marziacremona / sic-chip Goto Github PK

Hello Marzia,

I am interested in SIC-ChIP to analyze our ATAC-seq peak shape.
I am currently trying to test the program by following your instruction on github.
I typed as follow
Rscript ../SIC-ChIP.r --bw=coverage_test.bw --bed=peaks_test.bed --out=results

but I got an error pasted at the end of this comment.
Could you give me an advice to solve the problem?

Thank you for your help

Yusuke

Loading packages and functions...
In file included from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/scoped_ptr.hpp:13:0,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/graph/adjacency_list.hpp:23,
from picco.cpp:5:
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() )
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/RcppCommon.h:52,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/Rcpp.h:27,
from picco.cpp:4:
/mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/shared_ptr.hpp:17,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from picco.cpp:5:
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) )
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/RcppCommon.h:52,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/Rcpp.h:27,
from picco.cpp:4:
/mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from picco.cpp:5:
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/RcppCommon.h:52,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/Rcpp.h:27,
from picco.cpp:4:
/mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from picco.cpp:5:
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn()
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/RcppCommon.h:52,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/Rcpp.h:27,
from picco.cpp:4:
/mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from picco.cpp:5:
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr( std::auto_ptr && r ): px(r.get()), pn()
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/RcppCommon.h:52,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/Rcpp.h:27,
from picco.cpp:4:
/mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from picco.cpp:5:
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr & r )
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/RcppCommon.h:52,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/Rcpp.h:27,
from picco.cpp:4:
/mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from picco.cpp:5:
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
shared_ptr & operator=( std::auto_ptr && r )
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/RcppCommon.h:52,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/Rcpp.h:27,
from picco.cpp:4:
/mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/shared_ptr.hpp:17:0,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/vector_property_map.hpp:14,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/property_map/property_map.hpp:602,
from /mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/graph/adjacency_list.hpp:28,
from picco.cpp:5:
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function 'boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)':
/mnt/gpfsA/home/miyanari/miniconda3/lib/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this );
^~~~~~~~
In file included from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/locale_conv.h:41:0,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/locale:43,
from /mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/iomanip:43,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/RcppCommon.h:52,
from /mnt/gpfsA/home/miyanari/tools/R-3.5.3/RLIB/Rcpp/include/Rcpp.h:27,
from picco.cpp:4:
/mnt/gpfsA/home/miyanari/miniconda3/x86_64-conda_cos6-linux-gnu/include/c++/7.3.0/bits/unique_ptr.h:51:28: note: declared here
template class auto_ptr;
^~~~~~~~

Importing coverage function for each peak...
Error in checkForRemoteErrors(val) :
27 nodes produced errors; first error: GRanges objects don't support [[, as.list(), lapply(), or unlist() at
the moment
Calls: importPeaks.bw ... clusterApplyLB -> dynamicClusterApply -> checkForRemoteErrors
Execution halted