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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Issue installing CNVnator #59

Closed sukesh14 closed 3 years ago

sukesh14 commented 7 years ago

Dear Sir,

Please find the below error while installing the CNVnator. Kindly help me to troubleshoot this error. I installed root v6 and CNVnator 0.27 and 0.3 versions on ubuntu 14.04

root@sukesh-Precision-Tower-7810:/home/sukesh/Downloads/CNVnator_v0.2.7/src# make g++ -pthread -m64 -DCNVNATOR_VERSION=\"v0.2.7\" -I/home/sukesh/Downloads/root-6.08.04/bin//include -Isamtools -c cnvnator.cpp -o obj/cnvnator.o In file included from cnvnator.cpp:8:0: HisMaker.hh:11:20: fatal error: TFrame.h: No such file or directory

include 

                ^

compilation terminated. make: *** [obj/cnvnator.o] Error 1

Thanks Sukesh

abyzov commented 7 years ago

Hi, most likely your ROOTSYS variable is set incorrectly.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

sukesh14 commented 7 years ago

Dear Sir,

Thanks for your prompt reply. The path for root system and library is mentioned as below before installing the CNVnator v0.27 or v 0.3. I don't know whether i am mentioning the correct path or not.

export ROOTSYS=/home/sukesh/Downloads/root-6.08.04/ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib.

After mentioning the above paths, i still get the errors.

/home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:776:53: error: invalid type in declaration before ‘;’ token typedef basic_string_view u16string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:777:29: error: ‘char32_t’ was not declared in this scope typedef basic_string_view u32string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:777:37: error: template argument 1 is invalid typedef basic_string_view u32string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:777:37: error: template argument 2 is invalid /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:777:53: error: invalid type in declaration before ‘;’ token typedef basic_string_view u32string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:786:30: error: ‘hash’ is not a class template struct _LIBCPP_TYPE_VIS_ONLY hash<std::experimental::basic_string_view<_CharT, _Traits> > ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:794:60: error: wrong number of template arguments (1, should be 2) hash<std::experimental::basic_string_view<_CharT, _Traits> >::operator()( ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:786:89: error: provided for ‘template<class _CharT, class _Traits> struct std::hash’ struct _LIBCPP_TYPE_VIS_ONLY hash<std::experimental::basic_string_view<_CharT, _Traits> > ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:795:77: error: non-member function ‘std::size_t std::operator()(const std::experimental::ROOT::basic_string_view<_CharT, _Traits>&)’ cannot have cv-qualifier const std::experimental::basic_string_view<_CharT, _Traits>& val) const _NOEXCEPT ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:795:77: error: ‘std::size_t std::operator()(const std::experimental::ROOT::basic_string_view<_CharT, _Traits>&)’ must be a nonstatic member function In file included from /home/sukesh/Downloads/root-6.08.04/include/TString.h:41:0, from /home/sukesh/Downloads/root-6.08.04/include/TNamed.h:29, from /home/sukesh/Downloads/root-6.08.04/include/TColor.h:16, from /home/sukesh/Downloads/root-6.08.04/include/TWbox.h:21, from /home/sukesh/Downloads/root-6.08.04/include/TFrame.h:17, from HisMaker.hh:11, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:32:4: error: expected unqualified-id before ‘using’ using basic_string_view = ::std::experimental::basic_string_view<_CharT,_Traits>; ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:35:12: error: ‘basic_string_view’ does not name a type typedef basic_string_view string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:36:12: error: ‘basic_string_view’ does not name a type typedef basic_string_view u16string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:37:12: error: ‘basic_string_view’ does not name a type typedef basic_string_view u32string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:38:12: error: ‘basic_string_view’ does not name a type typedef basic_string_view wstring_view; ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:48:28: error: ‘std::stod’ declared as an ‘inline’ variable inline double stod(std::string_view str, size_t pos) ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:48:23: error: ‘string_view’ is not a member of ‘std’ inline double stod(std::string_view str, size_t pos) ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:48:23: note: suggested alternatives: In file included from /home/sukesh/Downloads/root-6.08.04/include/RWrap_libcpp_string_view.h:520:0, from /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:26, from /home/sukesh/Downloads/root-6.08.04/include/TString.h:41, from /home/sukesh/Downloads/root-6.08.04/include/TNamed.h:29, from /home/sukesh/Downloads/root-6.08.04/include/TColor.h:16, from /home/sukesh/Downloads/root-6.08.04/include/TWbox.h:21, from /home/sukesh/Downloads/root-6.08.04/include/TFrame.h:17, from HisMaker.hh:11, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:775:39: note: ‘std::experimental::ROOT::string_view’ typedef basic_string_view string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:775:39: note: ‘std::experimental::ROOT::string_view’ In file included from /home/sukesh/Downloads/root-6.08.04/include/TString.h:41:0, from /home/sukesh/Downloads/root-6.08.04/include/TNamed.h:29, from /home/sukesh/Downloads/root-6.08.04/include/TColor.h:16, from /home/sukesh/Downloads/root-6.08.04/include/TWbox.h:21, from /home/sukesh/Downloads/root-6.08.04/include/TFrame.h:17, from HisMaker.hh:11, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:48:52: error: expected primary-expression before ‘’ token inline double stod(std::string_view str, size_t pos) ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:48:53: error: ‘pos’ was not declared in this scope inline double stod(std::string_view str, size_t pos) ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:48:56: error: expression list treated as compound expression in initializer [-fpermissive] inline double stod(std::string_view str, size_t pos) ^ /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:49:4: error: expected ‘,’ or ‘;’ before ‘{’ token { ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TNamed.h:29:0, from /home/sukesh/Downloads/root-6.08.04/include/TColor.h:16, from /home/sukesh/Downloads/root-6.08.04/include/TWbox.h:21, from /home/sukesh/Downloads/root-6.08.04/include/TFrame.h:17, from HisMaker.hh:11, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TString.h:116:13: error: expected type-specifier operator std::string_view() const { return std::string_view(Data(),fExtent); } ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h: In member function ‘TSubString::operator std::string() const’: /home/sukesh/Downloads/root-6.08.04/include/TString.h:117:42: error: ‘string_view’ is not a member of ‘std’ operator std::string() const { return std::string_view(Data(),fExtent).to_string(); } ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h:117:42: note: suggested alternatives: In file included from /home/sukesh/Downloads/root-6.08.04/include/RWrap_libcpp_string_view.h:520:0, from /home/sukesh/Downloads/root-6.08.04/include/RStringView.h:26, from /home/sukesh/Downloads/root-6.08.04/include/TString.h:41, from /home/sukesh/Downloads/root-6.08.04/include/TNamed.h:29, from /home/sukesh/Downloads/root-6.08.04/include/TColor.h:16, from /home/sukesh/Downloads/root-6.08.04/include/TWbox.h:21, from /home/sukesh/Downloads/root-6.08.04/include/TFrame.h:17, from HisMaker.hh:11, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:775:39: note: ‘std::experimental::ROOT::string_view’ typedef basic_string_view string_view; ^ /home/sukesh/Downloads/root-6.08.04/include/libcpp_string_view.h:775:39: note: ‘std::experimental::__ROOT::string_view’ In file included from /home/sukesh/Downloads/root-6.08.04/include/TNamed.h:29:0, from /home/sukesh/Downloads/root-6.08.04/include/TColor.h:16, from /home/sukesh/Downloads/root-6.08.04/include/TWbox.h:21, from /home/sukesh/Downloads/root-6.08.04/include/TFrame.h:17, from HisMaker.hh:11, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TString.h: At global scope: /home/sukesh/Downloads/root-6.08.04/include/TString.h:263:20: error: expected ‘,’ or ‘...’ before ‘&&’ token TString(TString &&s); // Move constructor ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h:263:23: error: invalid constructor; you probably meant ‘TString (const TString&)’ TString(TString &&s); // Move constructor ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h:269:18: error: ‘string_view’ in namespace ‘std’ does not name a type TString(const std::string_view &sub); ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h:269:36: error: ISO C++ forbids declaration of ‘sub’ with no type [-fpermissive] TString(const std::string_view &sub); ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h:290:13: error: expected type-specifier operator std::string_view() const { return std::string_view(GetPointer(),Length()); } ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h:297:32: error: ‘string_view’ in namespace ‘std’ does not name a type TString &operator=(const std::string_view &s); ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h:297:50: error: ISO C++ forbids declaration of ‘s’ with no type [-fpermissive] TString &operator=(const std::string_view &s); ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TNamed.h:29:0, from /home/sukesh/Downloads/root-6.08.04/include/TColor.h:16, from /home/sukesh/Downloads/root-6.08.04/include/TWbox.h:21, from /home/sukesh/Downloads/root-6.08.04/include/TFrame.h:17, from HisMaker.hh:11, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TString.h:787:32: error: ‘string_view’ in namespace ‘std’ does not name a type std::string printValue(const std::string_view val); ^ /home/sukesh/Downloads/root-6.08.04/include/TString.h:787:50: error: ISO C++ forbids declaration of ‘val’ with no type [-fpermissive] std::string printValue(const std::string_view val); ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TApplication.h:33:0, from HisMaker.hh:13, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TQObject.h:103:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template void EmitVA(const char signal_name, Int_t / nargs /, const T&... params); ^ /home/sukesh/Downloads/root-6.08.04/include/TQObject.h:103:97: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template void EmitVA(const char signal_name, Int_t / nargs /, const T&... params); ^ /home/sukesh/Downloads/root-6.08.04/include/TQObject.h:105:64: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default] void EmitVA(const char signal, Int_t nargs, va_list va) = delete; ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TInterpreter.h:30:0, from /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:40, from /home/sukesh/Downloads/root-6.08.04/include/TQObjectEmitVA.h:22, from /home/sukesh/Downloads/root-6.08.04/include/TQObject.h:215, from /home/sukesh/Downloads/root-6.08.04/include/TApplication.h:33, from HisMaker.hh:13, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TVirtualMutex.h: In member function ‘Int_t TLockGuard::UnLock()’: /home/sukesh/Downloads/root-6.08.04/include/TVirtualMutex.h:82:12: error: ‘tmp’ does not name a type auto tmp = fMutex; ^ /home/sukesh/Downloads/root-6.08.04/include/TVirtualMutex.h:84:14: error: ‘tmp’ was not declared in this scope return tmp->UnLock(); ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:40:0, from /home/sukesh/Downloads/root-6.08.04/include/TQObjectEmitVA.h:22, from /home/sukesh/Downloads/root-6.08.04/include/TQObject.h:215, from /home/sukesh/Downloads/root-6.08.04/include/TApplication.h:33, from HisMaker.hh:13, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TInterpreter.h: At global scope: /home/sukesh/Downloads/root-6.08.04/include/TInterpreter.h:67:4: warning: scoped enums only available with -std=c++11 or -std=gnu++11 [enabled by default] enum class EReturnType { kLong, kDouble, kString, kOther, kNoReturnType }; ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:40:0, from /home/sukesh/Downloads/root-6.08.04/include/TQObjectEmitVA.h:22, from /home/sukesh/Downloads/root-6.08.04/include/TQObject.h:215, from /home/sukesh/Downloads/root-6.08.04/include/TApplication.h:33, from HisMaker.hh:13, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TInterpreter.h:334:34: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template <typename U, typename... T> ^ /home/sukesh/Downloads/root-6.08.04/include/TInterpreter.h:335:74: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] void CallFunc_SetArgImpl(CallFunc_t func, const U& head, const T&... tail) ^ /home/sukesh/Downloads/root-6.08.04/include/TInterpreter.h:341:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template ^ /home/sukesh/Downloads/root-6.08.04/include/TInterpreter.h:342:61: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] void CallFunc_SetArguments(CallFunc_t func, const T&... args) ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TQObjectEmitVA.h:22:0, from /home/sukesh/Downloads/root-6.08.04/include/TQObject.h:215, from /home/sukesh/Downloads/root-6.08.04/include/TApplication.h:33, from HisMaker.hh:13, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:60:52: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default] TQConnection &operator=(const TQConnection &) = delete; ^ /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:76:50: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default] void ExecuteMethod(Int_t nargs, va_list va) = delete; ^ /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:78:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template inline void ExecuteMethod(const T&... params) ^ /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:78:67: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template inline void ExecuteMethod(const T&... params) ^ /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:93:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template inline void ExecuteMethod(Int_t / nargs /, const T&... params) ^ /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:93:86: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template inline void ExecuteMethod(Int_t / nargs /, const T&... params) ^ /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h: In member function ‘void TQConnection::ExecuteMethod(const T& ...)’: /home/sukesh/Downloads/root-6.08.04/include/TQConnection.h:80:28: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] if (!CheckSlot(sizeof...(params))) return; ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TQObject.h:215:0, from /home/sukesh/Downloads/root-6.08.04/include/TApplication.h:33, from HisMaker.hh:13, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TQObjectEmitVA.h: At global scope: /home/sukesh/Downloads/root-6.08.04/include/TQObjectEmitVA.h:25:19: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template inline ^ /home/sukesh/Downloads/root-6.08.04/include/TQObjectEmitVA.h:26:79: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] void TQObject::EmitVA(const char signal_name, Int_t / nargs /, const T&... params) ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TTree.h:66:0, from HisMaker.hh:18, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TClass.h:149:24: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default] Int_t fVerbLevel=0; ^ /home/sukesh/Downloads/root-6.08.04/include/TClass.h:150:7: error: ‘unordered_set’ in namespace ‘std’ does not name a type std::unordered_set fClassNamesSet; ^ /home/sukesh/Downloads/root-6.08.04/include/TClass.h:319:31: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default] TClass(const TClass& tc) = delete; ^ /home/sukesh/Downloads/root-6.08.04/include/TClass.h:320:39: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default] TClass& operator=(const TClass&) = delete; ^ /home/sukesh/Downloads/root-6.08.04/include/TClass.h: In member function ‘void TClass::Streamer(void, TBuffer&, const TClass) const’: /home/sukesh/Downloads/root-6.08.04/include/TClass.h:546:12: error: ‘t’ does not name a type auto t = fStreamerImpl.load(); ^ /home/sukesh/Downloads/root-6.08.04/include/TClass.h:547:32: error: ‘t’ was not declared in this scope t(this,obj,b,onfile_class); ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TTree.h:70:0, from HisMaker.hh:18, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TVirtualTreePlayer.h: At global scope: /home/sukesh/Downloads/root-6.08.04/include/TVirtualTreePlayer.h:47:11: error: ‘constexpr’ does not name a type static constexpr Long64_t kMaxEntries = std::numeric_limits::max(); ^ /home/sukesh/Downloads/root-6.08.04/include/TVirtualTreePlayer.h:47:11: note: C++11 ‘constexpr’ only available with -std=c++11 or -std=gnu++11 /home/sukesh/Downloads/root-6.08.04/include/TVirtualTreePlayer.h:53:55: error: ‘kMaxEntries’ was not declared in this scope ,Long64_t nentries=kMaxEntries, Long64_t firstentry=0) = 0; ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TTree.h:70:0, from HisMaker.hh:18, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TVirtualTreePlayer.h:85:56: error: ‘kMaxEntries’ was not declared in this scope ,Long64_t nentries=kMaxEntries, Long64_t firstentry=0) = 0; ^ /home/sukesh/Downloads/root-6.08.04/include/TVirtualTreePlayer.h:86:95: error: ‘kMaxEntries’ was not declared in this scope virtual Long64_t Process(const char filename,Option_t option="", Long64_t nentries=kMaxEntries, Long64_t firstentry=0) = 0; ^ /home/sukesh/Downloads/root-6.08.04/include/TVirtualTreePlayer.h:87:95: error: ‘kMaxEntries’ was not declared in this scope virtual Long64_t Process(TSelector selector,Option_t option="", Long64_t nentries=kMaxEntries, Long64_t firstentry=0) = 0; ^ In file included from HisMaker.hh:18:0, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TTree.h:154:43: error: ‘>>’ should be ‘> >’ within a nested template argument list std::vector<std::pair<Long64_t,TBranch>> fSortedBranches; ///<! Branches sorted by average task time ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:227:11: error: ‘constexpr’ does not name a type static constexpr Long64_t kMaxEntries = TVirtualTreePlayer::kMaxEntries; ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:227:11: note: C++11 ‘constexpr’ only available with -std=c++11 or -std=gnu++11 /home/sukesh/Downloads/root-6.08.04/include/TTree.h:361:103: error: ‘kMaxEntries’ was not declared in this scope virtual TTree CopyTree(const char selection, Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:367:119: error: ‘kMaxEntries’ was not declared in this scope virtual Long64_t Draw(const char varexp, const TCut& selection, Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:368:119: error: ‘kMaxEntries’ was not declared in this scope virtual Long64_t Draw(const char varexp, const char selection, Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); // MENU ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:374:169: error: ‘kMaxEntries’ was not declared in this scope virtual Int_t Fit(const char funcname, const char varexp, const char selection = "", Option_t option = "", Option_t goption = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); // MENU ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:486:136: error: ‘kMaxEntries’ was not declared in this scope TPrincipal Principal(const char varexp = "", const char selection = "", Option_t option = "np", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:489:101: error: ‘kMaxEntries’ was not declared in this scope virtual Long64_t Process(const char filename, Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); // MENU ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:495:100: error: ‘kMaxEntries’ was not declared in this scope virtual Long64_t Process(TSelector selector, Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:497:146: error: ‘kMaxEntries’ was not declared in this scope virtual Long64_t Project(const char hname, const char varexp, const char selection = "", Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:498:130: error: ‘kMaxEntries’ was not declared in this scope virtual TSQLResult Query(const char varexp = "", const char selection = "", Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:508:129: error: ‘kMaxEntries’ was not declared in this scope virtual Long64_t Scan(const char varexp = "", const char selection = "", Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); // MENU ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:551:61: error: ‘kMaxEntries’ was not declared in this scope virtual void SetMaxEntryLoop(Long64_t maxev = kMaxEntries) { fMaxEntryLoop = maxev; } // MENU ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h:567:153: error: ‘kMaxEntries’ was not declared in this scope virtual Int_t UnbinnedFit(const char funcname, const char varexp, const char selection = "", Option_t option = "", Long64_t nentries = kMaxEntries, Long64_t firstentry = 0); ^ /home/sukesh/Downloads/root-6.08.04/include/TTree.h: In member function ‘virtual void TTree::Draw(Option_t)’: /home/sukesh/Downloads/root-6.08.04/include/TTree.h:366:68: error: ‘kMaxEntries’ was not declared in this scope virtual void Draw(Option_t opt) { Draw(opt, "", "", kMaxEntries, 0); } ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TH1.h:65:0, from /home/sukesh/Downloads/root-6.08.04/include/TH1D.h:25, from HisMaker.hh:19, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h: At global scope: /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h:38:24: error: ‘shared_ptr’ in namespace ‘std’ does not name a type TFitResultPtr(const std::shared_ptr & p); ^ /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h:38:29: error: ISO C++ forbids declaration of ‘parameter’ with no type [-fpermissive] TFitResultPtr(const std::shared_ptr & p); ^ /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h:38:39: error: expected ‘,’ or ‘...’ before ‘<’ token TFitResultPtr(const std::shared_ptr & p); ^ /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h:38:4: error: ‘TFitResultPtr::TFitResultPtr(int)’ cannot be overloaded TFitResultPtr(const std::shared_ptr & p); ^ /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h:36:4: error: with ‘TFitResultPtr::TFitResultPtr(int)’ TFitResultPtr(int status = -1): fStatus(status), fPointer(0) {}; ^ /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h:59:4: error: ‘shared_ptr’ in namespace ‘std’ does not name a type std::shared_ptr fPointer; //! Smart Pointer to TFitResult class ^ /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h: In constructor ‘TFitResultPtr::TFitResultPtr(int)’: /home/sukesh/Downloads/root-6.08.04/include/TFitResultPtr.h:36:53: error: class ‘TFitResultPtr’ does not have any field named ‘fPointer’ TFitResultPtr(int status = -1): fStatus(status), fPointer(0) {}; ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TFormula.h:26:0, from /home/sukesh/Downloads/root-6.08.04/include/TF1.h:29, from HisMaker.hh:23, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h: At global scope: /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:44:10: error: expected nested-name-specifier before ‘EReturnType’ using EReturnType = TInterpreter::EReturnType; ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:44:10: error: using-declaration for non-member at class scope /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:44:22: error: expected ‘;’ before ‘=’ token using EReturnType = TInterpreter::EReturnType; ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:44:22: error: expected unqualified-id before ‘=’ token /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:47:17: error: ‘EReturnType’ does not name a type static const EReturnType kLong = TInterpreter::EReturnType::kLong; ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:48:17: error: ‘EReturnType’ does not name a type static const EReturnType kDouble = TInterpreter::EReturnType::kDouble; ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:49:17: error: ‘EReturnType’ does not name a type static const EReturnType kString = TInterpreter::EReturnType::kString; ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:50:17: error: ‘EReturnType’ does not name a type static const EReturnType kOther = TInterpreter::EReturnType::kOther; ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:51:17: error: ‘EReturnType’ does not name a type static const EReturnType kNoReturnType = TInterpreter::EReturnType::kNoReturnType; ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:53:17: error: ‘EReturnType’ does not name a type static const EReturnType kNone = TInterpreter::EReturnType::kNoReturnType; ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:66:4: error: ‘EReturnType’ does not name a type EReturnType fRetType; //method return type ^ In file included from /home/sukesh/Downloads/root-6.08.04/include/TFormula.h:26:0, from /home/sukesh/Downloads/root-6.08.04/include/TF1.h:29, from HisMaker.hh:23, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:98:4: error: ‘EReturnType’ does not name a type EReturnType ReturnType(); ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:108:22: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template void SetParams(const T&... params) { ^ /home/sukesh/Downloads/root-6.08.04/include/TMethodCall.h:108:56: warning: variadic templates only available with -std=c++11 or -std=gnu++11 [enabled by default] template void SetParams(const T&... params) { ^ In file included from HisMaker.hh:23:0, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TF1.h:156:4: warning: scoped enums only available with -std=c++11 or -std=gnu++11 [enabled by default] enum class EAddToList { ^ /home/sukesh/Downloads/root-6.08.04/include/TF1.h:217:110: error: ‘EAddToList’ is not a class or namespace TF1(const char name, const char formula, Double_t xmin=0, Double_t xmax = 1, EAddToList addToGlobList = EAddToList::kDefault); ^ In file included from HisMaker.hh:23:0, from cnvnator.cpp:8: /home/sukesh/Downloads/root-6.08.04/include/TF1.h:218:110: error: ‘EAddToList’ is not a class or namespace TF1(const char name, Double_t xmin, Double_t xmax, Int_t npar,Int_t ndim = 1, EAddToList addToGlobList = EAddToList::kDefault); ^ /home/sukesh/Downloads/root-6.08.04/include/TF1.h:219:158: error: ‘EAddToList’ is not a class or namespace TF1(const char name, Double_t (fcn)(Double_t , Double_t ), Double_t xmin=0, Double_t xmax=1, Int_t npar=0, Int_t ndim = 1, EAddToList addToGlobList = EAddToList::kDefault); ^ /home/sukesh/Downloads/root-6.08.04/include/TF1.h:220:169: error: ‘EAddToList’ is not a class or namespace TF1(const char name, Double_t (fcn)(const Double_t , const Double_t ), Double_t xmin=0, Double_t xmax=1, Int_t npar=0,Int_t ndim = 1, EAddToList addToGlobList = EAddToList::kDefault); ^ /home/sukesh/Downloads/root-6.08.04/include/TF1.h:223:150: error: ‘EAddToList’ is not a class or namespace TF1(const char name, ROOT::Math::ParamFunctor f, Double_t xmin = 0, Double_t xmax = 1, Int_t npar = 0,Int_t ndim = 1, EAddToList addToGlobList = EAddToList::kDefault); ^ /home/sukesh/Downloads/root-6.08.04/include/TF1.h:234:118: error: ‘EAddToList’ is not a class or namespace TF1(const char name, Func f, Double_t xmin, Double_t xmax, Int_t npar,Int_t ndim = 1, EAddToList addToGlobList = EAddToList::kDefault ); ^ /home/sukesh/Downloads/root-6.08.04/include/TF1.h:238:117: error: ‘EAddToList’ is not a class or namespace TF1(const char name, Func f, Double_t xmin, Double_t xmax, Int_t npar, const char , EAddToList addToGlobList = EAddToList::kDefault ) : ^ /home/sukesh/Downloads/root-6.08.04/include/TF1.h:268:141: error: ‘EAddToList’ is not a class or namespace TF1(const char name, const PtrObj& p, MemFn memFn, Double_t xmin, Double_t xmax, Int_t npar,Int_t ndim = 1, EAddToList addToGlobList = EAddToList::kDefault) : ^ /home/sukesh/Downloads/root-6.08.04/include/TF1.h:289:154: error: ‘EAddToList’ is not a class or namespace TF1(const char name, const PtrObj& p, MemFn memFn, Double_t xmin, Double_t xmax, Int_t npar,const char , const char , EAddToList addToGlobList = EAddToList::kDefault) : ^ make: *** [obj/cnvnator.o] Error 1

Thanks Sukesh

abyzov commented 7 years ago

Hi, could be incompatibility with compiler. Are you able to run ROOT?

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

sukesh14 commented 7 years ago

Dear Sir.

I can run the ROOT from bin folder of ROOT using the command ./root. In the bashrc i mentioned path for thisroot.sh.

Thanks Sukesh

From: "abyzov" notifications@github.com To: "abyzovlab/CNVnator" CNVnator@noreply.github.com Cc: "sukesh14" sukesh.k@ktr.srmuniv.ac.in, "Author" author@noreply.github.com Sent: Wednesday, March 22, 2017 10:33:01 PM Subject: Re: [abyzovlab/CNVnator] Issue installing CNVnator (#59)

Hi, could be incompatibility with compiler. Are you able to run ROOT?

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or mute the thread .

abyzov commented 7 years ago

HI, which compiler are your using?

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

sukesh14 commented 7 years ago

Dear Sir,

Thanks for your reply. I am using g++ v4.8.4 and gcc 4.8.4 compilers.

Thanks Sukesh

sukesh14 commented 7 years ago

Dear Sir,

I installed CNVnator using cnvnator packager. (https://github.com/indraniel/cnvnator-packager). Can i use this software for plants?

abyzov commented 7 years ago

Great! Currently CNVnator is intended for diploid genomes. If the ploidy of plants you are aiming at studying is higher then CNVnator will have limited abilities.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

sukesh14 commented 7 years ago

Dear Sir,

Thank you for your information. I tried to predict the cnvs for rice genome. According to tutorial, i ran the first command to extract the regions for each chromosome separately using bam files. Now when i run the first step using the below command i did not get any error and one root file is created.

First command

./cnvnator -root newseec8.root -genome chr08.fasta -chrom chr08 -tree seechr08.bam

new root file is generated, but i could not know how to visualize this file in root software.

But, for second step for histogram - when i run this using the below command

./cnvnator -root newseec8.root -genome chr08.fasta -chrom chr08 -his 100

It gives me below message

Allocating memory ... Done. Calculating histograms with bin size of 100 for 'chr08' ... Making GC histogram for 'chr08' ... Can't open file with chromosome sequence. No chromosome/contig information parsed. Sequence length (0) is different from expectation (28443022) for 'chr08'. Doing nothing! Done.

I just want to know what is the mistake i committed for generating the histogram. And another question i wanted to know how to set the bin size. I tried bin size 4 by reading your paper, but still i get the same above message. We did whole genome sequencing using 10x.

Thanks Sukesh

From: "abyzov" notifications@github.com To: "abyzovlab/CNVnator" CNVnator@noreply.github.com Cc: "sukesh14" sukesh.k@ktr.srmuniv.ac.in, "Author" author@noreply.github.com Sent: Tuesday, March 28, 2017 10:35:46 AM Subject: Re: [abyzovlab/CNVnator] Issue installing CNVnator (#59)

Great! Currently CNVnator is intended for diploid genomes. If the ploidy of plants you are aiming at studying is higher then CNVnator will have limited abilities.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or mute the thread .

abyzov commented 7 years ago

Hi, files should be named as: chr1.fa, chr2.fa, etc.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

dangpandora commented 7 years ago

hello, sukesh14 @sukesh14 , I am running into exactly the same issue as you did, do you mind telling me how did you solve the issue at the end? is the compiler the reason causing problem ? Thanks a lot

sukesh14 commented 7 years ago

Dear Sir,

No. I tried the normal way for installing cnvnator, it did not work out. Later, i found cnvnator packager and installed it (https://github.com/indraniel/cnvnator-packagerIt worked out).

Root version was also another problem so i changed the root version 6.08 which is compatible with cnvnator 0.32.

From: "dangpandora" notifications@github.com To: "abyzovlab/CNVnator" CNVnator@noreply.github.com Cc: "sukesh14" sukesh.k@ktr.srmuniv.ac.in, "Mention" mention@noreply.github.com Sent: Wednesday, May 10, 2017 1:33:41 AM Subject: Re: [abyzovlab/CNVnator] Issue installing CNVnator (#59)

hello, sukesh14 @sukesh14 , I am running into exactly the same issue as you did, do you minding telling me how did you solve the issue at the end? is the compiler the reason causing problem ? Thanks a lot

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub , or mute the thread .

dangpandora commented 7 years ago

@sukesh14 Thank you very much for the quick reply, it helps

sukesh14 commented 7 years ago

Dear Sir,

I am predicting cnv regions for three rice genomes using three cnv softwares like pindel, cnvnator and breakdancer. We are considering the best results, if at least two softwares out of three predict the same results. I have a doubt, if we find overlap between CNVs reported by two softwares, should we take only overlapping regions for wet lab study or from smallest start coordinate to largest coordinate?

Thanks Sukesh

----- Original Message ----- From: "dangpandora" notifications@github.com To: "abyzovlab/CNVnator" CNVnator@noreply.github.com Cc: "sukesh14" sukesh.k@ktr.srmuniv.ac.in, "Mention" mention@noreply.github.com Sent: Wednesday, May 10, 2017 7:12:12 PM Subject: Re: [abyzovlab/CNVnator] Issue installing CNVnator (#59)

@sukesh14 Thank you very much for the quick reply, it helps

-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/abyzovlab/CNVnator/issues/59#issuecomment-300485471

abyzov commented 7 years ago

Hi, breakdance and pindel have better breakpoint resolution. So, I would think they you should consider their breakpoints for downstream experiments.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

zzy3ly commented 10 months ago

hello,i get this problem when i make.CNVnator V0.3.2and root6.22 the erro:/app/root/include/ROOT/libcpp_string_view.h:275:63: error: 'numeric_limits' is not a member of 'std' 275 | size_type max_size() const _NOEXCEPT { return (_VSTD::numeric_limits::max)(); } | ^~~~~~ /app/root/include/ROOT/libcpp_string_view.h:275:87: error: expected primary-expression before '>' token 275 | size_type max_size() const _NOEXCEPT { return (_VSTD::numeric_limits::max)(); } | ^ make: *** [Makefile:63: obj/cnvnator.o] Error 1