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This page was generated on 2024-07-12 17:38 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 1.8.18  (landing page)
Tomoyuki Furuta
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/GBScleanR
git_branch: RELEASE_3_19
git_last_commit: 743b56b
git_last_commit_date: 2024-06-11 02:38:49 -0400 (Tue, 11 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GBScleanR on nebbiolo1

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: 1.8.18
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GBScleanR_1.8.18.tar.gz
StartedAt: 2024-07-10 23:12:23 -0400 (Wed, 10 Jul 2024)
EndedAt: 2024-07-10 23:15:55 -0400 (Wed, 10 Jul 2024)
EllapsedTime: 212.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GBScleanR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GBScleanR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GBScleanR_1.8.18.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GBScleanR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* 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 ‘1.8.18’
* 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 ... 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 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
getGenotype,GbsrGenotypeData: no visible binding for global variable
  ‘variant_id’
Undefined global functions or variables:
  variant_id
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/GBScleanR.Rcheck/00check.log’
for details.


Installation output

GBScleanR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GBScleanR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-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-3.19-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-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> library(testthat)
> library(GBScleanR)
Loading required package: SeqArray
Loading required package: gdsfmt
> 
> test_check("GBScleanR")
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp9OVozt/sample29ddf218a7ad3.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmp9OVozt/sample29ddf218a7ad3.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf218a7ad3.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/Rtmp9OVozt/sample29ddf19e338a9.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmp9OVozt/sample29ddf19e338a9.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf19e338a9.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Overwrite the previous parents information.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp9OVozt/sample29ddf2fc91148.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmp9OVozt/sample29ddf2fc91148.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf2fc91148.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 Jul 10 23:15:00 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/Rtmp9OVozt/sample29ddf33fd9617.gds
    [Progress Info: sample29ddf33fd9617.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 Jul 10 23:15:00 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp9OVozt/sample29ddf33fd9617.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/Rtmp9OVozt/sample29ddf33fd9617.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf33fd9617.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Wed Jul 10 23:15:00 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/Rtmp9OVozt/sample29ddf33fd9617.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmp9OVozt/sample29ddf33fd9617.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf33fd9617.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/Rtmp9OVozt/sample29ddf27e20c5c.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmp9OVozt/sample29ddf27e20c5c.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf27e20c5c.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Reformatting FGT
The connection to the GDS file was closed.
Loading GDS file.
Reformatting FGT
The connection to the GDS file was closed.
Wed Jul 10 23:15:10 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/Rtmp9OVozt/sample29ddf2c5fd2b2.gds
    [Progress Info: sample29ddf2c5fd2b2.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 Jul 10 23:15:10 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp9OVozt/sample29ddf2c5fd2b2.gds' (53.4K)
    # of fragments: 108
    save to '/tmp/Rtmp9OVozt/sample29ddf2c5fd2b2.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf2c5fd2b2.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Wed Jul 10 23:15:10 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/Rtmp9OVozt/sample29ddf2c5fd2b2.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmp9OVozt/sample29ddf2c5fd2b2.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf2c5fd2b2.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
No parents info.
Wed Jul 10 23:15:11 2024
Variant Call Format (VCF) Import:
    file:
        out29ddf79b27f6d.vcf (47.7K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 48
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 48
    INFO:
    FORMAT: AD
Output:
    /tmp/Rtmp9OVozt/newgds29ddf3f5ba760.gds
    [Progress Info: newgds29ddf3f5ba760.gds.progress]
Parsing 'out29ddf79b27f6d.vcf':
+ genotype/data   { Bit2 2x48x109 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 2276a6d3559f512f3fded5cb78e0093c]
    variant.id  [md5: 5067da9b1128b3131157a723ebdc004a]
    position  [md5: 630c37d68ecd68809e92e692558fb2c0]
    chromosome  [md5: 7dd6a3505147f621e0e2a5f153f93d71]
    allele  [md5: c0b0e52ff9c6c25ab7b923dcc05e7c08]
    genotype  [md5: 3bfd93ab730fe3f5571bb7e7c6149e99]
    phase  [md5: 37885845e314013e92ab13716827d616]
    annotation/id  [md5: c1f22b852fd627cbb7f5883c2e9e2947]
    annotation/qual  [md5: d7998cb66ab7d94d09faaa26ce3a4224]
    annotation/filter  [md5: 07124a219364aec327cf7f38018ed199]
    annotation/format/AD  [md5: b4d095f8cc8dd805af828f7949edf0d0]
Done.
Wed Jul 10 23:15:11 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp9OVozt/newgds29ddf3f5ba760.gds' (18.4K)
    # of fragments: 107
    save to '/tmp/Rtmp9OVozt/newgds29ddf3f5ba760.gds.tmp'
    rename '/tmp/Rtmp9OVozt/newgds29ddf3f5ba760.gds.tmp' (17.8K, reduced: 636B)
    # of fragments: 54
Wed Jul 10 23:15:11 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/Rtmp9OVozt/newgds29ddf3f5ba760.gds' (28.0K)
    # of fragments: 69
    save to '/tmp/Rtmp9OVozt/newgds29ddf3f5ba760.gds.tmp'
    rename '/tmp/Rtmp9OVozt/newgds29ddf3f5ba760.gds.tmp' (27.8K, reduced: 108B)
    # of fragments: 60
No parents info.
Wed Jul 10 23:15:11 2024
Variant Call Format (VCF) Import:
    file:
        out29ddf10710984.vcf (90.2K)
    file format: VCFv4.2
    genome reference: <unknown>
    # of sets of chromosomes (ploidy): 2
    # of samples: 48
    genotype field: GT
    genotype storage: bit2
    compression method: customized
    # of samples: 48
    INFO:
    FORMAT: AD,FAD,FGT
Output:
    /tmp/Rtmp9OVozt/newgds29ddf232cf9bf.gds
    [Progress Info: newgds29ddf232cf9bf.gds.progress]
Parsing 'out29ddf10710984.vcf':
+ genotype/data   { Bit2 2x48x109 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 2276a6d3559f512f3fded5cb78e0093c]
    variant.id  [md5: 5067da9b1128b3131157a723ebdc004a]
    position  [md5: 630c37d68ecd68809e92e692558fb2c0]
    chromosome  [md5: 7dd6a3505147f621e0e2a5f153f93d71]
    allele  [md5: c0b0e52ff9c6c25ab7b923dcc05e7c08]
    genotype  [md5: 3bfd93ab730fe3f5571bb7e7c6149e99]
    phase  [md5: 37885845e314013e92ab13716827d616]
    annotation/id  [md5: c1f22b852fd627cbb7f5883c2e9e2947]
    annotation/qual  [md5: d7998cb66ab7d94d09faaa26ce3a4224]
    annotation/filter  [md5: 07124a219364aec327cf7f38018ed199]
    annotation/format/AD  [md5: b4d095f8cc8dd805af828f7949edf0d0]
    annotation/format/FAD  [md5: 9693ff978d26fee5c2b5d09a3bc62dd3]
    annotation/format/FGT  [md5: 149e182f3a3bba6243fdae39b8b766bf]
Done.
Wed Jul 10 23:15:11 2024
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp9OVozt/newgds29ddf232cf9bf.gds' (26.5K)
    # of fragments: 129
    save to '/tmp/Rtmp9OVozt/newgds29ddf232cf9bf.gds.tmp'
    rename '/tmp/Rtmp9OVozt/newgds29ddf232cf9bf.gds.tmp' (25.8K, reduced: 780B)
    # of fragments: 64
Wed Jul 10 23:15:11 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/Rtmp9OVozt/newgds29ddf232cf9bf.gds' (44.6K)
    # of fragments: 86
    save to '/tmp/Rtmp9OVozt/newgds29ddf232cf9bf.gds.tmp'
    rename '/tmp/Rtmp9OVozt/newgds29ddf232cf9bf.gds.tmp' (43.4K, reduced: 1.1K)
    # of fragments: 74
The connection to the GDS file was closed.
The connection to the GDS file was closed.
Loading GDS file.
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file '/tmp/Rtmp9OVozt/sample29ddf3231dcc7.gds' (95.5K)
    # of fragments: 69
    save to '/tmp/Rtmp9OVozt/sample29ddf3231dcc7.gds.tmp'
    rename '/tmp/Rtmp9OVozt/sample29ddf3231dcc7.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 
 27.822   0.750  28.666 

Example timings

GBScleanR.Rcheck/GBScleanR-Ex.timings

nameusersystemelapsed
GbsrGenotypeData-class0.0160.0000.017
GbsrScheme-class0.0470.0000.047
addScheme0.0050.0030.009
assignScheme0.0760.0040.079
boxplotGBSR0.8160.0440.859
closeGDS0.0010.0040.005
countGenotype0.6270.0360.662
countRead0.6550.0040.658
estGeno2.1240.0922.217
gbsrGDS2CSV0.0360.0000.036
gbsrGDS2VCF0.0010.0040.005
gbsrVCF2GDS0.1130.0160.130
getAllele0.0080.0000.008
getChromosome0.0050.0030.007
getCountAlleleAlt0.4460.0290.475
getCountAlleleMissing0.4400.0020.442
getCountAlleleRef0.3720.0010.373
getCountGenoAlt0.3920.0040.396
getCountGenoHet0.3940.0000.394
getCountGenoMissing0.4640.0000.464
getCountGenoRef0.4560.0000.456
getCountRead0.5570.0440.601
getCountReadAlt0.4670.0000.468
getCountReadRef0.4660.0030.469
getGenotype0.0270.0040.031
getHaplotype2.2250.0522.277
getInfo0.0050.0000.005
getMAC0.4610.0000.461
getMAF0.4190.0080.427
getMarID0.0080.0000.007
getMeanReadAlt0.4320.0000.431
getMeanReadRef0.3720.0000.371
getMedianReadAlt0.4220.0400.462
getMedianReadRef0.3970.0070.404
getParents0.0000.0080.008
getPosition0.0070.0000.006
getRead0.0030.0040.007
getReplicates0.0020.0040.006
getSDReadAlt0.4260.0000.426
getSDReadRef0.4430.0030.446
getSamID0.0070.0000.007
histGBSR0.6640.0000.664
initScheme0.0040.0040.008
isOpenGDS0.0030.0040.006
loadGDS0.0710.0160.086
makeScheme0.0090.0000.009
nmar0.0010.0040.005
nsam0.0020.0030.005
pairsGBSR0.5260.0400.566
plotDosage0.1780.0000.179
plotGBSR0.5460.0000.546
plotReadRatio0.1680.0000.168
reopenGDS0.0090.0000.008
resetCallFilter0.5390.0200.558
resetFilter1.4030.0241.428
resetMarFilter0.8240.0000.825
resetSamFilter0.9410.0721.013
setCallFilter0.9210.0200.942
setInfoFilter0.0060.0000.006
setMarFilter0.8400.0000.841
setParents2.1110.0522.164
setReplicates0.0060.0000.006
setSamFilter0.8040.0000.804
showScheme0.0070.0000.007
thinMarker0.4550.0000.455
validMar0.0070.0000.007
validSam0.0050.0000.005