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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:densvis.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings densvis_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/densvis.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘densvis/DESCRIPTION’ ... OK
* this is package ‘densvis’ version ‘1.19.0’
* 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 ‘densvis’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.22-bioc/meat/densvis.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
densmap 24.416   1.79  26.958
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/densvis.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL densvis
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘densvis’ ...
** this is package ‘densvis’ version ‘1.19.0’
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-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 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c densne.cpp -o densne.o
densne.cpp:181:24: warning: variable 'row_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:33: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:35: note: initialize the variable 'row_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                  ^
                                   = nullptr
densne.cpp:181:24: warning: variable 'col_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:40: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                       ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:56: note: initialize the variable 'col_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                       ^
                                                        = nullptr
densne.cpp:181:24: warning: variable 'val_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:47: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                              ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:71: note: initialize the variable 'val_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                                      ^
                                                                       = nullptr
densne.cpp:181:24: warning: variable 'val_D' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:54: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                                     ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:86: note: initialize the variable 'val_D' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                                                     ^
                                                                                      = nullptr
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c densvis.cpp -o densvis.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c sptree.cpp -o sptree.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 densvis.so RcppExports.o densne.o densvis.o sptree.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-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/4.5-x86_64/Resources/library/densvis/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
* DONE (densvis)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> library(testthat)
> library(densvis)
> 
> test_check("densvis")
OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
OMP: Warning #96: Cannot form a team with 48 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
 39.116   1.824  37.368 
/Users/biocbuild/.pyenv/versions/3.12.10/lib/python3.12/multiprocessing/resource_tracker.py:279: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '