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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Harman.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Harman_1.35.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Harman.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Harman/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Harman’ version ‘1.35.0’
* 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 ... WARNING
Found the following significant warnings:
  CMapSelectKFromN.h:52:18: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/Harman.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 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 ... 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
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Harman.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL Harman
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘Harman’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_ARRAYALIGNEMT=4 -D_USE_RCPP=1 -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -I.  -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c Harman.cpp -o Harman.o
In file included from Harman.cpp:181:
CMapSelectKFromN.h:52:18: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
   52 |   CFactorials<T>(size_t maxN)
      |                  ^~~~~~
CMapSelectKFromN.h:52:18: note: remove the ‘< >’
Harman.cpp: In function ‘SEXPREC* HarmanMain(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
Harman.cpp:3008:3: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
 3008 |   else
      |   ^~~~
Harman.cpp:3022:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
 3022 |     std::vector<unsigned int>    tr_std_tmp     = Rcpp::as<std::vector<unsigned int> >(tr) ;
      |     ^~~
In file included from Harman.cpp:182:
CSelectRandom.h: In instantiation of ‘std::vector<unsigned int>* CSelectRandom<T>::ReturnVectOf32bitIntegersInRange_CSTDLIB(size_t, size_t, size_t, size_t) [with T = double; size_t = long unsigned int]’:
Harman.cpp:1764:79:   required from here
 1764 |                                         t_v_random32bit = _RandomSelect->ReturnVectOf32bitIntegersInRange_CSTDLIB(max_combinations, 0, 0, i_XvectSize  ) ;
      |                                                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CSelectRandom.h:943:48: warning: comparison of integer expressions of different signedness: ‘long long int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  943 |                                 while (currval < howManyIN)
      |                                        ~~~~~~~~^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o Harman.so Harman.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 -- Sat Jan  4 07:03:07 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 
 28.079   0.137  31.270