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### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings mbkmeans_1.23.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/mbkmeans.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘mbkmeans/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mbkmeans’ version ‘1.23.0’
* 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 ‘mbkmeans’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘S4Vectors’
  All declared Imports should be used.
* 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 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 ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9.             └─HDF5Array::getHDF5DumpFile()
   10.               └─HDF5Array:::.get_dump_autofile()
   11.                 └─rhdf5::h5createFile(filepath)
   12.                   └─rhdf5::H5Fcreate(file)
  
  [ FAIL 2 | WARN 20 | SKIP 0 | PASS 22 ]
  > 
  > proc.time()
     user  system elapsed 
   13.558   0.901  14.453 
  
   *** caught segfault ***
  address 0x558, cause 'memory not mapped'
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/mbkmeans.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL mbkmeans
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘mbkmeans’ ...
** this is package ‘mbkmeans’ version ‘1.23.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppArmadillo/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/RcppArmadillo/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c mini_batch.cpp -o mini_batch.o
In file included from mini_batch.cpp:3:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include/ClusterRHeader.h: In member function ‘arma::mat clustR::ClustHeader::KMEANS_arma(arma::mat&, int, int, bool, std::string, Rcpp::Nullable<Rcpp::Matrix<14> >, int)’:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include/ClusterRHeader.h:862:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
  862 |         bool status;
      |              ^~~~~~
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include/ClusterRHeader.h: In instantiation of ‘T clustR::ClustHeader::GMM_arma_covariance_type(T, arma::mat&, int, std::string, std::string, int, int, bool, double, int) [with T = arma::gmm_priv::gmm_full<double>; arma::mat = arma::Mat<double>; std::string = std::__cxx11::basic_string<char>]’:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include/ClusterRHeader.h:1592:65:   required from here
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
 1530 |         bool status;
      |              ^~~~~~
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include/ClusterRHeader.h: In instantiation of ‘T clustR::ClustHeader::GMM_arma_covariance_type(T, arma::mat&, int, std::string, std::string, int, int, bool, double, int) [with T = arma::gmm_priv::gmm_diag<double>; arma::mat = arma::Mat<double>; std::string = std::__cxx11::basic_string<char>]’:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include/ClusterRHeader.h:1626:65:   required from here
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
g++ -std=gnu++11 -shared -L/usr/local/lib -o mbkmeans.so RcppExports.o mini_batch.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-mbkmeans/00new/mbkmeans/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 (mbkmeans)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(testthat)
> library(mbkmeans)
> 
> test_check("mbkmeans")
Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
[ FAIL 2 | WARN 20 | SKIP 0 | PASS 22 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_mbkmeans.R:57:5'): Length of cluster labels is the same as number of obs ──
Error in `H5Fclose(file$H5Identifier)`: HDF5. Object cache. Internal error detected.
Backtrace:
     ▆
  1. └─methods::as(m0, "HDF5Matrix") at test_mbkmeans.R:57:5
  2.   └─HDF5Array (local) asMethod(object)
  3.     ├─methods::as(as(from, "HDF5Array"), "HDF5Matrix")
  4.     │ └─methods:::.class1(object)
  5.     └─methods::as(from, "HDF5Array")
  6.       └─HDF5Array (local) asMethod(object)
  7.         └─HDF5Array::writeHDF5Array(from)
  8.           └─DelayedArray::BLOCK_write_to_sink(sink, x, verbose = verbose)
  9.             └─DelayedArray::sinkApply(...)
 10.               └─DelayedArray::gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
 11.                 └─DelayedArray (local) FUN(viewport, init, ...)
 12.                   └─DelayedArray (local) FUN(init, viewport, ...)
 13.                     ├─S4Arrays::write_block(sink, viewport, block)
 14.                     └─HDF5Array::write_block(sink, viewport, block)
 15.                       ├─rhdf5::h5write(...)
 16.                       └─rhdf5:::h5write.default(...)
 17.                         └─rhdf5:::h5closeitLoc(loc)
 18.                           └─rhdf5::H5Fclose(file$H5Identifier)
── Error ('test_minibatch.R:79:3'): all mini_batch methods give same result ────
Error in `H5Fcreate(file)`: HDF5. File accessibility. Unable to open file.
Backtrace:
     ▆
  1. └─methods::as(m0, "HDF5Matrix") at test_minibatch.R:79:3
  2.   └─HDF5Array (local) asMethod(object)
  3.     ├─methods::as(as(from, "HDF5Array"), "HDF5Matrix")
  4.     │ └─methods:::.class1(object)
  5.     └─methods::as(from, "HDF5Array")
  6.       └─HDF5Array (local) asMethod(object)
  7.         └─HDF5Array::writeHDF5Array(from)
  8.           └─HDF5Array::HDF5RealizationSink(...)
  9.             └─HDF5Array::getHDF5DumpFile()
 10.               └─HDF5Array:::.get_dump_autofile()
 11.                 └─rhdf5::h5createFile(filepath)
 12.                   └─rhdf5::H5Fcreate(file)

[ FAIL 2 | WARN 20 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
 13.558   0.901  14.453 

 *** caught segfault ***
address 0x558, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)