::1::priority_queue<Record , std::__1::vector<const Record ,
std::1::allocator<const Record > >, RecordPtrSortDescFunctor>'
requested here
queueType queue = new queueType();
^
StrandQueue.cpp:32:47: error: no member named 'top' in
'std::1::priority_queue<Record *, std::1::vector<const Record ,
std::__1::allocator<const Record > >, RecordPtrSortDescFunctor>'
return const_cast<Record *>(_queues[minIdx]->top());
StrandQueue.cpp:38:19: error: no member named 'pop' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[minIdx]->pop();
~~~~~~~~~~~~~~~ ^
StrandQueue.cpp:45:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[0]->empty()) return NULL;
~~~~~~~~~~ ^
StrandQueue.cpp:46:24: error: no member named 'top' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
record = _queues[0]->top();
~~~~~~~~~~ ^
StrandQueue.cpp:49:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[1]->empty()) return NULL;
~~~~~~~~~~ ^
StrandQueue.cpp:51:24: error: no member named 'top' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
record = _queues[1]->top();
~~~~~~~~~~ ^
StrandQueue.cpp:54:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[0]->empty()) return NULL;
~~~~~~~~~~ ^
StrandQueue.cpp:55:24: error: no member named 'top' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
record = _queues[2]->top();
~~~~~~~~~~ ^
StrandQueue.cpp:66:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[0]->empty()) return;
~~~~~~~~~~ ^
StrandQueue.cpp:67:15: error: no member named 'pop' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[0]->pop();
~~~~~~~~~~ ^
StrandQueue.cpp:70:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[1]->empty()) return;
~~~~~~~~~~ ^
StrandQueue.cpp:71:15: error: no member named 'pop' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[1]->pop();
~~~~~~~~~~ ^
StrandQueue.cpp:74:19: error: no member named 'empty' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
if (_queues[2]->empty()) return;
~~~~~~~~~~ ^
StrandQueue.cpp:75:15: error: no member named 'pop' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[2]->pop();
~~~~~~~~~~ ^
StrandQueue.cpp:85:15: error: no member named 'push' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[0]->push(record);
~~~~~~~~~~ ^
StrandQueue.cpp:88:15: error: no member named 'push' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[1]->push(record);
~~~~~~~~~~ ^
StrandQueue.cpp:91:15: error: no member named 'push' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
_queues[2]->push(record);
~~~~~~~~~~ ^
StrandQueue.cpp:101:26: error: no member named 'size' in
'std::__1::priority_queue<Record *, std::__1::vector<const Record *,
std::__1::allocator<const Record *> >, RecordPtrSortDescFunctor>'
sumSize += _queues[i]->size();
~~~~~~~~~~ ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [../../../../obj//StrandQueue.o] Error 1
make[1]: *** [Records] Error 2
make: *** [src/utils/FileRecordTools] Error 2
Please help me. I downloaded Xcode version 10 as well as command line tools.
arq5x
commented
5 years ago
Hi all, I am trying to set up bedtools2 and it fails at the "make" step.
The errors generated are as follows: Building BEDTools:
DETECTED_VERSION = v2.25.0 CURRENT_VERSION = Updating version file.
~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:805:36: note: expanded from macro 'static_assert'define static_assert(b, m) _Static_assert(b, m)
StrandQueue.cpp:13:26: note: in instantiation of template class 'std::1::priority_queue<Record , std::__1::vector<const Record , std::1::allocator<const Record > >, RecordPtrSortDescFunctor>' requested here queueType queue = new queueType(); ^ StrandQueue.cpp:32:47: error: no member named 'top' in 'std::1::priority_queue<Record *, std::1::vector<const Record , std::__1::allocator<const Record > >, RecordPtrSortDescFunctor>' return const_cast<Record *>(_queues[minIdx]->top());
~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:805:36: note: expanded from macro 'static_assert'define static_assert(b, m) _Static_assert(b, m)
StrandQueue.cpp:13:26: note: in instantiation of template class 'std::1::priority_queue<Record , std::__1::vector<const Record , std::1::allocator<const Record > >, RecordPtrSortDescFunctor>' requested here queueType queue = new queueType(); ^ StrandQueue.cpp:32:47: error: no member named 'top' in 'std::1::priority_queue<Record *, std::1::vector<const Record , std::__1::allocator<const Record > >, RecordPtrSortDescFunctor>' return const_cast<Record *>(_queues[minIdx]->top());
Please help me. I downloaded Xcode version 10 as well as command line tools.