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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GBScleanR_2.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GBScleanR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GBScleanR’ version ‘2.0.3’
* 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 ‘GBScleanR’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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 ‘/home/biocbuild/R/R-4.4.2/site-library/GBScleanR/libs/GBScleanR.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (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 ... ERROR
Running examples in ‘GBScleanR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estGeno
> ### Title: Genotype estimation using a hiden Morkov model
> ### Aliases: estGeno estGeno,GbsrGenotypeData-method
> 
> ### ** Examples
> 
> # Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
> gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
> gds <- loadGDS(gds_fn)
Loading GDS file.
> 
> # Find the IDs of parental samples.
> parents <- grep("Founder", getSamID(gds), value = TRUE)
> 
> # Set the parents and flip allele information
> # if the reference sample (Founder1 in our case) has homozygous
> # alternative genotype at some markers of which alleles will
> # be swapped to make the reference sample have homozygous
> # reference genotype.
> gds <- setParents(gds, parents = parents)
> 
> # Initialize a scheme object stored in the slot of the GbsrGenotypeData.
> # We chose `crosstype = "pair"` because two inbred founders were mated
> # in our breeding scheme.
> # We also need to specify the mating matrix which has two rows and
> # one column with integers 1 and 2 indicating a sample (founder)
> # with the memberID 1 and a sample (founder) with the memberID 2
> # were mated.
> gds <- initScheme(gds, mating = cbind(c(1:2)))
> 
> # Add information of the next cross conducted in our scheme.
> # We chose 'crosstype = "selfing"', which do not require a
> # mating matrix.
> gds <- addScheme(gds, crosstype = "selfing")
As `mating` was not specified, set the following mating design.
     [,1]
[1,]    3
[2,]    3
> 
> # Execute error correction by estimating genotype and haplotype of
> # founders and offspring.
> gds <- estGeno(gds)
Member IDs were not assigned to samples.
Assign 4 to all samples as member ID.
Set the number of threads: 1
Start cleaning...
Preparing genotype and haplotype pattern table...
Possible allele dosages: 0 1 2
Number of possible founder genotypes: 2
Member ID(s) to be processed: 4
Number of offspring haplotypes: 4

Now cleaning chr 1...

Cycle 1: 

Forward round of genotype estimation ...

Founder genotype probability calculation ...                                                                      
 *** caught bus error ***
address 0x11, cause 'invalid alignment'

Traceback:
 1: run_viterbi(p_ref = param_list$reads$p_ref, p_alt = param_list$reads$p_alt,     ref = param_list$reads$ref, alt = param_list$reads$alt, eseq_in = param_list$error_rate,     bias = param_list$bias, mismap = param_list$mismap, trans_prob = trans_prob,     init_prob = init_prob, nonzero_prob = nonzero_prob, n_pgeno = param_list$pat$n_p_pat,     n_hap = param_list$pat$n_hap_pat, n_offspring = param_list$n_samples,     n_founder = param_list$n_parents, n_marker = param_list$n_mar,     n_nonzero_prob = n_nonzero_prob, het = param_list$het_parent,     pedigree = pedigree - 1, possiblehap = possiblehap - 1, possiblegeno = param_list$pat$possiblegeno -         1, p_geno_fix = param_list$p_geno_fix - 1, ploidy = param_list$n_ploidy)
 2: .getBestSeq(param_list = param_list, outprob = outprob)
 3: .runCycle(param_list = param_list, outprob = FALSE, outgeno = FALSE)
 4: .cleanEachChr(object = object, chr_i = chr_i, node = node, error_rate = error_rate,     recomb_rate = recomb_rate, call_threshold = call_threshold,     het_parent = het_parent, optim = optim, iter = iter, parentless = parentless,     dummy_reads = dummy_reads, pat = pat)
 5: .local(object, node, recomb_rate, error_rate, call_threshold,     het_parent, optim, iter, n_threads, dummy_reads, ...)
 6: estGeno(gds)
 7: estGeno(gds)
An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R/bin/BATCH: line 60: 2708008 Segmentation fault      (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  29: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  30: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
  31: source_file(path, env = env(env), desc = desc, error_call = error_call)
  32: FUN(X[[i]], ...)
  33: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
  34: doTryCatch(return(expr), name, parentenv, handler)
  35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  36: tryCatchList(expr, classes, parentenv, handlers)
  37: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
  38: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
  39: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
  40: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
  41: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
  42: test_check("GBScleanR")
  An irrecoverable exception occurred. R is aborting now ...
* 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: 2 ERRORs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GBScleanR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL GBScleanR
###
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* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘GBScleanR’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gbsrCalcProb.cpp -o gbsrCalcProb.o
gbsrCalcProb.cpp: In function ‘std::vector<double> calcGenoprob(const double&, const double&, const double&, const double&, const double&, const bool&, const int&)’:
gbsrCalcProb.cpp:25:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   25 |     for(int g = 0; g < prob.size(); ++g){
      |                    ~~^~~~~~~~~~~~~
gbsrCalcProb.cpp:37:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   37 |         for(int g = 0; g < prob.size(); ++g){
      |                        ~~^~~~~~~~~~~~~
gbsrCalcProb.cpp: In function ‘void calcMissmap(std::vector<double>&, const double&, const double&, const bool&, const int&)’:
gbsrCalcProb.cpp:72:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   72 |         } else if(g == ploidy){
      |                   ~~^~~~~~~~~
gbsrCalcProb.cpp:74:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   74 |                 if(h == ploidy){
      |                    ~~^~~~~~~~~
gbsrCalcProb.cpp:87:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   87 |                 } else if(h == ploidy){
      |                           ~~^~~~~~~~~
gbsrCalcProb.cpp:127:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  127 |                 } else if(g == ploidy){
      |                           ~~^~~~~~~~~
gbsrCalcProb.cpp: In function ‘void offsetProb(std::vector<double>&, const bool&, const int&)’:
gbsrCalcProb.cpp:170:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  170 |             if(g == 0 && g == ploidy){
      |                          ~~^~~~~~~~~
gbsrCalcProb.cpp:185:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  185 |                 if(g == 0 && g == ploidy){
      |                              ~~^~~~~~~~~
In file included from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel.h:24,
                 from gbsrCalcProb.cpp:3:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gbsrFB.cpp -o gbsrFB.o
In file included from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel.h:24,
                 from gbsrFB.cpp:3:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
gbsrFB.cpp: In member function ‘virtual void ParFB::operator()(size_t, size_t)’:
gbsrFB.cpp:109:17: warning: ‘hap_offset_ij’ may be used uninitialized [-Wmaybe-uninitialized]
  109 |             int hap_offset_ij;
      |                 ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gbsrIPO.cpp -o gbsrIPO.o
gbsrIPO.cpp: In member function ‘virtual void ParGenoProb::operator()(size_t, size_t)’:
gbsrIPO.cpp:57:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   57 |                 for(int g = 0; g < prob.size(); ++g){
      |                                ~~^~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel.h:24,
                 from gbsrIPO.cpp:3:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gbsrStats.cpp -o gbsrStats.o
In file included from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel.h:24,
                 from gbsrStats.cpp:3:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gbsrViterbi.cpp -o gbsrViterbi.o
In file included from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel.h:24,
                 from gbsrViterbi.cpp:3:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gbsrutil.cpp -o gbsrutil.o
In file included from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/RcppParallel.h:24,
                 from gbsrutil.cpp:3:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29:   required from here
  251 |             return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31:   required from here
  291 |                   && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o GBScleanR.so RcppExports.o gbsrCalcProb.o gbsrFB.o gbsrIPO.o gbsrStats.o gbsrViterbi.o gbsrutil.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.4.2/site-library/00LOCK-GBScleanR/00new/GBScleanR/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 (GBScleanR)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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.

> library(testthat)
> library(GBScleanR)
Loading required package: SeqArray
Loading required package: gdsfmt
> 
> test_check("GBScleanR")
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample295228526b81b0.gds' (95.5K)
    # of fragments: 69
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample295228526b81b0.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample295228526b81b0.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952286704b930.gds' (95.5K)
    # of fragments: 69
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952286704b930.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952286704b930.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample29522835641f49.gds' (95.5K)
    # of fragments: 69
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample29522835641f49.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample29522835641f49.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Fri Feb 14 07:00:25 2025
Variant Call Format (VCF) Import:
    file:
        sample.vcf (210.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 102
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 102
    INFO:
    FORMAT: AD
Output:
    /home/biocbuild/tmp/RtmpRe4yXJ/sample2952281943b421.gds
    [Progress Info: sample2952281943b421.gds.progress]
Parsing 'sample.vcf':
+ genotype/data   { Bit2 2x102x242 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 338086c89cac9760256e9d1ec0a77327]
    variant.id  [md5: 6f6b771cc6816e18766cd7b202765193]
    position  [md5: f3033fec247b8ec6980e81005e257bd8]
    chromosome  [md5: 891ee7d299e1dba9146b8ae33476741c]
    allele  [md5: 9fc3f097ae98a7ebff52fac77379926e]
    genotype  [md5: b83af5eb9818d83c2ccaa40d494f15a8]
    phase  [md5: 9d686e01959b61df5fdc1a4684bd72b3]
    annotation/id  [md5: 021994c12424cab1e907740e364c7c24]
    annotation/qual  [md5: 5a566f4332739a2b28d23b215163b70a]
    annotation/filter  [md5: cb74cdb22966d99a9290a2c804a10580]
    annotation/format/AD  [md5: f8b130e5e4e497ee162cf32b15b0ac3a]
Done.
Fri Feb 14 07:00:25 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281943b421.gds' (53.4K)
    # of fragments: 108
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281943b421.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281943b421.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Fri Feb 14 07:00:25 2025
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281943b421.gds' (95.5K)
    # of fragments: 69
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281943b421.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281943b421.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample29522853941bd4.gds' (95.5K)
    # of fragments: 69
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample29522853941bd4.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample29522853941bd4.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Reformatting FGT
The connection to the GDS file was closed.
Loading GDS file.
Reformatting FGT
The connection to the GDS file was closed.
Fri Feb 14 07:00:35 2025
Variant Call Format (VCF) Import:
    file:
        sample.vcf (210.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 102
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 102
    INFO:
    FORMAT: AD
Output:
    /home/biocbuild/tmp/RtmpRe4yXJ/sample2952284818218a.gds
    [Progress Info: sample2952284818218a.gds.progress]
Parsing 'sample.vcf':
+ genotype/data   { Bit2 2x102x242 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 338086c89cac9760256e9d1ec0a77327]
    variant.id  [md5: 6f6b771cc6816e18766cd7b202765193]
    position  [md5: f3033fec247b8ec6980e81005e257bd8]
    chromosome  [md5: 891ee7d299e1dba9146b8ae33476741c]
    allele  [md5: 9fc3f097ae98a7ebff52fac77379926e]
    genotype  [md5: b83af5eb9818d83c2ccaa40d494f15a8]
    phase  [md5: 9d686e01959b61df5fdc1a4684bd72b3]
    annotation/id  [md5: 021994c12424cab1e907740e364c7c24]
    annotation/qual  [md5: 5a566f4332739a2b28d23b215163b70a]
    annotation/filter  [md5: cb74cdb22966d99a9290a2c804a10580]
    annotation/format/AD  [md5: f8b130e5e4e497ee162cf32b15b0ac3a]
Done.
Fri Feb 14 07:00:36 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952284818218a.gds' (53.4K)
    # of fragments: 108
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952284818218a.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952284818218a.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Fri Feb 14 07:00:36 2025
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952284818218a.gds' (95.5K)
    # of fragments: 69
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952284818218a.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952284818218a.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
No parents info.
Fri Feb 14 07:00:36 2025
Variant Call Format (VCF) Import:
    file:
        out295228587ba7b9.vcf (62.7K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 52
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 52
    INFO:
    FORMAT: AD
Output:
    /home/biocbuild/tmp/RtmpRe4yXJ/newgds2952282f5eb33b.gds
    [Progress Info: newgds2952282f5eb33b.gds.progress]
Parsing 'out295228587ba7b9.vcf':
+ genotype/data   { Bit2 2x52x134 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 049a9a693f44aa0d136f3cddec7ad058]
    variant.id  [md5: 441d827c7d85c2700e57f543b5f92644]
    position  [md5: d5d5ac1ab397dfd2487a374f1c3dd344]
    chromosome  [md5: f785006ea07dfd7ebb0ee4fa9406bd41]
    allele  [md5: 9251984e8fd3badbb0ed1c7f9f4cec6f]
    genotype  [md5: d7111a37561faaba003ccae9232ac725]
    phase  [md5: d634739ce7a02de445dd0d45d4df3ab8]
    annotation/id  [md5: 795e705ebed3eda3023a013fb007e395]
    annotation/qual  [md5: 16bccb2f34bf7b073bc77ed6324bd8f8]
    annotation/filter  [md5: 6c94e626de06715b8a42c54193c99715]
    annotation/format/AD  [md5: 5de4a6c7a0241204d8ea91e1ba85e1ec]
Done.
Fri Feb 14 07:00:36 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952282f5eb33b.gds' (21.6K)
    # of fragments: 107
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952282f5eb33b.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952282f5eb33b.gds.tmp' (21.0K, reduced: 636B)
    # of fragments: 54
Fri Feb 14 07:00:36 2025
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952282f5eb33b.gds' (34.0K)
    # of fragments: 69
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952282f5eb33b.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952282f5eb33b.gds.tmp' (33.9K, reduced: 108B)
    # of fragments: 60
No parents info.
Fri Feb 14 07:00:36 2025
Variant Call Format (VCF) Import:
    file:
        out2952282f138bc0.vcf (118.9K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 52
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 52
    INFO:
    FORMAT: AD,FAD,FGT
Output:
    /home/biocbuild/tmp/RtmpRe4yXJ/newgds2952285e8eeeff.gds
    [Progress Info: newgds2952285e8eeeff.gds.progress]
Parsing 'out2952282f138bc0.vcf':
+ genotype/data   { Bit2 2x52x134 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 049a9a693f44aa0d136f3cddec7ad058]
    variant.id  [md5: 441d827c7d85c2700e57f543b5f92644]
    position  [md5: d5d5ac1ab397dfd2487a374f1c3dd344]
    chromosome  [md5: f785006ea07dfd7ebb0ee4fa9406bd41]
    allele  [md5: 9251984e8fd3badbb0ed1c7f9f4cec6f]
    genotype  [md5: d7111a37561faaba003ccae9232ac725]
    phase  [md5: d634739ce7a02de445dd0d45d4df3ab8]
    annotation/id  [md5: 795e705ebed3eda3023a013fb007e395]
    annotation/qual  [md5: 16bccb2f34bf7b073bc77ed6324bd8f8]
    annotation/filter  [md5: 6c94e626de06715b8a42c54193c99715]
    annotation/format/AD  [md5: 5de4a6c7a0241204d8ea91e1ba85e1ec]
    annotation/format/FAD  [md5: 46c1030cb5c6405e4b8d304e57d15385]
    annotation/format/FGT  [md5: 8169f11eff06fa489c2554b66f257eac]
Done.
Fri Feb 14 07:00:36 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952285e8eeeff.gds' (31.7K)
    # of fragments: 129
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952285e8eeeff.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952285e8eeeff.gds.tmp' (31.0K, reduced: 780B)
    # of fragments: 64
Fri Feb 14 07:00:36 2025
Loading GDS file.
Reformatting FGT
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Working on 'annotation/format/FAD' ...
Working on 'annotation/format/FGT' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952285e8eeeff.gds' (55.4K)
    # of fragments: 86
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952285e8eeeff.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/newgds2952285e8eeeff.gds.tmp' (53.9K, reduced: 1.5K)
    # of fragments: 74
The connection to the GDS file was closed.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281beac015.gds' (95.5K)
    # of fragments: 69
    save to '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281beac015.gds.tmp'
    rename '/home/biocbuild/tmp/RtmpRe4yXJ/sample2952281beac015.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
As `mating` was not specified, set the following mating design.
     [,1]
[1,]    3
[2,]    3
Member IDs were not assigned to samples.
Assign 4 to all samples as member ID.
Set the number of threads: 1
Start cleaning...
Preparing genotype and haplotype pattern table...
Possible allele dosages: 0 1 2
Number of possible founder genotypes: 2
Member ID(s) to be processed: 4
Number of offspring haplotypes: 4

Now cleaning chr 1...

Cycle 1: 

Forward round of genotype estimation ...

Founder genotype probability calculation ...                                                                      
 *** caught segfault ***
address 0xffffa727daa0, cause 'invalid permissions'

Traceback:
 1: run_viterbi(p_ref = param_list$reads$p_ref, p_alt = param_list$reads$p_alt,     ref = param_list$reads$ref, alt = param_list$reads$alt, eseq_in = param_list$error_rate,     bias = param_list$bias, mismap = param_list$mismap, trans_prob = trans_prob,     init_prob = init_prob, nonzero_prob = nonzero_prob, n_pgeno = param_list$pat$n_p_pat,     n_hap = param_list$pat$n_hap_pat, n_offspring = param_list$n_samples,     n_founder = param_list$n_parents, n_marker = param_list$n_mar,     n_nonzero_prob = n_nonzero_prob, het = param_list$het_parent,     pedigree = pedigree - 1, possiblehap = possiblehap - 1, possiblegeno = param_list$pat$possiblegeno -         1, p_geno_fix = param_list$p_geno_fix - 1, ploidy = param_list$n_ploidy)
 2: .getBestSeq(param_list = param_list, outprob = outprob)
 3: .runCycle(param_list = param_list, outprob = FALSE, outgeno = FALSE)
 4: .cleanEachChr(object = object, chr_i = chr_i, node = node, error_rate = error_rate,     recomb_rate = recomb_rate, call_threshold = call_threshold,     het_parent = het_parent, optim = optim, iter = iter, parentless = parentless,     dummy_reads = dummy_reads, pat = pat)
 5: .local(object, node, recomb_rate, error_rate, call_threshold,     het_parent, optim, iter, n_threads, dummy_reads, ...)
 6: estGeno(gds)
 7: estGeno(gds)
 8: eval(code, test_env)
 9: eval(code, test_env)
10: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
11: doTryCatch(return(expr), name, parentenv, handler)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
14: doTryCatch(return(expr), name, parentenv, handler)
15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
16: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
18: test_code(desc, code, env = parent.frame(), reporter = reporter)
19: test_that("estGeno", {    gds <- loadGDS(gds_fn)    gds <- setParents(gds, grep("Founder", getSamID(gds), value = TRUE))    gds <- initScheme(gds, cbind(c(1:2)))    gds <- addScheme(gds, "self")    gds <- estGeno(gds)    p_hap <- getHaplotype(gds, parents = "only")    expect_true(all(p_hap[, 1, ] == 1))    expect_true(all(p_hap[, 2, ] == 2))    hap <- getHaplotype(gds)    expect_true(all(dim(hap) == c(2, nsam(gds), nmar(gds))))    p_geno <- getGenotype(gds, node = "parents")    expect_true(nrow(p_geno) == sum(getParents(gds, TRUE)) *         2)    expect_true(ncol(p_geno) == nmar(gds, FALSE))    cor_geno <- getGenotype(gds, "cor")    expect_equal(dim(cor_geno), c(nsam(gds), nmar(gds)))    closeGDS(gds)})
20: eval(code, test_env)
21: eval(code, test_env)
22: withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error)
23: doTryCatch(return(expr), name, parentenv, handler)
24: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
26: doTryCatch(return(expr), name, parentenv, handler)
27: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
28: tryCatchList(expr, classes, parentenv, handlers)
29: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
30: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
31: source_file(path, env = env(env), desc = desc, error_call = error_call)
32: FUN(X[[i]], ...)
33: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
38: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
39: test_files_serial(test_dir = test_dir, test_package = test_package,     test_paths = test_paths, load_helpers = load_helpers, reporter = reporter,     env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     desc = desc, load_package = load_package, error_call = error_call)
40: test_files(test_dir = path, test_paths = test_paths, test_package = package,     reporter = reporter, load_helpers = load_helpers, env = env,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     load_package = load_package, parallel = parallel)
41: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
42: test_check("GBScleanR")
An irrecoverable exception occurred. R is aborting now ...