Multiple platform build/check report for BioC 3.7 - CHECK report for SeqArray on merida2

Package: SeqArray

Version: 1.20.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SeqArray_1.20.2.tar.gz

StartedAt: 2018-10-17 00:00:13 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:04:06 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 232.8 seconds

RetCode: 0

Status: OK

CheckDir: SeqArray.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SeqArray.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SeqArray_1.20.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.20.2’
* 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 ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SeqArray
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SeqArray’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ConvToGDS.cpp -o ConvToGDS.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c FileMerge.cpp -o FileMerge.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c GetData.cpp -o GetData.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Index.cpp -o Index.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Methods.cpp -o Methods.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_SeqArray.c -o R_SeqArray.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ReadBySample.cpp -o ReadBySample.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ReadByVariant.cpp -o ReadByVariant.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SeqArray.cpp -o SeqArray.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c pkg_test.cpp -o pkg_test.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c samtools_ext.c -o samtools_ext.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/gdsfmt/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c vectorization.c -o vectorization.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/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
* DONE (SeqArray)


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 (Sys.info()[['sysname']] != "Windows")
+ {
+ 	# according to the limit of 32-bit 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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


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

# of selected samples: 5
# of selected variants: 10
Running the examples in 'KG_P1_SampData()':
Running the examples in 'SeqArray-package()':
Wed Oct 17 00:02:34 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:34 2018
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 17 00:02:34 2018
File: /Users/biocbuild/bbs-3.7-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: <None>
    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):
    <None>
# of selected samples: 5
# of selected variants: 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

$qual
[1] "rs114199731"

$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] "rs35583437"

$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] "rs12347"

$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] "rs41269293"

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

$phase
[1] 0 0 0 0 0

$qual
[1] "rs2072183"

$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] "rs4253027"

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

$phase
[1] 0 0 0 0 0

$qual
[1] "rs2490763"

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

$phase
[1] 0 0 0 0 0

$qual
[1] "rs11180483"

$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] "rs35349730"

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

$phase
[1] 0 0 0 0 0

$qual
[1] "rs62078800"

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

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

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

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

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

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Running the examples in 'seqApply()':
# of selected samples: 5
# of selected variants: 10
      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,]    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,]    1   NA    1    0    1
  [2,]    0   NA    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   NA    1    1    1
  [2,]    0   NA    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    1    1    1    0    1
      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   NA    0    0    0
  [2,]    0   NA    0    0    0
      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,]   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,]   01   ff   01   00   01
  [2,]   00   ff   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   ff   01   01   01
  [2,]   00   ff   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   01   01   01   00   01
      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   ff   00   00   00
  [2,]   00   ff   00   00   00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    1    0    1    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0   NA    0   NA    0    0    NA
[2,]    0    0    0    0   NA    0   NA    1    0    NA
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    1    0    1    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    1    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    1    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   01   00   01   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   01   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   ff   00   ff   00   00    ff
[2,]   00   00   00   00   ff   00   ff   01   00    ff
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   01   00   01   00   00    00
[2,]   00   00   00   00   00   00   00   01   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   00   00   01   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   01   00   00    00
[2,]   00   00   00   00   00   00   00   01   00    00
$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] "rs114199731"

$DP
      index
sample [,1]
  [1,]    1
  [2,]   11
  [3,]   52
  [4,]   53
  [5,]   26

$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] "rs35583437"

$DP
      index
sample [,1]
  [1,]    7
  [2,]    5
  [3,]   14
  [4,]   24
  [5,]  191

$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] "rs12347"

$DP
      index
sample [,1]
  [1,]   12
  [2,]   79
  [3,]   31
  [4,]   70
  [5,]  133

$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] "rs41269293"

$DP
      index
sample [,1]
  [1,]   18
  [2,]   34
  [3,]   56
  [4,]   29
  [5,]  111

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

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs2072183"

$DP
      index
sample [,1]
  [1,]   15
  [2,]   21
  [3,]   31
  [4,]   68
  [5,]  149

$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] "rs4253027"

$DP
      index
sample [,1]
  [1,]    2
  [2,]   59
  [3,]   30
  [4,]   67
  [5,]   37

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

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs2490763"

$DP
      index
sample [,1]
  [1,]   21
  [2,]   68
  [3,]   40
  [4,]   43
  [5,]   64

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

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs11180483"

$DP
      index
sample [,1]
  [1,]   20
  [2,]   55
  [3,]   17
  [4,]   42
  [5,]  189

$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] "rs35349730"

$DP
      index
sample [,1]
  [1,]    9
  [2,]  130
  [3,]   81
  [4,]   44
  [5,]   13

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

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs62078800"

$DP
      index
sample [,1]
  [1,]    3
  [2,]    1
  [3,]    1
  [4,]   27
  [5,]   27

0
0
1
0
3
0
3
4
0
0
[1] 1
$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] "rs114199731"

[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] "rs35583437"

[1] 3
$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] "rs12347"

[1] 4
$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] "rs41269293"

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

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs2072183"

[1] 6
$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] "rs4253027"

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

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs2490763"

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

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs11180483"

[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] "rs35349730"

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

$phase
[1] 0 0 0 0 0

$rsid
[1] "rs62078800"

# 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,]    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,]    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,]    1   NA    1    0    1
  [2,]    0   NA    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   NA    1    1    1
  [2,]    0   NA    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    1    1    1    0    1
      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   NA    0    0    0
  [2,]    0   NA    0    0    0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    1    0    1    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0   NA    0   NA    0    0    NA
[2,]    0    0    0    0   NA    0   NA    1    0    NA
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    1    0    1    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    1    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    1    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
$sample.id
[1] "NA06985"

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

$sample.id
[1] "NA06989"

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

$sample.id
[1] "NA07000"

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

$sample.id
[1] "NA07048"

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

$sample.id
[1] "NA07346"

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

Running the examples in 'seqAsVCF()':
Running the examples in 'seqBED2GDS()':
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Wed Oct 17 00:02:35 2018
PLINK BED to SeqArray GDS Format:
    BED file: '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/SNPRelate/extdata/plinkhapmap.bed.gz' in the SNP-major mode (Sample X SNP)
    FAM file: '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/SNPRelate/extdata/plinkhapmap.fam.gz' (60 samples)
    BIM file: '/Library/Frameworks/R.framework/Versions/3.5/Resources/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 17 00:02:35 2018
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 17 00:02:35 2018
File: /Users/biocbuild/bbs-3.7-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: <None>
    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):
    <None>
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
Annotation, sample variable(s):
    family, Integer, <NA>
    father, Integer, <NA>
    mother, Integer, <NA>
    sex, String, <NA>
    phenotype, Integer, <NA>
Running the examples in 'seqBlockApply()':
# of selected samples: 5
# of selected variants: 10
      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,]    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,]    1   NA    1    0    1
  [2,]    0   NA    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   NA    1    1    1
  [2,]    0   NA    0    0    0
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]    0    0    0    0    0
  [2,]    1    1    1    0    1
      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   NA    0    0    0
  [2,]    0   NA    0    0    0
      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,]   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,]   01   ff   01   00   01
  [2,]   00   ff   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   ff   01   01   01
  [2,]   00   ff   00   00   00
      sample
allele [,1] [,2] [,3] [,4] [,5]
  [1,]   00   00   00   00   00
  [2,]   01   01   01   00   01
      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   ff   00   00   00
  [2,]   00   ff   00   00   00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    1    0    1    0    0    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0   NA    0   NA    0    0    NA
[2,]    0    0    0    0   NA    0   NA    1    0    NA
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    1    0    1    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]    0    0    0    0    0    0    1    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    1    0    0     0
[2,]    0    0    0    0    0    0    0    1    0     0
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   01   00   01   00   00   00   00    00
[2,]   00   00   00   00   00   00   00   01   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   ff   00   ff   00   00    ff
[2,]   00   00   00   00   ff   00   ff   01   00    ff
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   01   00   01   00   00    00
[2,]   00   00   00   00   00   00   00   01   00    00
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]   00   00   00   00   00   00   01   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   01   00   00    00
[2,]   00   00   00   00   00   00   00   01   00    00
      variant
sample [,1] [,2] [,3]
  [1,]    2    2    1
  [2,]    2    2    2
  [3,]    2    2    2
  [4,]    2    2    2
  [5,]    2    2    2
      variant
sample [,1] [,2] [,3]
  [1,]    2    1    2
  [2,]    2   NA    2
  [3,]    2    1    2
  [4,]    2    2    2
  [5,]    2    1    2
      variant
sample [,1] [,2] [,3]
  [1,]    2    1    2
  [2,]   NA    1    2
  [3,]    1    1    2
  [4,]    1    2    2
  [5,]    1    1    2
      variant
sample [,1]
  [1,]    2
  [2,]   NA
  [3,]    2
  [4,]    2
  [5,]    2
$dos
      variant
sample [,1] [,2] [,3]
  [1,]    2    2    1
  [2,]    2    2    2
  [3,]    2    2    2
  [4,]    2    2    2
  [5,]    2    2    2

$pos
[1] 112960987  48692052   7950283

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

$pos
[1] 28362841 44545705 50408787

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

$pos
[1] 101635488  74071367  88522150

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

$pos
[1] 9877205

Running the examples in 'seqClose-methods()':
Running the examples in 'seqDelete()':
Wed Oct 17 00:02:35 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:35 2018
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 17 00:02:35 2018
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' (184.5K)
    # of fragments: 70
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (51.9K, reduced: 132.6K)
    # of fragments: 58
Running the examples in 'seqDigest()':

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

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

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
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: 6241aec3c4bfa09b0ef7efaa9f7a5e59]
    position  [md5: b9b4e3f1b3aabe5f7d57692caae7b567]
    chromosome  [md5: ad0dc5f9be8bbc63ecd7a51a76cb0dc5]
    allele  [md5: f770ac938a0865d071f30da0b0fd661d]
    genotype  [md5: 6d28b76c5a101ee2b8fc1d406ecbe02f]
  [md5: f2b08fa659c10fc5a5582c65f52aa854]
    phase  [md5: fbfc323ca650cabd3df3affdc857c9da]
  [md5: fbfc323ca650cabd3df3affdc857c9da]
    annotation/id  [md5: d3ffc05abf9d714539b72faa0bc8bb21]
    annotation/qual  [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
    annotation/filter  [md5: 155aaa7359e27197a75f997dc645e48d]
    annotation/info/AA  [md5: be6b50ec9d81c6076dfa2d63f3b1ef66]
    annotation/info/AC  [md5: 4659fcd926477e4657010f159031f7f0]
    annotation/info/AN  [md5: 7612db10f5f04927a15c87c872beaa76]
    annotation/info/DP  [md5: 87a19bd2de4a19efde14b169a2cd3c6e]
    annotation/info/HM2  [md5: e5d63d253a319ea5e1ed341108d45d8b]
    annotation/info/HM3  [md5: 7cb62f0c1698b1ee5ad3610a0f25173c]
    annotation/info/OR  [md5: 4d67cb4077f1c5faa2678ce1dbf0ec56]
    annotation/info/GP  [md5: 46673c5ba130c5ed45fcf4772eea05f5]
    annotation/info/BN  [md5: b1b4eda47bd1a9991821225cd0c0e7c4]
    annotation/format/DP  [md5: a6f12cf35ac873fcc0faf84474689367]
  [md5: fd3692517995bcaa0b04ac21bb10e314]
    sample.annotation/family  [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (17.9K)
    # 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: 6241aec3c4bfa09b0ef7efaa9f7a5e59]
    position  [md5: b9b4e3f1b3aabe5f7d57692caae7b567]
    chromosome  [md5: ad0dc5f9be8bbc63ecd7a51a76cb0dc5]
    allele  [md5: f770ac938a0865d071f30da0b0fd661d]
    genotype  [md5: 6d28b76c5a101ee2b8fc1d406ecbe02f]
  [md5: f2b08fa659c10fc5a5582c65f52aa854]
    phase  [md5: fbfc323ca650cabd3df3affdc857c9da]
  [md5: fbfc323ca650cabd3df3affdc857c9da]
    annotation/id  [md5: d3ffc05abf9d714539b72faa0bc8bb21]
    annotation/qual  [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
    annotation/filter  [md5: 155aaa7359e27197a75f997dc645e48d]
    annotation/format/DP  [md5: a6f12cf35ac873fcc0faf84474689367]
  [md5: fd3692517995bcaa0b04ac21bb10e314]
    sample.annotation/family  [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (12.6K)
    # of fragments: 107
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (12.0K, reduced: 600B)
    # of fragments: 57
Export to 'tmp.gds'
    sample.id (8)  [md5: 7269c374a455e3c2d046ce1e3b2854a8]
    variant.id (100)  [md5: 6241aec3c4bfa09b0ef7efaa9f7a5e59]
    position  [md5: b9b4e3f1b3aabe5f7d57692caae7b567]
    chromosome  [md5: ad0dc5f9be8bbc63ecd7a51a76cb0dc5]
    allele  [md5: f770ac938a0865d071f30da0b0fd661d]
    genotype  [md5: 6d28b76c5a101ee2b8fc1d406ecbe02f]
  [md5: f2b08fa659c10fc5a5582c65f52aa854]
    phase  [md5: fbfc323ca650cabd3df3affdc857c9da]
  [md5: fbfc323ca650cabd3df3affdc857c9da]
    annotation/id  [md5: d3ffc05abf9d714539b72faa0bc8bb21]
    annotation/qual  [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
    annotation/filter  [md5: 155aaa7359e27197a75f997dc645e48d]
    annotation/info/AA  [md5: be6b50ec9d81c6076dfa2d63f3b1ef66]
    annotation/info/AC  [md5: 4659fcd926477e4657010f159031f7f0]
    annotation/info/AN  [md5: 7612db10f5f04927a15c87c872beaa76]
    annotation/info/DP  [md5: 87a19bd2de4a19efde14b169a2cd3c6e]
    annotation/info/HM2  [md5: e5d63d253a319ea5e1ed341108d45d8b]
    annotation/info/HM3  [md5: 7cb62f0c1698b1ee5ad3610a0f25173c]
    annotation/info/OR  [md5: 4d67cb4077f1c5faa2678ce1dbf0ec56]
    annotation/info/GP  [md5: 46673c5ba130c5ed45fcf4772eea05f5]
    annotation/info/BN  [md5: b1b4eda47bd1a9991821225cd0c0e7c4]
    sample.annotation/family  [md5: a1636dca6fa325e6f3e397cc2520d862]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (14.8K)
    # 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: 6241aec3c4bfa09b0ef7efaa9f7a5e59]
    position  [md5: b9b4e3f1b3aabe5f7d57692caae7b567]
    chromosome  [md5: ad0dc5f9be8bbc63ecd7a51a76cb0dc5]
    allele  [md5: f770ac938a0865d071f30da0b0fd661d]
    genotype  [md5: 6d28b76c5a101ee2b8fc1d406ecbe02f]
  [md5: f2b08fa659c10fc5a5582c65f52aa854]
    phase  [md5: fbfc323ca650cabd3df3affdc857c9da]
  [md5: fbfc323ca650cabd3df3affdc857c9da]
    annotation/id  [md5: d3ffc05abf9d714539b72faa0bc8bb21]
    annotation/qual  [md5: 3ed8eb4b551fd4ee34f546f1170b1ed7]
    annotation/filter  [md5: 155aaa7359e27197a75f997dc645e48d]
    annotation/info/AA  [md5: be6b50ec9d81c6076dfa2d63f3b1ef66]
    annotation/info/AC  [md5: 4659fcd926477e4657010f159031f7f0]
    annotation/info/AN  [md5: 7612db10f5f04927a15c87c872beaa76]
    annotation/info/DP  [md5: 87a19bd2de4a19efde14b169a2cd3c6e]
    annotation/info/HM2  [md5: e5d63d253a319ea5e1ed341108d45d8b]
    annotation/info/HM3  [md5: 7cb62f0c1698b1ee5ad3610a0f25173c]
    annotation/info/OR  [md5: 4d67cb4077f1c5faa2678ce1dbf0ec56]
    annotation/info/GP  [md5: 46673c5ba130c5ed45fcf4772eea05f5]
    annotation/info/BN  [md5: b1b4eda47bd1a9991821225cd0c0e7c4]
    annotation/format/DP  [md5: a6f12cf35ac873fcc0faf84474689367]
  [md5: fd3692517995bcaa0b04ac21bb10e314]
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (17.5K)
    # of fragments: 144
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (16.7K, reduced: 828B)
    # of fragments: 75
Running the examples in 'seqGDS2SNP()':
Wed Oct 17 00:02:37 2018
SeqArray GDS to SNP GDS Format:
    # of samples: 90
    # of variants: 1,348
    genotype compression: ZIP_RA
    annotation compression: LZMA_RA

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Done.
Wed Oct 17 00:02:37 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (27.7K)
    # of fragments: 31
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (27.5K, reduced: 192B)
    # of fragments: 15
Wed Oct 17 00:02:37 2018
Running the examples in 'seqGDS2VCF()':
# of selected samples: 5
Wed Oct 17 00:02:37 2018
VCF Export: tmp.vcf.gz
    5 samples, 1,348 variants
    INFO Field: AA, AC, AN, DP, HM2, HM3, OR, GP, BN
    FORMAT Field: DP

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 1s
Wed Oct 17 00:02:38 2018    Done.
Wed Oct 17 00:02:38 2018
VCF Export: tmp1.vcf.gz
    5 samples, 1,348 variants
    INFO Field: <none>
    FORMAT Field: <none>

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Wed Oct 17 00:02:38 2018    Done.
Wed Oct 17 00:02:38 2018
VCF Export: tmp2.vcf.gz
    5 samples, 1,348 variants
    INFO Field: BN, GP, AA, DP, HM2
    FORMAT Field: <none>

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Wed Oct 17 00:02:38 2018    Done.
# of selected samples: 90
# of selected variants: 1,348
Wed Oct 17 00:02:38 2018
VCF Export: tmp.vcf.gz
    90 samples, 1,348 variants
    INFO Field: AA, AC, AN, DP, HM2, HM3, OR, GP, BN
    FORMAT Field: DP

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Wed Oct 17 00:02:38 2018    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 17 00:02:38 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:38 2018
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 17 00:02:38 2018
Wed Oct 17 00:02:38 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:38 2018
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 17 00:02:38 2018
Wed Oct 17 00:02:38 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:38 2018
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 17 00:02:38 2018
Wed Oct 17 00:02:38 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:38 2018
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 17 00:02:38 2018
Wed Oct 17 00:02:38 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:38 2018
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 17 00:02:38 2018
Wed Oct 17 00:02:38 2018
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:
    /Users/biocbuild/bbs-3.7-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 17 00:02:39 2018
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 17 00:02:39 2018
File: /Users/biocbuild/bbs-3.7-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: <None>
    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):
    <None>
Wed Oct 17 00:02:39 2018
Preparing merging 2 GDS files:
    opening '/Library/Frameworks/R.framework/Versions/3.5/Resources/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:
    /Users/biocbuild/bbs-3.7-bioc/meat/SeqArray.Rcheck/tests/output.gds
Variables:
    sample.id  [md5: 43f95e0eb5cfeff96c9872fd6ab895e4]
    variant.id  [md5: ae004cdebf8eab2e7883a2182caa3967]
    position  [md5: aab908c919d5d6024d3ba1b7e8951830]
    chromosome  [md5: 2a27ef622bc33533749d1a2985dc6a4a]
    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 17 00:02:39 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'output.gds' (265.7K)
    # of fragments: 157
    save to 'output.gds.tmp'
    rename 'output.gds.tmp' (264.7K, reduced: 1.0K)
    # of fragments: 71
Wed Oct 17 00:02:39 2018
Running the examples in 'seqMissing()':

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

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Running the examples in 'seqNumAllele()':
Running the examples in 'seqOpen()':
Running the examples in 'seqOptimize()':
Wed Oct 17 00:02:39 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:40 2018
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 17 00:02:40 2018
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 'seqSNP2GDS()':
Wed Oct 17 00:02:40 2018
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 17 00:02:42 2018
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 17 00:02:42 2018
File: /Users/biocbuild/bbs-3.7-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: <None>
    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):
    <None>
Annotation, FORMAT variable(s):
    GT, 1, String, Genotype
Annotation, sample variable(s):
    family.id, String, <NA>
    father.id, String, <NA>
    mother.id, String, <NA>
    sex, String, <NA>
    pop.group, String, <NA>
Running the examples in 'seqSetFilter-methods()':
Running the examples in 'seqSetFilterCond()':
# of selected variants: 241

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

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
# of selected variants: 72
Running the examples in 'seqStorageOption()':
Wed Oct 17 00:02:42 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: customized
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 17 00:02:42 2018
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 17 00:02:42 2018
Wed Oct 17 00:02:42 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: customized
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 17 00:02:43 2018
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 17 00:02:43 2018
Wed Oct 17 00:02:43 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: customized
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 17 00:02:43 2018
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 17 00:02:43 2018
Wed Oct 17 00:02:43 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: customized
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: 1122d969fd5f1591a58effa1038dda3b]
    genotype  [md5: 30c2fcc33d9e0a5b42c629bdcc307f5f]
    phase  [md5: 54b8a7f61c639556b75e22340c45e276]
    annotation/id  [md5: 945dc5acd51d875f792a8f4e5a846afa]
    annotation/qual  [md5: 2d95cddb8b3f3555f0d5db4d7140979c]
    annotation/filter  [md5: f9941c922320aca8ff482466453cfc9a]
    annotation/info/AA  [md5: b493afbacec86f22050ae823486328cc]
    annotation/info/AC  [md5: d318f101c7e5f9b1915566e07d9d18e9]
    annotation/info/AN  [md5: 336c3c85a089ac2dca4d764c2a25aa1f]
    annotation/info/DP  [md5: 7f0b1f9249325d70688cd329b2c68405]
    annotation/info/HM2  [md5: 4423a47770a5636e1f90f02c41adc9cc]
    annotation/info/HM3  [md5: 4f1323efa931fa98f38a80a53f4bb1da]
    annotation/info/OR  [md5: 1079eaa7ad2d24a2c3ba7f7da8b25e11]
    annotation/info/GP  [md5: 2e0f54a5b11378c554da151824da40ff]
    annotation/info/BN  [md5: 1c1d591ea2f9e6bd1ae986dd73f4120e]
    annotation/format/DP  [md5: 0520c9ff2cc9ca7f51000500430b75d6]
Done.
Wed Oct 17 00:02:43 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp4.gds' (234.7K)
    # of fragments: 159
    save to 'tmp4.gds.tmp'
    rename 'tmp4.gds.tmp' (233.7K, reduced: 1.0K)
    # of fragments: 70
Wed Oct 17 00:02:43 2018
Running the examples in 'seqSummary()':
File: /Library/Frameworks/R.framework/Versions/3.5/Resources/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: <None>
    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, <NA>
File: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/SeqArray/extdata/CEU_Exon.gds
Format Version: v1.0
Reference: human_b36_both.fasta
Sample ID: no duplicate.
    sample.id: 'md5' passes
Variant ID: no duplicate.
    variant.id: 'md5' passes
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Genotypes:
    genotype/data: 'md5' passes
    genotype/˜data: no digest
    genotype/@data: 'md5' passes
    position: 'md5' passes
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' passes
Alleles:
    ALT: <None>
    tabulation: 2, 1346(99.9%); 3, 2(0.1%)
    chromosome: 'md5' passes
Annotation, ID:
    annotation/id: 'md5' passes
Annotation, Quality:
    Min: NA, 1st Qu: NA, Median: NA, Mean: NaN, 3rd Qu: NA, Max: NA, NA's: 1348
    annotation/qual: 'md5' passes
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, <NA>
Ploidy: 2
Number of samples: 90
Number of variants: 1,348
Number of selected samples: 90
Number of selected variants: 1,348
Alleles:
    ALT: <None>
    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, <NA>
Reference: human_b36_both.fasta
Annotation, FILTER:
    PASS, All filters passed, 1348(100.0%)
    q10, Quality below 10, 0(0.0%)
Alleles:
    ALT: <None>
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 17 00:02:43 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:43 2018
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 17 00:02:43 2018
Running the examples in 'seqVCF2GDS()':
Wed Oct 17 00:02:43 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:44 2018
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 17 00:02:44 2018
Wed Oct 17 00:02:44 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
    calculating the total number of variants ...
    the total number of variants for import: 1,348
    Writing to 2 files:
        tmp_p2_tmp01_66cf1fc5eb5c [1..674]
        tmp_p2_tmp02_66cf7adef54f [675..1,348]
    Done (Wed Oct 17 00:02:44 2018).
Output:
    tmp_p2.gds
Merging:
    opening 'tmp_p2_tmp01_66cf1fc5eb5c' ... [done]
    opening 'tmp_p2_tmp02_66cf7adef54f' ... [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 17 00:02:44 2018
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 17 00:02:44 2018
Wed Oct 17 00:02:44 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:44 2018
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 17 00:02:44 2018
Wed Oct 17 00:02:44 2018
Variant Call Format (VCF) Import:
    file(s):
        CEU_Exon.vcf.gz (226.0K)
    file format: VCFv4.0
    the number of sets of chromosomes (ploidy): 2
    the number of samples: 90
    genotype storage: bit2
    compression method: ZIP_RA
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 17 00:02:44 2018
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 17 00:02:44 2018
Running the examples in 'seqVCF_Header()':
Running the examples in 'seqVCF_SampID()':
# of selected variants: 898
# 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 17 00:03:58 2018 
*********************************************** 
Number of test functions: 27 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SeqArray RUnit Tests - 27 test functions, 0 errors, 0 failures
Number of test functions: 27 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
100.001   5.101 105.701

name	user	system	elapsed
SeqArray-package	0.571	0.060	0.652
SeqVarGDSClass-class	0.121	0.015	0.137
seqAlleleFreq	0.044	0.006	0.051
seqApply	0.182	0.033	0.217
seqAsVCF	0.005	0.001	0.006
seqBED2GDS	0.369	0.230	0.606
seqBlockApply	0.079	0.012	0.094
seqDelete	0.226	0.025	0.252
seqDigest	0.041	0.002	0.044
seqExampleFileName	0.004	0.000	0.005
seqExport	1.041	0.991	2.057
seqGDS2SNP	0.053	0.022	0.077
seqGDS2VCF	0.699	0.034	0.745
seqGetData	0.068	0.005	0.073
seqGetFilter	0.048	0.003	0.053
seqMerge	1.378	0.125	1.534
seqMissing	0.065	0.004	0.069
seqNumAllele	0.007	0.001	0.008
seqOpen	0.056	0.003	0.060
seqOptimize	0.248	0.029	0.283
seqParallel	0.202	0.156	0.258
seqParallelSetup	0.083	0.061	0.126
seqSNP2GDS	1.796	0.166	1.971
seqSetFilter	0.100	0.016	0.117
seqSetFilterCond	0.053	0.007	0.059
seqStorageOption	0.795	0.108	0.916
seqSummary	0.233	0.029	0.263
seqSystem	0.001	0.001	0.001
seqTranspose	0.247	0.021	0.276
seqVCF2GDS	0.903	0.313	1.062
seqVCF_Header	0.091	0.011	0.104
seqVCF_SampID	0.004	0.001	0.006

CHECK report for SeqArray on merida2

Summary

Command output

Installation output

Tests output

Example timings