Install log for 'specProc'

* installing *source* package ‘specProc’ ...
** this is package ‘specProc’ version ‘0.8.3’
** package ‘specProc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 23.1.3’
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/specProc/src'
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c baseline.cpp -o baseline.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c cellpca.cpp -o cellpca.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c colMedians.cpp -o colMedians.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c computeGroupedMeans.cpp -o computeGroupedMeans.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c computeMeans.cpp -o computeMeans.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c ddc.cpp -o ddc.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c robust_pca.cpp -o robust_pca.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c som.cpp -o som.o
/usr/local/clang23/bin/clang++ -std=gnu++20 -I"/data/localhost/ripley/R/R-clang/include" -DNDEBUG  -I'/data/localhost/ripley/R/test-clang/Rcpp/include' -I'/data/localhost/ripley/R/test-clang/RcppEigen/include' -isystem /usr/local/clang23/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw   -c voigt.cpp -o voigt.o
In file included from robust_pca.cpp:2:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/localhost/ripley/R/test-clang/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 ddc.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/localhost/ripley/R/test-clang/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 robust_pca.cpp:2:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/localhost/ripley/R/test-clang/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 
      |         ^
/data/localhost/ripley/R/test-clang/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 ddc.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/localhost/ripley/R/test-clang/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 
      |         ^
/data/localhost/ripley/R/test-clang/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 cellpca.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/localhost/ripley/R/test-clang/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 som.cpp:2:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/localhost/ripley/R/test-clang/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 cellpca.cpp:In file included from 4som.cpp:
:In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:225:
:
In file included from In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h/data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h::2529:
:
In file included from In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h/data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse::2929:
:
In file included from In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse/data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU::2935:
:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35/data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:
:78/data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h::978:: 9:warning:  variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]warning: 
variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
      7878 |  |     IInnddeexx  nnssuuppeerr__eett__ppoosstt  ==  00;;  ////  NNuummbbeerr  ooff  rreellaaxxeedd  ssnnooddeess  iinn  ppoossttoorrddeerreedd  eettrreeee  

            | |         ^        ^

/data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h/data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h::7979::99::  warning: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]variable 'nsuper_et' set but not used [-Wunused-but-set-variable]

      7979 |  |     IInnddeexx  nnssuuppeerr__eett  ==  00;;  ////  NNuummbbeerr  ooff  rreellaaxxeedd  ssnnooddeess  iinn  tthhee  oorriiggiinnaall  eettrreeee  

            | |         ^        ^

In file included from RcppExports.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:26:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseCore:61:
/data/localhost/ripley/R/test-clang/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 robust_pca.cpp:2:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/localhost/ripley/R/test-clang/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 ddc.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/localhost/ripley/R/test-clang/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 RcppExports.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/Sparse:29:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/Eigen/SparseLU:35:
/data/localhost/ripley/R/test-clang/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 
      |         ^
/data/localhost/ripley/R/test-clang/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 cellpca.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/localhost/ripley/R/test-clang/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 som.cpp:2:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/localhost/ripley/R/test-clang/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 RcppExports.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:31:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/data/localhost/ripley/R/test-clang/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 robust_pca.cpp:2:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/localhost/ripley/R/test-clang/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 ddc.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/localhost/ripley/R/test-clang/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 cellpca.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from In file included from som.cpp/data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h::237:
:
In file included from In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h/data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra::2545:
:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37/data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:
:In file included from 246/data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra::745::
 /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.hwarning: :246variable 'count' set but not used [-Wunused-but-set-variable]:
7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |     246i | n t  icnotu ncto u=n t0 ;=
       0| ;      ^

      |       ^
In file included from RcppExports.cpp:4:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigen.h:25:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/RcppEigenForward.h:37:
In file included from /data/localhost/ripley/R/test-clang/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/data/localhost/ripley/R/test-clang/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;
      |       ^
5 warnings generated.
5 warnings generated.
5 warnings generated.
5 warnings generated.
5 warnings generated.
/usr/local/clang23/bin/clang++ -std=gnu++20 -shared -L/usr/local/clang/lib64 -L/usr/local/clang23/lib -L/usr/local/clang23/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o specProc.so RcppExports.o baseline.o cellpca.o colMedians.o computeGroupedMeans.o computeMeans.o ddc.o robust_pca.o som.o voigt.o
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/specProc/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-clang/specProc/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-clang/specProc/src'
installing to /data/localhost/ripley/R/packages/tests-clang/specProc.Rcheck/00LOCK-specProc/00new/specProc/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** 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 (specProc)