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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeMixT_1.99.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/DeMixT.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-03-31 22:59:24 UTC
* using option ‘--no-vignettes’
* checking for file ‘DeMixT/DESCRIPTION’ ... OK
* this is package ‘DeMixT’ version ‘1.99.0’
* 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 ... NOTE
Found the following hidden files and directories:
  inst/doc/.gitkeep
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DeMixT’ can be installed ... OK
* used C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking installed package size ... INFO
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    7.3Mb
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
DeMixT_GS : IF_inverse: no visible global function definition for ‘is’
plot_dim: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
DeMixT_S2 21.546  0.155   21.89
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/DeMixT.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeMixT
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘DeMixT’ ...
** this is package ‘DeMixT’ version ‘1.99.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -I/Library/Frameworks/R.framework/Resources/include -fPIC  -falign-functions=64 -Wall -g -O2  -c DeMixNB.c -o DeMixNB.o
In file included from DeMixNB.c:6:
./DeMixNB.h:4:15: warning: unused function 'stirling_approx' [-Wunused-function]
    4 | static double stirling_approx(double z)
      |               ^~~~~~~~~~~~~~~
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -I/Library/Frameworks/R.framework/Resources/include -fPIC  -falign-functions=64 -Wall -g -O2  -c DeMixT.c -o DeMixT.o
DeMixT.c:37:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
   37 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |           ^
DeMixT.c:37:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
   37 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |                      ^
DeMixT.c:37:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
   37 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |                                 ^
DeMixT.c:37:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
   37 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |                                             ^
DeMixT.c:591:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
  591 |     double obj_old, obj_new;
      |            ^
DeMixT.c:591:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
  591 |     double obj_old, obj_new;
      |                     ^
DeMixT.c:1280:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
 1280 |     double obj_old, obj_new;
      |            ^
DeMixT.c:1280:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
 1280 |     double obj_old, obj_new;
      |                     ^
DeMixT.c:1307:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
 1307 |         double obj_old, obj_new;
      |                ^
DeMixT.c:1307:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
 1307 |         double obj_old, obj_new;
      |                         ^
DeMixT.c:1322:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
 1322 |     double obj_old, obj_new;
      |            ^
DeMixT.c:1322:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
 1322 |     double obj_old, obj_new;
      |                     ^
12 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -I/Library/Frameworks/R.framework/Resources/include -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -I/Library/Frameworks/R.framework/Resources/include -fPIC  -falign-functions=64 -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -I/Library/Frameworks/R.framework/Resources/include -fPIC  -falign-functions=64 -Wall -g -O2   -c Profile_2D.cpp -o Profile_2D.o
Profile_2D.cpp:15:20: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
   15 |     double tmp_pos[integ];
      |                    ^~~~~
Profile_2D.cpp:15:20: note: read of non-const variable 'integ' is not allowed in a constant expression
Profile_2D.cpp:14:6: note: declared here
   14 |         int integ=200;
      |             ^
Profile_2D.cpp:987:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
  987 |         int i=1;
      |             ^
Profile_2D.cpp:1022:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
 1022 |         int i=1;
      |             ^
Profile_2D.cpp:1057:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
 1057 |         int i=1;
      |             ^
Profile_2D.cpp:1437:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
 1437 |         int i=1;
      |             ^
Profile_2D.cpp:1460:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
 1460 |         int i=1;
      |             ^
Profile_2D.cpp:1484:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
 1484 |         int i=1;
      |             ^
Profile_2D.cpp:1508:6: warning: variable 'i' set but not used [-Wunused-but-set-variable]
 1508 |         int i=1;
      |             ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -I/Library/Frameworks/R.framework/Resources/include -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
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 DeMixT.so DeMixNB.o DeMixT.o init.o registerDynamicSymbol.o Profile_2D.o RcppExports.o -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 /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-DeMixT/00new/DeMixT/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (DeMixT)