##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqVarTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SeqVarTools_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/SeqVarTools.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SeqVarTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqVarTools' version '1.43.0'
* 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 code 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 ... NOTE
checkRd: (-1) getGenotype.Rd:40: Lost braces
    40 |   \item{sparse}{Logical for whether to return the alterate allele dosage as a sparse matrix using the \pkg{link{Matrix}} package. In most cases, setting \code{sparse=TRUE} will dramatically reduce the size of the returned object.}
       |                                                                                                                ^
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/SeqVarTools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SeqVarTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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-3.20-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=97264 on localhost:11825 at 09:45:23.043
starting worker pid=101996 on localhost:11825 at 09:45:23.236
starting worker pid=108004 on localhost:11825 at 09:45:23.420
starting worker pid=81500 on localhost:11825 at 09:45:24.272
starting worker pid=69212 on localhost:11825 at 09:45:24.384
starting worker pid=59264 on localhost:11825 at 09:45:24.448
starting worker pid=104788 on localhost:11825 at 09:45:24.599
starting worker pid=68048 on localhost:11825 at 09:45:24.824
starting worker pid=110568 on localhost:11825 at 09:45:24.883
starting worker pid=102584 on localhost:11825 at 09:45:25.024
starting worker pid=110872 on localhost:11825 at 09:45:25.124
starting worker pid=14980 on localhost:11825 at 09:45:25.388
starting worker pid=111792 on localhost:11825 at 09:45:25.459
starting worker pid=94052 on localhost:11825 at 09:45:25.892
starting worker pid=108572 on localhost:11825 at 09:45:26.079
starting worker pid=74312 on localhost:11825 at 09:45:26.170
starting worker pid=138140 on localhost:11825 at 09:45:26.259
starting worker pid=104132 on localhost:11825 at 09:45:26.351
starting worker pid=113156 on localhost:11825 at 09:45:26.453
starting worker pid=95888 on localhost:11825 at 09:45:26.511
starting worker pid=109548 on localhost:11825 at 09:45:26.610
starting worker pid=74504 on localhost:11825 at 09:45:26.679
starting worker pid=124228 on localhost:11825 at 09:45:26.953
starting worker pid=97384 on localhost:11825 at 09:45:27.018
starting worker pid=33876 on localhost:11825 at 09:45:27.212
starting worker pid=109748 on localhost:11825 at 09:45:27.341
starting worker pid=135808 on localhost:11825 at 09:45:27.453
starting worker pid=64284 on localhost:11825 at 09:45:27.783
starting worker pid=102976 on localhost:11825 at 09:45:27.970
starting worker pid=98708 on localhost:11825 at 09:45:28.222
starting worker pid=125600 on localhost:11825 at 09:45:28.289
starting worker pid=70708 on localhost:11825 at 09:45:47.365
starting worker pid=96080 on localhost:11825 at 09:45:47.645
starting worker pid=141012 on localhost:11825 at 09:45:47.778
starting worker pid=93464 on localhost:11825 at 09:45:47.850
starting worker pid=98724 on localhost:11825 at 09:45:48.028
starting worker pid=107684 on localhost:11825 at 09:45:48.210
starting worker pid=118124 on localhost:11825 at 09:45:48.371
starting worker pid=109072 on localhost:11825 at 09:45:48.519
starting worker pid=78344 on localhost:11825 at 09:45:48.929
starting worker pid=101444 on localhost:11825 at 09:45:48.980
starting worker pid=114860 on localhost:11825 at 09:45:49.194
starting worker pid=65584 on localhost:11825 at 09:45:49.453
starting worker pid=115120 on localhost:11825 at 09:45:49.526
starting worker pid=114212 on localhost:11825 at 09:45:49.586
starting worker pid=106820 on localhost:11825 at 09:45:49.640
starting worker pid=70376 on localhost:11825 at 09:45:49.698
starting worker pid=81904 on localhost:11825 at 09:45:49.822
starting worker pid=93168 on localhost:11825 at 09:45:49.912
starting worker pid=33100 on localhost:11825 at 09:45:49.989
starting worker pid=114336 on localhost:11825 at 09:45:50.097
starting worker pid=94580 on localhost:11825 at 09:45:50.230
starting worker pid=96776 on localhost:11825 at 09:45:50.365
starting worker pid=105948 on localhost:11825 at 09:45:50.585
starting worker pid=114456 on localhost:11825 at 09:45:50.646
starting worker pid=112472 on localhost:11825 at 09:45:50.803
starting worker pid=101296 on localhost:11825 at 09:45:50.888
starting worker pid=115308 on localhost:11825 at 09:45:51.350
starting worker pid=97204 on localhost:11825 at 09:45:51.446
starting worker pid=60228 on localhost:11825 at 09:45:51.719
starting worker pid=85308 on localhost:11825 at 09:45:51.787
starting worker pid=102840 on localhost:11825 at 09:45:51.866
starting worker pid=3844 on localhost:11825 at 09:46:26.434
starting worker pid=107944 on localhost:11825 at 09:46:26.658
starting worker pid=121820 on localhost:11825 at 09:46:26.815
starting worker pid=84500 on localhost:11825 at 09:46:26.867
starting worker pid=107880 on localhost:11825 at 09:46:27.083
starting worker pid=99136 on localhost:11825 at 09:46:27.235
starting worker pid=114080 on localhost:11825 at 09:46:27.394
starting worker pid=119140 on localhost:11825 at 09:46:27.575
starting worker pid=98372 on localhost:11825 at 09:46:28.059
starting worker pid=112332 on localhost:11825 at 09:46:28.298
starting worker pid=113404 on localhost:11825 at 09:46:28.365
starting worker pid=1736 on localhost:11825 at 09:46:28.525
starting worker pid=120080 on localhost:11825 at 09:46:28.661
starting worker pid=97380 on localhost:11825 at 09:46:28.901
starting worker pid=92416 on localhost:11825 at 09:46:28.969
starting worker pid=104464 on localhost:11825 at 09:46:29.127
starting worker pid=114880 on localhost:11825 at 09:46:29.305
starting worker pid=17060 on localhost:11825 at 09:46:29.383
starting worker pid=75436 on localhost:11825 at 09:46:29.517
starting worker pid=75256 on localhost:11825 at 09:46:29.722
starting worker pid=8520 on localhost:11825 at 09:46:30.017
starting worker pid=120132 on localhost:11825 at 09:46:30.099
starting worker pid=20924 on localhost:11825 at 09:46:30.217
starting worker pid=108336 on localhost:11825 at 09:46:30.296
starting worker pid=114660 on localhost:11825 at 09:46:30.384
starting worker pid=105548 on localhost:11825 at 09:46:30.475
starting worker pid=71296 on localhost:11825 at 09:46:30.541
starting worker pid=48208 on localhost:11825 at 09:46:30.691
starting worker pid=79040 on localhost:11825 at 09:46:30.897
starting worker pid=65316 on localhost:11825 at 09:46:30.962
starting worker pid=39232 on localhost:11825 at 09:46:31.022
starting worker pid=125044 on localhost:11825 at 09:46:49.684
starting worker pid=107888 on localhost:11825 at 09:46:50.177
starting worker pid=108408 on localhost:11825 at 09:46:50.356
starting worker pid=90776 on localhost:11825 at 09:46:50.689
starting worker pid=66268 on localhost:11825 at 09:46:50.785
starting worker pid=70172 on localhost:11825 at 09:46:51.134
starting worker pid=81656 on localhost:11825 at 09:46:51.215
starting worker pid=107816 on localhost:11825 at 09:46:51.471
starting worker pid=121652 on localhost:11825 at 09:46:51.669
starting worker pid=114048 on localhost:11825 at 09:46:51.737
starting worker pid=113424 on localhost:11825 at 09:46:51.922
starting worker pid=59912 on localhost:11825 at 09:46:52.023
starting worker pid=117080 on localhost:11825 at 09:46:52.075
starting worker pid=122100 on localhost:11825 at 09:46:52.317
starting worker pid=87620 on localhost:11825 at 09:46:52.589
starting worker pid=123484 on localhost:11825 at 09:46:52.762
starting worker pid=115472 on localhost:11825 at 09:46:52.843
starting worker pid=85312 on localhost:11825 at 09:46:52.910
starting worker pid=111164 on localhost:11825 at 09:46:53.046
starting worker pid=104920 on localhost:11825 at 09:46:53.108
starting worker pid=30880 on localhost:11825 at 09:46:53.171
starting worker pid=117476 on localhost:11825 at 09:46:53.352
starting worker pid=123624 on localhost:11825 at 09:46:53.448
starting worker pid=99332 on localhost:11825 at 09:46:53.608
starting worker pid=103428 on localhost:11825 at 09:46:53.774
starting worker pid=96408 on localhost:11825 at 09:46:53.847
starting worker pid=118032 on localhost:11825 at 09:46:53.918
starting worker pid=118484 on localhost:11825 at 09:46:54.023
starting worker pid=89060 on localhost:11825 at 09:46:54.261
starting worker pid=121684 on localhost:11825 at 09:46:54.493
starting worker pid=119428 on localhost:11825 at 09:46:54.576
starting worker pid=122904 on localhost:11825 at 09:47:27.525
starting worker pid=103688 on localhost:11825 at 09:47:27.678
starting worker pid=38292 on localhost:11825 at 09:47:27.752
starting worker pid=114132 on localhost:11825 at 09:47:28.341
starting worker pid=113748 on localhost:11825 at 09:47:28.434
starting worker pid=118308 on localhost:11825 at 09:47:28.562
starting worker pid=60568 on localhost:11825 at 09:47:28.705
starting worker pid=50284 on localhost:11825 at 09:47:28.912
starting worker pid=112624 on localhost:11825 at 09:47:29.099
starting worker pid=87392 on localhost:11825 at 09:47:29.336
starting worker pid=22472 on localhost:11825 at 09:47:29.634
starting worker pid=52988 on localhost:11825 at 09:47:29.917
starting worker pid=133092 on localhost:11825 at 09:47:30.007
starting worker pid=93800 on localhost:11825 at 09:47:30.155
starting worker pid=116676 on localhost:11825 at 09:47:30.221
starting worker pid=91740 on localhost:11825 at 09:47:30.384
starting worker pid=115272 on localhost:11825 at 09:47:30.492
starting worker pid=120068 on localhost:11825 at 09:47:30.733
starting worker pid=51488 on localhost:11825 at 09:47:30.827
starting worker pid=123864 on localhost:11825 at 09:47:30.941
starting worker pid=118576 on localhost:11825 at 09:47:31.158
starting worker pid=110176 on localhost:11825 at 09:47:31.216
starting worker pid=107208 on localhost:11825 at 09:47:31.321
starting worker pid=115844 on localhost:11825 at 09:47:31.389
starting worker pid=135788 on localhost:11825 at 09:47:31.493
starting worker pid=90328 on localhost:11825 at 09:47:31.642
starting worker pid=51312 on localhost:11825 at 09:47:31.841
starting worker pid=115048 on localhost:11825 at 09:47:31.880
starting worker pid=126812 on localhost:11825 at 09:47:32.089
starting worker pid=86204 on localhost:11825 at 09:47:32.146
starting worker pid=52932 on localhost:11825 at 09:47:32.219
# 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 -- Mon Jun 10 09:48:07 2024 
*********************************************** 
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 
  24.67   16.31  201.14