##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqVarTools.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SeqVarTools_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/SeqVarTools.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SeqVarTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqVarTools' version '1.36.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SeqVarTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under '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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL SeqVarTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'SeqVarTools' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SeqVarTools)

R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

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

> library(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-3.16-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
starting worker pid=44536 on localhost:11633 at 06:10:31.441
starting worker pid=93608 on localhost:11633 at 06:10:31.451
starting worker pid=86156 on localhost:11633 at 06:10:31.456
starting worker pid=94084 on localhost:11633 at 06:10:31.470
starting worker pid=13248 on localhost:11633 at 06:10:31.479
starting worker pid=80944 on localhost:11633 at 06:10:31.487
starting worker pid=56944 on localhost:11633 at 06:10:31.504
starting worker pid=71368 on localhost:11633 at 06:10:31.515
starting worker pid=43692 on localhost:11633 at 06:10:31.523
starting worker pid=72300 on localhost:11633 at 06:10:31.525
starting worker pid=83492 on localhost:11633 at 06:10:31.534
starting worker pid=88572 on localhost:11633 at 06:10:31.555
starting worker pid=91648 on localhost:11633 at 06:10:31.564
starting worker pid=82472 on localhost:11633 at 06:10:31.580
starting worker pid=77140 on localhost:11633 at 06:10:31.584
starting worker pid=96904 on localhost:11633 at 06:10:31.607
starting worker pid=77756 on localhost:11633 at 06:10:31.610
starting worker pid=92316 on localhost:11633 at 06:10:31.619
starting worker pid=38536 on localhost:11633 at 06:10:31.626
starting worker pid=69536 on localhost:11633 at 06:10:31.755
starting worker pid=91948 on localhost:11633 at 06:10:31.769
starting worker pid=20972 on localhost:11633 at 06:10:31.784
starting worker pid=94980 on localhost:11633 at 06:10:31.794
starting worker pid=86252 on localhost:11633 at 06:10:31.806
starting worker pid=81168 on localhost:11633 at 06:10:31.814
starting worker pid=57596 on localhost:11633 at 06:10:31.819
starting worker pid=53540 on localhost:11633 at 06:10:31.836
starting worker pid=83048 on localhost:11633 at 06:10:31.855
starting worker pid=123256 on localhost:11633 at 06:10:31.855
starting worker pid=69508 on localhost:11633 at 06:10:31.869
starting worker pid=79624 on localhost:11633 at 06:10:31.874
starting worker pid=91240 on localhost:11633 at 06:10:40.658
starting worker pid=78944 on localhost:11633 at 06:10:40.668
starting worker pid=94860 on localhost:11633 at 06:10:40.670
starting worker pid=76220 on localhost:11633 at 06:10:40.680
starting worker pid=85212 on localhost:11633 at 06:10:40.681
starting worker pid=91624 on localhost:11633 at 06:10:40.688
starting worker pid=6892 on localhost:11633 at 06:10:40.697
starting worker pid=85216 on localhost:11633 at 06:10:40.702
starting worker pid=94276 on localhost:11633 at 06:10:40.708
starting worker pid=130892 on localhost:11633 at 06:10:40.728
starting worker pid=93732 on localhost:11633 at 06:10:40.736
starting worker pid=113740 on localhost:11633 at 06:10:40.740
starting worker pid=10488 on localhost:11633 at 06:10:40.767
starting worker pid=51376 on localhost:11633 at 06:10:40.795
starting worker pid=90836 on localhost:11633 at 06:10:40.801
starting worker pid=87844 on localhost:11633 at 06:10:40.816
starting worker pid=46692 on localhost:11633 at 06:10:40.874
starting worker pid=77952 on localhost:11633 at 06:10:40.881
starting worker pid=92068 on localhost:11633 at 06:10:40.884
starting worker pid=90148 on localhost:11633 at 06:10:40.897
starting worker pid=53812 on localhost:11633 at 06:10:40.907
starting worker pid=103328 on localhost:11633 at 06:10:40.907
starting worker pid=26748 on localhost:11633 at 06:10:40.908
starting worker pid=72752 on localhost:11633 at 06:10:40.912
starting worker pid=59964 on localhost:11633 at 06:10:40.914
starting worker pid=93080 on localhost:11633 at 06:10:40.933
starting worker pid=59740 on localhost:11633 at 06:10:40.955
starting worker pid=45964 on localhost:11633 at 06:10:40.999
starting worker pid=79596 on localhost:11633 at 06:10:41.009
starting worker pid=69316 on localhost:11633 at 06:10:41.043
starting worker pid=36304 on localhost:11633 at 06:10:41.059
starting worker pid=73884 on localhost:11633 at 06:10:56.015
starting worker pid=87104 on localhost:11633 at 06:10:56.015
starting worker pid=21024 on localhost:11633 at 06:10:56.032
starting worker pid=95016 on localhost:11633 at 06:10:56.042
starting worker pid=67160 on localhost:11633 at 06:10:56.086
starting worker pid=74824 on localhost:11633 at 06:10:56.101
starting worker pid=97880 on localhost:11633 at 06:10:56.122
starting worker pid=82972 on localhost:11633 at 06:10:56.131
starting worker pid=96896 on localhost:11633 at 06:10:56.187
starting worker pid=26128 on localhost:11633 at 06:10:56.188
starting worker pid=67724 on localhost:11633 at 06:10:56.189
starting worker pid=92860 on localhost:11633 at 06:10:56.192
starting worker pid=52112 on localhost:11633 at 06:10:56.204
starting worker pid=85256 on localhost:11633 at 06:10:56.209
starting worker pid=54972 on localhost:11633 at 06:10:56.250
starting worker pid=92268 on localhost:11633 at 06:10:56.265
starting worker pid=37288 on localhost:11633 at 06:10:56.266
starting worker pid=70328 on localhost:11633 at 06:10:56.266
starting worker pid=94288 on localhost:11633 at 06:10:56.277
starting worker pid=24608 on localhost:11633 at 06:10:56.283
starting worker pid=97008 on localhost:11633 at 06:10:56.311
starting worker pid=64660 on localhost:11633 at 06:10:56.336
starting worker pid=80784 on localhost:11633 at 06:10:56.336
starting worker pid=97740 on localhost:11633 at 06:10:56.339
starting worker pid=89556 on localhost:11633 at 06:10:56.345
starting worker pid=90056 on localhost:11633 at 06:10:56.349
starting worker pid=93836 on localhost:11633 at 06:10:56.405
starting worker pid=91936 on localhost:11633 at 06:10:56.407
starting worker pid=133524 on localhost:11633 at 06:10:56.411
starting worker pid=108424 on localhost:11633 at 06:10:56.473
starting worker pid=91328 on localhost:11633 at 06:10:56.475
starting worker pid=96832 on localhost:11633 at 06:11:04.894
starting worker pid=95768 on localhost:11633 at 06:11:04.943
starting worker pid=73480 on localhost:11633 at 06:11:04.960
starting worker pid=48756 on localhost:11633 at 06:11:04.964
starting worker pid=124332 on localhost:11633 at 06:11:04.970
starting worker pid=83148 on localhost:11633 at 06:11:04.972
starting worker pid=42768 on localhost:11633 at 06:11:04.987
starting worker pid=84756 on localhost:11633 at 06:11:04.996
starting worker pid=132052 on localhost:11633 at 06:11:04.997
starting worker pid=72708 on localhost:11633 at 06:11:05.006
starting worker pid=92644 on localhost:11633 at 06:11:05.009
starting worker pid=92216 on localhost:11633 at 06:11:05.017
starting worker pid=134916 on localhost:11633 at 06:11:05.028
starting worker pid=30924 on localhost:11633 at 06:11:05.030
starting worker pid=73312 on localhost:11633 at 06:11:05.031
starting worker pid=95860 on localhost:11633 at 06:11:05.039
starting worker pid=92508 on localhost:11633 at 06:11:05.097
starting worker pid=116136 on localhost:11633 at 06:11:05.097
starting worker pid=73700 on localhost:11633 at 06:11:05.214
starting worker pid=83708 on localhost:11633 at 06:11:05.223
starting worker pid=108608 on localhost:11633 at 06:11:05.270
starting worker pid=57692 on localhost:11633 at 06:11:05.273
starting worker pid=73476 on localhost:11633 at 06:11:05.296
starting worker pid=84772 on localhost:11633 at 06:11:05.300
starting worker pid=84036 on localhost:11633 at 06:11:05.306
starting worker pid=86212 on localhost:11633 at 06:11:05.315
starting worker pid=48584 on localhost:11633 at 06:11:05.317
starting worker pid=25112 on localhost:11633 at 06:11:05.318
starting worker pid=95224 on localhost:11633 at 06:11:05.319
starting worker pid=77344 on localhost:11633 at 06:11:05.328
starting worker pid=97252 on localhost:11633 at 06:11:05.337
starting worker pid=95964 on localhost:11633 at 06:11:20.495
starting worker pid=81644 on localhost:11633 at 06:11:20.528
starting worker pid=79924 on localhost:11633 at 06:11:20.550
starting worker pid=86756 on localhost:11633 at 06:11:20.554
starting worker pid=92392 on localhost:11633 at 06:11:20.598
starting worker pid=131608 on localhost:11633 at 06:11:20.652
starting worker pid=22692 on localhost:11633 at 06:11:20.653
starting worker pid=36872 on localhost:11633 at 06:11:20.654
starting worker pid=82640 on localhost:11633 at 06:11:20.659
starting worker pid=84552 on localhost:11633 at 06:11:20.659
starting worker pid=97892 on localhost:11633 at 06:11:20.666
starting worker pid=22464 on localhost:11633 at 06:11:20.704
starting worker pid=17236 on localhost:11633 at 06:11:20.707
starting worker pid=78828 on localhost:11633 at 06:11:20.707
starting worker pid=72936 on localhost:11633 at 06:11:20.735
starting worker pid=77752 on localhost:11633 at 06:11:20.744
starting worker pid=79556 on localhost:11633 at 06:11:20.755
starting worker pid=137188 on localhost:11633 at 06:11:20.768
starting worker pid=84796 on localhost:11633 at 06:11:20.768
starting worker pid=60516 on localhost:11633 at 06:11:20.769
starting worker pid=99500 on localhost:11633 at 06:11:20.773
starting worker pid=76528 on localhost:11633 at 06:11:20.787
starting worker pid=79544 on localhost:11633 at 06:11:20.841
starting worker pid=85776 on localhost:11633 at 06:11:20.883
starting worker pid=87096 on localhost:11633 at 06:11:20.884
starting worker pid=64816 on localhost:11633 at 06:11:20.884
starting worker pid=82328 on localhost:11633 at 06:11:20.909
starting worker pid=99236 on localhost:11633 at 06:11:20.933
starting worker pid=6248 on localhost:11633 at 06:11:20.962
starting worker pid=78176 on localhost:11633 at 06:11:20.964
starting worker pid=80976 on localhost:11633 at 06:11:20.985
# 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 Mar 23 06:11:40 2023 
*********************************************** 
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 
  22.65    2.03   88.40