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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 version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-04 00:08:56 UTC
* 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 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... INFO
  specified C++17
* 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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Harman/libs/Harman.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/Harman.Rcheck/00check.log’
for details.

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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/Resources/library’
* installing *source* package ‘Harman’ ...
** this is package ‘Harman’ version ‘1.39.0’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++17
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Harman.cpp -o Harman.o
In file included from Harman.cpp:182:
./CSelectRandom.h:283:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable]
  283 |                         size_t seed ;
      |                                ^
./CSelectRandom.h:372:11: warning: variable 'seed' set but not used [-Wunused-but-set-variable]
  372 |                         size_t seed ;
      |                                ^
./CSelectRandom.h:392:11: warning: unused variable 'currindex' [-Wunused-variable]
  392 |                  size_t currindex ;
      |                         ^~~~~~~~~
./CSelectRandom.h:394:35: warning: unused variable 'it1' [-Wunused-variable]
  394 |                         std::vector<double>::iterator  it1, it2 ;
      |                                                        ^~~
./CSelectRandom.h:394:40: warning: unused variable 'it2' [-Wunused-variable]
  394 |                         std::vector<double>::iterator  it1, it2 ;
      |                                                             ^~~
./CSelectRandom.h:638:20: warning: unused variable 'ts1' [-Wunused-variable]
  638 |                         struct timespec ts1, ts2 ;
      |                                         ^~~
./CSelectRandom.h:638:25: warning: unused variable 'ts2' [-Wunused-variable]
  638 |                         struct timespec ts1, ts2 ;
      |                                              ^~~
./CSelectRandom.h:639:11: warning: unused variable 'time1' [-Wunused-variable]
  639 |                         double time1, time2 ;
      |                                ^~~~~
./CSelectRandom.h:639:18: warning: unused variable 'time2' [-Wunused-variable]
  639 |                         double time1, time2 ;
      |                                       ^~~~~
./CSelectRandom.h:932:18: warning: variable 'reject' set but not used [-Wunused-but-set-variable]
  932 |                         long long int reject ;
      |                                       ^
./CSelectRandom.h:1019:23: warning: unused variable 'randData2' [-Wunused-variable]
 1019 |                                 size_t randData1, randData2  ;
      |                                                   ^~~~~~~~~
./CSelectRandom.h:1021:12: warning: variable 'reject' set but not used [-Wunused-but-set-variable]
 1021 |                                 size_t reject ;
      |                                        ^
Harman.cpp:2480:12: warning: variable 'count' set but not used [-Wunused-but-set-variable]
 2480 |     size_t count ;
      |            ^
13 warnings generated.
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
installing to /Library/Frameworks/R.framework/Versions/4.6/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 version 4.6.0 alpha (2026-03-28 r89739)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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 -- Fri Apr  3 20:09:24 2026 
*********************************************** 
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 
 12.184   0.134  13.665