Merge pull request #25231 from veprbl/root_6.09.02

root: 6.08.02 -> 6.09.02

pkgs/applications/science/misc/root/ROOT-8728-extra.patch

@@ -0,0 +1,200 @@
+diff --git a/core/base/inc/ROOT/StringConv.hxx b/core/base/inc/ROOT/StringConv.hxx
+index 629fc18..4efa54a 100644
+--- a/core/base/inc/ROOT/StringConv.hxx
++++ b/core/base/inc/ROOT/StringConv.hxx
+@@ -89,7 +89,7 @@ EFromHumanReadableSize FromHumanReadableSize(std::string_view str, T &value)
+       size_t size = str.size();
+       size_t cur;
+       // Parse leading numeric factor
+-      const double coeff = stod(str, &cur);
++      const double coeff = stod(static_cast<std::string>(str), &cur);
+ 
+       // Skip any intermediate white space
+       while (cur<size && isspace(str[cur])) ++cur;
+diff --git a/core/metacling/src/TCling.cxx b/core/metacling/src/TCling.cxx
+index d71cb74..076facb 100644
+--- a/core/metacling/src/TCling.cxx
++++ b/core/metacling/src/TCling.cxx
+@@ -756,7 +756,7 @@ int TCling_GenerateDictionary(const std::vector<std::string> &classes,
+                gSystem->PrependPathName(dirbase, header);
+                dir = gSystem->DirName(dir);
+             }
+-            fileContent += TString("#include \"") + header + "\"\n";
++            fileContent += (TString("#include \"") + header + "\"\n").Data();
+          }
+       }
+       for (it = fwdDecls.begin(); it != fwdDecls.end(); ++it) {
+@@ -1061,7 +1061,7 @@ TCling::TCling(const char *name, const char *title)
+       ROOT::TMetaUtils::SetPathsForRelocatability(clingArgsStorage);
+ 
+       // Add -I early so ASTReader can find the headers.
+-      std::string interpInclude(TROOT::GetEtcDir());
++      std::string interpInclude(TROOT::GetEtcDir().Data());
+       clingArgsStorage.push_back("-I" + interpInclude);
+ 
+       // Add include path to etc/cling. FIXME: This is a short term solution. The
+@@ -1070,7 +1070,7 @@ TCling::TCling(const char *name, const char *title)
+       clingArgsStorage.push_back("-I" + interpInclude + "/cling");
+ 
+       // Add the root include directory and etc/ to list searched by default.
+-      clingArgsStorage.push_back(std::string("-I" + TROOT::GetIncludeDir()));
++      clingArgsStorage.push_back(std::string(("-I" + TROOT::GetIncludeDir()).Data()));
+ 
+       // Add the current path to the include path
+       // TCling::AddIncludePath(".");
+diff --git a/hist/hist/src/TFormula.cxx b/hist/hist/src/TFormula.cxx
+index abf3929..e7dad98 100644
+--- a/hist/hist/src/TFormula.cxx
++++ b/hist/hist/src/TFormula.cxx
+@@ -1677,7 +1677,7 @@ void TFormula::ProcessFormula(TString &formula)
+          if(fun.fName.Contains("::")) // add support for nested namespaces
+          {
+             // look for last occurence of "::"
+-            std::string name(fun.fName);
++            std::string name(fun.fName.Data());
+             size_t index = name.rfind("::");
+             assert(index != std::string::npos);
+             TString className = fun.fName(0,fun.fName(0,index).Length());
+@@ -1869,7 +1869,7 @@ void TFormula::ProcessFormula(TString &formula)
+ 
+          // save copy of inputFormula in a std::strig for the unordered map
+          // and also formula is same as FClingInput typically and it will be modified
+-         std::string inputFormula = std::string(formula);
++         std::string inputFormula = std::string(formula.Data());
+ 
+ 
+          // valid input formula - try to put into Cling
+diff --git a/main/src/nbmain.cxx b/main/src/nbmain.cxx
+index 55d4f2f..8490149 100644
+--- a/main/src/nbmain.cxx
++++ b/main/src/nbmain.cxx
+@@ -173,9 +173,9 @@ static bool CreateStamp(string dest)
+ 
+ int main()
+ {
+-   string rootbin(TROOT::GetBinDir());
+-   string rootlib(TROOT::GetLibDir());
+-   string rootetc(TROOT::GetEtcDir());
++   string rootbin(TROOT::GetBinDir().Data());
++   string rootlib(TROOT::GetLibDir().Data());
++   string rootetc(TROOT::GetEtcDir().Data());
+ 
+    // If needed, install ROOT notebook files in the user's home directory
+ #ifdef WIN32
+diff --git a/math/minuit/src/TMinuitMinimizer.cxx b/math/minuit/src/TMinuitMinimizer.cxx
+index 4e2082a..18215c0 100644
+--- a/math/minuit/src/TMinuitMinimizer.cxx
++++ b/math/minuit/src/TMinuitMinimizer.cxx
+@@ -454,7 +454,7 @@ std::string TMinuitMinimizer::VariableName(unsigned int ivar) const {
+    // return the variable name
+    if (!CheckMinuitInstance()) return std::string();
+    if (!CheckVarIndex(ivar)) return std::string();
+-   return std::string(fMinuit->fCpnam[ivar]);
++   return std::string(fMinuit->fCpnam[ivar].Data());
+ }
+ 
+ int TMinuitMinimizer::VariableIndex(const std::string & ) const {
+diff --git a/tmva/tmva/src/Factory.cxx b/tmva/tmva/src/Factory.cxx
+index 36060ef..a1bbe34 100644
+--- a/tmva/tmva/src/Factory.cxx
++++ b/tmva/tmva/src/Factory.cxx
+@@ -390,7 +390,7 @@ TMVA::MethodBase* TMVA::Factory::BookMethod( TMVA::DataLoader *loader, TString t
+    // initialize methods
+    IMethod* im;
+    if (!boostNum) {
+-      im = ClassifierFactory::Instance().Create( std::string(theMethodName),
++      im = ClassifierFactory::Instance().Create( std::string(theMethodName.Data()),
+                                                  fJobName,
+                                                  methodTitle,
+                                                  loader->DefaultDataSetInfo(),
+@@ -933,7 +933,7 @@ void TMVA::Factory::TrainAllMethods()
+ 
+        // recreate
+        m = dynamic_cast<MethodBase*>( ClassifierFactory::Instance()
+-                   .Create( std::string(Types::Instance().GetMethodName(methodType)),
++                   .Create( std::string(Types::Instance().GetMethodName(methodType).Data()),
+                       dataSetInfo, weightfile ) );
+        if( m->GetMethodType() == Types::kCategory ){
+       MethodCategory *methCat = (dynamic_cast<MethodCategory*>(m));
+diff --git a/tmva/tmva/src/MethodBoost.cxx b/tmva/tmva/src/MethodBoost.cxx
+index 1349e5d..2125ab3 100644
+--- a/tmva/tmva/src/MethodBoost.cxx
++++ b/tmva/tmva/src/MethodBoost.cxx
+@@ -389,7 +389,7 @@ void TMVA::MethodBoost::Train()
+       // the first classifier shows the option string output, the rest not
+       if (fCurrentMethodIdx>0) TMVA::MsgLogger::InhibitOutput();
+ 
+-      IMethod* method = ClassifierFactory::Instance().Create(std::string(fBoostedMethodName),
++      IMethod* method = ClassifierFactory::Instance().Create(std::string(fBoostedMethodName.Data()),
+                                                              GetJobName(),
+                                                              Form("%s_B%04i", fBoostedMethodTitle.Data(),fCurrentMethodIdx),
+                                                              DataInfo(),
+diff --git a/tmva/tmva/src/MethodCategory.cxx b/tmva/tmva/src/MethodCategory.cxx
+index c2cbe80..d278cca 100644
+--- a/tmva/tmva/src/MethodCategory.cxx
++++ b/tmva/tmva/src/MethodCategory.cxx
+@@ -147,7 +147,7 @@ TMVA::IMethod* TMVA::MethodCategory::AddMethod( const TCut& theCut,
+                                                 const TString& theTitle,
+                                                 const TString& theOptions )
+ {
+-   std::string addedMethodName = std::string(Types::Instance().GetMethodName(theMethod));
++   std::string addedMethodName = std::string(Types::Instance().GetMethodName(theMethod).Data());
+ 
+    Log() << kINFO << "Adding sub-classifier: " << addedMethodName << "::" << theTitle << Endl;
+ 
+diff --git a/tmva/tmva/src/MethodCompositeBase.cxx b/tmva/tmva/src/MethodCompositeBase.cxx
+index 98fa5da..96bd9a3 100644
+--- a/tmva/tmva/src/MethodCompositeBase.cxx
++++ b/tmva/tmva/src/MethodCompositeBase.cxx
+@@ -194,7 +194,7 @@ void TMVA::MethodCompositeBase::ReadWeightsFromXML( void* wghtnode )
+          ((TMVA::MethodBoost*)this)->BookMethod( Types::Instance().GetMethodType( methodTypeName), methodName,  optionString );
+       }
+       fMethods.push_back(ClassifierFactory::Instance().Create(
+-                                                              std::string(methodTypeName),jobName, methodName,DataInfo(),optionString));
++                                                              std::string(methodTypeName.Data()),jobName, methodName,DataInfo(),optionString));
+ 
+       fMethodWeight.push_back(methodWeight);
+       MethodBase* meth = dynamic_cast<MethodBase*>(fMethods.back());
+@@ -259,7 +259,7 @@ void  TMVA::MethodCompositeBase::ReadWeightsFromStream( std::istream& istr )
+             ((TMVA::MethodBoost*)this)->BookMethod( Types::Instance().GetMethodType( methodName), methodTitle,  optionString );
+       }
+       else methodTitle=Form("%s (%04i)",GetMethodName().Data(),fCurrentMethodIdx);
+-      fMethods.push_back(ClassifierFactory::Instance().Create( std::string(methodName), jobName,
++      fMethods.push_back(ClassifierFactory::Instance().Create( std::string(methodName.Data()), jobName,
+                                                                methodTitle,DataInfo(), optionString) );
+       fMethodWeight.push_back( methodWeight );
+       if(MethodBase* m = dynamic_cast<MethodBase*>(fMethods.back()) )
+diff --git a/tmva/tmva/src/Reader.cxx b/tmva/tmva/src/Reader.cxx
+index 94a8b28..0b67867 100644
+--- a/tmva/tmva/src/Reader.cxx
++++ b/tmva/tmva/src/Reader.cxx
+@@ -401,7 +401,7 @@ TMVA::IMethod* TMVA::Reader::BookMVA( const TString& methodTag, const TString& w
+ 
+ TMVA::IMethod* TMVA::Reader::BookMVA( TMVA::Types::EMVA methodType, const TString& weightfile )
+ {
+-   IMethod* im = ClassifierFactory::Instance().Create(std::string(Types::Instance().GetMethodName( methodType )),
++   IMethod* im = ClassifierFactory::Instance().Create(std::string(Types::Instance().GetMethodName( methodType ).Data()),
+                                                       DataInfo(), weightfile );
+ 
+    MethodBase *method = (dynamic_cast<MethodBase*>(im));
+@@ -440,7 +440,7 @@ TMVA::IMethod* TMVA::Reader::BookMVA( TMVA::Types::EMVA methodType, const char*
+ #if ROOT_VERSION_CODE >= ROOT_VERSION(5,26,00)
+ 
+    // books MVA method from weightfile
+-   IMethod* im = ClassifierFactory::Instance().Create(std::string(Types::Instance().GetMethodName( methodType )),
++   IMethod* im = ClassifierFactory::Instance().Create(std::string(Types::Instance().GetMethodName( methodType ).Data()),
+                                                       DataInfo(), "" );
+ 
+    MethodBase *method = (dynamic_cast<MethodBase*>(im));
+diff -aru a/core/base/inc/TString.h b/core/base/inc/TString.h
+--- a/core/base/inc/TString.h
++++ b/core/base/inc/TString.h
+@@ -106,7 +106,7 @@
+    char          operator[](Ssiz_t i) const;     // Index with bounds checking
+ 
+    operator std::string_view() const { return std::string_view(Data(),fExtent); }
+-   operator std::string() const { return std::string_view(Data(),fExtent).to_string(); }
++   operator std::string() const { return static_cast<std::string>(std::string_view(Data(),fExtent)); }
+ 
+    const char   *Data() const;
+    Ssiz_t        Length() const          { return fExtent; }

pkgs/applications/science/misc/root/default.nix

@@ -1,18 +1,19 @@
 { stdenv, fetchurl, fetchpatch, cmake, pcre, pkgconfig, python2
-, libX11, libXpm, libXft, libXext, zlib, lzma, gsl, Cocoa }:
+, libX11, libXpm, libXft, libXext, mesa, zlib, libxml2, lzma, gsl
+, Cocoa, OpenGL }:
 
 stdenv.mkDerivation rec {
   name = "root-${version}";
-  version = "6.08.02";
+  version = "6.09.02";
 
   src = fetchurl {
     url = "https://root.cern.ch/download/root_v${version}.source.tar.gz";
-    sha256 = "0530v1r4rvds52hgb13f00l3phhn76z6vii550mwv8bj3sl5070k";
+    sha256 = "0fc6b0l7bw66cyckxs4ikvyzcv1zlfx88205jx153smdhih0jj2k";
   };
 
-  buildInputs = [ cmake pcre pkgconfig python2 zlib lzma gsl ]
+  buildInputs = [ cmake pcre pkgconfig python2 zlib libxml2 lzma gsl ]
-    ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext ]
+    ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext mesa ]
-    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa ]
+    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
     ;
 
   patches = [
@@ -20,6 +21,13 @@ stdenv.mkDerivation rec {
 
     # this prevents thisroot.sh from setting $p, which interferes with stdenv setup
     ./thisroot.patch
+
+    # https://sft.its.cern.ch/jira/browse/ROOT-8728
+    (fetchpatch {
+      url = "https://sft.its.cern.ch/jira/secure/attachment/20025/0001-std-string_view-has-no-more-to_string.patch";
+      sha256 = "0ngyk960xfrcsj4vhr1ax8h85fx0g1cfycxi3k35a6ych2zmyg8q";
+    })
+    ./ROOT-8728-extra.patch
   ];
 
   preConfigure = ''
@@ -47,7 +55,7 @@ stdenv.mkDerivation rec {
     "-Dmonalisa=OFF"
     "-Dmysql=OFF"
     "-Dodbc=OFF"
-    "-Dopengl=OFF"
+    "-Dopengl=ON"
     "-Doracle=OFF"
     "-Dpgsql=OFF"
     "-Dpythia6=OFF"
@@ -55,7 +63,7 @@ stdenv.mkDerivation rec {
     "-Drfio=OFF"
     "-Dsqlite=OFF"
     "-Dssl=OFF"
-    "-Dxml=OFF"
+    "-Dxml=ON"
     "-Dxrootd=OFF"
   ]
   ++ stdenv.lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${stdenv.lib.getDev stdenv.cc.libc}/include";

pkgs/applications/science/misc/root/sw_vers.patch

@@ -25,7 +25,7 @@ diff --git a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake
 -                  COMMAND cut -d . -f 2
 -                  OUTPUT_VARIABLE MACOSX_MINOR OUTPUT_STRIP_TRAILING_WHITESPACE)
 -
--  if(MACOSX_VERSION VERSION_GREATER 10.7 AND ${CMAKE_CXX_COMPILER_ID} STREQUAL Clang)
+-  if(MACOSX_VERSION VERSION_GREATER 10.7 AND ${CMAKE_CXX_COMPILER_ID} MATCHES Clang)
      set(libcxx ON CACHE BOOL "Build using libc++" FORCE)
 -  endif()
  

pkgs/applications/science/physics/sherpa/default.nix

@@ -13,6 +13,9 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  # LLVM 4 doesn't allow ambigous type in std::abs argument
+  patches = stdenv.lib.optional stdenv.cc.isClang [ ./explicit_overloads.patch ];
+
   configureFlags = [
     "--with-sqlite3=${sqlite.dev}"
     "--enable-hepmc2=${hepmc}"

pkgs/applications/science/physics/sherpa/explicit_overloads.patch

@@ -0,0 +1,119 @@
+diff --git a/ATOOLS/Phys/Flavour.C b/ATOOLS/Phys/Flavour.C
+index 1986348..740eea3 100644
+--- a/ATOOLS/Phys/Flavour.C
++++ b/ATOOLS/Phys/Flavour.C
+@@ -298,8 +298,8 @@ std::string Flavour::IDName() const
+ 
+ bool Flavour::IsDiQuark() const 
+ {
+-  if(abs(Kfcode())>=1103&&abs(Kfcode())<=5505) {
+-    double help=abs(Kfcode())/100.0-int(abs(Kfcode())/100.0); 
++  if(abs((long)Kfcode())>=1103&&abs((long)Kfcode())<=5505) {
++    double help=abs((long)Kfcode())/100.0-int(abs((long)Kfcode())/100.0); 
+     if(help<0.031) return true;
+   }
+   return false;
+@@ -307,27 +307,27 @@ bool Flavour::IsDiQuark() const
+ 
+ bool Flavour::IsBaryon() const 
+ {
+-  if (abs(Kfcode())%10000<1000) return false;
++  if (abs((long)Kfcode())%10000<1000) return false;
+   return !IsDiQuark();
+ }
+ 
+ bool Flavour::IsB_Hadron() const 
+ {
+-  if (abs(Kfcode())<100)                            return 0;
++  if (abs((long)Kfcode())<100)                            return 0;
+   if (Kfcode()-100*int(Kfcode()/100)<10)                 return 0;
+-  if (abs((Kfcode()-100*int(Kfcode()/100))/10)==5)       return 1;
+-  if (abs((Kfcode()-1000*int(Kfcode()/1000))/100)==5)    return 1;
+-  if (abs((Kfcode()-10000*int(Kfcode()/10000))/1000)==5) return 1;
++  if (abs((long)(Kfcode()-100*int(Kfcode()/100))/10)==5)       return 1;
++  if (abs((long)(Kfcode()-1000*int(Kfcode()/1000))/100)==5)    return 1;
++  if (abs((long)(Kfcode()-10000*int(Kfcode()/10000))/1000)==5) return 1;
+   return 0;
+ }
+ 
+ bool Flavour::IsC_Hadron() const 
+ {
+-  if (abs(Kfcode())<100)                            return 0;
++  if (abs((long)Kfcode())<100)                            return 0;
+   if (Kfcode()-100*int(Kfcode()/100)<10)                 return 0;
+-  if (abs((Kfcode()-100*int(Kfcode()/100))/10)==4)       return 1;
+-  if (abs((Kfcode()-1000*int(Kfcode()/1000))/100)==4)    return 1;
+-  if (abs((Kfcode()-10000*int(Kfcode()/10000))/1000)==4) return 1;
++  if (abs((long)(Kfcode()-100*int(Kfcode()/100))/10)==4)       return 1;
++  if (abs((long)(Kfcode()-1000*int(Kfcode()/1000))/100)==4)    return 1;
++  if (abs((long)(Kfcode()-10000*int(Kfcode()/10000))/1000)==4) return 1;
+   return 0;
+ }
+ 
+diff --git a/AddOns/Pythia/Pythia_Jet_Criterion.C b/AddOns/Pythia/Pythia_Jet_Criterion.C
+index bbe9597..c1201e1 100644
+--- a/AddOns/Pythia/Pythia_Jet_Criterion.C
++++ b/AddOns/Pythia/Pythia_Jet_Criterion.C
+@@ -117,8 +117,8 @@ namespace PYTHIA {
+       double Qsq = sign * Q.Abs2();
+       // Mass term of radiator
+       DEBUG_VAR(ampl->MS());
+-      double m2Rad = ( abs(RadAfterBranch.Flav().Kfcode()) >= 4
+-                   && abs(RadAfterBranch.Flav().Kfcode()) < 7)
++      double m2Rad = ( abs((long)RadAfterBranch.Flav().Kfcode()) >= 4
++                   && abs((long)RadAfterBranch.Flav().Kfcode()) < 7)
+                    ? ampl->MS()->Mass2(RadAfterBranch.Flav())
+                    : 0.;
+       // Construct 2->3 variables for FSR
+diff --git a/BEAM/Main/EPA.C b/BEAM/Main/EPA.C
+index 861a1b2..340ac33 100644
+--- a/BEAM/Main/EPA.C
++++ b/BEAM/Main/EPA.C
+@@ -54,7 +54,7 @@ double EPA::CosInt::GetCosInt(double X)
+ 
+ double EPA::phi(double x, double qq)
+ {
+-  if (abs(m_beam.Kfcode()) == kf_p_plus) {
++  if (abs((long)m_beam.Kfcode()) == kf_p_plus) {
+     const double a = 7.16;
+     const double b = -3.96;
+     const double c = .028;
+@@ -179,7 +179,7 @@ bool EPA::CalculateWeight(double x,double q2)
+     m_weight=0.0;
+     return 1;
+   }
+-  if (abs(m_beam.Kfcode()) == kf_e) {
++  if (abs((long)m_beam.Kfcode()) == kf_e) {
+     double f = alpha/M_PI*(1+sqr(1-m_x))/m_x*log(2.*m_energy/m_mass);
+     if (f < 0) f = 0.;
+     m_weight = f;
+@@ -187,7 +187,7 @@ bool EPA::CalculateWeight(double x,double q2)
+ 	     <<"energy = "<<m_energy<<", "<<"mass = "<<m_mass<<".\n";
+     return 1;    
+   }
+-  else if (abs(m_beam.Kfcode()) == kf_p_plus) {
++  else if (abs((long)m_beam.Kfcode()) == kf_p_plus) {
+     const double qz = 0.71;
+     double f, qmi, qma;
+     qma=m_q2Max/qz;
+diff --git a/PDF/Remnant/Hadron_Remnant.C b/PDF/Remnant/Hadron_Remnant.C
+index 243717c..58c2278 100644
+--- a/PDF/Remnant/Hadron_Remnant.C
++++ b/PDF/Remnant/Hadron_Remnant.C
+@@ -188,13 +188,13 @@ ATOOLS::Flavour Hadron_Remnant::Opposite(ATOOLS::Flavour flav) const
+     if (m_constit[i]==flav && !found) found=true;
+     else rem[j++]=m_constit[i].Kfcode();
+   }
+-  Flavour anti=Flavour((kf_code)(abs(rem[0])*1000+abs(rem[1])*100+3));
++  Flavour anti=Flavour((kf_code)(abs((long)rem[0])*1000+abs((long)rem[1])*100+3));
+   if (rem[0]!=rem[1]) {
+     if (ran->Get()<0.25) 
+-      anti=Flavour((kf_code)(abs(rem[0])*1000+abs(rem[1])*100+1));
++      anti=Flavour((kf_code)(abs((long)rem[0])*1000+abs((long)rem[1])*100+1));
+   }
+   else {
+-    anti=Flavour((kf_code)(abs(rem[0])*1100+3));
++    anti=Flavour((kf_code)(abs((long)rem[0])*1100+3));
+   }
+   if (flav.IsAnti()) anti=anti.Bar();
+   return anti;

pkgs/top-level/all-packages.nix

@@ -18002,7 +18002,7 @@ with pkgs;
   megam = callPackage ../applications/science/misc/megam { };
 
   root = callPackage ../applications/science/misc/root {
-    inherit (darwin.apple_sdk.frameworks) Cocoa;
+    inherit (darwin.apple_sdk.frameworks) Cocoa OpenGL;
   };
 
   simgrid = callPackage ../applications/science/misc/simgrid { };