Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 778/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GBScleanR 2.3.2  (landing page)
Tomoyuki Furuta
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/GBScleanR
git_branch: devel
git_last_commit: d1bad5d
git_last_commit_date: 2025-06-17 21:55:38 -0400 (Tue, 17 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GBScleanR on lconway

To the developers/maintainers of the GBScleanR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GBScleanR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GBScleanR
Version: 2.3.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GBScleanR_2.3.2.tar.gz
StartedAt: 2025-08-08 21:07:19 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 21:12:37 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 318.9 seconds
RetCode: 0
Status:   OK  
CheckDir: GBScleanR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GBScleanR_2.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/GBScleanR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GBScleanR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GBScleanR’ version ‘2.3.2’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... 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 ... 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/GBScleanR/libs/GBScleanR.so’:
  Found ‘__ZNSt3__14coutE’, 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
getHaplotype 4.495 24.939  29.646
estGeno      4.510 24.811  29.553
setParents   4.379 24.842  29.505
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/GBScleanR.Rcheck/00check.log’
for details.


Installation output

GBScleanR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GBScleanR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘GBScleanR’ ...
** this is package ‘GBScleanR’ version ‘2.3.2’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrCalcProb.cpp -o gbsrCalcProb.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrFB.cpp -o gbsrFB.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrIPO.cpp -o gbsrIPO.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrStats.cpp -o gbsrStats.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrViterbi.cpp -o gbsrViterbi.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gbsrutil.cpp -o gbsrutil.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GBScleanR.so RcppExports.o gbsrCalcProb.o gbsrFB.o gbsrIPO.o gbsrStats.o gbsrViterbi.o gbsrutil.o -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)

Tests output

GBScleanR.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 '/private/tmp/Rtmp23Mmsc/sample5a32237ca9cb.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/Rtmp23Mmsc/sample5a32237ca9cb.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/sample5a32237ca9cb.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 '/private/tmp/Rtmp23Mmsc/sample5a325f926adf.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/Rtmp23Mmsc/sample5a325f926adf.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/sample5a325f926adf.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 '/private/tmp/Rtmp23Mmsc/sample5a322f59f508.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/Rtmp23Mmsc/sample5a322f59f508.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/sample5a322f59f508.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 Aug  8 21:11:41 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
    INFO:
    FORMAT: AD
Output:
    /tmp/Rtmp23Mmsc/sample5a32553b56a5.gds
    [Progress Info: sample5a32553b56a5.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 Aug  8 21:11:41 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp23Mmsc/sample5a32553b56a5.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/Rtmp23Mmsc/sample5a32553b56a5.gds.tmp'
    rename '/tmp/Rtmp23Mmsc/sample5a32553b56a5.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Fri Aug  8 21:11:41 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 '/private/tmp/Rtmp23Mmsc/sample5a32553b56a5.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/Rtmp23Mmsc/sample5a32553b56a5.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/sample5a32553b56a5.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 '/private/tmp/Rtmp23Mmsc/sample5a321c4035c6.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/Rtmp23Mmsc/sample5a321c4035c6.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/sample5a321c4035c6.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 Aug  8 21:11:53 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
    INFO:
    FORMAT: AD
Output:
    /tmp/Rtmp23Mmsc/sample5a32c0980a9.gds
    [Progress Info: sample5a32c0980a9.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 Aug  8 21:11:53 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp23Mmsc/sample5a32c0980a9.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/Rtmp23Mmsc/sample5a32c0980a9.gds.tmp'
    rename '/tmp/Rtmp23Mmsc/sample5a32c0980a9.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Fri Aug  8 21:11:53 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 '/private/tmp/Rtmp23Mmsc/sample5a32c0980a9.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/Rtmp23Mmsc/sample5a32c0980a9.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/sample5a32c0980a9.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
No parents info.
Fri Aug  8 21:11:53 2025
Variant Call Format (VCF) Import:
    file:
        out5a321af3be9c.vcf (55.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 57
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    INFO:
    FORMAT: AD
Output:
    /tmp/Rtmp23Mmsc/newgds5a3232995c9b.gds
    [Progress Info: newgds5a3232995c9b.gds.progress]
Parsing 'out5a321af3be9c.vcf':
+ genotype/data   { Bit2 2x57x108 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 820910163b62629f6ffd72700d5df905]
    variant.id  [md5: 0aa4d804f140678b2c36e2e8b471c56f]
    position  [md5: 1fe4867125c51a87c4304a83fd1969d6]
    chromosome  [md5: 598b6ec8fd1dc1e566e3ef982cde1fae]
    allele  [md5: 40581aa6531ed768b3f62da08c37c6fc]
    genotype  [md5: 5478bd77e559ef7b63c5dc99cd781ae8]
    phase  [md5: ca93fc31bef9f95528125a0bca7efd97]
    annotation/id  [md5: 7f75301764af65a067787e6329e5da5c]
    annotation/qual  [md5: 082d6e4f882c64bb5b18ac3c370b7797]
    annotation/filter  [md5: 5d108a27592cc50b48852c89de77e770]
    annotation/format/AD  [md5: 7c354ebd2d87de4339add7b1a367f06b]
Done.
Fri Aug  8 21:11:53 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp23Mmsc/newgds5a3232995c9b.gds' (20.1K)
    # of fragments: 107
    save to '/tmp/Rtmp23Mmsc/newgds5a3232995c9b.gds.tmp'
    rename '/tmp/Rtmp23Mmsc/newgds5a3232995c9b.gds.tmp' (19.4K, reduced: 636B)
    # of fragments: 54
Fri Aug  8 21:11:53 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 '/private/tmp/Rtmp23Mmsc/newgds5a3232995c9b.gds' (31.0K)
    # of fragments: 69
    save to '/private/tmp/Rtmp23Mmsc/newgds5a3232995c9b.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/newgds5a3232995c9b.gds.tmp' (30.9K, reduced: 108B)
    # of fragments: 60
No parents info.
Fri Aug  8 21:11:54 2025
Variant Call Format (VCF) Import:
    file:
        out5a3270bc5636.vcf (105.0K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 57
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    INFO:
    FORMAT: AD,FAD,FGT
Output:
    /tmp/Rtmp23Mmsc/newgds5a324ccd9e66.gds
    [Progress Info: newgds5a324ccd9e66.gds.progress]
Parsing 'out5a3270bc5636.vcf':
+ genotype/data   { Bit2 2x57x108 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 820910163b62629f6ffd72700d5df905]
    variant.id  [md5: 0aa4d804f140678b2c36e2e8b471c56f]
    position  [md5: 1fe4867125c51a87c4304a83fd1969d6]
    chromosome  [md5: 598b6ec8fd1dc1e566e3ef982cde1fae]
    allele  [md5: 40581aa6531ed768b3f62da08c37c6fc]
    genotype  [md5: 5478bd77e559ef7b63c5dc99cd781ae8]
    phase  [md5: ca93fc31bef9f95528125a0bca7efd97]
    annotation/id  [md5: 7f75301764af65a067787e6329e5da5c]
    annotation/qual  [md5: 082d6e4f882c64bb5b18ac3c370b7797]
    annotation/filter  [md5: 5d108a27592cc50b48852c89de77e770]
    annotation/format/AD  [md5: 7c354ebd2d87de4339add7b1a367f06b]
    annotation/format/FAD  [md5: e36dd50098e3c94b1f6a8ccdabf94e31]
    annotation/format/FGT  [md5: 6edb35d82975d6bcd682a43f117cfef8]
Done.
Fri Aug  8 21:11:54 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp23Mmsc/newgds5a324ccd9e66.gds' (29.3K)
    # of fragments: 129
    save to '/tmp/Rtmp23Mmsc/newgds5a324ccd9e66.gds.tmp'
    rename '/tmp/Rtmp23Mmsc/newgds5a324ccd9e66.gds.tmp' (28.5K, reduced: 780B)
    # of fragments: 64
Fri Aug  8 21:11:54 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 '/private/tmp/Rtmp23Mmsc/newgds5a324ccd9e66.gds' (50.2K)
    # of fragments: 86
    save to '/private/tmp/Rtmp23Mmsc/newgds5a324ccd9e66.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/newgds5a324ccd9e66.gds.tmp' (48.8K, reduced: 1.4K)
    # 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 '/private/tmp/Rtmp23Mmsc/sample5a325eb210ef.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/Rtmp23Mmsc/sample5a325eb210ef.gds.tmp'
    rename '/private/tmp/Rtmp23Mmsc/sample5a325eb210ef.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 ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Backward round of genotype estimation  ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Paramter optimization ...

Cycle 2: 

Forward round of genotype estimation ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Backward round of genotype estimation  ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Paramter optimization ...

Cycle 3: 

Forward round of genotype estimation ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Backward round of genotype estimation  ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Paramter optimization ...

Cycle 4: 

Forward round of genotype estimation ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Backward round of genotype estimation  ...

Founder genotype probability calculation ...                                                                      
Founder genotype probability calculation at marker#: 10                                                                      
Founder genotype probability calculation at marker#: 20                                                                      
Founder genotype probability calculation at marker#: 30                                                                      
Founder genotype probability calculation at marker#: 40                                                                      
Founder genotype probability calculation at marker#: 50                                                                      
Founder genotype probability calculation at marker#: 60                                                                      
Founder genotype probability calculation at marker#: 70                                                                      
Founder genotype probability calculation at marker#: 80                                                                      
Founder genotype probability calculation at marker#: 90                                                                      
Founder genotype probability calculation at marker#: 100                                                                      
Founder genotype probability calculation at marker#: 110                                                                      
Founder genotype probability calculation at marker#: 120                                                                      
Founder genotype probability calculation at marker#: 130                                                                      
Founder genotype probability calculation at marker#: 140                                                                      
Founder genotype probability calculation at marker#: 150                                                                      
Founder genotype probability calculation at marker#: 160                                                                      
Founder genotype probability calculation at marker#: 170                                                                      
Founder genotype probability calculation at marker#: 180                                                                      
Founder genotype probability calculation at marker#: 190                                                                      
Founder genotype probability calculation at marker#: 200                                                                      
Founder genotype probability calculation at marker#: 210                                                                      
Founder genotype probability calculation at marker#: 220                                                                      
Founder genotype probability calculation at marker#: 230                                                                      
Founder genotype probability calculation at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 240                                                                      
Backtracking best genotype sequences at marker#: 230                                                                      
Backtracking best genotype sequences at marker#: 220                                                                      
Backtracking best genotype sequences at marker#: 210                                                                      
Backtracking best genotype sequences at marker#: 200                                                                      
Backtracking best genotype sequences at marker#: 190                                                                      
Backtracking best genotype sequences at marker#: 180                                                                      
Backtracking best genotype sequences at marker#: 170                                                                      
Backtracking best genotype sequences at marker#: 160                                                                      
Backtracking best genotype sequences at marker#: 150                                                                      
Backtracking best genotype sequences at marker#: 140                                                                      
Backtracking best genotype sequences at marker#: 130                                                                      
Backtracking best genotype sequences at marker#: 120                                                                      
Backtracking best genotype sequences at marker#: 110                                                                      
Backtracking best genotype sequences at marker#: 100                                                                      
Backtracking best genotype sequences at marker#: 90                                                                      
Backtracking best genotype sequences at marker#: 80                                                                      
Backtracking best genotype sequences at marker#: 70                                                                      
Backtracking best genotype sequences at marker#: 60                                                                      
Backtracking best genotype sequences at marker#: 50                                                                      
Backtracking best genotype sequences at marker#: 40                                                                      
Backtracking best genotype sequences at marker#: 30                                                                      
Backtracking best genotype sequences at marker#: 20                                                                      
Backtracking best genotype sequences at marker#: 10                                                                      
Backtracking best genotype sequences: Done!                                                                      
Offspring genotype probability calculation ...                                                                      
                                                                      
Summarizing output ...

Done!
The connection to the GDS file was closed.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 271 ]
> 
> proc.time()
   user  system elapsed 
 32.210  26.811  59.828 

Example timings

GBScleanR.Rcheck/GBScleanR-Ex.timings

nameusersystemelapsed
GbsrGenotypeData-class0.0150.0050.027
GbsrScheme-class0.0100.0010.012
addScheme0.0230.0030.026
assignScheme0.1150.0040.119
boxplotGBSR0.9490.0330.986
closeGDS0.0040.0020.006
countGenotype0.7780.0080.790
countRead0.7950.0070.807
estGeno 4.51024.81129.553
gbsrGDS2CSV0.0200.0030.023
gbsrGDS2VCF0.0050.0020.007
gbsrVCF2GDS0.0860.0440.142
getAllele0.0060.0020.009
getChromosome0.0060.0020.008
getCountAlleleAlt0.4640.0090.479
getCountAlleleMissing0.4470.0050.455
getCountAlleleRef0.4230.0050.431
getCountGenoAlt0.4480.0050.456
getCountGenoHet0.4470.0060.458
getCountGenoMissing0.4170.0080.432
getCountGenoRef0.4270.0070.437
getCountRead0.4500.0070.463
getCountReadAlt0.4280.0070.437
getCountReadRef0.4220.0070.432
getFixedParameter0.0740.0430.126
getGenotype0.0400.0020.042
getHaplotype 4.49524.93929.646
getInfo0.0060.0020.008
getMAC0.4450.0070.454
getMAF0.4710.0090.481
getMarID0.0070.0060.012
getMeanReadAlt0.4420.0070.450
getMeanReadRef0.4540.0080.462
getMedianReadAlt0.4940.0070.504
getMedianReadRef0.4310.0060.439
getParents0.0080.0020.011
getPloidy0.0050.0020.007
getPosition0.0060.0040.010
getRead0.0090.0020.010
getReplicates0.0070.0040.012
getSDReadAlt0.4420.0080.452
getSDReadRef0.4520.0090.463
getSamID0.0060.0030.008
histGBSR0.7160.0060.725
initScheme0.0080.0020.011
isOpenGDS0.0070.0020.009
loadGDS0.0810.0430.133
makeScheme0.0090.0020.011
nmar0.0050.0010.006
nsam0.0050.0010.006
pairsGBSR0.5990.0060.608
plotDosage0.2710.0070.280
plotGBSR0.6530.0060.662
plotReadRatio0.2470.0040.252
reopenGDS0.0070.0020.010
resetCallFilter0.5690.0670.651
resetFilter1.4900.0681.578
resetMarFilter0.8420.0060.853
resetSamFilter0.9060.0490.972
setCallFilter1.0310.0781.129
setFixedParameter0.0730.0400.122
setInfoFilter0.0050.0010.007
setMarFilter0.8520.0060.864
setParents 4.37924.84229.505
setPloidy0.0050.0010.008
setReplicates0.0060.0020.008
setSamFilter0.8640.0070.877
showScheme0.0080.0020.010
thinMarker0.4380.0040.444
validMar0.0060.0040.009
validSam0.0040.0030.006