Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-17 13:21:33 -0400 (Mon, 17 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for GBScleanR on palomino3


To the developers/maintainers of the GBScleanR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 723/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GBScleanR 1.0.5  (landing page)
Tomoyuki Furuta
Snapshot Date: 2022-10-16 13:55:18 -0400 (Sun, 16 Oct 2022)
git_url: https://git.bioconductor.org/packages/GBScleanR
git_branch: RELEASE_3_15
git_last_commit: 6388d36
git_last_commit_date: 2022-09-07 07:11:14 -0400 (Wed, 07 Sep 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GBScleanR
Version: 1.0.5
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GBScleanR_1.0.5.tar.gz
StartedAt: 2022-10-17 00:19:31 -0400 (Mon, 17 Oct 2022)
EndedAt: 2022-10-17 00:22:43 -0400 (Mon, 17 Oct 2022)
EllapsedTime: 191.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GBScleanR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GBScleanR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GBScleanR_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/GBScleanR.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GBScleanR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GBScleanR' version '1.0.5'
* 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 whether package 'GBScleanR' can be installed ... OK
* 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 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.callFilterScan: no visible global function definition for 'quantile'
.cleanEachChr_ds: no visible global function definition for
  'dosage_viterbi'
.countGeno: no visible global function definition for 'slot<-'
.countRead: no visible global function definition for 'slot<-'
.df.maker: no visible global function definition for 'getQtileReadRef'
.df.maker: no visible global function definition for 'getQtileReadAlt'
.modGDS: no visible global function definition for 'moveto.gdsn'
.modGDS: no visible global function definition for 'setdim.gdsn'
.saveADB: no visible global function definition for 'append.gdsn'
.saveDosage: no visible global function definition for 'append.gdsn'
.saveGeno: no visible global function definition for 'append.gdsn'
.saveHap: no visible global function definition for 'append.gdsn'
.saveMR: no visible global function definition for 'append.gdsn'
.savePGeno: no visible global function definition for 'append.gdsn'
gbsrVCF2GDS: no visible global function definition for 'seqNumAllele'
loadGDS: no visible global function definition for 'seqNumAllele'
addScheme,GbsrGenotypeData: no visible global function definition for
  'slot<-'
estDosage,GbsrGenotypeData: no visible binding for global variable
  'het_parent'
initScheme,GbsrGenotypeData: no visible global function definition for
  'slot<-'
resetMarFilter,GbsrGenotypeData: no visible global function definition
  for 'slot<-'
resetSamFilter,GbsrGenotypeData: no visible global function definition
  for 'slot<-'
setParents,GbsrGenotypeData: no visible global function definition for
  'slot<-'
smoothReadRatio,GbsrGenotypeData: no visible global function definition
  for 'calc_ratio'
validMar<-,GbsrGenotypeData: no visible global function definition for
  'slot<-'
validSam<-,GbsrGenotypeData: no visible global function definition for
  'slot<-'
Undefined global functions or variables:
  append.gdsn calc_ratio dosage_viterbi getQtileReadAlt getQtileReadRef
  het_parent moveto.gdsn quantile seqNumAllele setdim.gdsn slot<-
Consider adding
  importFrom("methods", "slot<-")
  importFrom("stats", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'boxplotGBSR.Rd':
  'calcReadStats'

Missing link or links in documentation object 'countGenotype.Rd':
  'ScanAnnotationDataFrame'

Missing link or links in documentation object 'countRead.Rd':
  'ScanAnnotationDataFrame'

Missing link or links in documentation object 'gbsrGDS2VCF.Rd':
  'openGDS'

Missing link or links in documentation object 'getCountAlleleAlt.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountAlleleMissing.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountAlleleRef.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountGenoAlt.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountGenoHet.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountGenoMissing.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountGenoRef.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountRead.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountReadAlt.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getCountReadRef.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getMAC.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getMAF.Rd':
  'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getMeanReadAlt.Rd':
  'calcReadStats' 'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getMeanReadRef.Rd':
  'calcReadStats' 'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getMedianReadAlt.Rd':
  'calcReadStats' 'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getMedianReadRef.Rd':
  'calcReadStats' 'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getSDReadAlt.Rd':
  'calcReadStats' 'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'getSDReadRef.Rd':
  'calcReadStats' 'ScanAnnotationDataFrame' 'getValidSnp'

Missing link or links in documentation object 'histGBSR.Rd':
  'calcReadStats'

Missing link or links in documentation object 'pairsGBSR.Rd':
  'calcReadStats'

Missing link or links in documentation object 'plotGBSR.Rd':
  'calcReadStats'

Missing link or links in documentation object 'resetCallFilter.Rd':
  'setFiltGenotype'

Missing link or links in documentation object 'resetMarFilter.Rd':
  'setSnpFilter'

Missing link or links in documentation object 'resetSamFilter.Rd':
  'setScanFilter'

Missing link or links in documentation object 'setMarFilter.Rd':
  'getValidSnp'

Missing link or links in documentation object 'setSamFilter.Rd':
  'getValidScan'

Missing link or links in documentation object 'subsetGDS.Rd':
  'openGDS'

Missing link or links in documentation object 'thinMarker.Rd':
  'getValidSnp'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'GbsrGenotypeData-class':
Slots for class 'GbsrGenotypeData'
  Code: .S3Class marker sample scheme
  Inherited: .S3Class
  Docs: data marker sample scheme

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'countRead'
  'q'

Undocumented arguments in documentation object '.makeFilter'
  'object' 'valid' 'parents' 'chr'

Undocumented arguments in documentation object 'estDosage'
  'recomb_rate' 'error_rate' 'smooth' 'mindp'

Documented arguments not in \usage in documentation object 'gbsrGDS2VCF':
  'node'

Undocumented arguments in documentation object 'getMedianReadAlt'
  'q'

Undocumented arguments in documentation object 'getMedianReadRef'
  'q'

Undocumented arguments in documentation object 'getSamID'
  'parents'

Undocumented arguments in documentation object 'plotSmoothedRatio'
  'line_color'
Documented arguments not in \usage in documentation object 'plotSmoothedRatio':
  'node'

Undocumented arguments in documentation object 'smoothReadRatio'
  'node' 'verbose'

Undocumented arguments in documentation object 'validMar'
  'value'

Undocumented arguments in documentation object 'validSam'
  'value'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/GBScleanR/libs/x64/GBScleanR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'GBScleanR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GbsrGenotypeData-class
> ### Title: Class 'GbsrGenotypeData'
> ### Aliases: GbsrGenotypeData-class GbsrGenotypeData
> 
> ### ** Examples
> 
> # `loadGDS()` initialize the `GbsrGenotypeData` object.
> 
> # Load a GDS file and instantiate a `GbsrGenotypeData` object.
> gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
> gds <- loadGDS(gds_fn)
Loading GDS file.
Error in seqOpen(gds.fn = x, readonly = FALSE) : 
  'F:/biocbuild/bbs-3.15-bioc/R/library/GBScleanR/extdata/sample.gds' is a SNP GDS file, please use SNPRelate::snpgdsOpen().
Or use SeqArray::seqSNP2GDS() for converting SNP GDS to SeqArray GDS.
Calls: loadGDS -> seqOpen
Execution halted
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 4 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/GBScleanR.Rcheck/00check.log'
for details.


Installation output

GBScleanR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GBScleanR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GBScleanR' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GBSR_HMM.cpp -o GBSR_HMM.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GBSR_stats.cpp -o GBSR_stats.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -shared -s -static-libgcc -o GBScleanR.dll tmp.def GBSR_HMM.o GBSR_stats.o RcppExports.o -LF:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GBScleanR/00new/GBScleanR/libs/x64
** 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
** 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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
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.
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.
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.
Mon Oct 17 00:22:20 2022
Variant Call Format (VCF) Import:
    file(s):
        sample.vcf (210.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 102
    genotype storage: bit2
    compression method: customized
    # of samples: 102
Output:
    F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29602a429cc.gds
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.
Mon Oct 17 00:22:21 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29602a429cc.gds' (53.4K)
    # of fragments: 108
    save to 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29602a429cc.gds.tmp'
    rename 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29602a429cc.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Mon Oct 17 00:22:21 2022
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29602a429cc.gds' (95.5K)
    # of fragments: 69
    save to 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29602a429cc.gds.tmp'
    rename 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29602a429cc.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
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.
 <None> <None> <None> <None> <None> <None> <None> <None> <None> <None>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.
Mon Oct 17 00:22:26 2022
Variant Call Format (VCF) Import:
    file(s):
        sample.vcf (210.3K)
    file format: VCFv4.2
    genome reference: <unknown>
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 102
    genotype storage: bit2
    compression method: customized
    # of samples: 102
Output:
    F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29606d8747c8.gds
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.
Mon Oct 17 00:22:26 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29606d8747c8.gds' (53.4K)
    # of fragments: 108
    save to 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29606d8747c8.gds.tmp'
    rename 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29606d8747c8.gds.tmp' (52.8K, reduced: 648B)
    # of fragments: 54
Mon Oct 17 00:22:26 2022
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29606d8747c8.gds' (95.5K)
    # of fragments: 69
    save to 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29606d8747c8.gds.tmp'
    rename 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\sample29606d8747c8.gds.tmp' (95.4K, reduced: 108B)
    # of fragments: 60
Loading GDS file.
The connection to the GDS file was closed.
Mon Oct 17 00:22:26 2022
Variant Call Format (VCF) Import:
    file(s):
        out2960179c7b62.vcf (56.9K)
    file format: VCFv4.2
    genome reference: <unknown>
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 53
    genotype storage: bit2
    compression method: customized
    # of samples: 53
Output:
    F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29602aa068a.gds
Parsing 'out2960179c7b62.vcf':
+ genotype/data   { Bit2 2x53x119 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 61c4e5ba4151bcbb94a2559728d80550]
    variant.id  [md5: 2fe225cdcc03c6b25f94e65209f47935]
    position  [md5: f93416ea74a78595c069b66357889408]
    chromosome  [md5: 2c63827bd00e7c6bf967d1b3564fb864]
    allele  [md5: f70a2741045aa8c954d5bd3d892dab72]
    genotype  [md5: 98080f194327c67b224d3e1c281a05ec]
    phase  [md5: 4e1ccc07da202ba5cbba4c2c98b780e0]
    annotation/id  [md5: b5fb805ca6c6086ce3ebae2c7a9e567f]
    annotation/qual  [md5: e5b0890672db1d9613363930dd2f3aba]
    annotation/filter  [md5: 9987a60b68575dbedaa31b344ec7e745]
    annotation/format/AD  [md5: c7df797d631dd67c164bbac2bb43fd4f]
Done.
Mon Oct 17 00:22:26 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29602aa068a.gds' (20.6K)
    # of fragments: 107
    save to 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29602aa068a.gds.tmp'
    rename 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29602aa068a.gds.tmp' (20.0K, reduced: 636B)
    # of fragments: 54
Mon Oct 17 00:22:26 2022
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/AD' ...
Clean up the fragments of GDS file:
    open the file 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29602aa068a.gds' (31.9K)
    # of fragments: 69
    save to 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29602aa068a.gds.tmp'
    rename 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29602aa068a.gds.tmp' (31.8K, reduced: 108B)
    # of fragments: 60
Loading GDS file.
The connection to the GDS file was closed.
Mon Oct 17 00:22:27 2022
Variant Call Format (VCF) Import:
    file(s):
        out296078b178b1.vcf (120.9K)
    file format: VCFv4.2
    genome reference: <unknown>
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 53
    genotype storage: bit2
    compression method: customized
    # of samples: 53
Output:
    F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29605d6c43d7.gds
Parsing 'out296078b178b1.vcf':
+ genotype/data   { Bit2 2x53x119 ZIP_ra, 16B }
Digests:
    sample.id  [md5: 61c4e5ba4151bcbb94a2559728d80550]
    variant.id  [md5: 2fe225cdcc03c6b25f94e65209f47935]
    position  [md5: f93416ea74a78595c069b66357889408]
    chromosome  [md5: 2c63827bd00e7c6bf967d1b3564fb864]
    allele  [md5: f70a2741045aa8c954d5bd3d892dab72]
    genotype  [md5: 98080f194327c67b224d3e1c281a05ec]
    phase  [md5: 4e1ccc07da202ba5cbba4c2c98b780e0]
    annotation/id  [md5: b5fb805ca6c6086ce3ebae2c7a9e567f]
    annotation/qual  [md5: e5b0890672db1d9613363930dd2f3aba]
    annotation/filter  [md5: 9987a60b68575dbedaa31b344ec7e745]
    annotation/format/AD  [md5: c7df797d631dd67c164bbac2bb43fd4f]
    annotation/format/CFT  [md5: ec03c57c3e89d8724a190a1ce6c5fd4e]
    annotation/format/FAD  [md5: ae443b9d0b0be83988d925fa3ba70e91]
    annotation/format/FGT  [md5: 9d2d7d59295e7348b100d04e81c16aab]
Done.
Mon Oct 17 00:22:27 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29605d6c43d7.gds' (31.8K)
    # of fragments: 140
    save to 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29605d6c43d7.gds.tmp'
    rename 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29605d6c43d7.gds.tmp' (31.0K, reduced: 852B)
    # of fragments: 69
Mon Oct 17 00:22:27 2022
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 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29605d6c43d7.gds' (51.3K)
    # of fragments: 94
    save to 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29605d6c43d7.gds.tmp'
    rename 'F:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpQJZc6x\newgds29605d6c43d7.gds.tmp' (51.2K, reduced: 180B)
    # of fragments: 79
Loading GDS file.
The connection to the GDS file was closed.
Loading GDS file.
Set the number of threads: 1
Start cleaning...

Now cleaning chr 1...

Cycle 1: Forward path...

Forward founder genotype probability calculation at marker#: 10                                                                      
Forward founder genotype probability calculation at marker#: 20                                                                      
Forward founder genotype probability calculation at marker#: 30                                                                      
Forward founder genotype probability calculation at marker#: 40                                                                      
Forward founder genotype probability calculation at marker#: 50                                                                      
Forward founder genotype probability calculation at marker#: 60                                                                      
Forward founder genotype probability calculation at marker#: 70                                                                      
Forward founder genotype probability calculation at marker#: 80                                                                      
Forward founder genotype probability calculation at marker#: 90                                                                      
Forward founder genotype probability calculation at marker#: 100                                                                      
Forward founder genotype probability calculation at marker#: 110                                                                      
Forward founder genotype probability calculation at marker#: 120                                                                      
Forward founder genotype probability calculation at marker#: 130                                                                      
Forward founder genotype probability calculation at marker#: 140                                                                      
Forward founder genotype probability calculation at marker#: 150                                                                      
Forward founder genotype probability calculation at marker#: 160                                                                      
Forward founder genotype probability calculation at marker#: 170                                                                      
Forward founder genotype probability calculation at marker#: 180                                                                      
Forward founder genotype probability calculation at marker#: 190                                                                      
Forward founder genotype probability calculation at marker#: 200                                                                      
Forward founder genotype probability calculation at marker#: 210                                                                      
Forward founder genotype probability calculation at marker#: 220                                                                      
Forward founder genotype probability calculation at marker#: 230                                                                      
Forward founder genotype probability calculation at marker#: 240                                                                      
Forward founder genotype probability calculation: Done!                                                                      
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!                                                                      
                                                                      
Cycle 1: Backward path...

Forward founder genotype probability calculation at marker#: 10                                                                      
Forward founder genotype probability calculation at marker#: 20                                                                      
Forward founder genotype probability calculation at marker#: 30                                                                      
Forward founder genotype probability calculation at marker#: 40                                                                      
Forward founder genotype probability calculation at marker#: 50                                                                      
Forward founder genotype probability calculation at marker#: 60                                                                      
Forward founder genotype probability calculation at marker#: 70                                                                      
Forward founder genotype probability calculation at marker#: 80                                                                      
Forward founder genotype probability calculation at marker#: 90                                                                      
Forward founder genotype probability calculation at marker#: 100                                                                      
Forward founder genotype probability calculation at marker#: 110                                                                      
Forward founder genotype probability calculation at marker#: 120                                                                      
Forward founder genotype probability calculation at marker#: 130                                                                      
Forward founder genotype probability calculation at marker#: 140                                                                      
Forward founder genotype probability calculation at marker#: 150                                                                      
Forward founder genotype probability calculation at marker#: 160                                                                      
Forward founder genotype probability calculation at marker#: 170                                                                      
Forward founder genotype probability calculation at marker#: 180                                                                      
Forward founder genotype probability calculation at marker#: 190                                                                      
Forward founder genotype probability calculation at marker#: 200                                                                      
Forward founder genotype probability calculation at marker#: 210                                                                      
Forward founder genotype probability calculation at marker#: 220                                                                      
Forward founder genotype probability calculation at marker#: 230                                                                      
Forward founder genotype probability calculation at marker#: 240                                                                      
Forward founder genotype probability calculation: Done!                                                                      
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!                                                                      
                                                                      
Cycle 1: Estimating allele read bias and mismapping pattern...

Cycle 2: Forward path...

Forward founder genotype probability calculation at marker#: 10                                                                      
Forward founder genotype probability calculation at marker#: 20                                                                      
Forward founder genotype probability calculation at marker#: 30                                                                      
Forward founder genotype probability calculation at marker#: 40                                                                      
Forward founder genotype probability calculation at marker#: 50                                                                      
Forward founder genotype probability calculation at marker#: 60                                                                      
Forward founder genotype probability calculation at marker#: 70                                                                      
Forward founder genotype probability calculation at marker#: 80                                                                      
Forward founder genotype probability calculation at marker#: 90                                                                      
Forward founder genotype probability calculation at marker#: 100                                                                      
Forward founder genotype probability calculation at marker#: 110                                                                      
Forward founder genotype probability calculation at marker#: 120                                                                      
Forward founder genotype probability calculation at marker#: 130                                                                      
Forward founder genotype probability calculation at marker#: 140                                                                      
Forward founder genotype probability calculation at marker#: 150                                                                      
Forward founder genotype probability calculation at marker#: 160                                                                      
Forward founder genotype probability calculation at marker#: 170                                                                      
Forward founder genotype probability calculation at marker#: 180                                                                      
Forward founder genotype probability calculation at marker#: 190                                                                      
Forward founder genotype probability calculation at marker#: 200                                                                      
Forward founder genotype probability calculation at marker#: 210                                                                      
Forward founder genotype probability calculation at marker#: 220                                                                      
Forward founder genotype probability calculation at marker#: 230                                                                      
Forward founder genotype probability calculation at marker#: 240                                                                      
Forward founder genotype probability calculation: Done!                                                                      
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!                                                                      
                                                                      
Cycle 2: Backward path...

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

Done!
The connection to the GDS file was closed.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 272 ]
> 
> proc.time()
   user  system elapsed 
  15.04    2.51   18.64 

Example timings

GBScleanR.Rcheck/GBScleanR-Ex.timings

nameusersystemelapsed