Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-07 20:26 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 780/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GBScleanR 1.8.0  (landing page)
Tomoyuki Furuta
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/GBScleanR
git_branch: RELEASE_3_19
git_last_commit: 1e30a82
git_last_commit_date: 2024-04-30 11:39:37 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 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: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2024-06-05 20:31:26 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 20:34:49 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 203.4 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GBScleanR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GBScleanR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GBScleanR’ version ‘1.8.0’
* 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 ... NOTE
.replaceGT: no visible global function definition for ‘copyto.gdsn’
Undefined global functions or variables:
  copyto.gdsn
* checking Rd files ... NOTE
checkRd: (-1) boxplotGBSR.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxplotGBSR.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) histGBSR.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pairsGBSR.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotGBSR.Rd:66: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
getHaplotype 2.043  8.701  10.810
estGeno      1.582  8.166   9.785
setParents   1.477  8.083   9.594
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/library’
* installing *source* package ‘GBScleanR’ ...
** 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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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/RtmpXIx6gp/sample66c86e883f52.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpXIx6gp/sample66c86e883f52.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/sample66c86e883f52.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/RtmpXIx6gp/sample66c86e94033e.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpXIx6gp/sample66c86e94033e.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/sample66c86e94033e.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.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/private/tmp/RtmpXIx6gp/sample66c82ed6a7a8.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpXIx6gp/sample66c82ed6a7a8.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/sample66c82ed6a7a8.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 Jun  5 20:34:19 2024
Variant Call Format (VCF) Import:
    file:
        sample.vcf (210.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 102
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 102
    INFO:
    FORMAT: AD
Output:
    /tmp/RtmpXIx6gp/sample66c84647f49c.gds
    [Progress Info: sample66c84647f49c.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 Jun  5 20:34:19 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpXIx6gp/sample66c84647f49c.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/RtmpXIx6gp/sample66c84647f49c.gds.tmp'
    rename '/tmp/RtmpXIx6gp/sample66c84647f49c.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Wed Jun  5 20:34:19 2024
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/RtmpXIx6gp/sample66c84647f49c.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpXIx6gp/sample66c84647f49c.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/sample66c84647f49c.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/RtmpXIx6gp/sample66c84101175b.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpXIx6gp/sample66c84101175b.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/sample66c84101175b.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.
 <None> <None> <None> <None> <None> <None> <None> <None> <None> <None>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 Jun  5 20:34:25 2024
Variant Call Format (VCF) Import:
    file:
        sample.vcf (210.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 102
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 102
    INFO:
    FORMAT: AD
Output:
    /tmp/RtmpXIx6gp/sample66c82bfb7bde.gds
    [Progress Info: sample66c82bfb7bde.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 Jun  5 20:34:26 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpXIx6gp/sample66c82bfb7bde.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/RtmpXIx6gp/sample66c82bfb7bde.gds.tmp'
    rename '/tmp/RtmpXIx6gp/sample66c82bfb7bde.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Wed Jun  5 20:34:26 2024
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/RtmpXIx6gp/sample66c82bfb7bde.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpXIx6gp/sample66c82bfb7bde.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/sample66c82bfb7bde.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
No parents info.
Wed Jun  5 20:34:26 2024
Variant Call Format (VCF) Import:
    file:
        out66c8532cf42d.vcf (46.6K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 45
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 45
    INFO:
    FORMAT: AD
Output:
    /tmp/RtmpXIx6gp/newgds66c87532e457.gds
    [Progress Info: newgds66c87532e457.gds.progress]
Parsing 'out66c8532cf42d.vcf':
+ genotype/data   { Bit2 2x45x113 ZIP_ra, 16B }
Digests:
    sample.id  [md5: f643a0c48fd986343dded66cfb55ce28]
    variant.id  [md5: 33cb6463b8609dcab434773f65b64bb0]
    position  [md5: 6ed719ffec7f1ef381131b1b0f616e7a]
    chromosome  [md5: ac620ef2962685e4e48a4266f49f2e79]
    allele  [md5: b316e83a9ba46280baa329458eb813c5]
    genotype  [md5: cf0afed1b3579ea20bf24e526fa966c7]
    phase  [md5: c26f6378ac7a8c600f965683fa33f341]
    annotation/id  [md5: b282fc98002e02da40f95d9ebc9e7311]
    annotation/qual  [md5: b5e5f5a0a4a78969f23b027601107d05]
    annotation/filter  [md5: f8f4c2d07bf641d466c85241c6fd5ee9]
    annotation/format/AD  [md5: 831c65feb3af769246fa8f77f5c5b436]
Done.
Wed Jun  5 20:34:26 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpXIx6gp/newgds66c87532e457.gds' (18.1K)
    # of fragments: 107
    save to '/tmp/RtmpXIx6gp/newgds66c87532e457.gds.tmp'
    rename '/tmp/RtmpXIx6gp/newgds66c87532e457.gds.tmp' (17.5K, reduced: 636B)
    # of fragments: 54
Wed Jun  5 20:34:26 2024
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/RtmpXIx6gp/newgds66c87532e457.gds' (27.2K)
    # of fragments: 69
    save to '/private/tmp/RtmpXIx6gp/newgds66c87532e457.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/newgds66c87532e457.gds.tmp' (27.1K, reduced: 108B)
    # of fragments: 60
No parents info.
Wed Jun  5 20:34:26 2024
Variant Call Format (VCF) Import:
    file:
        out66c84c6f9713.vcf (98.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 45
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 45
    INFO:
    FORMAT: AD,CFT,FAD,FGT
Output:
    /tmp/RtmpXIx6gp/newgds66c841376788.gds
    [Progress Info: newgds66c841376788.gds.progress]
Parsing 'out66c84c6f9713.vcf':
+ genotype/data   { Bit2 2x45x113 ZIP_ra, 16B }
Digests:
    sample.id  [md5: f643a0c48fd986343dded66cfb55ce28]
    variant.id  [md5: 33cb6463b8609dcab434773f65b64bb0]
    position  [md5: 6ed719ffec7f1ef381131b1b0f616e7a]
    chromosome  [md5: ac620ef2962685e4e48a4266f49f2e79]
    allele  [md5: b316e83a9ba46280baa329458eb813c5]
    genotype  [md5: cf0afed1b3579ea20bf24e526fa966c7]
    phase  [md5: c26f6378ac7a8c600f965683fa33f341]
    annotation/id  [md5: b282fc98002e02da40f95d9ebc9e7311]
    annotation/qual  [md5: b5e5f5a0a4a78969f23b027601107d05]
    annotation/filter  [md5: f8f4c2d07bf641d466c85241c6fd5ee9]
    annotation/format/AD  [md5: 831c65feb3af769246fa8f77f5c5b436]
    annotation/format/CFT  [md5: 94d3eb0236ae46a8d30a49682724f2c6]
    annotation/format/FAD  [md5: 5095d00f998fcc433189353f80b5af74]
    annotation/format/FGT  [md5: e5564a07d96d6eb6e582e1cddd5eae4d]
Done.
Wed Jun  5 20:34:26 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/RtmpXIx6gp/newgds66c841376788.gds' (27.1K)
    # of fragments: 140
    save to '/tmp/RtmpXIx6gp/newgds66c841376788.gds.tmp'
    rename '/tmp/RtmpXIx6gp/newgds66c841376788.gds.tmp' (26.3K, reduced: 852B)
    # of fragments: 69
Wed Jun  5 20:34:26 2024
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/RtmpXIx6gp/newgds66c841376788.gds' (44.3K)
    # of fragments: 91
    save to '/private/tmp/RtmpXIx6gp/newgds66c841376788.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/newgds66c841376788.gds.tmp' (43.1K, reduced: 1.1K)
    # of fragments: 79
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/RtmpXIx6gp/sample66c87b691df3.gds' (95.5K)
    # of fragments: 69
    save to '/private/tmp/RtmpXIx6gp/sample66c87b691df3.gds.tmp'
    rename '/private/tmp/RtmpXIx6gp/sample66c87b691df3.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...

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 ...                                                                      
                                                                      
Summarizing output ...

Done!
The connection to the GDS file was closed.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 271 ]
> 
> proc.time()
   user  system elapsed 
 13.701  12.087  26.076 

Example timings

GBScleanR.Rcheck/GBScleanR-Ex.timings

nameusersystemelapsed
GbsrGenotypeData-class0.0170.0020.021
GbsrScheme-class0.0640.0020.066
addScheme0.0070.0010.008
assignScheme0.2240.0020.227
boxplotGBSR0.4650.0120.477
closeGDS0.0040.0010.004
countGenotype0.6830.0040.687
countRead0.3260.0260.353
estGeno1.5828.1669.785
gbsrGDS2CSV0.0380.0040.041
gbsrGDS2VCF0.0060.0020.008
gbsrVCF2GDS0.1000.0430.155
getAllele0.0040.0020.007
getChromosome0.0060.0030.009
getCountAlleleAlt0.0110.0030.014
getCountAlleleMissing0.0130.0030.015
getCountAlleleRef0.0130.0030.016
getCountGenoAlt0.0100.0030.013
getCountGenoHet0.0110.0030.015
getCountGenoMissing0.0080.0020.010
getCountGenoRef0.0120.0030.015
getCountRead0.0370.0040.041
getCountReadAlt0.0190.0040.023
getCountReadRef0.0190.0040.024
getGenotype0.0680.0020.070
getHaplotype 2.043 8.70110.810
getInfo0.0060.0020.008
getMAC0.0130.0050.019
getMAF0.0150.0050.020
getMarID0.0070.0050.012
getMeanReadAlt0.0180.0050.023
getMeanReadRef0.0190.0060.025
getMedianReadAlt0.0150.0050.020
getMedianReadRef0.0140.0050.020
getParents0.0090.0020.011
getPosition0.0050.0040.010
getRead0.0080.0020.010
getSDReadAlt0.0180.0050.024
getSDReadRef0.0190.0040.023
getSamID0.0040.0010.006
histGBSR0.3070.0060.316
initScheme0.0090.0020.010
isOpenGDS0.0080.0020.010
loadGDS0.0850.0430.139
nmar0.0050.0020.006
nsam0.0050.0010.007
pairsGBSR0.1960.0150.213
plotDosage0.1940.0070.201
plotGBSR0.2190.0040.225
plotReadRatio0.2030.0030.208
reopenGDS0.0080.0020.011
resetCallFilter0.4160.4130.847
resetFilter0.4590.4200.894
resetMarFilter0.0250.0050.029
resetSamFilter0.1090.0480.166
setCallFilter0.7780.8331.636
setInfoFilter0.0040.0010.006
setMarFilter0.0250.0030.028
setParents1.4778.0839.594
setReplicates0.0050.0010.007
setSamFilter0.0190.0010.021
showScheme0.0070.0020.009
thinMarker0.0120.0020.015
validMar0.0050.0030.008
validSam0.0050.0020.007