Mock Version: 1.3.4
Mock Version: 1.3.4
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/BEDTools.spec'], chrootPath='/var/lib/mock/f28-build-11735377-873015/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0xb5f28ad0>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/BEDTools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: armv7hl
Building for target armv7hl
Wrote: /builddir/build/SRPMS/BEDTools-2.26.0-7.fc28.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/BEDTools.spec'], chrootPath='/var/lib/mock/f28-build-11735377-873015/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0xb5f28ad0>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/BEDTools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: armv7hl
Building for target armv7hl
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.XJ4wEG
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bedtools2
+ /usr/bin/gzip -dc /builddir/build/SOURCES/bedtools-2.26.0.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bedtools2
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ /usr/bin/cat /builddir/build/SOURCES/BEDTools-double-parenthesis.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch
+ /usr/bin/cat /builddir/build/SOURCES/0001-Ditch-bizarre-inclusion-then-mock-out-of-matplotlib-.patch
+ rm -rf src/utils/curl
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.BRARYu
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2
+ make -j4 'CXXFLAGS=-I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard' V=1
Building BEDTools:
=========================================================
 * Creating BamTools API
DETECTED_VERSION = v2.26.0
CURRENT_VERSION  = 
Updating version file.
- Building in src/utils/FileRecordTools
- Building in src/utils/FileRecordTools/FileReaders
- Building in src/utils/FileRecordTools/Records
- Building in src/utils/bedFile
  * compiling FileRecordMgr.cpp
  * compiling FileReader.cpp
  * compiling Record.cpp
  * compiling bedFile.cpp
  * compiling SingleLineDelimTextFileReader.cpp
  * compiling EmptyRecord.cpp
  * compiling FileRecordMergeMgr.cpp
  * compiling Bed3Interval.cpp
  * compiling FileRecordMgr.cpp
  * compiling BamFileReader.cpp
  * compiling Bed4Interval.cpp
  * compiling BufferedStreamMgr.cpp
  * compiling FileRecordMergeMgr.cpp
  * compiling BedGraphInterval.cpp
  * compiling InputStreamMgr.cpp
  * compiling Bed5Interval.cpp
- Building in FileReaders
make[2]: Nothing to be done for 'all'.
- Building in Records
  * compiling Bed6Interval.cpp
  * compiling PlusFields.cpp
  * compiling Bed6Interval.cpp
  * compiling BedPlusInterval.cpp
- Building in src/utils/BinTree
  * compiling BinTree.cpp
  * compiling Bed12Interval.cpp
  * compiling BedPlusInterval.cpp
  * compiling BamRecord.cpp
  * compiling BamRecord.cpp
  * compiling GffRecord.cpp
- Building in src/utils/version
- Building in src/utils/bedGraphFile
  * compiling version.cpp
  * compiling bedGraphFile.cpp
- Building in src/utils/chromsweep
  * compiling chromsweep.cpp
  * compiling GffRecord.cpp
  * compiling GffPlusRecord.cpp
- Building in src/utils/Contexts
  * compiling ContextBase.cpp
  * compiling GffPlusRecord.cpp
  * compiling VcfRecord.cpp
  * compiling VcfRecord.cpp
  * compiling NoPosPlusRecord.cpp
  * compiling BlockMgr.cpp
  * compiling NoPosPlusRecord.cpp
  * compiling ContextIntersect.cpp
  * compiling StrandQueue.cpp
  * compiling RecordMgr.cpp
  * compiling StrandQueue.cpp
  * compiling RecordList.cpp
  * compiling ContextFisher.cpp
  * compiling RecordList.cpp
  * compiling ContextMap.cpp
  * compiling ContextSample.cpp
  * compiling RecordKeyList.cpp
  * compiling ContextSpacing.cpp
  * compiling ContextMerge.cpp
  * compiling RecordKeyVector.cpp
  * compiling ContextJaccard.cpp
- Building in src/utils/general
  * compiling QuickString.cpp
  * compiling RecordKeyList.cpp
  * compiling ParseTools.cpp
- Building in src/utils/gzstream
g++ -I. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -march=armv7-a -mfpu=vfpv3-d16 -mtune=generic-armv7-a -mabi=aapcs-linux -mfloat-abi=hard  -c -o ../../../obj//gzstream.o gzstream.C -I.
  * compiling ContextClosest.cpp
  * compiling ContextSubtract.cpp
  * compiling CompressionTools.cpp
  * compiling PushBackStreamBuf.cpp
  * compiling Tokenizer.cpp
  * compiling CommonHelp.cpp
  * compiling ContextCoverage.cpp
- Building in src/utils/fileType
  * compiling fileType.cpp
  * compiling FileRecordTypeChecker.cpp
  * compiling ContextComplement.cpp
- Building in src/utils/bedFilePE
  * compiling bedFilePE.cpp
FileRecordTypeChecker.cpp: In member function 'bool FileRecordTypeChecker::isTextDelimtedFormat(const char*, size_t)':
FileRecordTypeChecker.cpp:355:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (int j=0; j < len; j++) {
                 ~~^~~~~
  * compiling ContextGroupBy.cpp
- Building in src/utils/KeyListOps
  * compiling KeyListOps.cpp
- Building in src/utils/NewChromsweep
  * compiling NewChromsweep.cpp
  * compiling CloseSweep.cpp
- Building in src/utils/sequenceUtilities
- Building in src/utils/tabFile
  * compiling tabFile.cpp
  * compiling sequenceUtils.cpp
  * compiling KeyListOpsMethods.cpp
- Building in src/utils/BamTools
 * compiling BamAlignment.cpp
- Building in src/utils/BamTools-Ancillary
  * compiling BamAncillary.cpp
  * compiling BamAncillary.cpp
In file included from /usr/include/c++/8/algorithm:62,
                 from ../../utils/fileType/FileRecordTypeChecker.h:18,
                 from ../../utils/FileRecordTools/Records/Record.h:14,
                 from ../../utils/FileRecordTools/Records/RecordKeyVector.h:12,
                 from KeyListOpsMethods.h:15,
                 from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from ../../utils/fileType/FileRecordTypeChecker.h:18,
                 from ../../utils/FileRecordTools/Records/Record.h:14,
                 from ../../utils/FileRecordTools/Records/RecordKeyVector.h:12,
                 from KeyListOpsMethods.h:15,
                 from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from ../../utils/fileType/FileRecordTypeChecker.h:18,
                 from ../../utils/FileRecordTools/Records/Record.h:14,
                 from ../../utils/FileRecordTools/Records/RecordKeyVector.h:12,
                 from KeyListOpsMethods.h:15,
                 from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from ../../utils/fileType/FileRecordTypeChecker.h:18,
                 from ../../utils/FileRecordTools/Records/Record.h:14,
                 from ../../utils/FileRecordTools/Records/RecordKeyVector.h:12,
                 from KeyListOpsMethods.h:15,
                 from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from ../../utils/fileType/FileRecordTypeChecker.h:18,
                 from ../../utils/FileRecordTools/Records/Record.h:14,
                 from ../../utils/FileRecordTools/Records/RecordKeyVector.h:12,
                 from KeyListOpsMethods.h:15,
                 from KeyListOpsMethods.cpp:8:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 * compiling BamMultiReader.cpp
/usr/include/c++/8/bits/stl_algo.h: In member function 'void KeyListOpsMethods::sortArray(bool, bool)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
- Building in src/utils/BlockedIntervals
  * compiling BlockedIntervals.cpp
 * compiling BamReader.cpp
- Building in src/utils/Fasta
  * compiling Fasta.cpp
- Building in src/utils/VectorOps
  * compiling VectorOps.cpp
 * compiling BamWriter.cpp
 * compiling SamHeader.cpp
Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSequence(std::__cxx11::string)':
Fasta.cpp:290:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
         fread(seq, sizeof(char), seqlen, file);
         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Fasta.cpp: In member function 'std::__cxx11::string FastaReference::getSubSequence(std::__cxx11::string, int, int)':
Fasta.cpp:332:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
         fread(seq, sizeof(char), (off_t) seqlen, file);
         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
                 from Fasta.h:12,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >'} changed in GCC 7.1
       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
                 from Fasta.h:12,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_map.h: In member function 'std::__cxx11::string FastaReference::sequenceNameStartingWith(std::__cxx11::string)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >'} changed in GCC 7.1
    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
- Building in src/utils/GenomeFile
  * compiling GenomeFile.cpp
In file included from /usr/include/c++/8/algorithm:62,
                 from VectorOps.h:21,
                 from VectorOps.cpp:15:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 * compiling SamProgram.cpp
In file included from /usr/include/c++/8/vector:69,
                 from Fasta.h:15,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const FastaIndexEntry&}; _Tp = FastaIndexEntry; _Alloc = std::allocator<FastaIndexEntry>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<FastaIndexEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
                 from VectorOps.h:15,
                 from VectorOps.cpp:15:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
                 from Fasta.h:18,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function '_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char>*, std::vector<std::__cxx11::basic_string<char> > >; _OIter = std::back_insert_iterator<std::vector<double> >; _UnaryOperation = double (*)(const std::__cxx11::basic_string<char>&)]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from Fasta.h:18,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/8/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
     __push_heap(_RandomAccessIterator __first,
     ^~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
     ^~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
                 from Fasta.h:18,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FastaIndexEntry, FastaIndexEntry)>]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
       std::__make_heap(__first, __middle, __comp);
       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from VectorOps.h:21,
                 from VectorOps.cpp:15:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from VectorOps.h:21,
                 from VectorOps.cpp:15:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GenomeFile.cpp: In member function 'void GenomeFile::loadGenomeFileIntoMap()':
GenomeFile.cpp:60:26: warning: variable 'c2' set but not used [-Wunused-but-set-variable]
                     long c2;
                          ^~
 * compiling SamProgramChain.cpp
/usr/include/c++/8/bits/stl_algo.h: In member function 'double VectorOps::GetMedian()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from VectorOps.h:21,
                 from VectorOps.cpp:15:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
                 from Fasta.h:12,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_map.h: In function 'std::ostream& operator<<(std::ostream&, FastaIndex&)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, FastaIndexEntry> >'} changed in GCC 7.1
    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
                 from Fasta.h:15,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from Fasta.h:18,
                 from Fasta.cpp:9:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastaIndexEntry*, std::vector<FastaIndexEntry> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from VectorOps.h:21,
                 from VectorOps.cpp:15:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::less<double> >]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from VectorOps.h:21,
                 from VectorOps.cpp:15:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from VectorOps.h:21,
                 from VectorOps.cpp:15:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<std::greater<double> >]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'std::__cxx11::string VectorOps::GetDistinctSortNum(bool)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
  * compiling split.cpp
 * compiling SamReadGroup.cpp
  * compiling NewGenomeFile.cpp
- Building in src/utils/RecordOutputMgr
- Building in src/utils/ToolBase
  * compiling RecordOutputMgr.cpp
  * compiling ToolBase.cpp
 * compiling SamReadGroupDictionary.cpp
 * compiling SamSequence.cpp
 * compiling SamSequenceDictionary.cpp
- Building in src/utils/driver
- Building in src/annotateBed
  * compiling BedtoolsDriver.cpp
  * compiling annotateMain.cpp
  * compiling annotateBed.cpp
annotateMain.cpp: In function 'int annotate_main(int, char**)':
annotateMain.cpp:39:10: warning: variable 'haveTitles' set but not used [-Wunused-but-set-variable]
     bool haveTitles     = false;
          ^~~~~~~~~~
 * compiling BamHeader_p.cpp
 * compiling BamMultiReader_p.cpp
- Building in src/bamToBed
  * compiling bamToBed.cpp
 * compiling BamRandomAccessController_p.cpp
- Building in src/bamToFastq
  * compiling bamToFastqMain.cpp
bamToBed.cpp: In function 'int bamtobed_main(int, char**)':
bamToBed.cpp:88:10: warning: variable 'useAlignmentScore' set but not used [-Wunused-but-set-variable]
     bool useAlignmentScore = false;
          ^~~~~~~~~~~~~~~~~
bamToFastqMain.cpp: In function 'int bamtofastq_main(int, char**)':
bamToFastqMain.cpp:38:10: warning: variable 'haveFastq2' set but not used [-Wunused-but-set-variable]
     bool haveFastq2    = false;
          ^~~~~~~~~~
  * compiling bamToFastq.cpp
 * compiling BamReader_p.cpp
- Building in src/bedToBam
  * compiling bedToBam.cpp
 * compiling BamWriter_p.cpp
- Building in src/bedpeToBam
  * compiling bedpeToBam.cpp
 * compiling BamIndexFactory_p.cpp
bedToBam.cpp: In function 'int bedtobam_main(int, char**)':
bedToBam.cpp:60:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
     bool haveMapQual     = false;
          ^~~~~~~~~~~
bedpeToBam.cpp: In function 'int bedpetobam_main(int, char**)':
bedpeToBam.cpp:61:10: warning: variable 'haveMapQual' set but not used [-Wunused-but-set-variable]
     bool haveMapQual     = false;
          ^~~~~~~~~~~
 * compiling BamStandardIndex_p.cpp
 * compiling BamToolsIndex_p.cpp
- Building in src/bedToIgv
  * compiling bedToIgv.cpp
In file included from /usr/include/c++/8/vector:69,
                 from src/api/BamAux.h:18,
                 from src/api/BamAlignment.h:14,
                 from src/api/internal/index/BamToolsIndex_p.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator<BamTools::Internal::BtiBlock>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<BamTools::Internal::BtiBlock>::iterator' {aka '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator<BamTools::Internal::BtiReferenceSummary>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<BamTools::Internal::BtiReferenceSummary>::iterator' {aka '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiReferenceSummary*, std::vector<BamTools::Internal::BtiReferenceSummary> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiReferenceSummary*, std::vector<BamTools::Internal::BtiReferenceSummary> >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
                 from src/api/BamAux.h:18,
                 from src/api/BamAlignment.h:14,
                 from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator<BamTools::Internal::BaiAlignmentChunk>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<BamTools::Internal::BaiAlignmentChunk>::iterator' {aka '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from src/api/BamAux.h:18,
                 from src/api/BamAlignment.h:14,
                 from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from src/api/BamAux.h:18,
                 from src/api/BamAlignment.h:14,
                 from src/api/internal/index/BamToolsIndex_p.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BaiAlignmentChunk*, std::vector<BamTools::Internal::BaiAlignmentChunk> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
                 from src/api/BamAux.h:18,
                 from src/api/BamAlignment.h:14,
                 from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from src/api/BamAux.h:18,
                 from src/api/BamAlignment.h:14,
                 from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ^~~~~~~~~~~~~~
src/api/internal/index/BamStandardIndex_p.cpp:761:1: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
 }
 ^
In file included from /usr/include/c++/8/vector:69,
                 from src/api/BamAux.h:18,
                 from src/api/BamAlignment.h:14,
                 from src/api/internal/index/BamStandardIndex_p.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
- Building in src/bed12ToBed6
  * compiling bed12ToBed6.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual bool BamTools::Internal::BamToolsIndex::Create()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BamTools::Internal::BtiBlock*, std::vector<BamTools::Internal::BtiBlock> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set<short unsigned int>&, std::vector<long long int>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
 * compiling BamDeviceFactory_p.cpp
In file included from /usr/include/c++/8/algorithm:62,
                 from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
     __final_insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from src/api/internal/index/BamStandardIndex_p.cpp:21:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
    std::__final_insertion_sort(__first, __last, __comp);
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
 * compiling BamFile_p.cpp
/usr/include/c++/8/bits/stl_algo.h: In member function 'void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
    std::__final_insertion_sort(__first, __last, __comp);
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
- Building in src/closestFile
  * compiling closestHelp.cpp
  * compiling closestFile.cpp
- Building in src/clusterBed
  * compiling clusterMain.cpp
  * compiling clusterBed.cpp
clusterMain.cpp: In function 'int cluster_main(int, char**)':
clusterMain.cpp:38:10: warning: variable 'haveMaxDistance' set but not used [-Wunused-but-set-variable]
     bool haveMaxDistance = false;
          ^~~~~~~~~~~~~~~
 * compiling BamFtp_p.cpp
 * compiling BamHttp_p.cpp
- Building in src/complementFile
  * compiling complementHelp.cpp
  * compiling complementFile.cpp
- Building in src/coverageFile
  * compiling coverageHelp.cpp
  * compiling coverageFile.cpp
 * compiling BamPipe_p.cpp
- Building in src/expand
  * compiling expand.cpp
 * compiling BgzfStream_p.cpp
 * compiling ByteArray_p.cpp
- Building in src/fastaFromBed
  * compiling fastaFromBedMain.cpp
  * compiling fastaFromBed.cpp
- Building in src/flankBed
  * compiling flankBedMain.cpp
 * compiling HostAddress_p.cpp
 * compiling HostInfo_p.cpp
src/api/internal/io/HostAddress_p.cpp: In member function 'bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const':
src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
             return m_ip4Address < m_ip4Address;
                    ~~~~~~~~~~~~~^~~~~~~~~~~~~~
src/api/internal/io/HostAddress_p.cpp: In member function 'void BamTools::Internal::HostAddress::Clear()':
src/api/internal/io/HostAddress_p.cpp:283:49: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct BamTools::Internal::IPv6Address'; use assignment or value-initialization instead [-Wclass-memaccess]
     memset(&m_ip6Address, 0, sizeof(IPv6Address));
                                                 ^
In file included from src/api/internal/io/HostAddress_p.cpp:10:
src/api/internal/io/HostAddress_p.h:30:8: note: 'struct BamTools::Internal::IPv6Address' declared here
 struct IPv6Address {
        ^~~~~~~~~~~
src/api/internal/io/HostAddress_p.cpp: In member function 'std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const':
src/api/internal/io/HostAddress_p.cpp:325:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
             if ( i != 0 )
             ^~
src/api/internal/io/HostAddress_p.cpp:327:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
                 ss << hex << ( (uint16_t(m_ip6Address[2*i]) << 8) |
                 ^~
- Building in src/genomeCoverageBed
  * compiling genomeCoverageMain.cpp
 * compiling HttpHeader_p.cpp
 * compiling ILocalIODevice_p.cpp
  * compiling flankBed.cpp
 * compiling RollingBuffer_p.cpp
 * compiling TcpSocketEngine_p.cpp
 * compiling TcpSocketEngine_unix_p.cpp
  * compiling genomeCoverageBed.cpp
- Building in src/getOverlap
  * compiling getOverlap.cpp
 * compiling TcpSocket_p.cpp
 * compiling SamFormatParser_p.cpp
genomeCoverageBed.cpp: In member function 'void BedGenomeCoverage::CoverageBam(std::__cxx11::string)':
genomeCoverageBed.cpp:322:23: warning: comparison of integer expressions of different signedness: 'CHRPOS' {aka 'unsigned int'} and 'int' [-Wsign-compare]
                 if(end<_fragmentSize) { //sometimes fragmentSize is bigger :(
                    ~~~^~~~~~~~~~~~~~
getOverlap.cpp: In function 'int getoverlap_main(int, char**)':
getOverlap.cpp:44:10: warning: variable 'haveColumns' set but not used [-Wunused-but-set-variable]
     bool haveColumns = false;
          ^~~~~~~~~~~
 * compiling SamFormatPrinter_p.cpp
- Building in src/groupBy
  * compiling groupBy.cpp
  * compiling groupByHelp.cpp
- Building in src/intersectFile
  * compiling intersectHelp.cpp
  * compiling intersectFile.cpp
- Building in src/fisher
  * compiling fisherHelp.cpp
- Building in src/jaccard
  * compiling jaccardHelp.cpp
 * compiling SamHeaderValidator_p.cpp
  * compiling fisher.cpp
  * compiling jaccard.cpp
- Building in src/linksBed
  * compiling linksMain.cpp
- Building in src/maskFastaFromBed
  * compiling maskFastaFromBedMain.cpp
 * compiling BamException_p.cpp
  * compiling kfunc.cpp
  * compiling linksBed.cpp
  * compiling maskFastaFromBed.cpp
 * linking lib/libbamtools.a
ar cr lib/libbamtools.a src/api/BamAlignment.o src/api/BamMultiReader.o src/api/BamReader.o src/api/BamWriter.o src/api/SamHeader.o src/api/SamProgram.o src/api/SamProgramChain.o src/api/SamReadGroup.o src/api/SamReadGroupDictionary.o src/api/SamSequence.o src/api/SamSequenceDictionary.o src/api/internal/bam/BamHeader_p.o src/api/internal/bam/BamMultiReader_p.o src/api/internal/bam/BamRandomAccessController_p.o src/api/internal/bam/BamReader_p.o src/api/internal/bam/BamWriter_p.o src/api/internal/index/BamIndexFactory_p.o src/api/internal/index/BamStandardIndex_p.o src/api/internal/index/BamToolsIndex_p.o src/api/internal/io/BamDeviceFactory_p.o src/api/internal/io/BamFile_p.o src/api/internal/io/BamFtp_p.o src/api/internal/io/BamHttp_p.o src/api/internal/io/BamPipe_p.o src/api/internal/io/BgzfStream_p.o src/api/internal/io/ByteArray_p.o src/api/internal/io/HostAddress_p.o src/api/internal/io/HostInfo_p.o src/api/internal/io/HttpHeader_p.o src/api/internal/io/ILocalIODevice_p.o src/api/internal/io/RollingBuffer_p.o src/api/internal/io/TcpSocketEngine_p.o src/api/internal/io/TcpSocketEngine_unix_p.o src/api/internal/io/TcpSocket_p.o src/api/internal/sam/SamFormatParser_p.o src/api/internal/sam/SamFormatPrinter_p.o src/api/internal/sam/SamHeaderValidator_p.o src/api/internal/utils/BamException_p.o
ranlib lib/libbamtools.a
- Building in src/mapFile
  * compiling mapHelp.cpp
- Building in src/mergeFile
  * compiling mergeHelp.cpp
  * compiling mapFile.cpp
  * compiling mergeFile.cpp
- Building in src/multiBamCov
  * compiling multiBamCovMain.cpp
- Building in src/multiIntersectBed
  * compiling multiIntersectBedMain.cpp
multiBamCovMain.cpp: In function 'int multibamcov_main(int, char**)':
multiBamCovMain.cpp:38:10: warning: variable 'haveBed' set but not used [-Wunused-but-set-variable]
     bool haveBed           = false;
          ^~~~~~~
multiBamCovMain.cpp:39:10: warning: variable 'haveBams' set but not used [-Wunused-but-set-variable]
     bool haveBams          = false;
          ^~~~~~~~
multiBamCovMain.cpp:47:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
     bool haveFraction       = false;
          ^~~~~~~~~~~~
  * compiling multiIntersectBed.cpp
- Building in src/nucBed
  * compiling nucBedMain.cpp
multiIntersectBedMain.cpp: In function 'int multiintersect_main(int, char**)':
multiIntersectBedMain.cpp:45:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
     bool haveFiles         = false;
          ^~~~~~~~~
multiIntersectBedMain.cpp:47:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
     bool haveGenome        = false;
          ^~~~~~~~~~
multiIntersectBedMain.cpp:48:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
     bool haveFiller        = true;
          ^~~~~~~~~~
  * compiling multiBamCov.cpp
  * compiling nucBed.cpp
- Building in src/pairToBed
  * compiling pairToBedMain.cpp
pairToBedMain.cpp: In function 'int pairtobed_main(int, char**)':
pairToBedMain.cpp:43:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
     bool haveFraction       = false;
          ^~~~~~~~~~~~
- Building in src/pairToPair
  * compiling pairToPairMain.cpp
- Building in src/randomBed
  * compiling randomBedMain.cpp
  * compiling pairToPair.cpp
  * compiling pairToBed.cpp
pairToPairMain.cpp: In function 'int pairtopair_main(int, char**)':
pairToPairMain.cpp:44:10: warning: variable 'haveFraction' set but not used [-Wunused-but-set-variable]
     bool haveFraction = false;
          ^~~~~~~~~~~~
pairToPair.cpp: In member function 'void PairToPair::FindOverlaps(const BEDPE&)':
pairToPair.cpp:112:14: warning: variable 'found1' set but not used [-Wunused-but-set-variable]
         bool found1 = false;
              ^~~~~~
pairToPair.cpp:113:14: warning: variable 'found2' set but not used [-Wunused-but-set-variable]
         bool found2 = false;
              ^~~~~~
  * compiling randomBed.cpp
- Building in src/regressTest
compiling RegressTest.cpp
pairToBed.cpp: In member function 'void BedIntersectPE::FindSpanningOverlaps(const BEDPE&, std::vector<BED>&, const string&)':
pairToBed.cpp:257:12: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
     CHRPOS spanLength = 0;
            ^~~~~~~~~~
pairToBed.cpp: In member function 'bool BedIntersectPE::FindOneOrMoreSpanningOverlaps(const BEDPE&, const string&)':
pairToBed.cpp:310:9: warning: variable 'spanLength' set but not used [-Wunused-but-set-variable]
     int spanLength = 0;
         ^~~~~~~~~~
- Building in src/reldist
  * compiling reldistMain.cpp
RegressTest.cpp: In member function 'bool RegressTest::executeAndCompareCorrectness(const fileListType&)':
RegressTest.cpp:431:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
  system(diffCmd.c_str());
  ~~~~~~^~~~~~~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::startMemoryProfile(bool)':
RegressTest.cpp:573:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
  fgets(sLine, 4192, fp);
  ~~~~~^~~~~~~~~~~~~~~~~
RegressTest.cpp: In member function 'bool RegressTest::calcMemoryStats()':
RegressTest.cpp:622:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(sLine, 4192, fp);
   ~~~~~^~~~~~~~~~~~~~~~~
- Building in src/sampleFile
  * compiling sampleHelp.cpp
  * compiling reldist.cpp
  * compiling sampleFile.cpp
reldist.cpp: In member function 'void RelativeDistance::ReportDistanceSummary()':
reldist.cpp:69:16: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'unsigned int' [-Wformat=]
         printf("%.2f\t%lu\t%lu\t%.3f\n",
                ^~~~~~~~~~~~~~~~~~~~~~~~
reldist.cpp:71:16:
                freqItr->second,
                ~~~~~~~~~~~~~~~
reldist.cpp:69:16: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
compiling regressTestMain.cpp
- Building in src/shiftBed
  * compiling shiftBedMain.cpp
- Building in src/shuffleBed
  * compiling shuffleBedMain.cpp
  * compiling shuffleBed.cpp
- Building in src/slopBed
  * compiling slopBedMain.cpp
  * compiling shiftBed.cpp
  * compiling slopBed.cpp
- Building in src/sortBed
  * compiling sortMain.cpp
slopBed.cpp: In member function 'void BedSlop::AddSlop(BED&)':
slopBed.cpp:85:47: warning: comparison of integer expressions of different signedness: 'long int' and 'CHRPOS' {aka 'unsigned int'} [-Wsign-compare]
         if ( ((int)bed.end + (long)_leftSlop) <= chromSize ) {
              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
slopBed.cpp:107:48: warning: comparison of integer expressions of different signedness: 'long int' and 'CHRPOS' {aka 'unsigned int'} [-Wsign-compare]
         if ( ((int)bed.end + (long)_rightSlop) <= chromSize )
              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
- Building in src/spacingFile
  * compiling spacingHelp.cpp
  * compiling sortBed.cpp
- Building in src/split
  * compiling splitBed.cpp
  * compiling splitBedMain.cpp
  * compiling spacingFile.cpp
- Building in src/subtractFile
  * compiling subtractHelp.cpp
  * compiling subtractFile.cpp
- Building in src/tagBam
  * compiling tagBamMain.cpp
- Building in src/unionBedGraphs
  * compiling unionBedGraphsMain.cpp
  * compiling tagBam.cpp
unionBedGraphsMain.cpp: In function 'int unionbedgraphs_main(int, char**)':
unionBedGraphsMain.cpp:46:10: warning: variable 'haveFiles' set but not used [-Wunused-but-set-variable]
     bool haveFiles         = false;
          ^~~~~~~~~
unionBedGraphsMain.cpp:48:10: warning: variable 'haveGenome' set but not used [-Wunused-but-set-variable]
     bool haveGenome        = false;
          ^~~~~~~~~~
unionBedGraphsMain.cpp:49:10: warning: variable 'haveFiller' set but not used [-Wunused-but-set-variable]
     bool haveFiller        = true;
          ^~~~~~~~~~
  * compiling unionBedGraphs.cpp
- Building in src/windowBed
  * compiling windowMain.cpp
- Building in src/windowMaker
  * compiling windowMakerMain.cpp
  * compiling windowMaker.cpp
  * compiling windowBed.cpp
- Building main bedtools binary.
done.
- Creating executables for old CLI.
DEPRECATION WARNING: python2 invoked with /usr/bin/python.
    Use /usr/bin/python3 or /usr/bin/python2
    /usr/bin/python will be removed or switched to Python 3 in the future.
    If you cannot make the switch now, please follow instructions at https://fedoraproject.org/wiki/Changes/Avoid_usr_bin_python_in_RPM_Build#Quick_Opt-Out
done.
+ cd docs
+ make clean html
rm -rf _build/*
sphinx-build -b html -d _build/doctrees   . _build/html
Running Sphinx v1.6.6
making output directory...
WARNING: sphinx.ext.pngmath has been deprecated. Please use sphinx.ext.imgmath instead.
loading pickled environment... not yet created
loading intersphinx inventory from http://bedtools.readthedocs.org/en/latest/objects.inv...
WARNING: intersphinx inventory 'http://bedtools.readthedocs.org/en/latest/objects.inv' not fetchable due to <class 'requests.exceptions.ConnectionError'>: HTTPConnectionPool(host='bedtools.readthedocs.org', port=80): Max retries exceeded with url: /en/latest/objects.inv (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0xb5154d90>: Failed to establish a new connection: [Errno -2] Name or service not known',))
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 52 source files that are out of date
updating environment: 52 added, 0 changed, 0 removed
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reading sources... [  3%] content/bedtools-suite
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reading sources... [100%] index
/builddir/build/BUILD/bedtools2/docs/content/history.rst:107: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/history.rst:110: WARNING: Block quote ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/history.rst:112: WARNING: Enumerated list ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/history.rst:115: WARNING: Block quote ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/related-tools.rst:3: WARNING: Duplicate explicit target name: "here".
/builddir/build/BUILD/bedtools2/docs/content/tools/closest.rst:355: WARNING: Content block expected for the "note" directive; none found.
/builddir/build/BUILD/bedtools2/docs/content/tools/cluster.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/tools/intersect.rst:67: WARNING: Block quote ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/tools/merge.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent.
looking for now-outdated files... /builddir/build/BUILD/bedtools2/docs/content/tools/merge.rst:238: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/tools/merge.rst:244: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/tools/merge.rst:250: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/tools/pairtopair.rst:30: WARNING: Block quote ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/tools/random.rst:11: WARNING: Explicit markup ends without a blank line; unexpected unindent.
/builddir/build/BUILD/bedtools2/docs/content/tools/shift.rst:: WARNING: image file not readable: content/tools/../images/tool-glyphs/shift-glyph.png
none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  1%] content/advanced-usage
writing output... [  3%] content/bedtools-suite
writing output... [  5%] content/example-usage
writing output... [  7%] content/faq
writing output... [  9%] content/general-usage
writing output... [ 11%] content/history
writing output... [ 13%] content/installation
writing output... [ 15%] content/overview
writing output... [ 17%] content/quick-start
writing output... [ 19%] content/related-tools
writing output... [ 21%] content/tips-and-tricks
writing output... [ 23%] content/tools/annotate
writing output... [ 25%] content/tools/bamtobed
writing output... [ 26%] content/tools/bamtofastq
writing output... [ 28%] content/tools/bed12tobed6
writing output... [ 30%] content/tools/bedpetobam
writing output... [ 32%] content/tools/bedtobam
writing output... [ 34%] content/tools/closest
writing output... [ 36%] content/tools/cluster
writing output... [ 38%] content/tools/complement
writing output... [ 40%] content/tools/coverage
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writing output... [ 65%] content/tools/maskfasta
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writing output... [ 69%] content/tools/multicov
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writing output... [ 76%] content/tools/pairtobed
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writing output... [100%] index
/builddir/build/BUILD/bedtools2/docs/content/faq.rst:18: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/builddir/build/BUILD/bedtools2/docs/content/faq.rst:67: WARNING: Could not lex literal_block as "bash". Highlighting skipped.
/builddir/build/BUILD/bedtools2/docs/content/related-tools.rst:79: WARNING: undefined label: bedtools:map (if the link has no caption the label must precede a section header)
generating indices... genindex
writing additional pages... search
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copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 20 warnings.
Build finished. The HTML pages are in _build/html.
+ cd ..
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.DYwLou
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm
++ dirname /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm
+ cd bedtools2
+ rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm
+ mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/bin
+ install -m 0755 bin/annotateBed bin/bamToBed bin/bamToFastq bin/bed12ToBed6 bin/bedToBam bin/bedToIgv bin/bedpeToBam bin/bedtools bin/closestBed bin/clusterBed bin/complementBed bin/coverageBed bin/expandCols bin/fastaFromBed bin/flankBed bin/genomeCoverageBed bin/getOverlap bin/groupBy bin/intersectBed bin/linksBed bin/mapBed bin/maskFastaFromBed bin/mergeBed bin/multiBamCov bin/multiIntersectBed bin/nucBed bin/pairToBed bin/pairToPair bin/randomBed bin/shiftBed bin/shuffleBed bin/slopBed bin/sortBed bin/subtractBed bin/tagBam bin/unionBedGraphs bin/windowBed bin/windowMaker /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/bin
+ mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/BEDTools
+ cp -a genomes/ /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/BEDTools
+ cp -a data/ /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/BEDTools
+ find /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/BEDTools -type f -exec chmod 0644 '{}' ';'
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 2.26.0-7.fc28 --unique-debug-suffix -2.26.0-7.fc28.arm --unique-debug-src-base BEDTools-2.26.0-7.fc28.arm --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bedtools2
extracting debug info from /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/bin/bedtools
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
3641 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
/sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs '' ''
Processing files: BEDTools-2.26.0-7.fc28.armv7hl
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.d0hnIs
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2
+ DOCDIR=/builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/doc/BEDTools
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/doc/BEDTools
+ cp -pr README.md /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/doc/BEDTools
+ cp -pr RELEASE_HISTORY /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/doc/BEDTools
+ cp -pr LICENSE /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/doc/BEDTools
+ cp -pr docs/_build/html/ /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm/usr/share/doc/BEDTools
+ exit 0
Provides: BEDTools = 2.26.0-7.fc28 BEDTools(armv7hl-32) = 2.26.0-7.fc28
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /bin/sh ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libc.so.6 libc.so.6(GLIBC_2.15) libc.so.6(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libm.so.6 libm.so.6(GLIBC_2.23) libm.so.6(GLIBC_2.4) libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.8) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(CXXABI_ARM_1.3.3) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.9) libz.so.1 rtld(GNU_HASH)
Processing files: BEDTools-debugsource-2.26.0-7.fc28.armv7hl
Provides: BEDTools-debugsource = 2.26.0-7.fc28 BEDTools-debugsource(armv7hl-32) = 2.26.0-7.fc28
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: BEDTools-debuginfo-2.26.0-7.fc28.armv7hl
Provides: BEDTools-debuginfo = 2.26.0-7.fc28 BEDTools-debuginfo(armv7hl-32) = 2.26.0-7.fc28 debuginfo(build-id) = e3e583006c770ef5c5792c742174ef9e0a807848
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: BEDTools-debugsource(armv7hl-32) = 2.26.0-7.fc28
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm
Wrote: /builddir/build/RPMS/BEDTools-2.26.0-7.fc28.armv7hl.rpm
Wrote: /builddir/build/RPMS/BEDTools-debugsource-2.26.0-7.fc28.armv7hl.rpm
Wrote: /builddir/build/RPMS/BEDTools-debuginfo-2.26.0-7.fc28.armv7hl.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.i2nwQv
+ umask 022
+ cd /builddir/build/BUILD
+ cd bedtools2
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/BEDTools-2.26.0-7.fc28.arm
+ exit 0
Child return code was: 0