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This page was generated on 2025-08-14 12:05 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 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 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-13 13:45 -0400 (Wed, 13 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 24.04.3 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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for GBScleanR on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GBScleanR_2.3.2.tar.gz
StartedAt: 2025-08-13 22:50:02 -0400 (Wed, 13 Aug 2025)
EndedAt: 2025-08-13 22:53:43 -0400 (Wed, 13 Aug 2025)
EllapsedTime: 221.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GBScleanR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GBScleanR_2.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GBScleanR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
* 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 ... 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 ‘/home/biocbuild/bbs-3.22-bioc/R/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 ... OK
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GBScleanR.Rcheck/00check.log’
for details.


Installation output

GBScleanR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GBScleanR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GBScleanR’ ...
** this is package ‘GBScleanR’ version ‘2.3.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c gbsrCalcProb.cpp -o gbsrCalcProb.o
gbsrCalcProb.cpp: In function ‘std::vector<double> calcGenoprob(const double&, const double&, const double&, const double&, const double&, const bool&, const int&)’:
gbsrCalcProb.cpp:25:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   25 |     for(int g = 0; g < prob.size(); ++g){
      |                    ~~^~~~~~~~~~~~~
gbsrCalcProb.cpp:37:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   37 |         for(int g = 0; g < prob.size(); ++g){
      |                        ~~^~~~~~~~~~~~~
gbsrCalcProb.cpp: In function ‘void calcMissmap(std::vector<double>&, const double&, const double&, const bool&, const int&)’:
gbsrCalcProb.cpp:72:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   72 |         } else if(g == ploidy){
      |                   ~~^~~~~~~~~
gbsrCalcProb.cpp:74:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   74 |                 if(h == ploidy){
      |                    ~~^~~~~~~~~
gbsrCalcProb.cpp:87:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   87 |                 } else if(h == ploidy){
      |                           ~~^~~~~~~~~
gbsrCalcProb.cpp:127:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  127 |                 } else if(g == ploidy){
      |                           ~~^~~~~~~~~
gbsrCalcProb.cpp: In function ‘void offsetProb(std::vector<double>&, const bool&, const int&)’:
gbsrCalcProb.cpp:170:28: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  170 |             if(g == 0 && g == ploidy){
      |                          ~~^~~~~~~~~
gbsrCalcProb.cpp:185:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  185 |                 if(g == 0 && g == ploidy){
      |                              ~~^~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c gbsrFB.cpp -o gbsrFB.o
gbsrFB.cpp: In member function ‘virtual void ParFB::operator()(size_t, size_t)’:
gbsrFB.cpp:109:17: warning: ‘hap_offset_ij’ may be used uninitialized [-Wmaybe-uninitialized]
  109 |             int hap_offset_ij;
      |                 ^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c gbsrIPO.cpp -o gbsrIPO.o
gbsrIPO.cpp: In member function ‘virtual void ParGenoProb::operator()(size_t, size_t)’:
gbsrIPO.cpp:57:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   57 |                 for(int g = 0; g < prob.size(); ++g){
      |                                ~~^~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c gbsrStats.cpp -o gbsrStats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c gbsrViterbi.cpp -o gbsrViterbi.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c gbsrutil.cpp -o gbsrutil.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o GBScleanR.so RcppExports.o gbsrCalcProb.o gbsrFB.o gbsrIPO.o gbsrStats.o gbsrViterbi.o gbsrutil.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-GBScleanR/00new/GBScleanR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GBScleanR)

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-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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 '/tmp/RtmpfH2hDZ/sample14fb6e325a7d25.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/RtmpfH2hDZ/sample14fb6e325a7d25.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e325a7d25.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 '/tmp/RtmpfH2hDZ/sample14fb6e209062d1.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/RtmpfH2hDZ/sample14fb6e209062d1.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e209062d1.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 '/tmp/RtmpfH2hDZ/sample14fb6e52ab460.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/RtmpfH2hDZ/sample14fb6e52ab460.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e52ab460.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.
Wed Aug 13 22:52:42 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/RtmpfH2hDZ/sample14fb6e33b39538.gds
    [Progress Info: sample14fb6e33b39538.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.
Wed Aug 13 22:52:43 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpfH2hDZ/sample14fb6e33b39538.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/RtmpfH2hDZ/sample14fb6e33b39538.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e33b39538.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Wed Aug 13 22:52:43 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 '/tmp/RtmpfH2hDZ/sample14fb6e33b39538.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/RtmpfH2hDZ/sample14fb6e33b39538.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e33b39538.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 '/tmp/RtmpfH2hDZ/sample14fb6e147e3d86.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/RtmpfH2hDZ/sample14fb6e147e3d86.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e147e3d86.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.
Wed Aug 13 22:52:55 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/RtmpfH2hDZ/sample14fb6e53318cb5.gds
    [Progress Info: sample14fb6e53318cb5.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.
Wed Aug 13 22:52:55 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpfH2hDZ/sample14fb6e53318cb5.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/RtmpfH2hDZ/sample14fb6e53318cb5.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e53318cb5.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Wed Aug 13 22:52:55 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 '/tmp/RtmpfH2hDZ/sample14fb6e53318cb5.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/RtmpfH2hDZ/sample14fb6e53318cb5.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e53318cb5.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
No parents info.
Wed Aug 13 22:52:55 2025
Variant Call Format (VCF) Import:
    file:
        out14fb6eeca47b9.vcf (55.5K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 50
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    INFO:
    FORMAT: AD
Output:
    /tmp/RtmpfH2hDZ/newgds14fb6e7d4fb852.gds
    [Progress Info: newgds14fb6e7d4fb852.gds.progress]
Parsing 'out14fb6eeca47b9.vcf':
+ genotype/data   { Bit2 2x50x123 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 39d26dc32c1637733cceddb89fbbc703]
    variant.id  [md5: 5a4e8bfc1e37fcd1800d6ca6831cbd4e]
    position  [md5: 061c7f1c440ab29afbd5a2a2ec150153]
    chromosome  [md5: f6bfc37d611c76b81e9d7b504bb3162c]
    allele  [md5: 80996bbbfdfba9c20e547d8048ffb3d9]
    genotype  [md5: 84bf4f6b6c790cbb96399e015c9d9a67]
    phase  [md5: f04c124a2e09d686b14b34a8479bd4a4]
    annotation/id  [md5: 866fd2c24ef64ec1a755f747f72c05ec]
    annotation/qual  [md5: aba5ad5b4581d374c611cfab79690308]
    annotation/filter  [md5: eb14a330fb0decef5fabef1ce0f58772]
    annotation/format/AD  [md5: 06deab95edf48789c654fc9454c126fa]
Done.
Wed Aug 13 22:52:55 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpfH2hDZ/newgds14fb6e7d4fb852.gds' (19.8K)
    # of fragments: 107
    save to '/tmp/RtmpfH2hDZ/newgds14fb6e7d4fb852.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/newgds14fb6e7d4fb852.gds.tmp' (19.2K, reduced: 636B)
    # of fragments: 54
Wed Aug 13 22:52:55 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 '/tmp/RtmpfH2hDZ/newgds14fb6e7d4fb852.gds' (30.6K)
    # of fragments: 69
    save to '/tmp/RtmpfH2hDZ/newgds14fb6e7d4fb852.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/newgds14fb6e7d4fb852.gds.tmp' (30.5K, reduced: 108B)
    # of fragments: 60
No parents info.
Wed Aug 13 22:52:56 2025
Variant Call Format (VCF) Import:
    file:
        out14fb6e611822fb.vcf (105.1K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 50
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    INFO:
    FORMAT: AD,FAD,FGT
Output:
    /tmp/RtmpfH2hDZ/newgds14fb6e7b8acc30.gds
    [Progress Info: newgds14fb6e7b8acc30.gds.progress]
Parsing 'out14fb6e611822fb.vcf':
+ genotype/data   { Bit2 2x50x123 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 39d26dc32c1637733cceddb89fbbc703]
    variant.id  [md5: 5a4e8bfc1e37fcd1800d6ca6831cbd4e]
    position  [md5: 061c7f1c440ab29afbd5a2a2ec150153]
    chromosome  [md5: f6bfc37d611c76b81e9d7b504bb3162c]
    allele  [md5: 80996bbbfdfba9c20e547d8048ffb3d9]
    genotype  [md5: 84bf4f6b6c790cbb96399e015c9d9a67]
    phase  [md5: f04c124a2e09d686b14b34a8479bd4a4]
    annotation/id  [md5: 866fd2c24ef64ec1a755f747f72c05ec]
    annotation/qual  [md5: aba5ad5b4581d374c611cfab79690308]
    annotation/filter  [md5: eb14a330fb0decef5fabef1ce0f58772]
    annotation/format/AD  [md5: 06deab95edf48789c654fc9454c126fa]
    annotation/format/FAD  [md5: 944183cc0816c44e67a8eeee16c7bf98]
    annotation/format/FGT  [md5: d1aaf43b9306a1e1f698baa58abbac39]
Done.
Wed Aug 13 22:52:57 2025
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpfH2hDZ/newgds14fb6e7b8acc30.gds' (28.7K)
    # of fragments: 129
    save to '/tmp/RtmpfH2hDZ/newgds14fb6e7b8acc30.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/newgds14fb6e7b8acc30.gds.tmp' (28.0K, reduced: 780B)
    # of fragments: 64
Wed Aug 13 22:52:57 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 '/tmp/RtmpfH2hDZ/newgds14fb6e7b8acc30.gds' (49.2K)
    # of fragments: 86
    save to '/tmp/RtmpfH2hDZ/newgds14fb6e7b8acc30.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/newgds14fb6e7b8acc30.gds.tmp' (47.9K, reduced: 1.3K)
    # 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 '/tmp/RtmpfH2hDZ/sample14fb6e2a1f8c34.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/RtmpfH2hDZ/sample14fb6e2a1f8c34.gds.tmp'
    rename '/tmp/RtmpfH2hDZ/sample14fb6e2a1f8c34.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 
 31.893   0.979  33.772 

Example timings

GBScleanR.Rcheck/GBScleanR-Ex.timings

nameusersystemelapsed
GbsrGenotypeData-class0.0120.0020.015
GbsrScheme-class0.0070.0040.011
addScheme0.0210.0040.025
assignScheme0.0950.0120.107
boxplotGBSR0.8710.0180.890
closeGDS0.0020.0020.004
countGenotype0.6850.0400.724
countRead0.7310.0000.731
estGeno3.3770.0783.457
gbsrGDS2CSV0.0170.0000.017
gbsrGDS2VCF0.0040.0000.004
gbsrVCF2GDS0.0780.0090.158
getAllele0.0050.0000.005
getChromosome0.0040.0010.005
getCountAlleleAlt0.3990.0010.401
getCountAlleleMissing0.4320.0010.433
getCountAlleleRef0.4200.0010.421
getCountGenoAlt0.5060.0010.507
getCountGenoHet0.5420.0000.542
getCountGenoMissing0.4250.0010.426
getCountGenoRef0.5020.0010.504
getCountRead0.5340.0010.535
getCountReadAlt0.4940.0020.496
getCountReadRef0.4460.0010.448
getFixedParameter0.0700.0150.158
getGenotype0.0350.0000.035
getHaplotype2.9680.0102.978
getInfo0.0050.0000.005
getMAC0.4340.0010.434
getMAF0.4450.0010.446
getMarID0.0050.0000.005
getMeanReadAlt0.4170.0010.418
getMeanReadRef0.4160.0010.417
getMedianReadAlt0.4810.0000.481
getMedianReadRef0.4030.0010.404
getParents0.0070.0000.007
getPloidy0.0040.0000.004
getPosition0.0040.0000.005
getRead0.0060.0000.007
getReplicates0.0050.0000.005
getSDReadAlt0.3950.0000.395
getSDReadRef0.3970.0020.400
getSamID0.0040.0010.005
histGBSR0.6970.0020.699
initScheme0.0060.0000.007
isOpenGDS0.0050.0000.005
loadGDS0.0770.0140.165
makeScheme0.0060.0010.007
nmar0.0040.0000.004
nsam0.0030.0010.004
pairsGBSR0.5310.0000.531
plotDosage0.2210.0000.222
plotGBSR0.6130.0030.616
plotReadRatio0.1890.0020.191
reopenGDS0.0050.0020.006
resetCallFilter0.5620.0220.669
resetFilter1.5000.0831.665
resetMarFilter0.7940.0000.794
resetSamFilter0.9520.0091.033
setCallFilter0.9260.0151.027
setFixedParameter0.0810.0070.163
setInfoFilter0.0050.0010.006
setMarFilter0.8760.0010.877
setParents2.9390.0552.994
setPloidy0.0040.0000.004
setReplicates0.0050.0000.005
setSamFilter0.8540.0040.858
showScheme0.0070.0000.006
thinMarker0.4310.0020.432
validMar0.0030.0010.005
validSam0.0040.0000.004