Compilation of qctools fail at random steps

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Issue #69 resolved
Shing Wan Choi created an issue

Hi Gavin,

Thanks for pointing out that I’ve posted to the wrong reporsitory, sorry about that.

I have now use the beta branch (178c78f30521) of qctools and still got some strange errors:

../genfile/src/CrossCohortBaselineRemapping.cpp: In member function ‘void genfile::CrossCohortBaselineRemapping::recompute_map()’:
../genfile/src/CrossCohortBaselineRemapping.cpp:50:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for( int i = 0; i < get_number_of_distinct_mapped_values(); ++i ) {
                                                             ^
../genfile/src/LongFormatSNPDataSource.cpp: In member function ‘void genfile::LongFormatSNPDataSource::setup(std::istream&)’:
../genfile/src/LongFormatSNPDataSource.cpp:276:65: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( alternate_alleles.size() + 1 != to_repr< int >( elts[4] )) {
                                                                 ^
Waf: Leaving directory `/sc/orga/projects/psychgen/ukb/software/src/qctool/build'
Build failed:  -> task failed (err #-1):
    {task: cxx get_ploidy_from_sex.cpp -> get_ploidy_from_sex_1.o}

If I rerun ./waf-1.5.18, I will then get another error but managed to move forward for a bit

In file included from ../3rd_party/boost_1_55_0/boost/assert.hpp:51:0,
                 from ../3rd_party/boost_1_55_0/boost/range/iterator_range_core.hpp:21,
                 from ../3rd_party/boost_1_55_0/boost/range/iterator_range.hpp:13,
                 from ../3rd_party/boost_1_55_0/boost/ptr_container/ptr_map_adapter.hpp:23,
                 from ../3rd_party/boost_1_55_0/boost/ptr_container/ptr_map.hpp:20,
                 from ../genfile/include/genfile/vcf/Types.hpp:15,
                 from ../genfile/include/genfile/VariantDataReader.hpp:22,
                 from ../genfile/include/genfile/SNPDataSink.hpp:19,
                 from ../genfile/src/ShapeITHaplotypesSNPDataSink.cpp:12:
../genfile/src/ShapeITHaplotypesSNPDataSink.cpp: In member function virtual void genfile::{anonymous}::HaplotypeWriter::initialise(std::size_t, std::size_t):
../genfile/src/ShapeITHaplotypesSNPDataSink.cpp:42:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     assert( (2*nSamples) == m_data.size() ) ;
                                         ^
../genfile/src/ShapeITHaplotypesSNPDataSink.cpp: In member function void genfile::{anonymous}::HaplotypeWriter::write_to_stream(std::ostream&) const:
../genfile/src/ShapeITHaplotypesSNPDataSink.cpp:86:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( std::size_t i = 0; i < m_data.size(); ++i ) {
                                             ^
../genfile/src/GenIntensityFileSNPDataSink.cpp: In member function virtual void genfile::{anonymous}::IntensityWriter::initialise(std::size_t, std::size_t):
../genfile/src/GenIntensityFileSNPDataSink.cpp:44:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if( (nSamples*2) != m_data.size() ) {
                                     ^
../genfile/src/GenIntensityFileSNPDataSink.cpp: In member function void genfile::{anonymous}::IntensityWriter::write_to_stream(std::ostream&) const:
../genfile/src/GenIntensityFileSNPDataSink.cpp:96:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( std::size_t i = 0; i < m_data.size(); ++i ) {
                                             ^
Waf: Leaving directory `/sc/orga/projects/psychgen/ukb/software/src/qctool/build'
Build failed:  -> task failed (err #-1):
    {task: cxx SNPInSetTest.cpp -> SNPInSetTest_1.o}

Is that normal? Do I just need to continuely re-run ./waf-1.5.18 until all file is successfully compiled?

g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/hpc/packages/minerva-common/gcc/4.8.2/libexec/gcc/x86_64-unknown-linux-gnu/4.8.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --prefix=/hpc/packages/minerva-common/gcc/4.8.2
Thread model: posix
gcc version 4.8.2 (GCC)

Comments (3)

  1. Gavin Band repo owner

    It is normal that it fails at ‘random’ steps. Restricting to one job (`./waf-1.5.18 -j 1`) will likely make this reproducible.

    Unfortunately your build output does not contain the errors that caused the build to fail. (The messages you reported are compiler warnings, but they don’t cause the build to fail). Can you run `./waf-1.5.18 -j 1` and post the full build output?

    Thanks,

    g.

  2. Shing Wan Choi reporter

    Odd, once I use -j 1, the build finished successfully. Maybe that has something to do with my server. Thank you Gavin!

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