Install log for 'pagoda2'

* installing *source* package ‘pagoda2’ ...
** this is package ‘pagoda2’ version ‘1.0.14’
** package ‘pagoda2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.3.19.1)’
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c binaryExport.cpp -o binaryExport.o
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c checkfunctions.cpp -o checkfunctions.o
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c edgeweights.cpp -o edgeweights.o
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c gradients.cpp -o gradients.o
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c largeVis.cpp -o largeVis.o
In file included from checkfunctions.cpp:2:
In file included from ./include/largeVis.h:9:
In file included from In file included from In file included from largeVis.cpp:In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.hedgeweights.cpp:In file included from RcppExports.cpp:9gradients.cpp54:
::
In file included from 3:
In file included from ./include/largeVis.h: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 :
./include/largeVis.h:In file included from ./include/largeVis.h/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h::9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from 25:
In file included from 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/Sparse26/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h: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::26:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore:/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h2961:
:29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:26:
:
29:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273::
In file included from In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore13In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseIn 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.h6126:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse:
/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]
::61:
  273 | ::  273/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    273 |       I26 :
273 In file included from   |   /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseCore Indewarning: :61ndex cvariable 'count' set but not used [-Wunused-but-set-variable]:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273ox :13 unt 
= 0c ;  273 |    
      |             ^
 : ou  Inn dex Ind  count = 0;
warning: variable 'count' set but not used [-Wunused-but-set-variable]
e        273 |   |             ^
 t = 0;
      |             ^x 
count =   Index count = 0;
      |             ^
 0;
      |             ^
In file included from RcppExports.cpp:5:
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 gradients.cpp:3:
In file included from In file included from ./include/largeVis.h:9checkfunctions.cppIn file included from :
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:2:
:edgeweights.cpp:25In file included from In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLUIn file included from :
./include/largeVis.h: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:78:9:359:
In file included from : :
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78largeVis.cppIn 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:
:./include/largeVis.h:warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
:   99:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h |   Ind:25:
In file included from 78:9: warning: 4:variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]e /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:29:
warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
In file included from :
In file included from ./include/largeVis.h:   
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/Sparse78   : | 789x29:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/SparseLU:35:
   Indn:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:sup/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h | :78  :25Ie9xe:nr_et_p warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
dex no:
 ssuper_In file included from t   /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h nsup:= 0; // Number oeet_p78rfost = 0; _et |   Ind29:
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:
ree_p/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h // Numbeox nsuper_et_pr of rel:78:9ost = 0; // Number of relaxedl:staxe  warning: d snodvariable 'nsuper_et_post' set but not used [-Wunused-but-set-variable] = 0es;
s   78 |   In  dex in// Nn auxed snopnmobostorddeedr of reered etrees in plsupers iaxed son postordered estordered n_et_potreeotee 
       s
| ree               ^

| t/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h        ^des in:79       po:9:s tor
=/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h  warning: 0d:|         ^
variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
   79 |   ;/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.her79::9: 79e:I9d warning: :nvariable 'nsuper_et' set but not used [-Wunused-but-set-variable]edetree  warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]

      | 
   79 |          ^   
 79/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h: |  In79: x/ I dndex nsuex nsuper_et = 0np;/e r Num_et = 0s/u9;/: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
p // Num    79 |   Index nbbseeuer rpe_ofr of relaxr_et = Nedet =u  m00 rel; // Number;besr  // Number of relaxed sno aodenxof relaxeded ssno  iondsnodeses i then postor des in in the f relaxed snodes intdere original etree 
      | h        ^d 
e original etree 
      |         ^
originetree 
      |         ^
a/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.hl etre: te 
      | 79:9he ori: warning:         ^
ginal etree 
      |         ^
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 checkfunctions.cpp:2:
In file included from ./include/largeVis.h:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:In file included from In file included from In file included from edgeweights.cppgradients.cppRcppExports.cpp25In file included from largeVis.cpp:4::
:
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::3:
In file included from :In file included from 9./include/largeVis.h46./include/largeVis.h:95:
::
In file included from :
In file included from ./include/largeVis.h: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 :
9In 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/RcppEigen.h:25/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h/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:72In file included from :In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h10: warning: 46/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:variable 'replacements' set but not used [-Wunused-but-set-variable]/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers31::46:
25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:31
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10:   :
 warning: :
/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]In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:

:
In file included from variable 'replacements' set but not used [-Wunused-but-set-variable]/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:
      727272/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/IterativeSolvers72 |                          | :46I                        Index |                         Index ren dpex:10 replar:
epl:a/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]
   72c ceewarning:  | mlacements variable 'replacements' set but not used [-Wunused-but-set-variable]eme=
 0;
         72 | n        ts                        In | = 0;
      | n                                      ^d        e
ts I=x replacne                              ^dex 0;
      |                               ^m repla

entscements = 0;
       = 0;
      |                               ^
|                               ^
In file included from checkfunctions.cpp:2In file included from largeVis.cppIn file included from :
In file included from ./include/largeVis.h:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.hIn file included from In file included from RcppExports.cpp:edgeweights.cpp5:gradients.cpp9::254:
In file included from :
::
In file included from 3:
In file included from ./include/largeVis.h:9:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.hIn file included from :
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:
:./include/largeVis.h25:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25:
In file included from ./include/largeVis.hIn 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:9/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:9:
246:In file included from :
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:25In file included from :7: warning: variable 'count' set but not used [-Wunused-but-set-variable]/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigen.h:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h:37:::
37:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra37In file included from :45:
:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h25
:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra:
In file included from /Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/RcppEigenForward.h
In file included from :45:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:37  :
:7:246In 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 |   246: 7 |  warning:   in/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/SparseExtra variable 'count' set but not used [-Wunused-but-set-variable]t i: :
45:
/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.hwarning:   246 |   ivariable 'count' set but not used [-Wunused-but-set-variable]
nt :  246c246:7: cou |   ionnt count nt countt = 0u =;
      warning: |       ^
n variable 'count' set but not used [-Wunused-but-set-variable]t
0;
      |       ^
= = 0   246 | 0;
      |       ^
  int c;
      |       ^
ount = 0;
      |       ^
edgeweights.cpp:123:12: warning: variable 'sum_weight' set but not used [-Wunused-but-set-variable]
  123 |     double sum_weight = 0;
      |            ^
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c misc2.cpp -o misc2.o
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c pagoda1_liftover.cpp -o pagoda1_liftover.o
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -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/RcppArmadillo/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppProgress/include' -I'/Volumes/Builds/packages/sonoma-arm64/Rlib/4.6/RcppEigen/include' -I/opt/R/arm64/include   -I"./include"   -fPIC  -falign-functions=64 -Wall -g -O2   -c rank.cpp -o rank.o
6 warnings generated.
5 warnings generated.
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o pagoda2.so RcppExports.o binaryExport.o checkfunctions.o edgeweights.o gradients.o largeVis.o misc2.o pagoda1_liftover.o rank.o -L. -lpthread -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Volumes/Builds/packages/sonoma-arm64/results/4.6/pagoda2.Rcheck/00LOCK-pagoda2/00new/pagoda2/libs
** generating debug symbols (dSYM)
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pagoda2)