R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
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> library(GenomicRanges)
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
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, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
> BiocGenerics:::testPackage("SeqVarTools")
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")'.
# of selected samples: 5
# of selected variants: 5
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 3
# of selected samples: 3
matching samples... 2 pairs identified!
matching variants... 1346 non-overlapping variant matches identified!
# of selected samples: 2
# of selected variants: 1,346
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 2
# of selected variants: 50
# of selected samples: 2
# of selected variants: 51
matching samples... 2 pairs identified!
matching variants... 26 non-overlapping variant matches identified!
# of selected variants: 26
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
File: F:\biocbuild\bbs-3.17-bioc\R\library\SeqArray\extdata\CEU_Exon.gds (287.6K)
+ [ ] *
|--+ description [ ] *
|--+ sample.id { Str8 90 LZMA_ra(34.7%), 257B } *
|--+ variant.id { Int32 1348 LZMA_ra(16.7%), 905B } *
|--+ position { Int32 1348 LZMA_ra(64.4%), 3.4K } *
|--+ chromosome { Str8 1348 LZMA_ra(4.39%), 157B } *
|--+ allele { Str8 1348 LZMA_ra(16.6%), 901B } *
|--+ genotype [ ] *
| |--+ data { Bit2 2x90x1348 LZMA_ra(26.3%), 15.6K } *
| |--+ ~data { Bit2 2x1348x90 LZMA_ra(29.2%), 17.3K } *
| |--+ extra.index { Int32 3x0 LZMA_ra, 18B } *
| \--+ extra { Int16 0 LZMA_ra, 18B }
|--+ phase [ ]
| |--+ data { Bit1 90x1348 LZMA_ra(0.86%), 137B } *
| |--+ ~data { Bit1 1348x90 LZMA_ra(0.86%), 137B } *
| |--+ extra.index { Int32 3x0 LZMA_ra, 18B } *
| \--+ extra { Bit1 0 LZMA_ra, 18B }
|--+ annotation [ ]
| |--+ id { Str8 1348 LZMA_ra(38.3%), 5.5K } *
| |--+ qual { Float32 1348 LZMA_ra(2.11%), 121B } *
| |--+ filter { Int32,factor 1348 LZMA_ra(2.11%), 121B } *
| |--+ info [ ]
| | |--+ AA { Str8 1328 LZMA_ra(22.1%), 593B } *
| | |--+ AC { Int32 1348 LZMA_ra(24.1%), 1.3K } *
| | |--+ AN { Int32 1348 LZMA_ra(19.6%), 1.0K } *
| | |--+ DP { Int32 1348 LZMA_ra(47.7%), 2.5K } *
| | |--+ HM2 { Bit1 1348 LZMA_ra(145.6%), 253B } *
| | |--+ HM3 { Bit1 1348 LZMA_ra(145.6%), 253B } *
| | |--+ OR { Str8 1348 LZMA_ra(19.6%), 341B } *
| | |--+ GP { Str8 1348 LZMA_ra(24.3%), 3.8K } *
| | \--+ BN { Int32 1348 LZMA_ra(20.7%), 1.1K } *
| \--+ format [ ]
| \--+ DP [ ] *
| |--+ data { VL_Int 90x1348 LZMA_ra(70.8%), 115.2K } *
| \--+ ~data { VL_Int 1348x90 LZMA_ra(65.1%), 105.9K } *
\--+ sample.annotation [ ]
\--+ family { Str8 90 LZMA_ra(55.0%), 221B } *
# of selected variants: 142
# of selected samples: 90
# of selected variants: 1,348
# of selected variants: 5
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 5
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 3
# of selected samples: 3
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 2
# of selected variants: 50
# of selected samples: 2
# of selected variants: 51
matching samples... 2 pairs identified!
matching variants... 26 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 26 variant matches identified!
# of selected variants: 26
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 3
# of selected samples: 3
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 1346 variant matches identified!
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 2
# of selected variants: 50
# of selected samples: 2
# of selected variants: 51
matching samples... 2 pairs identified!
matching variants... 26 variant matches identified!
matching samples... 2 pairs identified!
matching variants... 26 variant matches identified!
# of selected variants: 26
Warning in SeqVarTools:::.samplePairs1(samples) :
More than two samples for subject 4
Selecting first two samples: samp7, samp8
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected variants: 1,346
# of selected variants: 1,330
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 3
# of selected variants: 10
# of selected samples: 3
# of selected samples: 90
# of selected variants: 1,348
# of selected variants: 10
# of selected samples: 3
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
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# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected variants: 903
# of selected samples: 59
# of selected samples: 58
# of selected samples: 32
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 5
# of selected variants: 10
# of selected samples: 90
# of selected variants: 1,348
# of selected samples: 5
# of selected variants: 10
# of selected samples: 10
# of selected samples: 10
# of selected variants: 10
# of selected samples: 10
RUNIT TEST PROTOCOL -- Thu Dec 29 03:34:50 2022
***********************************************
Number of test functions: 152
Number of errors: 0
Number of failures: 0
1 Test Suite :
SeqVarTools RUnit Tests - 152 test functions, 0 errors, 0 failures
Number of test functions: 152
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.43 1.98 69.68