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### Running command:
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###   /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_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DeMixT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeMixT/DESCRIPTION’ ... OK
* this is package ‘DeMixT’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
  Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
  Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/DeMixT.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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: no visible global function definition for ‘qchisq’
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 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 ... WARNING
Codoc mismatches from Rd file 'DeMixT_preprocessing.Rd':
DeMixT_preprocessing
  Code: function(count.matrix, normal.id, tumor.id, selected.genes =
                 9000, cutoff_normal_range = c(0.1, 1),
                 cutoff_tumor_range = c(0, 2.5), cutoff_step = 0.2)
  Docs: function(count.matrix, normal.id, tumor.id, cutoff_normal_range
                 = c(0.1, 1), cutoff_tumor_range = c(0, 2.5),
                 cutoff_step = 0.2)
  Argument names in code not in docs:
    selected.genes
  Mismatches in argument names:
    Position: 4 Code: selected.genes Docs: cutoff_normal_range
    Position: 5 Code: cutoff_normal_range Docs: cutoff_tumor_range
    Position: 6 Code: cutoff_tumor_range Docs: cutoff_step

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'detect_suspicious_sample_by_hierarchical_clustering_2comp.Rd'
  ‘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 44.708  0.146  45.006
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘calibrate’
* 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: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DeMixT.c -o DeMixT.o
DeMixT.c:37:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
  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]
  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]
  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]
  double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                     ^
DeMixT.c:591:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
                    ^
DeMixT.c:591:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
           ^
DeMixT.c:1280:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
           ^
DeMixT.c:1280:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
                    ^
DeMixT.c:1307:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
        double obj_old, obj_new;
               ^
DeMixT.c:1307:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
        double obj_old, obj_new;
                        ^
DeMixT.c:1322:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
           ^
DeMixT.c:1322:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
                    ^
12 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Profile_2D.cpp -o Profile_2D.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o DeMixT.so DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ 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::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ 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::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
** testing if installed package keeps a record of temporary installation path
* DONE (DeMixT)