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This page was generated on 2024-03-29 11:35:58 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 769/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GBScleanR 1.6.0  (landing page)
Tomoyuki Furuta
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/GBScleanR
git_branch: RELEASE_3_18
git_last_commit: f849068
git_last_commit_date: 2023-10-24 11:38:50 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.6.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GBScleanR_1.6.0.tar.gz
StartedAt: 2024-03-27 22:37:59 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 22:40:50 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 171.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GBScleanR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GBScleanR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GBScleanR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘GBScleanR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GBScleanR’ version ‘1.6.0’
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
* 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 R 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 ... NOTE
.replaceGT: no visible global function definition for ‘copyto.gdsn’
Undefined global functions or variables:
  copyto.gdsn
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘BasicUsageOfGBScleanR.rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GBScleanR.Rcheck/00check.log’
for details.



Installation output

GBScleanR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL GBScleanR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘GBScleanR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gbsrCalcProb.cpp -o gbsrCalcProb.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gbsrFB.cpp -o gbsrFB.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gbsrIPO.cpp -o gbsrIPO.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gbsrStats.cpp -o gbsrStats.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gbsrViterbi.cpp -o gbsrViterbi.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c gbsrutil.cpp -o gbsrutil.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.18-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-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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/Rtmph35crU/sample1e22d828b93642.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmph35crU/sample1e22d828b93642.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d828b93642.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/Rtmph35crU/sample1e22d8135014e9.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmph35crU/sample1e22d8135014e9.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d8135014e9.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 '/tmp/Rtmph35crU/sample1e22d82bdac0d4.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmph35crU/sample1e22d82bdac0d4.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d82bdac0d4.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 Mar 27 22:40:10 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/Rtmph35crU/sample1e22d84a67be17.gds
    [Progress Info: sample1e22d84a67be17.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 Mar 27 22:40:10 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmph35crU/sample1e22d84a67be17.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/Rtmph35crU/sample1e22d84a67be17.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d84a67be17.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Wed Mar 27 22:40:10 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 '/tmp/Rtmph35crU/sample1e22d84a67be17.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmph35crU/sample1e22d84a67be17.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d84a67be17.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/Rtmph35crU/sample1e22d8c3603c9.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmph35crU/sample1e22d8c3603c9.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d8c3603c9.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 Mar 27 22:40:14 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/Rtmph35crU/sample1e22d89d202e1.gds
    [Progress Info: sample1e22d89d202e1.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 Mar 27 22:40:14 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmph35crU/sample1e22d89d202e1.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/Rtmph35crU/sample1e22d89d202e1.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d89d202e1.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Wed Mar 27 22:40:14 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 '/tmp/Rtmph35crU/sample1e22d89d202e1.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmph35crU/sample1e22d89d202e1.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d89d202e1.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
No parents info.
Wed Mar 27 22:40:14 2024
Variant Call Format (VCF) Import:
    file:
        out1e22d850703422.vcf (47.5K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 46
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 46
    INFO:
    FORMAT: AD
Output:
    /tmp/Rtmph35crU/newgds1e22d810fd7abc.gds
    [Progress Info: newgds1e22d810fd7abc.gds.progress]
Parsing 'out1e22d850703422.vcf':
+ genotype/data   { Bit2 2x46x113 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 59ebe6c53120b5967ec0075e8bb44929]
    variant.id  [md5: 33cb6463b8609dcab434773f65b64bb0]
    position  [md5: 76d9fc8f2e338a5b54e231a60afbe01b]
    chromosome  [md5: ac620ef2962685e4e48a4266f49f2e79]
    allele  [md5: 3c98b9041c2b373ef5c3d96d50df3dfa]
    genotype  [md5: 2ecd7f5b3ce0c43410f28e8f5c68af9a]
    phase  [md5: f4c15d6b53753444ca0d1438c2bede8c]
    annotation/id  [md5: 0a6157566ca2ad920f237386dce63459]
    annotation/qual  [md5: b5e5f5a0a4a78969f23b027601107d05]
    annotation/filter  [md5: f8f4c2d07bf641d466c85241c6fd5ee9]
    annotation/format/AD  [md5: 67c17861e79e08d7c3f5f8d7a70c28f4]
Done.
Wed Mar 27 22:40:14 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmph35crU/newgds1e22d810fd7abc.gds' (18.3K)
    # of fragments: 107
    save to '/tmp/Rtmph35crU/newgds1e22d810fd7abc.gds.tmp'
    rename '/tmp/Rtmph35crU/newgds1e22d810fd7abc.gds.tmp' (17.7K, reduced: 636B)
    # of fragments: 54
Wed Mar 27 22:40:14 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 '/tmp/Rtmph35crU/newgds1e22d810fd7abc.gds' (27.7K)
    # of fragments: 69
    save to '/tmp/Rtmph35crU/newgds1e22d810fd7abc.gds.tmp'
    rename '/tmp/Rtmph35crU/newgds1e22d810fd7abc.gds.tmp' (27.6K, reduced: 108B)
    # of fragments: 60
No parents info.
Wed Mar 27 22:40:14 2024
Variant Call Format (VCF) Import:
    file:
        out1e22d83b507e1f.vcf (100.2K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 46
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 46
    INFO:
    FORMAT: AD,CFT,FAD,FGT
Output:
    /tmp/Rtmph35crU/newgds1e22d82f722a77.gds
    [Progress Info: newgds1e22d82f722a77.gds.progress]
Parsing 'out1e22d83b507e1f.vcf':
+ genotype/data   { Bit2 2x46x113 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 59ebe6c53120b5967ec0075e8bb44929]
    variant.id  [md5: 33cb6463b8609dcab434773f65b64bb0]
    position  [md5: 76d9fc8f2e338a5b54e231a60afbe01b]
    chromosome  [md5: ac620ef2962685e4e48a4266f49f2e79]
    allele  [md5: 3c98b9041c2b373ef5c3d96d50df3dfa]
    genotype  [md5: 2ecd7f5b3ce0c43410f28e8f5c68af9a]
    phase  [md5: f4c15d6b53753444ca0d1438c2bede8c]
    annotation/id  [md5: 0a6157566ca2ad920f237386dce63459]
    annotation/qual  [md5: b5e5f5a0a4a78969f23b027601107d05]
    annotation/filter  [md5: f8f4c2d07bf641d466c85241c6fd5ee9]
    annotation/format/AD  [md5: 67c17861e79e08d7c3f5f8d7a70c28f4]
    annotation/format/CFT  [md5: 846528d2958c107116dfa2c148636a2c]
    annotation/format/FAD  [md5: b37a75ac4a2c6f89c49b928cf7f1caa2]
    annotation/format/FGT  [md5: 72861decd4d5b56a9f81958bdb08c2e6]
Done.
Wed Mar 27 22:40:14 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmph35crU/newgds1e22d82f722a77.gds' (27.5K)
    # of fragments: 140
    save to '/tmp/Rtmph35crU/newgds1e22d82f722a77.gds.tmp'
    rename '/tmp/Rtmph35crU/newgds1e22d82f722a77.gds.tmp' (26.7K, reduced: 852B)
    # of fragments: 69
Wed Mar 27 22:40:14 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 '/tmp/Rtmph35crU/newgds1e22d82f722a77.gds' (45.3K)
    # of fragments: 91
    save to '/tmp/Rtmph35crU/newgds1e22d82f722a77.gds.tmp'
    rename '/tmp/Rtmph35crU/newgds1e22d82f722a77.gds.tmp' (44.2K, 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 '/tmp/Rtmph35crU/sample1e22d8789a04c9.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmph35crU/sample1e22d8789a04c9.gds.tmp'
    rename '/tmp/Rtmph35crU/sample1e22d8789a04c9.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 
 12.708   1.293  13.988 

Example timings

GBScleanR.Rcheck/GBScleanR-Ex.timings

nameusersystemelapsed
GbsrGenotypeData-class0.0120.0000.014
GbsrScheme-class0.0390.0040.044
addScheme0.0070.0000.007
assignScheme0.0670.0000.067
boxplotGBSR0.4380.0000.438
closeGDS0.0040.0000.003
countGenotype0.2590.0240.284
countRead0.2760.0190.294
estGeno2.2710.1082.380
gbsrGDS2CSV0.0270.0040.031
gbsrGDS2VCF0.0040.0000.004
gbsrVCF2GDS0.0780.0040.083
getAllele0.0050.0000.005
getChromosome0.0050.0000.005
getCountAlleleAlt0.0130.0000.013
getCountAlleleMissing0.0130.0000.013
getCountAlleleRef0.0100.0040.013
getCountGenoAlt0.0120.0010.014
getCountGenoHet0.0110.0030.013
getCountGenoMissing0.0130.0000.012
getCountGenoRef0.0110.0010.013
getCountRead0.0270.0030.029
getCountReadAlt0.0170.0000.017
getCountReadRef0.0170.0000.017
getGenotype0.0530.0000.053
getHaplotype2.2260.0642.291
getInfo0.0040.0000.005
getMAC0.0130.0000.012
getMAF0.0130.0000.013
getMarID0.0040.0000.005
getMeanReadAlt0.0150.0000.016
getMeanReadRef0.0160.0000.016
getMedianReadAlt0.0150.0000.016
getMedianReadRef0.0160.0000.015
getParents0.0070.0000.006
getPosition0.0040.0000.004
getRead0.0060.0000.007
getSDReadAlt0.0120.0040.016
getSDReadRef0.0130.0040.016
getSamID0.0050.0000.005
histGBSR0.2240.0040.228
initScheme0.0060.0000.006
isOpenGDS0.0050.0000.005
loadGDS0.0640.0080.071
nmar0.0030.0000.004
nsam0.0040.0000.004
pairsGBSR0.1510.0000.151
plotDosage0.1740.0000.174
plotGBSR0.1900.0040.194
plotReadRatio0.1480.0040.152
reopenGDS0.0060.0000.006
resetCallFilter0.3430.0400.383
resetFilter0.3160.0960.413
resetMarFilter0.0240.0040.028
resetSamFilter0.0900.0040.103
setCallFilter0.6100.1480.758
setInfoFilter0.0020.0040.006
setMarFilter0.0250.0000.026
setParents1.6980.0321.730
setReplicates0.0040.0010.004
setSamFilter0.0330.0020.035
showScheme0.0070.0000.006
thinMarker0.0140.0000.014
validMar0.0050.0000.005
validSam0.0050.0000.005