Error in run_ld_clumping.ipynb

When I am running run_ld_clumping.ipynb from ‘end to end GWAS PheWAS’ in jupterlab on DNAnexus , I encounter the problem that 

[Errno 2] No such file or directory: '/opt/notebooks/bgen.tgz/build/apps/bgenix'.
I investigated further and found no bgenix in the folder'/opt/notebooks/bgen.tgz/build/apps'.

Then I run bgenix installation line by line in bash on DNAnexus. Here is the error report:


cd bgen.tgz/ 
./waf ​ 
bash: cd: bgen.tgz/: No such file or directory Waf: Entering directory /opt/notebooks/bgen.tgz/build' Creating release build... [20/85] Linking build/3rd_party/boost_1_55_0/libboost.a [22/85] Linking build/3rd_party/sqlite3/libsqlite3.a [34/85] Linking build/3rd_party/zstd-1.1.0/libzstd.a [40/85] Linking build/db/libdb.a [44/85] Compiling src/View.cpp [57/85] Linking build/appcontext/libappcontext.a [69/85] Creating build/bgen_revision_autogenerated.hpp [70/85] Compiling src/IndexQuery.cpp [71/85] Compiling src/MissingValue.cpp [72/85] Compiling src/View.cpp [73/85] Compiling src/bgen.cpp [74/85] Compiling src/zlib.cpp In file included from ../3rd_party/boost_1_55_0/boost/mpl/aux_/na_assert.hpp:23, from ../3rd_party/boost_1_55_0/boost/mpl/arg.hpp:25, from ../3rd_party/boost_1_55_0/boost/mpl/placeholders.hpp:24, from ../3rd_party/boost_1_55_0/boost/iterator/iterator_categories.hpp:17, from ../3rd_party/boost_1_55_0/boost/iterator/detail/facade_iterator_category.hpp:7, from ../3rd_party/boost_1_55_0/boost/iterator/iterator_facade.hpp:14, from ../3rd_party/boost_1_55_0/boost/filesystem/path.hpp:28, from ../3rd_party/boost_1_55_0/boost/filesystem.hpp:16, from ../src/View.cpp:15: ../3rd_party/boost_1_55_0/boost/mpl/assert.hpp:187:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 187 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 188 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ ../3rd_party/boost_1_55_0/boost/mpl/assert.hpp:187:21: note: remove parentheses 187 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 188 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | ); | ~ | - ../3rd_party/boost_1_55_0/boost/mpl/assert.hpp:192:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 192 | failed ************ (boost::mpl::not_<Pred>::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | ); | ~ ../3rd_party/boost_1_55_0/boost/mpl/assert.hpp:192:21: note: remove parentheses 192 | failed ************ (boost::mpl::not_<Pred>::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 193 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 | ); | ~ | - ../src/View.cpp: In member function ‘void genfile::bgen::View::setup(const std::string&)’: ../src/View.cpp:180:43: error: ‘streampos’ is not a member of ‘std::ios’ {aka ‘std::basic_ios<char>’} 180 | std::ios::streampos origin = m_stream->tellg() ; | ^~~~~~~~~ ../src/View.cpp:182:76: error: ‘origin’ was not declared in this scope 182 | m_file_metadata.size = m_stream->tellg() - origin ; | ^~~~~~ ../src/View.cpp:212:48: warning: comparison of integer expressions of different signedness: ‘std::streamsize’ {aka ‘long int’} and ‘std::vector<unsigned char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 212 | if( m_stream->gcount() != m_postheader_data.size() ) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ At global scope: cc1plus: note: unrecognized command-line option ‘-Wno-c++11-long-long’ may have been intended to silence earlier diagnostics Waf: Leaving directory /opt/notebooks/bgen.tgz/build' Build failed -> task in 'bgen' failed with exit status 1 (run with -v to display more information)


Thank you!