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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:scMitoMut.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings scMitoMut_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/scMitoMut.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-13 07:25:48 UTC
* checking for file ‘scMitoMut/DESCRIPTION’ ... OK
* this is package ‘scMitoMut’ version ‘1.7.0’
* 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 ‘scMitoMut’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 ... NOTE
export_dt: no visible binding for global variable ‘af’
export_dt: no visible binding for global variable ‘fwd_depth’
export_dt: no visible binding for global variable ‘rev_depth’
export_dt: no visible binding for global variable ‘coverage’
export_dt: no visible binding for global variable ‘alt_count’
export_dt: no visible binding for global variable ‘alt_depth’
export_dt: no visible binding for global variable ‘mut_status’
export_dt: no visible binding for global variable ‘cell_barcode’
export_dt: no visible binding for global variable ‘n’
export_dt: no visible binding for global variable ‘loc’
filter_loc: no visible binding for global variable ‘mut_cell_n’
plot_locus: no visible binding for global variable ‘alt_depth’
plot_locus: no visible binding for global variable ‘depth’
plot_locus: no visible binding for global variable ‘af’
plot_locus: no visible binding for global variable ‘highlight’
process_locus_bb: no visible binding for global variable ‘alt_depth’
process_locus_bb: no visible binding for global variable ‘fwd_depth’
process_locus_bb: no visible binding for global variable ‘rev_depth’
process_locus_bm: no visible binding for global variable ‘alt_depth’
process_locus_bm: no visible binding for global variable ‘fwd_depth’
process_locus_bm: no visible binding for global variable ‘rev_depth’
process_locus_summary: no visible binding for global variable
  ‘alt_depth’
process_locus_summary: no visible binding for global variable
  ‘fwd_depth’
process_locus_summary: no visible binding for global variable
  ‘rev_depth’
read_locus: no visible binding for global variable ‘cell_barcode’
read_locus: no visible binding for global variable ‘fwd_depth’
read_locus: no visible binding for global variable ‘rev_depth’
read_locus: no visible binding for global variable ‘coverage’
read_locus: no visible binding for global variable ‘alt’
read_locus: no visible binding for global variable ‘af’
read_mgatk: no visible binding for global variable ‘fwd_depth’
read_mgatk: no visible binding for global variable ‘rev_depth’
Undefined global functions or variables:
  af alt alt_count alt_depth cell_barcode coverage depth fwd_depth
  highlight loc mut_cell_n mut_status n rev_depth
* 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 ... ERROR
Running examples in ‘scMitoMut-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: subset_cell
> ### Title: Subset cell and loci
> ### Aliases: subset_cell subset_loc
> 
> ### ** Examples
> 
> ## Use the example data
> f <- system.file("extdata", "mini_dataset.tsv.gz", package = "scMitoMut")
> 
> ## Create a temporary h5 file
> ## In real case, we keep the h5 in project folder for future use
> f_h5_tmp <- tempfile(fileext = ".h5")
> 
> ## Load the data with parse_table function
> f_h5 <- parse_table(f, sep = "\t", h5_file = f_h5_tmp)
> 
> ## open the h5 file and create a mtmutObj object
> x <- open_h5_file(f_h5)
> x
mtmutObj object
-------------------------------------------------
h5 file: /tmp/RtmpXpDepg/file2e46e75614f96.h5
Available loci: 16
Selected loci: 16
Available cells: 1359
Selected cells: 1359
Loci passed the filter: 0
filter parameters: 
	min_cell: 1
	model: bb
	p_threshold: 0.05
	alt_count_threshold: 0
	p_adj_method: fdr
> ## subset cell and loci
> x <- subset_cell(x, x$cell_list[1:10])
> x <- subset_loc(x, x$loc_list[1:10])
> x
mtmutObj object
-------------------------------------------------
h5 file: /tmp/RtmpXpDepg/file2e46e75614f96.h5
Available loci: 16
Selected loci: 10
Available cells: 1359
Selected cells: 10
Loci passed the filter: 0
filter parameters: 
	min_cell: 1
	model: bb
	p_threshold: 0.05
	alt_count_threshold: 0
	p_adj_method: fdr
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("subset_cell", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  25.203 2.132 24.616 2.306 1.052 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')

 *** caught segfault ***
address 0x632b2ce8c078, cause 'invalid permissions'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
export_dt    5.825   1.86   5.954
plot_heatmap 5.731   0.65   4.711
* 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:
  chrM.9804
  chrM.9840
  chrM.12889
  chrM.16093
  chrM.16147
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
  > 
  > proc.time()
     user  system elapsed 
    4.864   0.300   4.664 
  
   *** caught segfault ***
  address 0x6279bb0bcb10, cause 'invalid permissions'
  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: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/scMitoMut.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL scMitoMut
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘scMitoMut’ ...
** this is package ‘scMitoMut’ version ‘1.7.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c em_bm.cpp -o em_bm.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c mle_bb.cpp -o mle_bb.o
g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o scMitoMut.so RcppExports.o em_bm.o mle_bb.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-scMitoMut/00new/scMitoMut/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 (scMitoMut)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(scMitoMut)
> 
> test_check("scMitoMut")
chrM.200
chrM.204
chrM.310
chrM.824
chrM.1000
chrM.1001
chrM.1227
chrM.2285
chrM.6081
chrM.9429
chrM.9728
chrM.9804
chrM.9840
chrM.12889
chrM.16093
chrM.16147
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
  4.864   0.300   4.664 

 *** caught segfault ***
address 0x6279bb0bcb10, cause 'invalid permissions'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)