##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decontX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decontX_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/decontX.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decontX/DESCRIPTION’ ... OK
* this is package ‘decontX’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decontX’ can be installed ... WARNING
Found the following significant warnings:
  matrixSums.c:108:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  matrixSums.c:158:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  matrixSums.c:293:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  matrixSums.c:343:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/decontX.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
decontX                     12.260  0.415  12.726
plotDecontXContamination    11.461  0.194  11.666
decontPro                   11.266  0.354  11.655
plotDecontXMarkerPercentage 10.303  0.207  10.520
plotDecontXMarkerExpression 10.158  0.169  10.344
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/decontX.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decontX
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘decontX’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++17
using SDK: ‘MacOSX11.3.sdk’


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c DecontX.cpp -o DecontX.o
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/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]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from DecontX.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
DecontX.cpp:321:10: warning: variable 'x' set but not used [-Wunused-but-set-variable]
  double x;
         ^
6 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/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]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
5 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c matrixNorm.cpp -o matrixNorm.o


clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c matrixSums.c -o matrixSums.o
matrixSums.c:108:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  if (!isFactor(R_group) | !isFactor(R_pgroup)) {
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                         ||
matrixSums.c:108:7: note: cast one or both operands to int to silence this warning
matrixSums.c:158:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  if (!isFactor(R_group) | !isFactor(R_pgroup)) {
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                         ||
matrixSums.c:158:7: note: cast one or both operands to int to silence this warning
matrixSums.c:293:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  if (!isFactor(R_group) | !isFactor(R_pgroup)) {
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                         ||
matrixSums.c:293:7: note: cast one or both operands to int to silence this warning
matrixSums.c:343:7: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  if (!isFactor(R_group) | !isFactor(R_pgroup)) {
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                         ||
matrixSums.c:343:7: note: cast one or both operands to int to silence this warning
4 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c matrixSumsSparse.cpp -o matrixSumsSparse.o
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/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]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from matrixSumsSparse.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
5 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -c stanExports_shrinkage.cc -o stanExports_shrinkage.o
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/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]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_shrinkage.cc:5:
./stanExports_shrinkage.h:515:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
In file included from stanExports_shrinkage.cc:5:
In file included from ./stanExports_shrinkage.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable]
      const T x_extrema = 1 / (1 + a);
              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here
      temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2);
      ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
               x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol);
                   ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here
   rx = detail::ibeta_inv_imp(
                ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
   return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol);
          ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here
  return boost::math::ibeta_inv(a, b, p, boost_policy_t<>());
                      ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o decontX.so DecontX.o RcppExports.o matrixNorm.o matrixSums.o matrixSumsSparse.o stanExports_shrinkage.o -L/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-decontX/00new/decontX/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (decontX)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(decontX)
> 
> test_check("decontX")
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:04 2024 .. Analyzing all cells
Wed Apr 17 11:20:04 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:04 2024 .... Generating UMAP
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:11 2024 .... Estimating contamination
Wed Apr 17 11:20:11 2024 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 7.731286 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:11 2024 .. Analyzing cells in batch '1'
Wed Apr 17 11:20:11 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:11 2024 .... Generating UMAP
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:16 2024 .... Estimating contamination
Wed Apr 17 11:20:16 2024 .. Calculating final decontaminated matrix
Wed Apr 17 11:20:16 2024 .. Analyzing cells in batch '2'
Wed Apr 17 11:20:16 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:16 2024 .... Generating UMAP
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:21 2024 .... Estimating contamination
Wed Apr 17 11:20:21 2024 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 10.06067 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:22 2024 .. Analyzing all cells
Wed Apr 17 11:20:22 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:22 2024 .... Generating UMAP and estimating cell types
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:26 2024 .... Estimating contamination
Wed Apr 17 11:20:26 2024 ...... Completed iteration: 9 | converge: 0.0009154
Wed Apr 17 11:20:26 2024 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 4.986596 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:27 2024 .. Analyzing all cells
Wed Apr 17 11:20:27 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:27 2024 .... Generating UMAP and estimating cell types
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:32 2024 .... Estimating contamination
Wed Apr 17 11:20:32 2024 ...... Completed iteration: 10 | converge: 0.02021
Wed Apr 17 11:20:32 2024 ...... Completed iteration: 20 | converge: 0.00284
Wed Apr 17 11:20:32 2024 ...... Completed iteration: 30 | converge: 0.0009675
Wed Apr 17 11:20:32 2024 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 4.980826 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:32 2024 .. Analyzing all cells
Wed Apr 17 11:20:32 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:32 2024 .... Generating UMAP and estimating cell types
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:37 2024 .... Estimating contamination
Wed Apr 17 11:20:37 2024 ...... Completed iteration: 9 | converge: 0.0009154
Wed Apr 17 11:20:37 2024 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 5.007973 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:38 2024 .. Analyzing all cells
Wed Apr 17 11:20:38 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:38 2024 .... Generating UMAP and estimating cell types
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:43 2024 .... Estimating contamination
Wed Apr 17 11:20:43 2024 ...... Completed iteration: 9 | converge: 0.0008168
Wed Apr 17 11:20:43 2024 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 5.231474 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:43 2024 .. Analyzing all cells
Wed Apr 17 11:20:43 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:43 2024 .... Generating UMAP and estimating cell types
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:48 2024 .... Estimating contamination
Wed Apr 17 11:20:48 2024 ...... Completed iteration: 10 | converge: 0.02021
Wed Apr 17 11:20:48 2024 ...... Completed iteration: 20 | converge: 0.00284
Wed Apr 17 11:20:48 2024 ...... Completed iteration: 30 | converge: 0.0009675
Wed Apr 17 11:20:48 2024 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 5.154388 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:49 2024 .. Analyzing all cells
Wed Apr 17 11:20:49 2024 .... Converting to sparse matrix
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:49 2024 .. Analyzing all cells
Wed Apr 17 11:20:49 2024 .... Converting to sparse matrix
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Apr 17 11:20:49 2024 .. Analyzing all cells
Wed Apr 17 11:20:49 2024 .... Converting to sparse matrix
Wed Apr 17 11:20:49 2024 .... Generating UMAP
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Wed Apr 17 11:20:54 2024 .... Generating UMAP
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Found more than one class "dist" in cache; using the first, from namespace 'spam'
Also defined by 'BiocGenerics'
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000765 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.65 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1:    100        -8039.760             1.000            1.000
Chain 1:    200        -5731.482             0.701            1.000
Chain 1:    300        -5570.966             0.477            0.403
Chain 1:    400        -5510.810             0.361            0.403
Chain 1:    500        -5480.807             0.290            0.029
Chain 1:    600        -5451.166             0.242            0.029
Chain 1:    700        -5416.328             0.209            0.011
Chain 1:    800        -5401.248             0.183            0.011
Chain 1:    900        -5395.230             0.163            0.006   MEDIAN ELBO CONVERGED
Chain 1: 
Chain 1: Drawing a sample of size 1000 from the approximate posterior... 
Chain 1: COMPLETED.
[ FAIL 0 | WARN 13 | SKIP 2 | PASS 19 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-decon.R:27:1', 'test-decon.R:48:1'

[ FAIL 0 | WARN 13 | SKIP 2 | PASS 19 ]
> 
> proc.time()
   user  system elapsed 
 81.964   1.548  83.305