Multiple platform build/check report for BioC 3.6 - CHECK report for SeqArray on veracruz1

Package: SeqArray

Version: 1.18.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqArray_1.18.2.tar.gz

StartedAt: 2018-04-12 09:26:15 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 09:30:09 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 234.8 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 --no-vignettes --timings SeqArray_1.18.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.18.2’
* 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  6.0Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   1.6Mb
* 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
File ‘SeqArray/libs/SeqArray.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqArray’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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/3.4/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 vectorization.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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


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 object is masked from 'package:base':

    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()':
Thu Apr 12 09:29:01 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 }
Hash function 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.
Thu Apr 12 09:29:01 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.1K)
    # of fragments: 154
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:01 2018
File: /Users/biocbuild/bbs-3.6-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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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

$qual
[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)
Thu Apr 12 09:29:02 2018
PLINK BED to SeqArray GDS Format:
    BED file: "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/SNPRelate/extdata/plinkhapmap.bed.gz" in the SNP-major mode (Sample X SNP)
    FAM file: '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/SNPRelate/extdata/plinkhapmap.fam.gz' (60 samples)
    BIM file: '/Library/Frameworks/R.framework/Versions/3.4/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.
Thu Apr 12 09:29:02 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
Thu Apr 12 09:29:02 2018
File: /Users/biocbuild/bbs-3.6-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()':
Thu Apr 12 09:29:02 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 }
Hash function 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.
Thu Apr 12 09:29:02 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.1K)
    # of fragments: 154
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:02 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' (184.0K)
    # of fragments: 66
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (51.4K, reduced: 132.6K)
    # of fragments: 54
Running the examples in 'seqDigest()':

[..................................................]  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' (17.4K)
    # of fragments: 145
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (16.6K, reduced: 864B)
    # of fragments: 73
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' (12.1K)
    # of fragments: 103
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (11.5K, reduced: 600B)
    # of fragments: 53
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' (14.3K)
    # of fragments: 129
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (13.6K, reduced: 756B)
    # of fragments: 66
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' (17.0K)
    # of fragments: 140
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (16.2K, reduced: 828B)
    # of fragments: 71
Running the examples in 'seqGDS2SNP()':
Thu Apr 12 09:29:04 2018
SeqArray GDS to SNP GDS Format:

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Done.
Thu Apr 12 09:29:04 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (30.3K)
    # of fragments: 31
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (30.1K, reduced: 192B)
    # of fragments: 15
Thu Apr 12 09:29:04 2018
Running the examples in 'seqGDS2VCF()':
# of selected samples: 5
Thu Apr 12 09:29:04 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 0s
Thu Apr 12 09:29:04 2018    Done.
Thu Apr 12 09:29:04 2018
VCF Export: tmp1.vcf.gz
    5 samples, 1,348 variants
    INFO Field: <none>
    FORMAT Field: <none>

[..................................................]  0%, ETC: ---    
[==================================================] 100%, completed in 0s
Thu Apr 12 09:29:04 2018    Done.
Thu Apr 12 09:29:04 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
Thu Apr 12 09:29:04 2018    Done.
# of selected samples: 90
# of selected variants: 1,348
Thu Apr 12 09:29:04 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
Thu Apr 12 09:29:04 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()':
Thu Apr 12 09:29:04 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 }
Hash function 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.
Thu Apr 12 09:29:05 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp1.gds' (46.2K)
    # of fragments: 152
    save to 'tmp1.gds.tmp'
    rename 'tmp1.gds.tmp' (45.1K, reduced: 1.0K)
    # of fragments: 65
Thu Apr 12 09:29:05 2018
Thu Apr 12 09:29:05 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 }
Hash function 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.
Thu Apr 12 09:29:05 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp2.gds' (45.9K)
    # of fragments: 152
    save to 'tmp2.gds.tmp'
    rename 'tmp2.gds.tmp' (44.9K, reduced: 1.0K)
    # of fragments: 65
Thu Apr 12 09:29:05 2018
Thu Apr 12 09:29:05 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 }
Hash function 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.
Thu Apr 12 09:29:05 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp3.gds' (46.2K)
    # of fragments: 152
    save to 'tmp3.gds.tmp'
    rename 'tmp3.gds.tmp' (45.1K, reduced: 1.0K)
    # of fragments: 65
Thu Apr 12 09:29:05 2018
Thu Apr 12 09:29:05 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 }
Hash function 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.
Thu Apr 12 09:29:05 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp4.gds' (45.9K)
    # of fragments: 152
    save to 'tmp4.gds.tmp'
    rename 'tmp4.gds.tmp' (44.9K, reduced: 1.0K)
    # of fragments: 65
Thu Apr 12 09:29:05 2018
Thu Apr 12 09:29:05 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 }
Hash function 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.
Thu Apr 12 09:29:05 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp5.gds' (44.0K)
    # of fragments: 152
    save to 'tmp5.gds.tmp'
    rename 'tmp5.gds.tmp' (42.9K, reduced: 1.0K)
    # of fragments: 65
Thu Apr 12 09:29:05 2018
Thu Apr 12 09:29:05 2018
Preparing merging 5 GDS files:
    opening 'tmp1.gds' ... [done]
    opening 'tmp2.gds' ... [done]
    opening 'tmp3.gds' ... [done]
    opening 'tmp4.gds' ... [done]
    opening 'tmp5.gds' ... [done]
    228,388 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-3.6-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.
Thu Apr 12 09:29:05 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.0K)
    # of fragments: 149
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.0K, reduced: 996B)
    # of fragments: 66
Thu Apr 12 09:29:05 2018
File: /Users/biocbuild/bbs-3.6-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>
Thu Apr 12 09:29:05 2018
Preparing merging 2 GDS files:
    opening '/Users/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/SeqArray/extdata/CEU_Exon.gds' ... [done]
    opening 'test.gds' ... [done]
    612,005 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-3.6-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.
Thu Apr 12 09:29:05 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'output.gds' (244.7K)
    # of fragments: 153
    save to 'output.gds.tmp'
    rename 'output.gds.tmp' (243.7K, reduced: 1.0K)
    # of fragments: 67
Thu Apr 12 09:29:05 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()':
Thu Apr 12 09:29:05 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 }
Hash function 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.
Thu Apr 12 09:29:06 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.1K)
    # of fragments: 154
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:06 2018
Working on 'genotype' ...
Working on 'phase' ...
Working on 'annotation/format/DP' ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (332.8K)
    # of fragments: 82
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (332.7K, reduced: 108B)
    # of fragments: 73
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()':
Thu Apr 12 09:29:06 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.
Thu Apr 12 09:29:08 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
Thu Apr 12 09:29:08 2018
File: /Users/biocbuild/bbs-3.6-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()':
Thu Apr 12 09:29:08 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 }
Hash function 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.
Thu Apr 12 09:29:08 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp1.gds' (185.1K)
    # of fragments: 154
    save to 'tmp1.gds.tmp'
    rename 'tmp1.gds.tmp' (184.0K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:08 2018
Thu Apr 12 09:29:08 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 }
Hash function 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.
Thu Apr 12 09:29:08 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp2.gds' (184.1K)
    # of fragments: 154
    save to 'tmp2.gds.tmp'
    rename 'tmp2.gds.tmp' (183.0K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:08 2018
Thu Apr 12 09:29:08 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 }
Hash function 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.
Thu Apr 12 09:29:08 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp3.gds' (227.7K)
    # of fragments: 146
    save to 'tmp3.gds.tmp'
    rename 'tmp3.gds.tmp' (226.7K, reduced: 984B)
    # of fragments: 64
Thu Apr 12 09:29:08 2018
Thu Apr 12 09:29:08 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 }
Hash function 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.
Thu Apr 12 09:29:09 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp4.gds' (234.3K)
    # of fragments: 154
    save to 'tmp4.gds.tmp'
    rename 'tmp4.gds.tmp' (233.2K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:09 2018
Running the examples in 'seqSummary()':
File: /Users/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/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: /Users/biocbuild/bbs-3.6-bioc/meat/SeqArray.Rcheck/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()':
Thu Apr 12 09:29:09 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 }
Hash function 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.
Thu Apr 12 09:29:09 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.1K)
    # of fragments: 154
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:09 2018
Running the examples in 'seqVCF2GDS()':
Thu Apr 12 09:29:09 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 }
Hash function 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.
Thu Apr 12 09:29:09 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (185.1K)
    # of fragments: 154
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (184.0K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:09 2018
Thu Apr 12 09:29:09 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_182531689160a [1..674]
        tmp_p2_tmp02_18253205f615 [675..1,348]
    Done (Thu Apr 12 09:29:09 2018).
Output:
    tmp_p2.gds
Merging:
    opening 'tmp_p2_tmp01_182531689160a' ... [done]
    opening 'tmp_p2_tmp02_18253205f615' ... [done]
Hash function 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.
Thu Apr 12 09:29:09 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp_p2.gds' (185.2K)
    # of fragments: 155
    save to 'tmp_p2.gds.tmp'
    rename 'tmp_p2.gds.tmp' (184.1K, reduced: 1.0K)
    # of fragments: 66
Thu Apr 12 09:29:09 2018
Thu Apr 12 09:29:09 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 }
Hash function 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.
Thu Apr 12 09:29:09 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (167.9K)
    # of fragments: 95
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (167.3K, reduced: 588B)
    # of fragments: 46
Thu Apr 12 09:29:09 2018
Thu Apr 12 09:29:09 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 }
Hash function 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.
Thu Apr 12 09:29:10 2018
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'tmp.gds' (36.8K)
    # of fragments: 82
    save to 'tmp.gds.tmp'
    rename 'tmp.gds.tmp' (36.3K, reduced: 504B)
    # of fragments: 40
Thu Apr 12 09:29:10 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 -- Thu Apr 12 09:30:04 2018 
*********************************************** 
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SeqArray RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 82.316   4.011  87.567

name	user	system	elapsed
SeqArray-package	0.643	0.053	0.753
SeqVarGDSClass-class	0.320	0.004	0.326
seqAlleleFreq	0.042	0.003	0.045
seqApply	0.130	0.017	0.149
seqAsVCF	0.004	0.001	0.004
seqBED2GDS	0.310	0.135	0.463
seqBlockApply	0.054	0.009	0.063
seqDelete	0.167	0.022	0.196
seqDigest	0.030	0.002	0.032
seqExampleFileName	0.003	0.001	0.004
seqExport	0.777	0.907	1.779
seqGDS2SNP	0.019	0.005	0.024
seqGDS2VCF	0.362	0.010	0.384
seqGetData	0.062	0.006	0.069
seqGetFilter	0.042	0.003	0.049
seqMerge	1.020	0.113	1.163
seqMissing	0.054	0.004	0.059
seqNumAllele	0.005	0.001	0.006
seqOpen	0.038	0.003	0.040
seqOptimize	0.178	0.022	0.214
seqParallel	0.133	0.095	0.183
seqParallelSetup	0.065	0.039	0.110
seqSNP2GDS	1.543	0.202	1.793
seqSetFilter	0.079	0.016	0.099
seqSetFilterCond	0.052	0.006	0.062
seqStorageOption	0.600	0.078	0.692
seqSummary	0.170	0.017	0.188
seqSystem	0.001	0.000	0.001
seqTranspose	0.196	0.020	0.224
seqVCF2GDS	0.563	0.195	0.790
seqVCF_Header	0.053	0.002	0.059
seqVCF_SampID	0.003	0.000	0.003

CHECK report for SeqArray on veracruz1

Summary

Command output

Installation output

Tests output

Example timings