Wham installation fails

I tried to install Whamg on Ubuntu 18.04, I have installed OpenMP and CMake, but when I run
git clone --recursive  https://github.com/zeeev/wham.git; cd wham; make

I got:
enrico@godzilla:/media/mothra/enrico/whamg$ git clone --recursive  https://github.com/zeeev/wham.git; cd wham; make
Cloning into 'wham'...
remote: Enumerating objects: 2958, done.
remote: Total 2958 (delta 0), reused 0 (delta 0), pack-reused 2958
Receiving objects: 100% (2958/2958), 95.44 MiB | 11.17 MiB/s, done.
Resolving deltas: 100% (1922/1922), done.
Submodule 'src/Complete-Striped-Smith-Waterman-Library' (https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.git) registered for path 'src/Complete-Striped-Smith-Waterman-Library'
Submodule 'src/bamtools' (https://github.com/pezmaster31/bamtools.git) registered for path 'src/bamtools'
Submodule 'src/fastahack' (https://github.com/ekg/fastahack.git) registered for path 'src/fastahack'
Submodule 'src/seqan' (https://github.com/seqan/seqan.git) registered for path 'src/seqan'
Cloning into '/media/mothra/enrico/whamg/wham/src/Complete-Striped-Smith-Waterman-Library'...
remote: Enumerating objects: 9, done.
remote: Counting objects: 100% (9/9), done.
remote: Compressing objects: 100% (7/7), done.
remote: Total 1579 (delta 2), reused 8 (delta 2), pack-reused 1570
Receiving objects: 100% (1579/1579), 12.18 MiB | 11.11 MiB/s, done.
Resolving deltas: 100% (980/980), done.
Cloning into '/media/mothra/enrico/whamg/wham/src/bamtools'...
remote: Enumerating objects: 291, done.
remote: Counting objects: 100% (291/291), done.
remote: Compressing objects: 100% (193/193), done.
remote: Total 5148 (delta 176), reused 160 (delta 94), pack-reused 4857
Receiving objects: 100% (5148/5148), 6.28 MiB | 10.84 MiB/s, done.
Resolving deltas: 100% (3549/3549), done.
Cloning into '/media/mothra/enrico/whamg/wham/src/fastahack'...
remote: Enumerating objects: 227, done.
remote: Total 227 (delta 0), reused 0 (delta 0), pack-reused 227
Receiving objects: 100% (227/227), 51.19 KiB | 6.40 MiB/s, done.
Resolving deltas: 100% (128/128), done.
Cloning into '/media/mothra/enrico/whamg/wham/src/seqan'...
remote: Enumerating objects: 82092, done.
remote: Total 82092 (delta 0), reused 0 (delta 0), pack-reused 82092
Receiving objects: 100% (82092/82092), 148.96 MiB | 11.06 MiB/s, done.
Resolving deltas: 100% (60918/60918), done.
Submodule path 'src/Complete-Striped-Smith-Waterman-Library': checked out '8c9933a1685e0ab50c7d8b7926c9068bc0c9d7d2'
Submodule path 'src/bamtools': checked out '2d7685d2aeedd11c46ad3bd67886d9ed65c30f3e'
Submodule path 'src/fastahack': checked out '0a8ca3de9239b061839418b306bb6a9072990158'
Submodule path 'src/seqan': checked out '7f3ca44fbe777f3b637ff57ccc1dcd975cca1661'
mkdir bin
cd src/bamtools && mkdir -p build && cd build && cmake .. && make
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /media/mothra/enrico/whamg/wham/src/bamtools/build
make[1]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[2]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target SharedHeaders
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[  0%] Built target SharedHeaders
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target BamTools-static
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[  1%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o
[  2%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o
[  3%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o
[  4%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o
[  5%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o
[  6%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o
[  7%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
[  8%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
[  9%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
[ 10%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
[ 11%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
[ 12%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o
[ 12%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
[ 13%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 14%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
[ 15%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
[ 16%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
[ 17%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
          ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 18%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o
[ 19%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 20%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
[ 21%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
[ 22%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
[ 23%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o
[ 24%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o
[ 25%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o
[ 26%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
             return m_ip4Address < m_ip4Address;
                    ~~~~~~~~~~~~~^~~~~~~~~~~~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
             if ( i != 0 )
             ^~
/media/mothra/enrico/whamg/wham/src/bamtools/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) |
                 ^~
[ 27%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
[ 28%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
[ 29%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
[ 30%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
[ 31%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
[ 32%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
[ 33%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
[ 34%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
[ 35%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 36%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 37%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
[ 38%] Linking CXX static library ../../../lib/libbamtools.a
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 38%] Built target BamTools-static
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target BamTools
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
[ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
[ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o
[ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o
[ 42%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
[ 43%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o
[ 44%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
[ 45%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
[ 46%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o
[ 47%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
[ 48%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
[ 49%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
[ 50%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
[ 51%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o
[ 52%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o
[ 53%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o
[ 54%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o
[ 55%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )
          ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 56%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o
[ 57%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o
[ 58%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o
[ 59%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o
[ 60%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
[ 61%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o
[ 62%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o
[ 63%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o
[ 64%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]
             return m_ip4Address < m_ip4Address;
                    ~~~~~~~~~~~~~^~~~~~~~~~~~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
             if ( i != 0 )
             ^~
/media/mothra/enrico/whamg/wham/src/bamtools/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) |
                 ^~
[ 65%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o
[ 66%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o
[ 67%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o
[ 68%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o
[ 69%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o
[ 70%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o
[ 71%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
[ 72%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
[ 73%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
[ 74%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
[ 75%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
[ 76%] Linking CXX shared library ../../../lib/libbamtools.so
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 76%] Built target BamTools
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target APIHeaders
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 76%] Built target APIHeaders
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target AlgorithmsHeaders
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 76%] Built target AlgorithmsHeaders
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target jsoncpp
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 77%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o
[ 78%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o
[ 79%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o
[ 80%] Linking CXX static library ../../../../lib/libjsoncpp.a
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 80%] Built target jsoncpp
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target BamTools-utils
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
[ 82%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
[ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
[ 85%] Linking CXX static library ../../../lib/libbamtools-utils.a
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 85%] Built target BamTools-utils
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Scanning dependencies of target bamtools_cmd
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
[ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
[ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
[ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
[ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
[ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::ReadNamesFileReader::Read(std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:415:74: error: no matching function for call to ‘make_pair<std::__cxx11::string, bool>(__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type&, bool)’
         resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ;
                                                                          ^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/string:40,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
     make_pair(_T1&& __x, _T2&& __y)
     ^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:415:74: note:   cannot convert ‘fields.std::vector<std::__cxx11::basic_string<char> >::operator[](1)’ (type ‘__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type {aka std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’
         resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ;
                                                                          ^
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::StatsFileReader::ParseReadGroupLine(const string&, std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:612:75: error: no matching function for call to ‘make_pair<std::__cxx11::string, ReadGroupResolver>(const string&, ReadGroupResolver&)’
     readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) );
                                                                           ^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/string:40,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
     make_pair(_T1&& __x, _T2&& __y)
     ^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:612:61: note:   cannot convert ‘name’ (type ‘const string {aka const std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’
     readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) );
                                                             ^~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::ResolveToolPrivate::MakeStats()’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1019:93: error: no matching function for call to ‘make_pair<std::__cxx11::string, bool>(std::__cxx11::string&, const bool&)’
         else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) );
                                                                                ^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/string:40,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
     make_pair(_T1&& __x, _T2&& __y)
     ^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1019:68: note:   cannot convert ‘al.BamTools::BamAlignment::Name’ (type ‘std::__cxx11::string {aka std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’
         else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) );
                                                                 ~~~^~~~
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘void BamTools::ResolveTool::ResolveToolPrivate::ParseHeader(const BamTools::SamHeader&)’:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1051:93: error: no matching function for call to ‘make_pair<std::__cxx11::string, ReadGroupResolver>(const string&, ReadGroupResolver)’
         m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) );
                                                                                ^
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/string:40,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,
                 from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
     make_pair(_T1&& __x, _T2&& __y)
     ^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed:
/media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1051:70: note:   cannot convert ‘rg.BamTools::SamReadGroup::ID’ (type ‘const string {aka const std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’
         m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) );
                                                                   ~~~^~
src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:254: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o' failed
make[3]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o] Error 1
make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
CMakeFiles/Makefile2:520: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/all' failed
make[2]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/all] Error 2
make[2]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Makefile:129: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build'
Makefile:26: recipe for target 'src/bamtools/lib/libbamtools.a' failed
make: *** [src/bamtools/lib/libbamtools.a] Error 2

Thank you in advance for any help!

I was in the same situation. I tried sudo make and installed it successfully.

still not working:
git clone --recursive  https://github.com/zeeev/wham.git; cd wham; sudo make; Cloning into 'wham'... remote: Enumerating objects: 2958, done. remote: Total 2958 (delta 0), reused 0 (delta 0), pack-reused 2958 Receiving objects: 100% (2958/2958), 95.44 MiB | 11.16 MiB/s, done. Resolving deltas: 100% (1922/1922), done. Submodule 'src/Complete-Striped-Smith-Waterman-Library' (https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.git) registered for path 'src/Complete-Striped-Smith-Waterman-Library' Submodule 'src/bamtools' (https://github.com/pezmaster31/bamtools.git) registered for path 'src/bamtools' Submodule 'src/fastahack' (https://github.com/ekg/fastahack.git) registered for path 'src/fastahack' Submodule 'src/seqan' (https://github.com/seqan/seqan.git) registered for path 'src/seqan' Cloning into '/media/mothra/enrico/whamg/wham/src/Complete-Striped-Smith-Waterman-Library'... remote: Enumerating objects: 9, done.         remote: Counting objects: 100% (9/9), done.         remote: Compressing objects: 100% (7/7), done.         remote: Total 1579 (delta 2), reused 8 (delta 2), pack-reused 1570         Receiving objects: 100% (1579/1579), 12.18 MiB | 11.02 MiB/s, done. Resolving deltas: 100% (980/980), done. Cloning into '/media/mothra/enrico/whamg/wham/src/bamtools'... remote: Enumerating objects: 291, done.         remote: Counting objects: 100% (291/291), done.         remote: Compressing objects: 100% (193/193), done.         remote: Total 5148 (delta 176), reused 160 (delta 94), pack-reused 4857         Receiving objects: 100% (5148/5148), 6.28 MiB | 10.47 MiB/s, done. Resolving deltas: 100% (3549/3549), done. Cloning into '/media/mothra/enrico/whamg/wham/src/fastahack'... remote: Enumerating objects: 227, done.         remote: Total 227 (delta 0), reused 0 (delta 0), pack-reused 227         Receiving objects: 100% (227/227), 51.19 KiB | 4.65 MiB/s, done. Resolving deltas: 100% (128/128), done. Cloning into '/media/mothra/enrico/whamg/wham/src/seqan'... remote: Enumerating objects: 82092, done.         remote: Total 82092 (delta 0), reused 0 (delta 0), pack-reused 82092         Receiving objects: 100% (82092/82092), 148.96 MiB | 11.03 MiB/s, done. Resolving deltas: 100% (60918/60918), done. Submodule path 'src/Complete-Striped-Smith-Waterman-Library': checked out '8c9933a1685e0ab50c7d8b7926c9068bc0c9d7d2' Submodule path 'src/bamtools': checked out '2d7685d2aeedd11c46ad3bd67886d9ed65c30f3e' Submodule path 'src/fastahack': checked out '0a8ca3de9239b061839418b306bb6a9072990158' Submodule path 'src/seqan': checked out '7f3ca44fbe777f3b637ff57ccc1dcd975cca1661' [sudo] password for enrico:  mkdir bin cd src/bamtools && mkdir -p build && cd build && cmake .. && make -- The C compiler identification is GNU 7.5.0 -- The CXX compiler identification is GNU 7.5.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /media/mothra/enrico/whamg/wham/src/bamtools/build make[1]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[2]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target SharedHeaders make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [  0%] Built target SharedHeaders make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target BamTools-static make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [  1%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o [  2%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o [  3%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o [  4%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o [  5%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o [  6%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o [  7%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o [  8%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o [  9%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o [ 10%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o [ 11%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o [ 12%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o [ 12%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o [ 13%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 14%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o [ 15%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o [ 16%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o [ 17%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]      if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )           ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o [ 19%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o [ 20%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o [ 21%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o [ 22%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]      if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]      if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 23%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o [ 24%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o [ 25%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o [ 26%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]              return m_ip4Address < m_ip4Address;                     ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]              if ( i != 0 )              ^~ /media/mothra/enrico/whamg/wham/src/bamtools/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) |                  ^~ [ 27%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o [ 28%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o [ 29%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o [ 30%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o [ 31%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o [ 32%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o [ 33%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o [ 34%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o [ 35%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 36%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 37%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o [ 38%] Linking CXX static library ../../../lib/libbamtools.a make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 38%] Built target BamTools-static make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target BamTools make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o [ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o [ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o [ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o [ 42%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o [ 43%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o [ 44%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o [ 45%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o [ 46%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o [ 47%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o [ 48%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o [ 49%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o [ 50%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o [ 51%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 52%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o [ 53%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o [ 54%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o [ 55%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]      if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof(uint64_t)) )           ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o [ 57%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o [ 58%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o [ 59%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o [ 60%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]      if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]      if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) {           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ [ 61%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o [ 62%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o [ 63%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o [ 64%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘bool BamTools::Internal::HostAddress::operator<(const BamTools::Internal::HostAddress&) const’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:266:33: warning: self-comparison always evaluates to false [-Wtautological-compare]              return m_ip4Address < m_ip4Address;                     ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp: In member function ‘std::__cxx11::string BamTools::Internal::HostAddress::GetIPString() const’: /media/mothra/enrico/whamg/wham/src/bamtools/src/api/internal/io/HostAddress_p.cpp:325:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]              if ( i != 0 )              ^~ /media/mothra/enrico/whamg/wham/src/bamtools/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) |                  ^~ [ 65%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o [ 66%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o [ 67%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o [ 68%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o [ 69%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o [ 70%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o [ 71%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o [ 72%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o [ 73%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 74%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 75%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o [ 76%] Linking CXX shared library ../../../lib/libbamtools.so make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 76%] Built target BamTools make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target APIHeaders make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 76%] Built target APIHeaders make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target AlgorithmsHeaders make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 76%] Built target AlgorithmsHeaders make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target jsoncpp make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 77%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o [ 78%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o [ 79%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o [ 80%] Linking CXX static library ../../../../lib/libjsoncpp.a make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 80%] Built target jsoncpp make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target BamTools-utils make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o [ 82%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o [ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o [ 85%] Linking CXX static library ../../../lib/libbamtools-utils.a make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 85%] Built target BamTools-utils make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Scanning dependencies of target bamtools_cmd make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' make[3]: Entering directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' [ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o [ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o [ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o [ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o [ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o [ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::ReadNamesFileReader::Read(std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:415:74: error: no matching function for call to ‘make_pair<std::__cxx11::string, bool>(__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type&, bool)’          resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ;                                                                           ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,                  from /usr/include/c++/7/bits/char_traits.h:39,                  from /usr/include/c++/7/string:40,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10: /usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)      make_pair(_T1&& __x, _T2&& __y)      ^~~~~~~~~ /usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:415:74: note:   cannot convert ‘fields.std::vector<std::__cxx11::basic_string<char> >::operator[](1)’ (type ‘__gnu_cxx::__alloc_traits<std::allocator<std::__cxx11::basic_string<char> > >::value_type {aka std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’          resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ;                                                                           ^ /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::StatsFileReader::ParseReadGroupLine(const string&, std::map<std::__cxx11::basic_string<char>, ReadGroupResolver>&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:612:75: error: no matching function for call to ‘make_pair<std::__cxx11::string, ReadGroupResolver>(const string&, ReadGroupResolver&)’      readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) );                                                                            ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,                  from /usr/include/c++/7/bits/char_traits.h:39,                  from /usr/include/c++/7/string:40,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10: /usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)      make_pair(_T1&& __x, _T2&& __y)      ^~~~~~~~~ /usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:612:61: note:   cannot convert ‘name’ (type ‘const string {aka const std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’      readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) );                                                              ^~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘bool BamTools::ResolveTool::ResolveToolPrivate::MakeStats()’: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1019:93: error: no matching function for call to ‘make_pair<std::__cxx11::string, bool>(std::__cxx11::string&, const bool&)’          else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) );                                                                                ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,                  from /usr/include/c++/7/bits/char_traits.h:39,                  from /usr/include/c++/7/string:40,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10: /usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)      make_pair(_T1&& __x, _T2&& __y)      ^~~~~~~~~ /usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1019:68: note:   cannot convert ‘al.BamTools::BamAlignment::Name’ (type ‘std::__cxx11::string {aka std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’          else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) );                                                                  ~~~^~~~ /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp: In member function ‘void BamTools::ResolveTool::ResolveToolPrivate::ParseHeader(const BamTools::SamHeader&)’: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1051:93: error: no matching function for call to ‘make_pair<std::__cxx11::string, ReadGroupResolver>(const string&, ReadGroupResolver)’          m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) );                                                                                ^ In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,                  from /usr/include/c++/7/bits/char_traits.h:39,                  from /usr/include/c++/7/string:40,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_tool.h:14,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.h:13,                  from /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:10: /usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)      make_pair(_T1&& __x, _T2&& __y)      ^~~~~~~~~ /usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed: /media/mothra/enrico/whamg/wham/src/bamtools/src/toolkit/bamtools_resolve.cpp:1051:70: note:   cannot convert ‘rg.BamTools::SamReadGroup::ID’ (type ‘const string {aka const std::__cxx11::basic_string<char>}’) to type ‘std::__cxx11::basic_string<char>&&’          m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) );                                                                    ~~~^~ src/toolkit/CMakeFiles/bamtools_cmd.dir/build.make:254: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o' failed make[3]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o] Error 1 make[3]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' CMakeFiles/Makefile2:520: recipe for target 'src/toolkit/CMakeFiles/bamtools_cmd.dir/all' failed make[2]: *** [src/toolkit/CMakeFiles/bamtools_cmd.dir/all] Error 2 make[2]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Makefile:129: recipe for target 'all' failed make[1]: *** [all] Error 2 make[1]: Leaving directory '/media/mothra/enrico/whamg/wham/src/bamtools/build' Makefile:26: recipe for target 'src/bamtools/lib/libbamtools.a' failed make: *** [src/bamtools/lib/libbamtools.a] Error 2


Use scissor test to limit clears to output rectangle (fixes #4)

This PR uses the scissor test to limit clears and draws to the output rectangle, resolving #4.

Very nice.  Thank you.


Add custom scriptblock feature

My initial code (pre-class) allowed the user to add a custom property based on a scriptblock. See how to add that feature to this module.

Added in https://github.com/jdhitsolutions/MyNumber/commit/86dd4851e8b0720488e6c546da12feb519c8f419


Scenario for this code

Explain when this code block will be executed, give an example when this values will <> 0 and this code will be run

For eg: We have 3 prizes and 10 winners to distribute among them:
Prize Neha: Probability = 0.3, Current Winners = 1
Prize Priya: Probability = 0.3, Current Winners = 2
Prize Kaya: Probability = 0.3, Current Winners = 0
Now, let's walk through the code:
Loop Initialization:
We enter the while loop because there are still winners left to distribute ($totalWinners = 10).
Filtering the prize:
We filter the prizes to find those with fewer winners than expected based on their probabilities.
Prize Neha needs 2 more winners (0.3 * 10 = 3 expected, but only 1 current).
Prize Priya needs 1 more winner (0.3 * 10 = 3 expected, but only 2 current).
Prize C needs 3 more winners (0.3 * 10 = 3 expected, but 0 current).
So, all prizes are included in $remainingPrizes.
Calculating Total Remaining Shortfall:
We calculate the total remaining shortfall, which is the sum of the differences between the expected and current winners for each prize:
Total shortfall = 2 (Prize Neha) + 1 (Prize Kaya) + 3 (Prize Kaya) = 6.
Redistributing Winners:
We redistribute the remaining 10 winners among the prizes in proportion to their shortfalls.
Prize A gets (2 / 6) * 10 = 3 winners.
Prize B gets (1 / 6) * 10 = 1.67 (round figure 2) winners.
Prize C gets (3 / 6) * 10 = 5 winners.
After redistribution, we update the number of winners for each prize accordingly.
Since redistribution occurred, we continue the loop.
Continue looping until there are no more winners to distribute or until no further redistribution occurs.


Feature request: force skip requests to wordpress

When you deal with a big project with at least 30-40 pages, that has some content that is coming from WP it becomes annoying to switch between branches/restart service because it causes regeneration and redownloading of all assets if there is a change of dependecies. It takes time, and even having a local version of  WP does not help a lot since Gatsby starts to query everything again. It would be nice to have an option that will force the use of the current version of downloaded assets as well as content data that was already downloaded without even making a single query to a data source.
I know Gatsby focused more and more on speeding up the production build time, however, development environment builds on local machine becomes time-consuming as well, especially when it comes to PR reviews or edits in gatsby-node.js.

Hi @lnikell , this is a great request! I've added 2 API's that are meant to help in (almost) this situation. There is options.develop.hardCacheData and options.develop.hardCacheMediaFiles. The media file hard-cache will work across sources, however the data hard cache will not. It would be possible to hard cache in a directory created from options.url though, so that could easily enable the functionality you're looking for :)
Currently we're working on shipping a stable release of this plugin and we're heavily focused on getting Preview to work as seamlessly and reliably as possible so we won't be prioritizing this now, but could in the future. If you're interested in opening a PR for this, you would want to change this line https://github.com/gatsbyjs/gatsby-source-wordpress-experimental/blob/master/plugin/src/utils/cache.js#L27 so that the cache directory includes a hash of the WP url.

Hi, @TylerBarnes thank you for the feedback. That's definitely will be very useful in the future. Actually can't wait to see it working :) Because Dev experience on any real WP project is not great. Please don't get me wrong.
I've checked options.develop.hardCacheMediaFiles it creates wordpress-cache indeed, but if I get you right it does not work at this moment, so it does not affect build time, etc. I will try to debug a bit the part of the code you sent, to understand better how does it work.

Ahh, dangit! definitely a regression. I'll fix this soon and add a test for it. I see that it's hard caching the files but not properly restoring them for some reason. And thank you for the feedback too, we need real-world honest feedback!

@lnikell , hardCacheMediaFiles is working on latest! There was some missing logic where fetching images where we could identify what the MediaItem node was weren't being hard cached.

thank you @TylerBarnes, already added it to a couple of projects,  very curious will it improve the experience or no :)

Closing this as hardCacheMediaFiles and hardCacheData are working on latest 👍


Feat: support Milvus more params

fix https://github.com/langchain-ai/langchain/issues/15442

Looks great. Thanks for the improvement!

@hwchase17


Clean up workspace dependencies after cargo remove

What does this PR try to resolve?
After successful removal of an inherited dependency from a workspace member, clean up the root workspace manifest.
This PR is part of the continued working on cargo remove (#11099, see deferred work).
How should we test and review this PR?
Make sure the tests cover all possible use cases. After posting this PR, I will post a short self-review regarding some design concerns.
Additional information
#11194 is currently blocked on this feature.

r? @weihanglo
(rust-highfive has picked a reviewer for you, use r? to override)

Recent push should fix these issues. No rush though :)

I believe @epage will be unavailable for the time being, so @weihanglo do you think you could take over reviewing this?
It'd be nice to get this and #11194 merged before the upcoming 1.66 cutoff so that it lands with cargo remove.

Absolutely yes! Will review it ASAP.
r? @weihanglo

The failing tests seem to be spurious and unrelated, although I don't have a way to retry.

The failing tests seem to be spurious and unrelated, although I don't have a way to retry.

See https://rust-lang.zulipchat.com/#narrow/stream/246057-t-cargo/topic/latest.20nightly.20broken

Okay, great! Tests seem to be passing now.

@bors r+

:pushpin: Commit 38b23d5c688dde85072b07ba2c93d78c6da0726a has been approved by epage
It is now in the queue for this repository.

:hourglass: Testing commit 38b23d5c688dde85072b07ba2c93d78c6da0726a with merge 65b21497703344724f54ba638bcf9ae91173aaff...

:sunny: Test successful - checks-actions
Approved by: epage
Pushing 65b21497703344724f54ba638bcf9ae91173aaff to master...

Should we backport this to 1.66 beta?

Bah, we didn't make the cut off?
We also have #11194 which is almost done.  Probably a topic for the next team meeting of whether

Let these come in the next release
Beta backport these
Mark cargo-remove as unstable in the beta, removing the cargo-rm alias (to not interfere with cargo-edit)

If we are fine with these behavior changes after 1.66 (which I think I am fine with), I lean towards letting them go into 1.67.  I tend to treat the bar for backports as high but am open to where others set the bar.

We discussed the options in the meeting, and I think we are comfortable with just continuing with this and #11194 landing in the next release. I think the impact should be small, and is unlikely to be a significant problem for users. That is:

This issue AFAIK just leaves a stale dependency in workspace.dependencies. That shouldn't cause any warnings or errors, and shouldn't be a significant problem for users. This would also require the combination of someone using cargo remove plus workspace inheritance plus removing the last remaining reference. I suspect that combination is a very small population of users.
#11194 may cause errors, but I think the combination of someone using cargo remove and using a patch or profile override is going to be extremely small (if not zero). And the consequence is not terrible, they will just get a warning about them being unused, and I think the user should be able to figure out what is going on. My comment at https://github.com/rust-lang/cargo/pull/11099#issuecomment-1253739902 about gc'ing unused things wasn't intended to be a high-priority issue, and I think it's find that it was deferred.


Fix docker-compose.yaml error

Switching from dictionary to array for node:volumes to fix the following error:

services.node.volumes contains an invalid type, it should be a string

@mart1n-xyz Thanks for flagging, will be fixed in next minor release (long syntax requires Dockerfile v >=3.2)


Add packages demoing and testing pathed exports for alpha/beta types

Adds two new private, unpublished packages to test per-package exports by path. These packages demonstrate using exports paths to provide alpha and beta APIs alongside public APIs in a single package. The APIs are deliberate simple and tautologically named.
I think it would be valuable to merge these, then follow up with additional PRs exploring the pattern more deeply. That will allow us to focus future PRs on the changes, rather than including a package scaffolding in every change. That said, if there is a better way to explore the pattern, e.g. using real packages in the repo instead of a demo package, I'm all ears!
If these packages serve no more purpose once we have explored the pattern, then we can delete them. There's no need to publish them ever - anything we want to test that requires publishing can be tested using an already-published package.
Guidance for reviewers
I suggest filtering to only .ts files so you can focus on the code. Most of the rest of the changes are just new package scaffolding.
The exception is the tsconfig - note that moduleResolution: "node16" seems to be needed to get the exports paths to resolve. I think this is consistent with the TypeScript docs.

I'm not opposed to temporarily adding private packages so we can test this thoroughly. Seems like a reasonable path to me. We should be sure to clearly document this in their READMEs though in case someone else stumbles onto them.


TAS: add e2e tests for rank ordering for Job

What type of PR is this?
/kind cleanup
What this PR does / why we need it:
Which issue(s) this PR fixes:
Part of #3450
Part of #3533
Special notes for your reviewer:

I was also thinking about an alternative assert that rack(pod0)==rack(pod1) and rack(pod2)==rack(pod3), but I think it will be harder to debug when the assert fails. With the exact assignment check we can easily see the full assignment.
I have confirmed locally that when not using TAS the distributions of pods is completely random (I commented out setting the TopologyName and TAS PodSet annotation), then got:

  [FAILED] Expected object to be comparable, diff:   map[string]string{
  - 	"0": "kind-worker",
  + 	"0": "kind-worker5",
  - 	"1": "kind-worker2",
  + 	"1": "kind-worker7",
    	"2": "kind-worker3",
    	"3": "kind-worker4",
    }

I ran it a 4 times and it failed all repeats.
Does this PR introduce a user-facing change?

NONE

/assign @PBundyra
cc @tenzen-y

/test pull-kueue-test-tas-e2e-main

LGTM, good job! I'll hold for @tenzen-y to take a look
/hold
/lgtm

/hold cancel

Do we have integration testing for this situation?

no, but we have unit testing which is quite useful here, because it is high-level.
So, personally I'm using unit tests for debugging, the e2e tests are useful to confirm the feature works.
I considered adding integration tests, but they are actually tricky, because TopologyUngater operates on pods, but we don't enable the k8s Job controller in the integaration tests. So, we would need to create the pods ourselves, just like in unit tests, so I don't see much gain.


OSX 10.13 "Multiple validation errors occured." for 1.7 (252)

After upgrading to High Sierra, Simple Comic would spawn "multiple validation errors occurred." error dialogs. This does not appear happen for 1.7.1 (253). The non-programmers would likely appreciate an update to the binary on http://dancingtortoise.com/simplecomic/.

i have this problem, how do i fix it?

You upgrade to 1.7.1. You can either compile it yourself or feel free to use the one I compiled. I'm sharing it because i know not everyone is comfortable with compiling their own.
https://www.dropbox.com/s/sf7eidl9eujtnl2/SimpleComic_1.7.1_253.zip?dl=1

Hi Brandon,
Much appreciated!
Regards,
Sean Ong
On 10 November 2017 at 13:45, Brandon Yap<EMAIL_ADDRESS>wrote:

You upgrade to 1.7.1. You can either compile it yourself or feel free to
use the one I compiled. I'm sharing it because i know not everyone is
comfortable with compiling their own.
https://www.dropbox.com/s/sf7eidl9eujtnl2/SimpleComic_1.7.1_253.zip?dl=1
—
You are receiving this because you commented.
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https://github.com/arauchfuss/Simple-Comic/issues/116#issuecomment-343359067,
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@PSiAU Thanks for the download, but in your build one of the buttons is missing, the full screen mode one. How do you add it back in?

Seems to be there for me. Not sure why that'd be missing.....could you do a screenshot?

Many thanks for that!
I notice the QuickLook plugin is no longer working for CBR files (still works for CBZ). Would that be related to this update or the fact I recently switched RAR expanders?

@PSiAU It's on the other side of the window.

The full screen button (for me atleast) is better than the go to full screen, as hitting the button gives a black background and gets rid of the bar at the top and bottom of the page.
The 2 show what i mean, the first is on your build:

And this same image again in the old build:

Hope you can see what i mean
Regards Dave
PS: Thanks for actually doing this for those of us not tech savvy!

No worries Dave.
I'm thinking Alex could have intentionally removed that from the codebase, because with new versions of macOS, the fullscreen functionality of the green button and the one you mentioned on the right side of the window should do the same thing thus making it redundant.

But they arent the same as the images show. Shame he removed it means i'll need to find another app now.

You upgrade to 1.7.1. You can either compile it yourself or feel free to use the one I compiled. I'm sharing it because i know not everyone is comfortable with compiling their own.
https://www.dropbox.com/s/sf7eidl9eujtnl2/SimpleComic_1.7.1_253.zip?dl=1

Good sir, would you mind re-uploading that 253 binary? The Dropbox link has gone expired.

I think I might have removed it by accident. Here's the new link.
https://www.dropbox.com/s/g7msn2bbrwkrddk/SimpleComic_1.7.1_253.zip?dl=1

@PSiAU Do you have any idea why it stopped working after Catalina? I just bought a new Mac which came with it already on, but for some reason the app opens, but it docent display any images

Same problem here with Catalina. Was using SimpleComic 1.7.1_253 before moving to Catalina and it was working fine. Thumbnails are displaying fine in finder but you just don't get a window for anything in SimpleComic. I tried to give the app full disk access in case that was related but nothing changed.

Thanks for the link @PSiAU! This seems to fix the issue… but unfortunately removes that all-too-handy full screen button (the Cmd+F view keeps showing the bottom bar for me) so I can't use it… :/
Does anyone know what's the cause of this "Multiple validation errors occurred" error that happens from time to time? Might try to fork this repo and fix that… without also removing the full screen button.

Try using my fork. I hopefully worked around the issue of the status bar taking up space when hidden.

@MaddTheSane Thanks! Not sure if I'm set up to build but will try tomorrow. :) The Cmd+F shortcut still plays an animation, though, which isn't ideal for me… what I liked about the old version as well is that it didn't really use Mac's native full screen mode but just made the window borderless + maximum size, and instantly transitioned.

If I remember well, cmd+/ switches the status bar on and off - even in full screen.

@kiwifb Aha, you're right. And it seems it remembers the setting, so you don't have to press that shortcut every time which is handy. Still (for me) the problem of getting rid of that maximizing/shrinking animation in and out of full screen mode. Not sure if the tradeoff of sometimes having to deal with the "validation error" message at times (& being forced to restart the application) is worth it… hmm…

@PSiAU  Thank you so much for posting this again. I just upgraded to High Sierra and was bummed out SimpleComic 1.8 wasn't working right. This fixed it!  (version 1.7.1_253)


CoffeeScript Standard Library

Just throwing this out there as a thought: what would be the pros/cons/technical issues of baking a standard library into CoffeeScript?
I use Underscore and consider its functions an essential extension of the JavaScript language. It would be nice to be able to call them without the "_." prefix.

This is old, but:
Now there is Sugar.js, an "ActiveSupport" for both clientside and serverside Javascript: http://sugarjs.com/api


FYI The Capslock key lights up correctly when enabled

I noticed the README says Capslock still needs work, but I'm happy to report that it's working fine here.

In older versions of the repo, the Type Cover of the first generation Surface Go had issues with the Caps Lock light. I still use my old "Cobalt Blue" first gen Type Cover and the Caps Lock light is working now.


Add 'embeddedsha' to record tested baseline for bundle

The primary change in this PR is very small: Add $bundle.embeddedsha to enable read-only vcpkg to provide useful error messages around baselines.
While investigating the general problem, I discovered several other functions that were generally 'unsafe' (they depend upon root / ".git"), but in the single context they're used are safe. I therefore refactored things to move those functions closer to their contexts and out of the public VcpkgPaths:: interface.

One main aspect of #197 was to get the date of the used vcpkg version for issues. You now always see in the issues how old the vcpkg version is they used to build a port (for example vcpkg version: 1a5075b 2021-11-17 (2 hours ago)). This is very helpful if people are using a (very) old version of vcpkg and you know the failure was fixed in a new version.
This feature gets removed with this PR

I see, I assumed it was primarily about the commit id. Let me see about adding date infromation.

I've restored the date display behavior for existing cases, however the read-only bundle probably needs a different treatment (the date information needs to come from somewhere else).


Guidance on configuring NFSv3 and/or NFSv4 across host, trident and ontap

Describe the solution you'd like
Configuring NFSv3 or NFSv4 on ONTAP can quite be complex task in the field and very easily lead to misconfigurations on a multitude of places (host, ontap svm (export policy, nfs settings, auth methods, trident).
In many cases people just might be wants just NFSv4 to work as NFSv3. When it comes to Kerberos, not many customers i worked with use this, if they do then its because the security team mandates it. But this is perhaps another story.
In many cases there are two parties involved, the devops team that sets up Trident and then the ONTAP administrator, and also the administrator who need to configure linux hosts. In my experience setting up Trident end-to-end with all this, could takes many days.
Perhaps consider some guidance on good defaults for example ONTAP NFS v3 and NFSv4 to help someone speed up the deployment of Trident.
In the best of worlds, why couldn't trident cli auto-configure an SVM for various common scenarios or give you configuration defaults to get started ?
Describe alternatives you've considered
Learn the nitty gritty details of configuring ONTAP and NFSv3 and NFSv4.

@martencassel, thanks for the feedback on Trident examples. We'll consider how to improve the documentation as far as having some quick start examples. To really understand how to apply different NFS options, in your StorageClass's mountOptions, you will want to refer to the NFS in NetApp ONTAP Technical Report.


MySQL: ERROR 2027 (HY000): Malformed packet

I am getting this Error Message when executing this query: SELECT * FROM table WHERE id = 0
I am not getting this message when executing the query in the mysql client binary
Sqlx version: 0.4.0-beta.1
Mariadb is installed with pacman

I dont know how to fix it but after switching to docker I am at least getting different errors

I just hit the same issue, can this be reopened?


Show Path to Public Pages

Describe the feature you'd like
our Bookstack is mainly for knowledge sharing, we have public and private pages, now if you have public page in private book and chapter you can't see them in the home page, so you can't access the pages without having link to the page or looking on the left history tab. if the question rises why not have them in different shelf and books, well it's a lot easier for those who have full access to manage and navigate the site.
Describe the benefits this feature would bring to BookStack users
this would allow easier access to pages as now it's pretty hard to access

Thanks for the suggestion @Zyzto.
I'm going to close this off as I can't see a way of this working without having options that are only useful to specific use-cases in certain situations. This would be fighting back against the permission system, and would have to be an option upon the current functionality as people would typically expect the items without view permission would be hidden.
Maybe #182 would be a more likely option for the fundamental visibility issue at play here.


400D and 500D Spherical embeddings for NER

Hello, thanks for your interesting paper. I used your released embeddings in our standard NER architecture to see if they are useful for an NER downstream task. You can see the comparison against other approaches on CoNLL-03. As the table shows, F1 score increases with more dimensions to the point of being comparable to vanilla GloVe. It would be interesting to see if this trend continues with dimensions higher than 300D and if at higher dimensionality it beats vanilla GloVe.
Would you be interested in also releasing spherical embeddings trained over the same data / parameters with 400D and 500D? If so, I'll test and report the numbers back.

Hi,
Thanks for your interest in our paper and for conducting the comparison! May I ask where did you obtain the pre-trained 100-d GloVe vectors? The "glove.6B.zip" version provided on the GloVe page is trained on both Wikipedia and the Gigaword corpus, while our released vectors are only trained on the Wikipedia corpus, which might make the comparison unfair.
Regarding higher dimensional embeddings, I haven't planned to release pre-trained embeddings with higher than 300 dimensions since I didn't see many people using >300-d embedding in their models, but you can always run our code on the Wikipedia corpus for arbitrary dimensions---both the code and the Wikipedia corpus are available in this repository. However, if you encounter any issues running our code, please let me know.
Best,
Yu

Thanks for your quick response - For vanilla GloVe, I used the embeddings released here by the authors of the Poincaré Glove embeddings. They trained all embeddings on a 1.4 billion token dump of Wikpedia, so the numbers should be roughly comparable.

Thanks for letting me know. As I said in my previous response, since >300-d embeddings are not very common in applications, I don't have the embeddings of our model with >300 dimensions. But you can always run the code on the processed Wikipedia corpus with arbitrary dimensions--Just let me know if you have any problems or issues running the code.
Best,
Yu


Syntax highlight based on inline script type

Just allows you to have inline scripts for recipes:
recipe:
    #!/usr/bin/env python
    import sys
    print("Hello from stderr", file=sys.stderr)

It would be nice if vscode-just could correctly syntax highlight these scripts, using the shebang to determine what syntax highlighting it should use.
This happens in the Markdown syntax highlighting in VS Code when you make an inline code block.

Oh man, how cool is that!?

I was exactly upto it and seems like relevant thing is: https://code.visualstudio.com/api/language-extensions/syntax-highlight-guide#embedded-languages

This is how vscode markdown does it: https://github.com/microsoft/vscode/blob/master/extensions/markdown-basics/syntaxes/markdown.tmLanguage.json

Parent repository: https://github.com/microsoft/vscode-markdown-tm-grammar


Problem with unsqueeze

Model loaded
Processing file: ./dataset/data/00002.jpg
Performing inversion...
Traceback (most recent call last):
  File "estimate_input_noise.py", line 70, in <module>
    outputs = invertor.perform_inversion(file_name, cond = None, init_noise_init = None, loss_weights= {'latents': 1. , 'pixels':1.} )
  File "/home/bazza/src/DIA/ddim_invertor.py", line 92, in perform_inversion
    cond = self.__tokens2conditioning(cond_out)
  File "/home/bazza/src/DIA/ddim_invertor.py", line 223, in __tokens2conditioning
    conditioning = self.ddim_sampler.model.cond_stage_model.transformer(inputs_embeds = tokens.unsqueeze(0))['last_hidden_state']
AttributeError: 'NoneType' object has no attribute 'unsqueeze'

Hi, it seems like the pickle with token inversion does not exist. Could you provide the code you ran to reproduce the problem?

Hi, Looks like pytorch overcame my 24gb video memory
I don't know why this is happening. But i don't know how to fix it.
Selected timesteps: tensor([4, 0, 5, 2, 3, 6, 7, 1])
  0%|                                                                             | 0/10 [00:06<?, ?it/s, loss=0.24, indices=tensor([4, 0, 5, 2, 3, 6, 7, 1])]
Traceback (most recent call last):
  File "estimate_CLIP_features.py", line 65, in <module>
    output = invertor.perform_cond_inversion_individual_timesteps(file_path, None, optimize_tokens=True)
  File "/home/bazza/src/DIA/ddim_invertor.py", line 290, in perform_cond_inversion_individual_timesteps
    loss.backward()
  File "/home/bazza/src/miniforge3/envs/dia_env/lib/python3.8/site-packages/torch/_tensor.py", line 363, in backward
    torch.autograd.backward(self, gradient, retain_graph, create_graph, inputs=inputs)
  File "/home/bazza/src/miniforge3/envs/dia_env/lib/python3.8/site-packages/torch/autograd/__init__.py", line 173, in backward
    Variable._execution_engine.run_backward(  # Calls into the C++ engine to run the backward pass
  File "/home/bazza/src/miniforge3/envs/dia_env/lib/python3.8/site-packages/torch/autograd/function.py", line 253, in apply
    return user_fn(self, *args)
  File "/home/bazza/src/DIA/stable-diffusion/ldm/modules/diffusionmodules/util.py", line 139, in backward
    input_grads = torch.autograd.grad(
  File "/home/bazza/src/miniforge3/envs/dia_env/lib/python3.8/site-packages/torch/autograd/__init__.py", line 275, in grad
    return Variable._execution_engine.run_backward(  # Calls into the C++ engine to run the backward pass
RuntimeError: CUDA error: out of memory
CUDA kernel errors might be asynchronously reported at some other API call,so the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1.

this generates the same result:
python estimate_CLIP_features.py --input_img dataset/data/00000.png

I believe that the first issue with unsqueeze was different from the second one. I referenced the second one in a new thread.
The first one was caused by trying to perform the noise inversion before the CLIP feature inversion. I added file check so now it should be clear why the error occured.


Incorrect Permissions for Security Groups/Rules

Under Permissions - Network Security Groups, the Actions specify Microsoft.Network/ruleTables but the provider operations should be Microsoft.Network/networkSecurityGroups.

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 8ea14a05-b98d-4cec-5f36-726f3c3d1da2
Version Independent ID: 6852fef5-f9f1-5893-258a-5d04c82dfcc8
Content: Create, change, or delete an Azure network security group
Content Source: articles/virtual-network/manage-network-security-group.md
Service: virtual-network
GitHub Login: @jimdial
Microsoft Alias: jdial

Thanks for the feedback! I have assigned the issue to the content author to investigate further and update the document as appropriate.

@wagesworld Thanks for catching. I've updated the article appropriately.  It will publish later today.  #please-close.