##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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.