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CHECK report for SeqArray on malbec2

This page was generated on 2019-10-16 12:02:32 -0400 (Wed, 16 Oct 2019).

Package 1490/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqArray 1.24.2
Xiuwen Zheng
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/SeqArray
Branch: RELEASE_3_9
Last Commit: 1ecfddf
Last Changed Date: 2019-07-11 22:49:49 -0400 (Thu, 11 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqArray
Version: 1.24.2
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SeqArray_1.24.2.tar.gz
StartedAt: 2019-10-16 04:55:46 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 05:00:04 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 257.8 seconds
RetCode: 0
Status:  OK 
CheckDir: SeqArray.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SeqArray_1.24.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqArray’ version ‘1.24.2’
* 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 ‘SeqArray’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.9Mb
* 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
':::' call which should be '::': ‘parallel:::mc.reset.stream’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘parallel:::cleanup’ ‘parallel:::prepareCleanup’
  ‘parallel:::processID’ ‘parallel:::readChild’
  ‘parallel:::selectChildren’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘SeqArray/libs/SeqArray.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’, ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

Installation output

SeqArray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SeqArray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘SeqArray’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c GetData.cpp -o GetData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Index.cpp -o Index.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c Methods.cpp -o Methods.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c pkg_test.cpp -o pkg_test.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c samtools_ext.c -o samtools_ext.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -I"/home/biocbuild/bbs-3.9-bioc/R/library/gdsfmt/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c vectorization.c -o vectorization.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-SeqArray/00new/SeqArray/libs
** R
** data
** 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 (SeqArray)

Tests output

SeqArray.Rcheck/tests/test.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> if (.Platform$OS.type != "windows")
+     BiocGenerics:::testPackage("SeqArray")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

The following object is masked from 'package:SeqArray':

    rowRanges

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:SeqArray':

    rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum


Attaching package: 'SummarizedExperiment'

The following object is masked from 'package:SeqArray':

    colData

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following objects are masked from 'package:SeqArray':

    alt, filt, fixed, geno, header, info, qual, ref

The following object is masked from 'package:base':

    tabulate

[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Running the examples in 'KG_P1_SampData()':
Running the examples in 'SeqArray-package()':
Wed Oct 16 04:58:10 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info/AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
    annotation/info/AC  [md5: 32e0060f853f014a2f0500092eb41a93]
    annotation/info/AN  [md5: 520c98d2b93738bf522425c1bab724d4]
    annotation/info/DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
    annotation/info/HM2  [md5: 38b58906766fb24600273356a0db9c50]
    annotation/info/HM3  [md5: 2125043130d80f3773acf690705b85e2]
    annotation/info/OR  [md5: e1829aa0fc0a84250f873500c0174857]
    annotation/info/GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
    annotation/info/BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format/DP  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Wed Oct 16 04:58:10 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.5K)
    # of fragments: 159
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.5K, reduced: 1.0K)
    # of fragments: 70
Wed Oct 16 04:58:10 2019
File: /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Chromosomes:
    Chr1 : 142, Chr2 : 59 , Chr3 : 81 , Chr4 : 48 , Chr5 : 61 , Chr6 : 99 
    Chr7 : 58 , Chr8 : 51 , Chr9 : 29 , Chr10: 70 , Chr11: 16 , Chr12: 62 
    Chr13: 11 , Chr14: 61 , Chr15: 46 , Chr16: 84 , Chr17: 100, Chr18: 54 
    Chr19: 111, Chr20: 59 , Chr21: 23 , Chr22: 23 
Alleles:
    ALT: 
    tabulation: 2, 1346(99.9%); 3, 2(0.1%)
Annotation, Quality:
    Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
Annotation, FILTER:
    PASS, All filters passed, 1348(100.0%)
    q10, Quality below 10, 0(0.0%)
Annotation, INFO variable(s):
    AA, ., String, Ancestral Allele
    AC, 1, Integer, Total number of alternate alleles in called genotypes
    AN, 1, Integer, Total number of alleles in called genotypes
    DP, 1, Integer, Total Depth
    HM2, 0, Flag, HapMap2 membership
    HM3, 0, Flag, HapMap3 membership
    OR, 1, String, Previous rs number
    GP, 1, String, GRCh37 position(s)
    BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
    DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
    
# of selected samples: 5
# of selected variants: 10
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    1    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs3762001"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs73134914"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs115805274"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    1
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs34424078"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    1    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs16940094"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    1    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs114467444"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs75372730"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs72483216"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs112301322"

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$qual
[1] "rs11554369"

# of selected samples: 90
# of selected variants: 1,348
Running the examples in 'SeqVarGDSClass()':
Running the examples in 'seqAlleleFreq()':

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
Running the examples in 'seqApply()':
# of selected samples: 5
# of selected variants: 10
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    1    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    1
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    1    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    1    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   01   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   01
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   01   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   01   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    1    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    1    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    1    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    1    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   01   00   00   00   00   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   00   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   01   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   00   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   00   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   00   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   00   00   00   00   00    00
[2,]   00   00   00   00   00   01   00   00   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   01   00   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   00   00    00
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    1    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs3762001"

$DP
      index
sample [,1]
  [1,]   16
  [2,]   64
  [3,]   61
  [4,]   84
  [5,]   89

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs73134914"

$DP
      index
sample [,1]
  [1,]    4
  [2,]    2
  [3,]    9
  [4,]   60
  [5,]  159

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs115805274"

$DP
      index
sample [,1]
  [1,]   27
  [2,]  111
  [3,]   42
  [4,]   96
  [5,]  153

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    1
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs34424078"

$DP
      index
sample [,1]
  [1,]   13
  [2,]   34
  [3,]   23
  [4,]   53
  [5,]  141

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    1    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs16940094"

$DP
      index
sample [,1]
  [1,]   43
  [2,]   62
  [3,]   50
  [4,]   52
  [5,]  127

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    1    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs114467444"

$DP
      index
sample [,1]
  [1,]   13
  [2,]    7
  [3,]   11
  [4,]   28
  [5,]   50

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs75372730"

$DP
      index
sample [,1]
  [1,]    2
  [2,]   15
  [3,]   38
  [4,]   18
  [5,]   63

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs72483216"

$DP
      index
sample [,1]
  [1,]   13
  [2,]  105
  [3,]   45
  [4,]   78
  [5,]   70

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs112301322"

$DP
      index
sample [,1]
  [1,]   12
  [2,]   59
  [3,]   66
  [4,]   84
  [5,]   77

$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs11554369"

$DP
      index
sample [,1]
  [1,]    8
  [2,]   31
  [3,]   54
  [4,]   41
  [5,]   46

1
0
0
1
1
1
0
0
0
0
[1] 1
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    1    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs3762001"

[1] 2
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs73134914"

[1] 3
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs115805274"

[1] 4
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    1
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs34424078"

[1] 5
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    1    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs16940094"

[1] 6
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    1    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs114467444"

[1] 7
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs75372730"

[1] 8
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs72483216"

[1] 9
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs112301322"

[1] 10
$geno
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs11554369"

# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    1    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    1
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    1    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    1    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    1    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    1    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    1    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    1    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
$sample.id
[1] "NA06985"

$genotype
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    1    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0

$sample.id
[1] "NA06989"

$genotype
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    1    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0

$sample.id
[1] "NA07000"

$genotype
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0

$sample.id
[1] "NA07048"

$genotype
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    1    0    0    0     0

$sample.id
[1] "NA07346"

$genotype
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    1    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0

Running the examples in 'seqAsVCF()':
Running the examples in 'seqBED2GDS()':
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Wed Oct 16 04:58:11 2019
PLINK BED to SeqArray GDS Format:
    BED file: '/home/biocbuild/bbs-3.9-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz' in the SNP-major mode (Sample X SNP)
    FAM file: '/home/biocbuild/bbs-3.9-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz' (60 samples)
    BIM file: '/home/biocbuild/bbs-3.9-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz' (5,000 variants)
    sample.id  [md5: b74526f3626e38cb16ca0f430e14a5ec]
    variant.id  [md5: 46b9b8513fddb695e351385ee3c6f177]
    position  [md5: 5ce9fe5d7fb8ed55cf8518b777951219]
    chromosome  [md5: 1e7c9ebb547f153137f8840b56220bf5]
    allele  [md5: 8ac94702b318deb38950aec11c50fb60]
    genotype  [md5: a4c1462aa0dbbf2333ef09a5fb02e67d]
    phase  [md5: 982a3a9e10be5cb4326775709384ee33]
    annotation/id  [md5: 2ffacef2573cdad31273b89903287925]
    annotation/qual  [md5: 0246b3fc665ce36bb8882d5d73bb7b4c]
    annotation/filter  [md5: e06fa4c84d9e6d743ee16d4e64ddacac]
    sample.annotation
Done.
Wed Oct 16 04:58:11 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (80.5K)
    # of fragments: 104
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (79.8K, reduced: 672B)
    # of fragments: 48
Wed Oct 16 04:58:11 2019
File: /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Format Version: v1.0
Reference: unknown
Ploidy: 2
Number of samples: 60
Number of variants: 5,000
Chromosomes:
    Chr1 : 365, Chr2 : 417, Chr3 : 339, Chr4 : 307, Chr5 : 313, Chr6 : 357
    Chr7 : 236, Chr8 : 249, Chr9 : 223, Chr10: 267, Chr11: 277, Chr12: 228
    Chr13: 185, Chr14: 141, Chr15: 156, Chr16: 150, Chr17: 108, Chr18: 143
    Chr19: 89 , Chr20: 117, Chr21: 69 , Chr22: 61 , Chr23: 203
Alleles:
    ALT: 
    tabulation: 2, 5000(100.0%)
Annotation, Quality:
    Min: 100, 1st Qu: 100, Median: 100, Mean: 100, 3rd Qu: 100, Max: 100
Annotation, FILTER:
    PASS, All filters passed, 5000(100.0%)
Annotation, INFO variable(s):
    
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
Annotation, sample variable(s):
    family, Integer, 
    father, Integer, 
    mother, Integer, 
    sex, String, 
    phenotype, Integer, 
Running the examples in 'seqBlockApply()':
# of selected samples: 5
# of selected variants: 10
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    1    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    1
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    1    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    1    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    0    0    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   01   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   01
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   01   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   01   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   00   00   00   00   00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    1    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    1    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    0    0    0     0
[2,]    0    0    0    0    0    1    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    1    0    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    0    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   01   00   00   00   00   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   00   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   01   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   00   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   00   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   00   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   00   00   00   00   00    00
[2,]   00   00   00   00   00   01   00   00   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   01   00   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   00   00    00
      variant
sample [,1] [,2] [,3]
  [1,]    1    2    2
  [2,]    2    2    2
  [3,]    2    2    2
  [4,]    2    2    2
  [5,]    2    2    2
      variant
sample [,1] [,2] [,3]
  [1,]    2    2    2
  [2,]    2    1    2
  [3,]    2    2    2
  [4,]    2    2    1
  [5,]    1    2    2
      variant
sample [,1] [,2] [,3]
  [1,]    2    2    2
  [2,]    2    2    2
  [3,]    2    2    2
  [4,]    2    2    2
  [5,]    2    2    2
      variant
sample [,1]
  [1,]    2
  [2,]    2
  [3,]    2
  [4,]    2
  [5,]    2
$dos
      variant
sample [,1] [,2] [,3]
  [1,]    1    2    2
  [2,]    2    2    2
  [3,]    2    2    2
  [4,]    2    2    2
  [5,]    2    2    2

$pos
[1] 143864805  72487157  80328908

$dos
      variant
sample [,1] [,2] [,3]
  [1,]    2    2    2
  [2,]    2    1    2
  [3,]    2    2    2
  [4,]    2    2    1
  [5,]    1    2    2

$pos
[1] 90751641 23316941 45492190

$dos
      variant
sample [,1] [,2] [,3]
  [1,]    2    2    2
  [2,]    2    2    2
  [3,]    2    2    2
  [4,]    2    2    2
  [5,]    2    2    2

$pos
[1]  3363976 30796109 35198045

$dos
      variant
sample [,1]
  [1,]    2
  [2,]    2
  [3,]    2
  [4,]    2
  [5,]    2

$pos
[1] 52444656

Running the examples in 'seqCheck()':
Open '/home/biocbuild/bbs-3.9-bioc/R/library/SeqArray/extdata/CEU_Exon.gds'
Hash check:
    sample.id:	'md5' [OK]
    variant.id:	'md5' [OK]
    position:	'md5' [OK]
    chromosome:	'md5' [OK]
    allele:	'md5' [OK]
    genotype/data:	'md5' [OK]
    genotype/@data:	'md5' [OK]
    phase/data:	'md5' [OK]
    annotation/id:	'md5' [OK]
    annotation/qual:	'md5' [OK]
    annotation/filter:	'md5' [OK]
    annotation/info/AA:	'md5' [OK]
    annotation/info/@AA:	'md5' [OK]
    annotation/info/AC:	'md5' [OK]
    annotation/info/AN:	'md5' [OK]
    annotation/info/DP:	'md5' [OK]
    annotation/info/HM2:	'md5' [OK]
    annotation/info/HM3:	'md5' [OK]
    annotation/info/OR:	'md5' [OK]
    annotation/info/GP:	'md5' [OK]
    annotation/info/BN:	'md5' [OK]
    annotation/format/DP/data:	'md5' [OK]
    annotation/format/DP/@data:	'md5' [OK]
Dimension check:
    variant.id	[OK]
    position	[OK]
    chromosome	[OK]
    allele	[OK]
    annotation/id	[OK]
    annotation/qual	[OK]
    annotation/filter	[OK]
    annotation/info/AA	[OK]
    annotation/info/AC	[OK]
    annotation/info/AN	[OK]
    annotation/info/DP	[OK]
    annotation/info/HM2	[OK]
    annotation/info/HM3	[OK]
    annotation/info/OR	[OK]
    annotation/info/GP	[OK]
    annotation/info/BN	[OK]
Running the examples in 'seqClose-methods()':
Running the examples in 'seqDelete()':
Delete INFO variable(s): HM2 AA
Delete FORMAT variable(s): DP
Delete Sample Annotation variable(s):
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (299.1K)
    # of fragments: 77
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (63.3K, reduced: 235.7K)
    # of fragments: 64
Running the examples in 'seqDigest()':
Running the examples in 'seqExampleFileName()':
Running the examples in 'seqExport()':
# of selected samples: 8
# of selected variants: 100
Export to 'tmp.gds'
    sample.id (8)  [md5: 7269c374a455e3c2d046ce1e3b2854a8]
    variant.id (100)  [md5: 5260e8825b753db5240e1adc3208fae4]
    position  [md5: c7ef4e9e68da9f32fa43f52f900b48c5]
    chromosome  [md5: 31101f0b9c3a15be71aa9904b49776e0]
    allele  [md5: 7b70b62ea10c297f4b44411c0247a346]
    genotype  [md5: 418d339cc0bad5eed558e6555970240b]
  [md5: 9af8a70f41fa6c1822aff9ec427e78bf]
    phase  [md5: fbfc323ca650cabd3df3affdc857c9da]
  [md5: fbfc323ca650cabd3df3affdc857c9da]
    annotation/id  [md5: 43e4c471f036cf267d9ad898c9a4d552]
    annotation/qual  [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
    annotation/filter  [md5: 155aaa7359e27197a75f997dc645e48d]
    annotation/info/AA  [md5: e8070827ea4aa58a1b22a6a0bbd04238]
    annotation/info/AC  [md5: 3683b41616fc897f3806db6c665eead2]
    annotation/info/AN  [md5: 2cbdb642a0402ace8a15642bad729454]
    annotation/info/DP  [md5: 3e41693488201ee0913f044ddff0b352]
    annotation/info/HM2  [md5: 9bdbd7c2223bca753a035e717be81c4b]
    annotation/info/HM3  [md5: 4c7060bd7024bc44392519fe36a927f9]
    annotation/info/OR  [md5: f82ffa7301b6d86fa158e0547a9d8823]
    annotation/info/GP  [md5: 86ccad572dbf631507a84ef6a586ba78]
    annotation/info/BN  [md5: 026894e1ea6f5f60c3faa919ad75a233]
    annotation/format/DP  [md5: 5dd8e77d8d141fb92fa329f10dd1ae12]
  [md5: 6ad9cf3b0c0b1868e9d81618948dc8fc]
    sample.annotation/family  [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (17.8K)
    # of fragments: 149
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (17.0K, reduced: 864B)
    # of fragments: 77
Export to 'tmp.gds'
    sample.id (8)  [md5: 7269c374a455e3c2d046ce1e3b2854a8]
    variant.id (100)  [md5: 5260e8825b753db5240e1adc3208fae4]
    position  [md5: c7ef4e9e68da9f32fa43f52f900b48c5]
    chromosome  [md5: 31101f0b9c3a15be71aa9904b49776e0]
    allele  [md5: 7b70b62ea10c297f4b44411c0247a346]
    genotype  [md5: 418d339cc0bad5eed558e6555970240b]
  [md5: 9af8a70f41fa6c1822aff9ec427e78bf]
    phase  [md5: fbfc323ca650cabd3df3affdc857c9da]
  [md5: fbfc323ca650cabd3df3affdc857c9da]
    annotation/id  [md5: 43e4c471f036cf267d9ad898c9a4d552]
    annotation/qual  [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
    annotation/filter  [md5: 155aaa7359e27197a75f997dc645e48d]
    annotation/format/DP  [md5: 5dd8e77d8d141fb92fa329f10dd1ae12]
  [md5: 6ad9cf3b0c0b1868e9d81618948dc8fc]
    sample.annotation/family  [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (12.5K)
    # of fragments: 107
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (11.9K, reduced: 600B)
    # of fragments: 57
Export to 'tmp.gds'
    sample.id (8)  [md5: 7269c374a455e3c2d046ce1e3b2854a8]
    variant.id (100)  [md5: 5260e8825b753db5240e1adc3208fae4]
    position  [md5: c7ef4e9e68da9f32fa43f52f900b48c5]
    chromosome  [md5: 31101f0b9c3a15be71aa9904b49776e0]
    allele  [md5: 7b70b62ea10c297f4b44411c0247a346]
    genotype  [md5: 418d339cc0bad5eed558e6555970240b]
  [md5: 9af8a70f41fa6c1822aff9ec427e78bf]
    phase  [md5: fbfc323ca650cabd3df3affdc857c9da]
  [md5: fbfc323ca650cabd3df3affdc857c9da]
    annotation/id  [md5: 43e4c471f036cf267d9ad898c9a4d552]
    annotation/qual  [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
    annotation/filter  [md5: 155aaa7359e27197a75f997dc645e48d]
    annotation/info/AA  [md5: e8070827ea4aa58a1b22a6a0bbd04238]
    annotation/info/AC  [md5: 3683b41616fc897f3806db6c665eead2]
    annotation/info/AN  [md5: 2cbdb642a0402ace8a15642bad729454]
    annotation/info/DP  [md5: 3e41693488201ee0913f044ddff0b352]
    annotation/info/HM2  [md5: 9bdbd7c2223bca753a035e717be81c4b]
    annotation/info/HM3  [md5: 4c7060bd7024bc44392519fe36a927f9]
    annotation/info/OR  [md5: f82ffa7301b6d86fa158e0547a9d8823]
    annotation/info/GP  [md5: 86ccad572dbf631507a84ef6a586ba78]
    annotation/info/BN  [md5: 026894e1ea6f5f60c3faa919ad75a233]
    sample.annotation/family  [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (14.7K)
    # of fragments: 133
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (14.0K, reduced: 756B)
    # of fragments: 70
Export to 'tmp.gds'
    sample.id (8)  [md5: 7269c374a455e3c2d046ce1e3b2854a8]
    variant.id (100)  [md5: 5260e8825b753db5240e1adc3208fae4]
    position  [md5: c7ef4e9e68da9f32fa43f52f900b48c5]
    chromosome  [md5: 31101f0b9c3a15be71aa9904b49776e0]
    allele  [md5: 7b70b62ea10c297f4b44411c0247a346]
    genotype  [md5: 418d339cc0bad5eed558e6555970240b]
  [md5: 9af8a70f41fa6c1822aff9ec427e78bf]
    phase  [md5: fbfc323ca650cabd3df3affdc857c9da]
  [md5: fbfc323ca650cabd3df3affdc857c9da]
    annotation/id  [md5: 43e4c471f036cf267d9ad898c9a4d552]
    annotation/qual  [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
    annotation/filter  [md5: 155aaa7359e27197a75f997dc645e48d]
    annotation/info/AA  [md5: e8070827ea4aa58a1b22a6a0bbd04238]
    annotation/info/AC  [md5: 3683b41616fc897f3806db6c665eead2]
    annotation/info/AN  [md5: 2cbdb642a0402ace8a15642bad729454]
    annotation/info/DP  [md5: 3e41693488201ee0913f044ddff0b352]
    annotation/info/HM2  [md5: 9bdbd7c2223bca753a035e717be81c4b]
    annotation/info/HM3  [md5: 4c7060bd7024bc44392519fe36a927f9]
    annotation/info/OR  [md5: f82ffa7301b6d86fa158e0547a9d8823]
    annotation/info/GP  [md5: 86ccad572dbf631507a84ef6a586ba78]
    annotation/info/BN  [md5: 026894e1ea6f5f60c3faa919ad75a233]
    annotation/format/DP  [md5: 5dd8e77d8d141fb92fa329f10dd1ae12]
  [md5: 6ad9cf3b0c0b1868e9d81618948dc8fc]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (17.4K)
    # of fragments: 144
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (16.6K, reduced: 828B)
    # of fragments: 75
Running the examples in 'seqGDS2SNP()':
Wed Oct 16 04:58:12 2019
SeqArray GDS to SNP GDS Format:
    # of samples: 90
    # of variants: 1,348
    genotype compression: LZMA_RA
    annotation compression: LZMA_RA

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
Done.
Wed Oct 16 04:58:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (26.5K)
    # of fragments: 31
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (26.3K, reduced: 192B)
    # of fragments: 15
Wed Oct 16 04:58:12 2019
Running the examples in 'seqGDS2VCF()':
# of selected samples: 5
Wed Oct 16 04:58:12 2019
VCF Export: tmp.vcf.gz
    5 samples, 1,348 variants
    INFO Field: AA, AC, AN, DP, HM2, HM3, OR, GP, BN
    FORMAT Field: DP
    output to BGZF format

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
Wed Oct 16 04:58:12 2019    Done.
Wed Oct 16 04:58:12 2019
VCF Export: tmp1.vcf.gz
    5 samples, 1,348 variants
    INFO Field: 
    FORMAT Field: 
    output to BGZF format

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
Wed Oct 16 04:58:12 2019    Done.
Wed Oct 16 04:58:12 2019
VCF Export: tmp2.vcf.gz
    5 samples, 1,348 variants
    INFO Field: BN, GP, AA, DP, HM2
    FORMAT Field: 
    output to BGZF format

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
Wed Oct 16 04:58:12 2019    Done.
# of selected samples: 90
# of selected variants: 1,348
Wed Oct 16 04:58:12 2019
VCF Export: tmp.vcf.gz
    90 samples, 1,348 variants
    INFO Field: AA, AC, AN, DP, HM2, HM3, OR, GP, BN
    FORMAT Field: DP
    output to BGZF format

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
Wed Oct 16 04:58:12 2019    Done.
Running the examples in 'seqGetData()':
# of selected samples: 5
# of selected variants: 10
Running the examples in 'seqGetFilter()':
# of selected samples: 5
# of selected variants: 10
Running the examples in 'seqMerge()':
Wed Oct 16 04:58:12 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp1.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x269 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: 31977a337486b43ef6f23727c03b93f1]
    position  [md5: da44a52891c27fdc773a5b99f8c02cf9]
    chromosome  [md5: b85b07da5fc3648b14c558491bcd05be]
    allele  [md5: cd5d2fa95a245204b6566b8ec0a8a33a]
    genotype  [md5: 412d90215ad9bd1c480ce7d58f884844]
    phase  [md5: 32f9b472c93c5421f2e327b8a2a048ae]
    annotation/id  [md5: 1365ee5e73e9030aebbee40c7f6bb25b]
    annotation/qual  [md5: 75d9516e34424c3ba8992777b7daea77]
    annotation/filter  [md5: faa4243cabb7df18c7e1d768687999de]
    annotation/info/AA  [md5: a5c30c16b0004b0987c892f4cedfd310]
    annotation/info/AC  [md5: f1502cc22c0190b135f50c4f149b4e01]
    annotation/info/AN  [md5: c21269493661db41bb776f4fdacfe74f]
    annotation/info/DP  [md5: 901bdf13cdb66e0d54005c6e2e1a5b5f]
    annotation/info/HM2  [md5: 2fdd6210a1f891a10555ad1d9046d0a2]
    annotation/info/HM3  [md5: 86d7e6f95e621ecaa6bbda882cb565e0]
    annotation/info/OR  [md5: 63361d188cefd769be41d5883d3b814b]
    annotation/info/GP  [md5: 92a9ae87dfc97e62a19c92f181e9d31f]
    annotation/info/BN  [md5: 2767eb7baa2d136a1c5987503bb23ee3]
    annotation/format/DP  [md5: f8694c788d23bbf67cb25ca9b2930709]
Done.
Wed Oct 16 04:58:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp1.gds' (46.5K)
    # of fragments: 157
    save to 'tmp1.gds.tmp'
    rename 'tmp1.gds.tmp' (45.5K, reduced: 1.0K)
    # of fragments: 69
Wed Oct 16 04:58:12 2019
Wed Oct 16 04:58:12 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp2.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x270 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: 702b2d499921b2746c717e94c10b850e]
    position  [md5: 338b3ef9c6450ead1c4eb1d5544aca4a]
    chromosome  [md5: a4d7b4e4cb2c1f8210a2c71dbab83bb5]
    allele  [md5: af20c8bbec9c885eb2ec0ac7200bc0fe]
    genotype  [md5: bb82d3855a2334cf988bce5c6ba94762]
    phase  [md5: d6d20b1a4b6720ab588b0b4297d9b32b]
    annotation/id  [md5: a21f24833e38262da8b7d957dd64785a]
    annotation/qual  [md5: 512c62a8e514115686234183d90daa00]
    annotation/filter  [md5: bbe72e6de6e452b05acb9d37d1d4efcf]
    annotation/info/AA  [md5: fe904ec6b205bf8a7884f57507eea0d6]
    annotation/info/AC  [md5: a651cc76f494587611a9c0e0d46d7839]
    annotation/info/AN  [md5: 526332c5f7156495d16763e3ae5f1609]
    annotation/info/DP  [md5: 8c3b67b68611ac59dd89a719e4fc515a]
    annotation/info/HM2  [md5: 227879b1605bf8aef6b7d50b80127a3e]
    annotation/info/HM3  [md5: 497750adc263e37255ff533a56c7a7b5]
    annotation/info/OR  [md5: f08c7fb2e2b68d0be4536db007f3488e]
    annotation/info/GP  [md5: 5ae337da74c76dce7ee5cd06c22c89ff]
    annotation/info/BN  [md5: 9244facc8572ffd3afbfed7db94c9412]
    annotation/format/DP  [md5: 49fc303177a01aa04578f0c0bb45ff94]
Done.
Wed Oct 16 04:58:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp2.gds' (46.3K)
    # of fragments: 157
    save to 'tmp2.gds.tmp'
    rename 'tmp2.gds.tmp' (45.2K, reduced: 1.0K)
    # of fragments: 69
Wed Oct 16 04:58:12 2019
Wed Oct 16 04:58:12 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp3.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x269 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: 79a9e2f03ab2a7992e93875c4cbf102d]
    position  [md5: 0774b9eeec510b900096be5d427cb3ba]
    chromosome  [md5: 14fc6ae2c5a3415c76c898555dcb5a16]
    allele  [md5: 084f88745d3947ed533e40271e1ea0d8]
    genotype  [md5: d414371adf89b3f6df652c23ae4e8ad3]
    phase  [md5: 32f9b472c93c5421f2e327b8a2a048ae]
    annotation/id  [md5: e3dbfc9e19459fd1eaf1f937b618a75b]
    annotation/qual  [md5: 75d9516e34424c3ba8992777b7daea77]
    annotation/filter  [md5: faa4243cabb7df18c7e1d768687999de]
    annotation/info/AA  [md5: 247fc1c43d33e10e2314255ca8683d69]
    annotation/info/AC  [md5: 1ccad5fd3121aaba325fbf501cc887ad]
    annotation/info/AN  [md5: da9c38467822d68e654fecb3bf9f3498]
    annotation/info/DP  [md5: 88b66f79339f655db1bb5699aaa670b2]
    annotation/info/HM2  [md5: 691d8e114b6e4a3922c686e83f0871fa]
    annotation/info/HM3  [md5: 33bb00f6c0fd2f9429825fc35329f076]
    annotation/info/OR  [md5: 3f5a355124218a349a40c13845212e02]
    annotation/info/GP  [md5: f165316874ce73a46652b5eb7de29d86]
    annotation/info/BN  [md5: 0234c15cbc2849ab0bf61cb55fa874c5]
    annotation/format/DP  [md5: 5ee17f959e045d7d71eb241e51c69c6f]
Done.
Wed Oct 16 04:58:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp3.gds' (46.6K)
    # of fragments: 157
    save to 'tmp3.gds.tmp'
    rename 'tmp3.gds.tmp' (45.5K, reduced: 1.0K)
    # of fragments: 69
Wed Oct 16 04:58:12 2019
Wed Oct 16 04:58:12 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp4.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x270 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: 596deceba4d6785759026d710ebbd6a5]
    position  [md5: 56e4e9c99e7a25933ea668686f3c81f1]
    chromosome  [md5: 0b766775d21b6b368c399aa2363946c5]
    allele  [md5: e8dc9d008e28d70c9014929bec8a72b8]
    genotype  [md5: 6f5d76b39c423e14bbce491ea5a5942b]
    phase  [md5: d6d20b1a4b6720ab588b0b4297d9b32b]
    annotation/id  [md5: b666b21b581036b7f45f2753d389058b]
    annotation/qual  [md5: 512c62a8e514115686234183d90daa00]
    annotation/filter  [md5: bbe72e6de6e452b05acb9d37d1d4efcf]
    annotation/info/AA  [md5: 136d498f7dc4879feeb9a03a3cf328fb]
    annotation/info/AC  [md5: 54348b0efa93fd1f7eb9d7b2767aa761]
    annotation/info/AN  [md5: bdbca84358d9cf22f172fb8e1a691531]
    annotation/info/DP  [md5: 7da7dae10b066a3b8e7bb7d6b070a2e8]
    annotation/info/HM2  [md5: 4db37a5a26c42890df37b183db37eac7]
    annotation/info/HM3  [md5: 3acca3d02fc51ef797290eb4857d35dd]
    annotation/info/OR  [md5: ea4ef9649f92c784e68a18294a4320be]
    annotation/info/GP  [md5: 2c66df855998e4c0715f2543a9b60672]
    annotation/info/BN  [md5: 463eb1f0a504213b9b86b3001315276b]
    annotation/format/DP  [md5: 34ac9d047be4554124d58b90d8e6abce]
Done.
Wed Oct 16 04:58:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp4.gds' (46.3K)
    # of fragments: 157
    save to 'tmp4.gds.tmp'
    rename 'tmp4.gds.tmp' (45.3K, reduced: 1.0K)
    # of fragments: 69
Wed Oct 16 04:58:12 2019
Wed Oct 16 04:58:12 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp5.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x270 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: bd7a9ec44d55514be411d70be3bc90b6]
    position  [md5: 787e53edad459d397d89f6572140398c]
    chromosome  [md5: 15b81663ef97a0890c343b8593ece496]
    allele  [md5: fc7e212f40d47b068f5a79f4624a094e]
    genotype  [md5: 3d8d5a11811c6b9259f1a51982bf5966]
    phase  [md5: d6d20b1a4b6720ab588b0b4297d9b32b]
    annotation/id  [md5: c9473ed3210534e6b2e098cbf7c8ec34]
    annotation/qual  [md5: 512c62a8e514115686234183d90daa00]
    annotation/filter  [md5: bbe72e6de6e452b05acb9d37d1d4efcf]
    annotation/info/AA  [md5: 77d5bcba4cb9ddc850ed1c13a01b17e7]
    annotation/info/AC  [md5: 19da63c0f0346353823ceb623b51fe9f]
    annotation/info/AN  [md5: 58a283bc70b7686719d659802434a4a3]
    annotation/info/DP  [md5: 438abf141332861815e877f5e4459bed]
    annotation/info/HM2  [md5: 725882b2b1b79c80db0ef0f9757c5b9e]
    annotation/info/HM3  [md5: 61e24df355c65a28074a344a874b7752]
    annotation/info/OR  [md5: b2bd6e5fda0e9a34705366f32b2cb6e4]
    annotation/info/GP  [md5: 47bd1383bc6a8e0591b7083cf4414494]
    annotation/info/BN  [md5: 4025eb570a89b5d0b7ccc571a94a0d40]
    annotation/format/DP  [md5: 5d164565b2a5cee1a3be107de4da8876]
Done.
Wed Oct 16 04:58:12 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp5.gds' (44.3K)
    # of fragments: 157
    save to 'tmp5.gds.tmp'
    rename 'tmp5.gds.tmp' (43.3K, reduced: 1.0K)
    # of fragments: 69
Wed Oct 16 04:58:12 2019
Wed Oct 16 04:58:12 2019
Preparing merging 5 GDS files:
    opening 'tmp1.gds'
    opening 'tmp2.gds'
    opening 'tmp3.gds'
    opening 'tmp4.gds'
    opening 'tmp5.gds'
    230,237 bytes in total
    90 samples in total (90 samples in common)
    [1 ] tmp1.gds (269 variants)
    [2 ] tmp2.gds (270 variants)
    [3 ] tmp3.gds (269 variants)
    [4 ] tmp4.gds (270 variants)
    [5 ] tmp5.gds (270 variants)
    1,348 variants in total, 0 variant in common
Output:
    /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Variables:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype, phase [1,2,3,4,5]
            [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
            [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info (AA,AC,AN,DP,HM2,HM3,OR,GP,BN)
        AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
        AC  [md5: 32e0060f853f014a2f0500092eb41a93]
        AN  [md5: 520c98d2b93738bf522425c1bab724d4]
        DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
        HM2  [md5: 38b58906766fb24600273356a0db9c50]
        HM3  [md5: 2125043130d80f3773acf690705b85e2]
        OR  [md5: e1829aa0fc0a84250f873500c0174857]
        GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
        BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format (DP)
        DP [1,2,3,4,5]  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
    sample.annotation ()
Done.
Wed Oct 16 04:58:13 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.4K)
    # of fragments: 153
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.5K, reduced: 996B)
    # of fragments: 70
Wed Oct 16 04:58:13 2019
File: /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Chromosomes:
    Chr1 : 142, Chr2 : 59 , Chr3 : 81 , Chr4 : 48 , Chr5 : 61 , Chr6 : 99 
    Chr7 : 58 , Chr8 : 51 , Chr9 : 29 , Chr10: 70 , Chr11: 16 , Chr12: 62 
    Chr13: 11 , Chr14: 61 , Chr15: 46 , Chr16: 84 , Chr17: 100, Chr18: 54 
    Chr19: 111, Chr20: 59 , Chr21: 23 , Chr22: 23 
Alleles:
    ALT: 
    tabulation: 2, 1346(99.9%); 3, 2(0.1%)
Annotation, Quality:
    Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
Annotation, FILTER:
    PASS, All filters passed, 1348(100.0%)
Annotation, INFO variable(s):
    AA, ., String, Ancestral Allele
    AC, 1, Integer, Total number of alternate alleles in called genotypes
    AN, 1, Integer, Total number of alleles in called genotypes
    DP, 1, Integer, Total Depth
    HM2, 0, Flag, HapMap2 membership
    HM3, 0, Flag, HapMap3 membership
    OR, 1, String, Previous rs number
    GP, 1, String, GRCh37 position(s)
    BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
    DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
    
Wed Oct 16 04:58:13 2019
Preparing merging 2 GDS files:
    opening '/home/biocbuild/bbs-3.9-bioc/R/library/SeqArray/extdata/CEU_Exon.gds'
    opening 'test.gds'
    612,969 bytes in total
    180 samples in total (0 sample in common)
    [1 ] CEU_Exon.gds (1,348 variants)
    [2 ] test.gds (1,348 variants)
    1,348 variants in total, 1,348 variants in common
Output:
    /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/output.gds
Variables:
    sample.id  [md5: 43f95e0eb5cfeff96c9872fd6ab895e4]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype [<<<<<<<<<<<<<<<<<<<<<<<<<]  [md5: 38110ba7c478e8e77a63637a77388330]
    phase [<<<<<<<<<<<<<<<<<<<<<<<<<]  [md5: 0eacab6c079033d11dcd127d9139de73]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info (AA,AC,AN,DP,HM2,HM3,OR,GP,BN)
        AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
        AC  [md5: 32e0060f853f014a2f0500092eb41a93]
        AN  [md5: 520c98d2b93738bf522425c1bab724d4]
        DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
        HM2  [md5: 38b58906766fb24600273356a0db9c50]
        HM3  [md5: 2125043130d80f3773acf690705b85e2]
        OR  [md5: e1829aa0fc0a84250f873500c0174857]
        GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
        BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format (DP)
        DP [<<<<<<<<<<<<<<<<<<<<<<<<<]  [md5: 2d4b87bb2cfabb8bb1c1cd633e25cd5c]
    sample.annotation (family)
        family  [md5: 18a957ad99f19f3bedab5893bfc237bf]
Done.
Wed Oct 16 04:58:13 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'output.gds' (244.4K)
    # of fragments: 157
    save to 'output.gds.tmp'
    rename 'output.gds.tmp' (243.4K, reduced: 1.0K)
    # of fragments: 71
Wed Oct 16 04:58:13 2019
Running the examples in 'seqMissing()':

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
Running the examples in 'seqNumAllele()':
Running the examples in 'seqOpen()':
Running the examples in 'seqOptimize()':
Wed Oct 16 04:58:13 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info/AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
    annotation/info/AC  [md5: 32e0060f853f014a2f0500092eb41a93]
    annotation/info/AN  [md5: 520c98d2b93738bf522425c1bab724d4]
    annotation/info/DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
    annotation/info/HM2  [md5: 38b58906766fb24600273356a0db9c50]
    annotation/info/HM3  [md5: 2125043130d80f3773acf690705b85e2]
    annotation/info/OR  [md5: e1829aa0fc0a84250f873500c0174857]
    annotation/info/GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
    annotation/info/BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format/DP  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Wed Oct 16 04:58:13 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.5K)
    # of fragments: 159
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.5K, reduced: 1.0K)
    # of fragments: 70
Wed Oct 16 04:58:13 2019
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/DP' ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (333.3K)
    # of fragments: 86
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (333.2K, reduced: 108B)
    # of fragments: 77
Running the examples in 'seqParallel()':
Enable the computing cluster with 2 forked R processes.
Stop the computing cluster.
Running the examples in 'seqParallelSetup()':
Enable the computing cluster with 2 forked R processes.
Stop the computing cluster.
Running the examples in 'seqRecompress()':
Open 'tmp.gds' ...
    sample.id	(deflated 0.4%)  ac460b05cf0de81d3a307259fb908238
    variant.id	(deflated 0.1%)  c9602a5420b6a5a148f5a0120a8750e1
    position	(deflated 0.0%)  a23801beb47fb2d7ca26b65d2b71e622
    chromosome	(deflated 0.6%)  a46ad5529a68298eb581c7c66b31b99b
    allele	(deflated 0.1%)  e65988a36b2675d1e4f6a9ad9d2774a9
    genotype/data	(deflated 0.0%)  318c71bd2c1878e7d05c6e4b8b3067ef
    genotype/~data	(deflated 0.0%)
    genotype/@data	(deflated 1.0%)  e4bff5c57a2a343d93a9a1462b13bc8f
    phase/data	(deflated 0.7%)  4873107397a2eec80cca77d8fa09592b
    phase/~data	(deflated 0.7%)
    annotation/id	(deflated 0.0%)  164df6a971c24c99ad386bbaf8759cb2
    annotation/qual	(deflated 0.8%)  ff3b3c516fe7081c406d4c26782b44e4
    annotation/filter	(deflated 0.8%)  5b09a6e58b307857c38e3d82284dfff0
    annotation/info/AA	(deflated 0.1%)  7bba129ada9e50a98db7451044abdde9
    annotation/info/@AA	(deflated 0.8%)  5b09a6e58b307857c38e3d82284dfff0
    annotation/info/AC	(deflated 0.1%)  79076139f25b3f78164182af5d86c680
    annotation/info/AN	(deflated 0.1%)  b4c305461e62a78dc439f7a1df50e5fc
    annotation/info/DP	(deflated 0.0%)  9f358649989b5fd48fba25b6b50af02f
    annotation/info/HM2	(deflated 0.4%)  9b792cdd10840bdda63d77a1ce065588
    annotation/info/HM3	(deflated 0.4%)  b936dc73a3ffa1241305dfdcc14d71e1
    annotation/info/OR	(deflated 0.3%)  6f6f800d686268b592ac50f10c5851b9
    annotation/info/GP	(deflated 0.0%)  a1ccfb37b78edd2bb1204c8b9c901b0a
    annotation/info/BN	(deflated 0.1%)  0ac62828c0c8d3d27cbd15aa975532fd
    annotation/format/DP/data	(deflated 0.0%)  1f03a59e8b55049b80f6ae42da163783
    annotation/format/DP/~data	(deflated 0.0%)
    annotation/format/DP/@data	(deflated 0.8%)  5b09a6e58b307857c38e3d82284dfff0
    sample.annotation/family	(deflated 0.5%)
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (299.1K)
    # of fragments: 77
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (299.0K, reduced: 27B)
    # of fragments: 77
Running the examples in 'seqResetVariantID()':
[ 1] tmp1.gds ...  [md5: c9602a5420b6a5a148f5a0120a8750e1]
    set new variant id: 1 ... 1348 [1348]
[ 2] tmp2.gds ...  [md5: 451be93e6c11061778420ac2850636f1]
    set new variant id: 1349 ... 2696 [1348]
Running the examples in 'seqSNP2GDS()':
Wed Oct 16 04:58:15 2019
SNP GDS to SeqArray GDS Format:
    sample.id  [md5: 8c16d801816b5acb9884930d1a61d479]
    variant.id  [md5: f82f4a0ec8ea0bef03f2fee13f7bdca5]
    position  [md5: 52c1144a14a83c5baa5c046dd637b7ca]
    chromosome  [md5: 95eec41652f7b63bc66f113836a28607]
    genotype  [md5: 9848dc57cdeff87e29d09b8341c41651]
    allele  [md5: ac3d0e4abdc8ac4bf6db6832fa3cc79a]
    phase  [md5: a759f1581057a88d45a9c4194b0b43a3]
    annotation/id  [md5: 244319c29efb59f5b7a09584a2bbf9bd]
    sample.annotation
    sample.annotation/family.id  [md5: dd38a34e070d5d4ca3c8322c2cfc41d7]
    sample.annotation/father.id  [md5: 99d5f5add61e93d35fe7f928a524a53b]
    sample.annotation/mother.id  [md5: 75bf5e4263df975637ddd055360ba593]
    sample.annotation/sex  [md5: a3615c4ac39a9f121c5eb897dc608495]
    sample.annotation/pop.group  [md5: 99a5577d77e6a3dbd9d3e1993a380b52]
Done.
Wed Oct 16 04:58:17 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (464.5K)
    # of fragments: 95
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (464.0K, reduced: 564B)
    # of fragments: 48
Wed Oct 16 04:58:17 2019
File: /home/biocbuild/bbs-3.9-bioc/meat/SeqArray.Rcheck/tests/tmp.gds
Format Version: v1.0
Reference: unknown
Ploidy: 2
Number of samples: 279
Number of variants: 9,088
Chromosomes:
    Chr1 : 716, Chr2 : 742, Chr3 : 609, Chr4 : 562, Chr5 : 566, Chr6 : 565
    Chr7 : 472, Chr8 : 488, Chr9 : 416, Chr10: 483, Chr11: 447, Chr12: 427
    Chr13: 344, Chr14: 282, Chr15: 262, Chr16: 278, Chr17: 207, Chr18: 266
    Chr19: 120, Chr20: 229, Chr21: 126, Chr22: 116, Chr23: 365
Alleles:
    ALT: 
    tabulation: 2, 9088(100.0%)
Annotation, Quality:
    Min: 100, 1st Qu: 100, Median: 100, Mean: 100, 3rd Qu: 100, Max: 100
Annotation, FILTER:
    PASS, All filters passed, 9088(100.0%)
Annotation, INFO variable(s):
    
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
Annotation, sample variable(s):
    family.id, String, 
    father.id, String, 
    mother.id, String, 
    sex, String, 
    pop.group, String, 
Running the examples in 'seqSetFilter-methods()':
Running the examples in 'seqSetFilterCond()':
# of selected variants: 241

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of selected variants: 98
# of selected variants: 241

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 0s
# of selected variants: 72
Running the examples in 'seqStorageOption()':
Wed Oct 16 04:58:17 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: customized
    # of samples: 90
Output:
    tmp1.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info/AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
    annotation/info/AC  [md5: 32e0060f853f014a2f0500092eb41a93]
    annotation/info/AN  [md5: 520c98d2b93738bf522425c1bab724d4]
    annotation/info/DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
    annotation/info/HM2  [md5: 38b58906766fb24600273356a0db9c50]
    annotation/info/HM3  [md5: 2125043130d80f3773acf690705b85e2]
    annotation/info/OR  [md5: e1829aa0fc0a84250f873500c0174857]
    annotation/info/GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
    annotation/info/BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format/DP  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Wed Oct 16 04:58:17 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp1.gds' (185.5K)
    # of fragments: 159
    save to 'tmp1.gds.tmp'
    rename 'tmp1.gds.tmp' (184.5K, reduced: 1.0K)
    # of fragments: 70
Wed Oct 16 04:58:17 2019
Wed Oct 16 04:58:17 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: customized
    # of samples: 90
Output:
    tmp2.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: 01bb26dcaafd0df48a31602185b65c92]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: f63a4d4efe99e6acab979b74d35136cb]
    genotype  [md5: 61b541faecd37d86a354a0020b754ce1]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: 91c1d0a0ac5571c0226fbd8727b114f1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info/AA  [md5: bc40b5045fcd40de3b0be5e513e5e836]
    annotation/info/AC  [md5: d428a081a2f32ecc51bf01762743e217]
    annotation/info/AN  [md5: 758c32f9b396ff0d4697a362ff2d6dea]
    annotation/info/DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
    annotation/info/HM2  [md5: 38b58906766fb24600273356a0db9c50]
    annotation/info/HM3  [md5: 2125043130d80f3773acf690705b85e2]
    annotation/info/OR  [md5: 7b7f8128d98d09f9183737df1d1a6a0a]
    annotation/info/GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
    annotation/info/BN  [md5: be4b0b7b40783bb7933c366bc39f218a]
    annotation/format/DP  [md5: ad5f45b991605297330efdb18bc6a268]
Done.
Wed Oct 16 04:58:17 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp2.gds' (184.6K)
    # of fragments: 159
    save to 'tmp2.gds.tmp'
    rename 'tmp2.gds.tmp' (183.5K, reduced: 1.0K)
    # of fragments: 70
Wed Oct 16 04:58:17 2019
Wed Oct 16 04:58:17 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: customized
    # of samples: 90
Output:
    tmp3.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348, 59.2K }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: 8070a7f5f2e17ee4435fbb45466e8213]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info/AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
    annotation/info/AC  [md5: 32e0060f853f014a2f0500092eb41a93]
    annotation/info/AN  [md5: 520c98d2b93738bf522425c1bab724d4]
    annotation/info/DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
    annotation/info/HM2  [md5: 38b58906766fb24600273356a0db9c50]
    annotation/info/HM3  [md5: 2125043130d80f3773acf690705b85e2]
    annotation/info/OR  [md5: e1829aa0fc0a84250f873500c0174857]
    annotation/info/GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
    annotation/info/BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format/DP  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Wed Oct 16 04:58:17 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp3.gds' (228.1K)
    # of fragments: 151
    save to 'tmp3.gds.tmp'
    rename 'tmp3.gds.tmp' (227.2K, reduced: 996B)
    # of fragments: 68
Wed Oct 16 04:58:17 2019
Wed Oct 16 04:58:17 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: customized
    # of samples: 90
Output:
    tmp4.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 LZ4_ra, 20B }
Digests:
    sample.id  [md5: a7b2eb225e6552690973f2f1b79dc73e]
    variant.id  [md5: 9f99987c0bc8217713b4a8a55a153626]
    position  [md5: 2499d10bd9660eafde7dadcb64988691]
    chromosome  [md5: 1e20e040c376abdd54f7851023ba4bab]
    allele  [md5: 072e0e67eb949fcf2eba36e2de04ffed]
    genotype  [md5: ca8fa50513a5500dfd5f39cf6a1e749b]
    phase  [md5: 54b8a7f61c639556b75e22340c45e276]
    annotation/id  [md5: 7ff9f8150de634e5a98b7b975268c968]
    annotation/qual  [md5: 2d95cddb8b3f3555f0d5db4d7140979c]
    annotation/filter  [md5: f9941c922320aca8ff482466453cfc9a]
    annotation/info/AA  [md5: b493afbacec86f22050ae823486328cc]
    annotation/info/AC  [md5: d318f101c7e5f9b1915566e07d9d18e9]
    annotation/info/AN  [md5: e503620a86e357b5f557a270b9d86f29]
    annotation/info/DP  [md5: 7f0b1f9249325d70688cd329b2c68405]
    annotation/info/HM2  [md5: 4423a47770a5636e1f90f02c41adc9cc]
    annotation/info/HM3  [md5: 4f1323efa931fa98f38a80a53f4bb1da]
    annotation/info/OR  [md5: d72964829bbd1d23736c625b279985d0]
    annotation/info/GP  [md5: 2e0f54a5b11378c554da151824da40ff]
    annotation/info/BN  [md5: 31d0303d62a38abc7d029484956188cb]
    annotation/format/DP  [md5: 0520c9ff2cc9ca7f51000500430b75d6]
Done.
Wed Oct 16 04:58:17 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp4.gds' (234.6K)
    # of fragments: 159
    save to 'tmp4.gds.tmp'
    rename 'tmp4.gds.tmp' (233.6K, reduced: 1.0K)
    # of fragments: 70
Wed Oct 16 04:58:17 2019
Running the examples in 'seqSummary()':
File: /home/biocbuild/bbs-3.9-bioc/R/library/SeqArray/extdata/CEU_Exon.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Chromosomes:
    Chr1 : 142, Chr2 : 59 , Chr3 : 81 , Chr4 : 48 , Chr5 : 61 , Chr6 : 99 
    Chr7 : 58 , Chr8 : 51 , Chr9 : 29 , Chr10: 70 , Chr11: 16 , Chr12: 62 
    Chr13: 11 , Chr14: 61 , Chr15: 46 , Chr16: 84 , Chr17: 100, Chr18: 54 
    Chr19: 111, Chr20: 59 , Chr21: 23 , Chr22: 23 
Alleles:
    ALT: 
    tabulation: 2, 1346(99.9%); 3, 2(0.1%)
Annotation, Quality:
    Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
Annotation, FILTER:
    PASS, All filters passed, 1348(100.0%)
    q10, Quality below 10, 0(0.0%)
Annotation, INFO variable(s):
    AA, ., String, Ancestral Allele
    AC, 1, Integer, Total number of alternate alleles in called genotypes
    AN, 1, Integer, Total number of alleles in called genotypes
    DP, 1, Integer, Total Depth
    HM2, 0, Flag, HapMap2 membership
    HM3, 0, Flag, HapMap3 membership
    OR, 1, String, Previous rs number
    GP, 1, String, GRCh37 position(s)
    BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
    DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
    family, String, 
File: /home/biocbuild/bbs-3.9-bioc/R/library/SeqArray/extdata/CEU_Exon.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Sample ID: no duplicate.
    sample.id:	'md5' [OK]
Variant ID: no duplicate.
    variant.id:	'md5' [OK]
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Genotypes:
    genotype/data:	'md5' [OK]
    genotype/~data:	no digest
    genotype/@data:	'md5' [OK]
    position:	'md5' [OK]
Chromosomes:
    Chr1 : 142, Chr2 : 59 , Chr3 : 81 , Chr4 : 48 , Chr5 : 61 , Chr6 : 99 
    Chr7 : 58 , Chr8 : 51 , Chr9 : 29 , Chr10: 70 , Chr11: 16 , Chr12: 62 
    Chr13: 11 , Chr14: 61 , Chr15: 46 , Chr16: 84 , Chr17: 100, Chr18: 54 
    Chr19: 111, Chr20: 59 , Chr21: 23 , Chr22: 23 
    chromosome:	'md5' [OK]
Alleles:
    ALT: 
    tabulation: 2, 1346(99.9%); 3, 2(0.1%)
    chromosome:	'md5' [OK]
Annotation, ID:
    annotation/id:	'md5' [OK]
Annotation, Quality:
    Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
    annotation/qual:	'md5' [OK]
Annotation, FILTER:
    PASS, All filters passed, 1348(100.0%)
    q10, Quality below 10, 0(0.0%)
Annotation, INFO variable(s):
    AA, ., String, Ancestral Allele
    AC, 1, Integer, Total number of alternate alleles in called genotypes
    AN, 1, Integer, Total number of alleles in called genotypes
    DP, 1, Integer, Total Depth
    HM2, 0, Flag, HapMap2 membership
    HM3, 0, Flag, HapMap3 membership
    OR, 1, String, Previous rs number
    GP, 1, String, GRCh37 position(s)
    BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
    DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
    family, String, 
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Number of selected samples: 90
Number of selected variants: 1,348
Alleles:
    ALT: 
    tabulation: 2, 1346(99.9%); 3, 2(0.1%)
Annotation, FILTER:
    PASS, All filters passed, 1348(100.0%)
    q10, Quality below 10, 0(0.0%)
Annotation, INFO variable(s):
    AA, ., String, Ancestral Allele
    AC, 1, Integer, Total number of alternate alleles in called genotypes
    AN, 1, Integer, Total number of alleles in called genotypes
    DP, 1, Integer, Total Depth
    HM2, 0, Flag, HapMap2 membership
    HM3, 0, Flag, HapMap3 membership
    OR, 1, String, Previous rs number
    GP, 1, String, GRCh37 position(s)
    BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
    DP, ., Integer, Read Depth from MOSAIK BAM
Annotation, sample variable(s):
    family, String, 
Reference: human_b36_both.fasta
Annotation, FILTER:
    PASS, All filters passed, 1348(100.0%)
    q10, Quality below 10, 0(0.0%)
Alleles:
    ALT: 
Annotation, INFO variable(s):
    AA, ., String, Ancestral Allele
    AC, 1, Integer, Total number of alternate alleles in called genotypes
    AN, 1, Integer, Total number of alleles in called genotypes
    DP, 1, Integer, Total Depth
    HM2, 0, Flag, HapMap2 membership
    HM3, 0, Flag, HapMap3 membership
    OR, 1, String, Previous rs number
    GP, 1, String, GRCh37 position(s)
    BN, 1, Integer, First dbSNP build #
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
    DP, ., Integer, Read Depth from MOSAIK BAM
# of selected samples: 5
# of selected variants: 10
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Number of selected samples: 5
Number of selected variants: 10
Running the examples in 'seqSystem()':
Running the examples in 'seqTranspose()':
Wed Oct 16 04:58:17 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info/AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
    annotation/info/AC  [md5: 32e0060f853f014a2f0500092eb41a93]
    annotation/info/AN  [md5: 520c98d2b93738bf522425c1bab724d4]
    annotation/info/DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
    annotation/info/HM2  [md5: 38b58906766fb24600273356a0db9c50]
    annotation/info/HM3  [md5: 2125043130d80f3773acf690705b85e2]
    annotation/info/OR  [md5: e1829aa0fc0a84250f873500c0174857]
    annotation/info/GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
    annotation/info/BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format/DP  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Wed Oct 16 04:58:17 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.5K)
    # of fragments: 159
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.5K, reduced: 1.0K)
    # of fragments: 70
Wed Oct 16 04:58:17 2019
Running the examples in 'seqVCF2GDS()':
Wed Oct 16 04:58:17 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info/AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
    annotation/info/AC  [md5: 32e0060f853f014a2f0500092eb41a93]
    annotation/info/AN  [md5: 520c98d2b93738bf522425c1bab724d4]
    annotation/info/DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
    annotation/info/HM2  [md5: 38b58906766fb24600273356a0db9c50]
    annotation/info/HM3  [md5: 2125043130d80f3773acf690705b85e2]
    annotation/info/OR  [md5: e1829aa0fc0a84250f873500c0174857]
    annotation/info/GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
    annotation/info/BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format/DP  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Wed Oct 16 04:58:18 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.5K)
    # of fragments: 159
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.5K, reduced: 1.0K)
    # of fragments: 70
Wed Oct 16 04:58:18 2019
Wed Oct 16 04:58:18 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
    calculating the total number of variants ...
    the total number of variants for import: 1,348
    Writing to 2 files:
        tmp_p2_tmp01_5e131b9d9b1e [1..674]
        tmp_p2_tmp02_5e1365116c87 [675..1,348]
    Done (Wed Oct 16 04:58:18 2019).
Output:
    tmp_p2.gds
Merging:
    opening 'tmp_p2_tmp01_5e131b9d9b1e' ... [done]
    opening 'tmp_p2_tmp02_5e1365116c87' ... [done]
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: fe72c1ff1844ce8eb7db6b1392f59dfa]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/info/AA  [md5: 6df3bcf4c07db5b94be51d1842154038]
    annotation/info/AC  [md5: 32e0060f853f014a2f0500092eb41a93]
    annotation/info/AN  [md5: 520c98d2b93738bf522425c1bab724d4]
    annotation/info/DP  [md5: a304721e223a79637ccedb5b5a6f2f8f]
    annotation/info/HM2  [md5: 38b58906766fb24600273356a0db9c50]
    annotation/info/HM3  [md5: 2125043130d80f3773acf690705b85e2]
    annotation/info/OR  [md5: e1829aa0fc0a84250f873500c0174857]
    annotation/info/GP  [md5: 7b29009823b6f3d1beb4afac91ce11a5]
    annotation/info/BN  [md5: 05f5e42981b9671fa0f931cd19d61339]
    annotation/format/DP  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Wed Oct 16 04:58:18 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp_p2.gds' (185.6K)
    # of fragments: 160
    save to 'tmp_p2.gds.tmp'
    rename 'tmp_p2.gds.tmp' (184.6K, reduced: 1.1K)
    # of fragments: 70
Wed Oct 16 04:58:18 2019
Wed Oct 16 04:58:18 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
    annotation/format/DP  [md5: 8e8a671fdd4c090f34f6c5451cf417fc]
Done.
Wed Oct 16 04:58:18 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (168.4K)
    # of fragments: 100
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (167.8K, reduced: 600B)
    # of fragments: 50
Wed Oct 16 04:58:18 2019
Wed Oct 16 04:58:18 2019
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (243.4K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    # of samples: 90
Output:
    tmp.gds
Parsing 'CEU_Exon.vcf.gz':
+ genotype/data   { Bit2 2x90x1348 ZIP_ra, 16B }
Digests:
    sample.id  [md5: d4d5be5fd4dc15775186933a968eeb86]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: f3c7091eb406b90b71be6234c1b996f2]
    chromosome  [md5: b65ee00d30fd4019558a228e14144303]
    allele  [md5: 9217bde736ad7a49d70b5788074a2f33]
    genotype  [md5: 55b7b3cb53dde7d9549ec1a9adb5eada]
    phase  [md5: f272efd2132d769ded473e188c68a710]
    annotation/id  [md5: ad224facbbf907a362af31fa4d9f8cf1]
    annotation/qual  [md5: 61fe29d41ab53d2a877966fca27ae725]
    annotation/filter  [md5: 87214e07213369b019511967d315e61b]
Done.
Wed Oct 16 04:58:18 2019
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (37.3K)
    # of fragments: 87
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (36.8K, reduced: 516B)
    # of fragments: 44
Wed Oct 16 04:58:18 2019
Running the examples in 'seqVCF_Header()':
Running the examples in 'seqVCF_SampID()':
# of selected variants: 898

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 8s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 8s

[..................................................]  0%, ETC: ---    
[=>................................................]  1%, ETC: 7.4m    
[==================================================] 100%, completed, 11s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 1s
# of selected variants: 655

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 4s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 4s

[..................................................]  0%, ETC: ---    
[=>................................................]  2%, ETC: 5.4m    
[==================================================] 100%, completed, 8s

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed, 3s
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348


RUNIT TEST PROTOCOL -- Wed Oct 16 04:59:59 2019 
*********************************************** 
Number of test functions: 28 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SeqArray RUnit Tests - 28 test functions, 0 errors, 0 failures
Number of test functions: 28 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 85.036  52.801 133.845

Example timings

SeqArray.Rcheck/SeqArray-Ex.timings

nameusersystemelapsed
SeqArray-package0.4750.0200.551
SeqVarGDSClass-class0.1220.0040.127
seqAlleleFreq0.0400.0080.048
seqApply0.1420.0160.158
seqAsVCF0.0000.0040.005
seqBED2GDS0.4020.0440.529
seqBlockApply0.0560.0080.064
seqCheck0.0320.0040.036
seqDelete0.0720.0040.077
seqDigest0.0260.0000.026
seqExampleFileName0.0010.0000.001
seqExport0.6620.1380.801
seqGDS2SNP0.0850.0080.094
seqGDS2VCF0.5460.0070.553
seqGetData0.0670.0090.075
seqGetFilter0.0380.0030.043
seqMerge1.0820.0591.142
seqMissing0.0540.0050.058
seqNumAllele0.0010.0030.005
seqOpen0.1210.0000.122
seqOptimize0.2010.0240.225
seqParallel0.1510.2330.235
seqParallelSetup0.0570.0840.096
seqRecompress1.2810.0501.304
seqResetVariantID0.0280.0080.035
seqSNP2GDS2.0150.0562.089
seqSetFilter0.0640.0110.075
seqSetFilterCond0.0520.0000.052
seqStorageOption0.6220.0390.662
seqSummary0.1880.0160.205
seqSystem000
seqTranspose0.1950.0040.199
seqVCF2GDS0.5940.2240.700
seqVCF_Header0.0740.0040.079
seqVCF_SampID0.0020.0000.002