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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings DeMixT_1.99.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/DeMixT.Rcheck’
* using R version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-01 02:28:42 UTC
* 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 ... WARNING
Found the following significant warnings:
  DeMixT.c:94:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
See ‘/home/biocbuild/bbs-3.23-bioc/meat/DeMixT.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    6.3Mb
    libs   1.6Mb
* 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 loading without being on the library search path ... 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 94.973  0.057  50.343
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/DeMixT.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL DeMixT
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘DeMixT’ ...
** this is package ‘DeMixT’ version ‘1.99.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security -c DeMixNB.c -o DeMixNB.o
In file included from DeMixNB.c:6:
DeMixNB.h:4:15: warning: ‘stirling_approx’ defined but not used [-Wunused-function]
    4 | static double stirling_approx(double z)
      |               ^~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security -c DeMixT.c -o DeMixT.o
DeMixT.c: In function ‘Tdemix’:
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: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:37:22: 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:37:11: 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: In function ‘gettumor’:
DeMixT.c:591:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
  591 |     double obj_old, obj_new;
      |                     ^~~~~~~
DeMixT.c:591:12: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
  591 |     double obj_old, obj_new;
      |            ^~~~~~~
DeMixT.c: In function ‘getpi’:
DeMixT.c:1280:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
 1280 |     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: In function ‘getspikeinpi’:
DeMixT.c:1307:25: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
 1307 |         double obj_old, obj_new;
      |                         ^~~~~~~
DeMixT.c:1307:16: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
 1307 |         double obj_old, obj_new;
      |                ^~~~~~~
DeMixT.c: In function ‘getpiT’:
DeMixT.c:1322:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
 1322 |     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: In function ‘Tdemix’:
DeMixT.c:195:11: warning: ‘Tavgtmp’ may be used uninitialized [-Wmaybe-uninitialized]
  195 |         if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
      |           ^
DeMixT.c:177:12: note: ‘Tavgtmp’ was declared here
  177 |     double Tavgtmp;
      |            ^~~~~~~
DeMixT.c:94:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   94 |   FD = calloc((size_t)nS ,sizeof(double *));
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from DeMixT.c:8:
/usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security  -c Profile_2D.cpp -o Profile_2D.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -shared -L/usr/local/lib -o DeMixT.so DeMixNB.o DeMixT.o init.o registerDynamicSymbol.o Profile_2D.o RcppExports.o -fopenmp -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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)