Install log for 'Seurat'

* installing *source* package ‘Seurat’ ...
** this is package ‘Seurat’ version ‘5.5.0’
** package ‘Seurat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using C++17
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c ModularityOptimizer.cpp -o ModularityOptimizer.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RModularityOptimizer.cpp -o RModularityOptimizer.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_manipulation.cpp -o data_manipulation.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c fast_NN_dist.cpp -o fast_NN_dist.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c integration.cpp -o integration.o
ModularityOptimizer.cpp:761:7: warning: unused variable 'n1_max' [-Wunused-variable]
  761 |   int n1_max = *std::max_element(node1.cbegin(), node1.cend());
      |       ^~~~~~
ModularityOptimizer.cpp:762:7: warning: unused variable 'n2_max' [-Wunused-variable]
  762 |   int n2_max = *std::max_element(node2.cbegin(), node2.cend());
      |       ^~~~~~
In file included from fast_NN_dist.cpp:1:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp.h:49:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp/Function.h:75:65: error: use of undeclared identifier 'R_NamespaceRegistry'
   75 |             Shield<SEXP> env(R_getVarEx(Rf_install(ns.c_str()), R_NamespaceRegistry, FALSE, R_UnboundValue));
      |                                                                 ^
1 error generated.
make: *** [fast_NN_dist.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from data_manipulation.cpp:1:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       Index count = 0;
      |             ^
273In file included from integration.cpp:1:
In file included from  |   /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25    Index count = 0;
      |             ^:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h
:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from integration.cpp:1:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
In file included from data_manipulation.cpp:1:
In file included from In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78In file included from RcppExports.cpp:4 | :  Index nsuper_et_post = 0; /:
/ N29:
uIn file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
mb   78 | In file included from e/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]r of relaxed 
 snode   78 |   Index  Index nsupersn_ inet_ postorderedps etree 
      |         ^
ouper_/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.hst = 0e:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
t; /_post = / N   79 | umber of relaxed snodes in postordered etree 
      |         ^
 /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h0; / Ind:79:9/ Number of re: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
laxex nsuped snode   er_et = 0; // Numbers in postordered etree 
      |         ^
79 |  of relaxed snodes in the original/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9:  e  Indetree 
      |         ^
warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
x nsuper_et =   79 |   Index  0; nsu// Numper_et = 0; // Nubermbe of rer olaxf relaed snoxeddes in the or snigiodenal etres in te 
he       |         ^original etree 
      |         ^

In file included from RModularityOptimizer.cpp:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:61:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from RModularityOptimizer.cpp:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from integration.cpp:1:
In file included from In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.hdata_manipulation.cpp:1:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:In file included from 31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h::25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:31:
:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:72:1046:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
72:10   72 | : warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
:                    warning: variable 'replacements' set but not used [-Wunused-but-set-variable]        Ind72 | 
                        ex Indreplacementsex repl   72 |                         Indacementex =  reps =lacements0;
 =       |                               ^
0;
 0;
      |       |                               ^
                              ^
In file included from RModularityOptimizer.cpp:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from RModularityOptimizer.cpp:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from integration.cpp:1In file included from data_manipulation.cpp:1:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count :
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45= 0;
      |       ^
:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from RModularityOptimizer.cpp:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp.h:49:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp/Function.h:75:65: error: use of undeclared identifier 'R_NamespaceRegistry'
   75 |             Shield<SEXP> env(R_getVarEx(Rf_install(ns.c_str()), R_NamespaceRegistry, FALSE, R_UnboundValue));
      |                                                                 ^
In file included from RcppExports.cpp:4:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp.h:49:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp/Function.h:75:65: error: use of undeclared identifier 'R_NamespaceRegistry'
In file included from integration.cpp:1:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp.h:49:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp/Function.h:75:65: error: use of undeclared identifier 'R_NamespaceRegistry'
      75 |        75 |          Shie   ld<SEXP     Shield<SEXP> env(R> env(R_ge_getVatVarEx(Rf_irExnstall(ns.c_st(RfIn file included from data_manipulation.cpp:1:
_r()), R_In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp.h:49iNamesnstapaceRe:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/Rcpp/include/Rcpp/Function.h:75:65gistry, FALSE, R_UnboundValue)): error: use of undeclared identifier 'R_NamespaceRegistry'
ll(ns.   ;
      |                                                                 ^
75c_str()), R_Name |             ShispaceReldegi<SEstrXP> env(R_getVarEx(Rf_install(y, ns.c_stFALr()), RSE, R_U_NamespnboaceundValue));
      |                                                                 ^
Registry, FALSE, R_UnboundValue));
      |                                                                 ^
5 warnings and 1 error generated.
make: *** [RModularityOptimizer.o] Error 1
2 warnings generated.
5 warnings and 1 error generated.
make: *** [RcppExports.o] Error 1
5 warnings and 1 error generated.
make: *** [integration.o] Error 1
5 warnings and 1 error generated.
make: *** [data_manipulation.o] Error 1
ERROR: compilation failed for package ‘Seurat’
* removing ‘/Volumes/Builds/packages/sonoma-arm64/results/4.6/Seurat.Rcheck/Seurat’