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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GBScleanR_2.1.7.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GBScleanR.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GBScleanR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GBScleanR' version '2.1.7'
* 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 whether package 'GBScleanR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 ... 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GbsrGenotypeData-class.Rd: SeqArray
  loadGDS.Rd: SeqArray
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'getPloidy' 'setPloidy'
Undocumented S4 methods:
  generic 'getPloidy' and siglist 'GbsrGenotypeData'
  generic 'setPloidy' and siglist 'GbsrGenotypeData'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... INFO
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 for x64 is not available
* 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: getErrorRate
> ### Title: Get allele read biases
> ### Aliases: getErrorRate getErrorRate,GbsrGenotypeData-method
> 
> ### ** Examples
> 
> # Create a GDS file from a sample VCF file.
> vcf_fn <- system.file("extdata", "sample.vcf", package = "GBScleanR")
> gds_fn <- tempfile("sample", fileext = ".gds")
> gbsrVCF2GDS(vcf_fn = vcf_fn, out_fn = gds_fn, force = TRUE)
Sat Mar 22 01:43:16 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:
    E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpa21kjH\sample71085dc87d5a.gds
    [Progress Info: sample71085dc87d5a.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.
Sat Mar 22 01:43:16 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpa21kjH\sample71085dc87d5a.gds' (53.4K)
    # of fragments: 108
    save to 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpa21kjH\sample71085dc87d5a.gds.tmp'
    rename 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpa21kjH\sample71085dc87d5a.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Sat Mar 22 01:43:16 2025
[1] "E:\\biocbuild\\bbs-3.21-bioc\\tmpdir\\Rtmpa21kjH\\sample71085dc87d5a.gds"
> 
> # Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
> gds <- loadGDS(gds_fn)
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpa21kjH\sample71085dc87d5a.gds' (95.5K)
    # of fragments: 69
    save to 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpa21kjH\sample71085dc87d5a.gds.tmp'
    rename 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmpa21kjH\sample71085dc87d5a.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
> 
> # Set fixed allele read biases.
> # Initialize the bias vector to be assinged.
> bias <- rep(NA, nmar(gds))
> 
> # As an example, select 20 markers randomly and assign 0 or 1 to them.
> # Since the bias set by setFixedParameter() function is the reference allele read
> # bias. Thus, the values 0 and 1 means that the marker only gives alternative
> # and reference allele reads, respectively.
> # Set these fixed biases if some of your markers are dominant markers.
> bias[sample(seq_along(bias), 20)] <- sample(c(0, 1), 20, replace = TRUE)
> 
> fixed_bias <- getErrorRate(gds)
Error in .local(object, valid, chr, ...) : 
  No record of marker wise error rates in the input GDS file.
Run estGeno() to obtain them.
Calls: getErrorRate -> getErrorRate -> .local
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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 ERROR, 1 WARNING, 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/GBScleanR.Rcheck/00check.log'
for details.