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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Harman.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Harman_1.39.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Harman.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Harman/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Harman’ version ‘1.39.0’
* 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 ‘Harman’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.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 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Harman
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘Harman’ ...
** this is package ‘Harman’ version ‘1.39.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"` -I.  -fPIC  -falign-functions=64 -Wall -g -O2   -c Harman.cpp -o Harman.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
In file included from Harman.cpp:182:
./CSelectRandom.h:283:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable]
                        size_t seed ;
                               ^
./CSelectRandom.h:372:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable]
                        size_t seed ;
                               ^
./CSelectRandom.h:392:11: warning: unused variable 'currindex' [-Wunused-variable]
                 size_t currindex ;
                        ^
./CSelectRandom.h:394:35: warning: unused variable 'it1' [-Wunused-variable]
                        std::vector<double>::iterator  it1, it2 ;
                                                       ^
./CSelectRandom.h:394:40: warning: unused variable 'it2' [-Wunused-variable]
                        std::vector<double>::iterator  it1, it2 ;
                                                            ^
./CSelectRandom.h:638:20: warning: unused variable 'ts1' [-Wunused-variable]
                        struct timespec ts1, ts2 ;
                                        ^
./CSelectRandom.h:638:25: warning: unused variable 'ts2' [-Wunused-variable]
                        struct timespec ts1, ts2 ;
                                             ^
./CSelectRandom.h:639:11: warning: unused variable 'time1' [-Wunused-variable]
                        double time1, time2 ;
                               ^
./CSelectRandom.h:639:18: warning: unused variable 'time2' [-Wunused-variable]
                        double time1, time2 ;
                                      ^
./CSelectRandom.h:932:18: warning: variable 'reject' set but not used [-Wunused-but-set-variable]
                        long long int reject ;
                                      ^
./CSelectRandom.h:1019:23: warning: unused variable 'randData2' [-Wunused-variable]
                                size_t randData1, randData2  ;
                                                  ^
./CSelectRandom.h:1021:12: warning: variable 'reject' set but not used [-Wunused-but-set-variable]
                                size_t reject ;
                                       ^
Harman.cpp:2480:12: warning: variable 'count' set but not used [-Wunused-but-set-variable]
    size_t count ;
           ^
13 warnings generated.
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Harman.so Harman.o -F/Library/Frameworks/R.framework/.. -framework R
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-Harman/00new/Harman/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 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 (Harman)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> BiocGenerics:::testPackage("Harman")
First clustering, now find top two k, done. Reclustering, done.


RUNIT TEST PROTOCOL -- Tue Dec  9 22:04:15 2025 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Harman RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 
Warning message:
In kClusterMethylation(betas[1, , drop = FALSE], row_ks = ks[1]) :
  All rows have a cluster size of 1
> 
> proc.time()
   user  system elapsed 
  9.010   1.134  10.753