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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DeMixT.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DeMixT_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DeMixT.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DeMixT/DESCRIPTION’ ... OK
* this is package ‘DeMixT’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'parallel', 'Rcpp', 'SummarizedExperiment', 'knitr', 'KernSmooth',
  'matrixcalc', 'rmarkdown', 'DSS', 'dendextend', 'psych', 'sva'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘DeMixT’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
  Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
  Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
See ‘/home/biocbuild/bbs-3.16-bioc/meat/DeMixT.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   4.1Mb
* 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 loading without being on the library search path ... 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: no visible global function definition for ‘qchisq’
DeMixT_preprocessing: no visible global function definition for
  ‘quantile_normalization’
detect_suspicious_sample_by_hierarchical_clustering_2comp :
  <anonymous>: no visible global function definition for ‘wilcox.test’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
  global function definition for ‘prcomp’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
  global function definition for ‘dist’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
  global function definition for ‘hclust’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
  global function definition for ‘par’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
  global function definition for ‘as.dendrogram’
detect_suspicious_sample_by_hierarchical_clustering_2comp: no visible
  global function definition for ‘legend’
plot_dim: no visible global function definition for ‘prcomp’
plot_dim: no visible global function definition for ‘rainbow’
plot_dim: no visible global function definition for ‘abline’
plot_dim: no visible global function definition for ‘segments’
plot_dim: no visible global function definition for ‘points’
plot_dim: no visible global function definition for ‘legend’
plot_sd: no visible global function definition for ‘par’
scale_normalization_75th_percentile: no visible global function
  definition for ‘median’
simulate_2comp: no visible global function definition for ‘SimpleList’
simulate_2comp: no visible global function definition for ‘DataFrame’
simulate_3comp: no visible global function definition for ‘SimpleList’
simulate_3comp: no visible global function definition for ‘DataFrame’
Undefined global functions or variables:
  DataFrame SimpleList abline as.dendrogram dist hclust legend median
  par points prcomp qchisq quantile_normalization rainbow segments
  wilcox.test
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "par", "points", "segments")
  importFrom("stats", "as.dendrogram", "dist", "hclust", "median",
             "prcomp", "qchisq", "wilcox.test")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in documentation object 'detect_suspicious_sample_by_hierarchical_clustering_2comp'
  ‘labels’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
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 98.952  0.068  50.371
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘calibrate’
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘demixt.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/DeMixT.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DeMixT
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -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:1307:18: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
 1307 |  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: 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 in this function [-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:94:8: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   94 |   FD = calloc(nS ,sizeof(double *));
      |        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from DeMixT.c:8:
/usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here
  542 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Profile_2D.cpp -o Profile_2D.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o DeMixT.so DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -fopenmp -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-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
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
** testing if installed package keeps a record of temporary installation path
* DONE (DeMixT)