##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqVarTools.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SeqVarTools_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SeqVarTools.Rcheck'
* using R version 4.4.0 (2024-04-24 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 '1.42.0'
* 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-3.19-bioc/meat/SeqVarTools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SeqVarTools
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 (2024-04-24 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-3.19-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=28396 on localhost:11228 at 06:21:24.570
starting worker pid=136788 on localhost:11228 at 06:21:24.574
starting worker pid=25080 on localhost:11228 at 06:21:24.655
starting worker pid=20200 on localhost:11228 at 06:21:24.660
starting worker pid=30604 on localhost:11228 at 06:21:24.664
starting worker pid=13000 on localhost:11228 at 06:21:24.671
starting worker pid=74780 on localhost:11228 at 06:21:24.672
starting worker pid=12080 on localhost:11228 at 06:21:24.674
starting worker pid=89216 on localhost:11228 at 06:21:24.734
starting worker pid=20072 on localhost:11228 at 06:21:24.741
starting worker pid=23768 on localhost:11228 at 06:21:24.741
starting worker pid=8436 on localhost:11228 at 06:21:24.744
starting worker pid=23660 on localhost:11228 at 06:21:24.749
starting worker pid=106308 on localhost:11228 at 06:21:24.766
starting worker pid=111636 on localhost:11228 at 06:21:24.808
starting worker pid=75476 on localhost:11228 at 06:21:24.822
starting worker pid=105876 on localhost:11228 at 06:21:24.828
starting worker pid=4496 on localhost:11228 at 06:21:24.830
starting worker pid=12980 on localhost:11228 at 06:21:24.863
starting worker pid=54636 on localhost:11228 at 06:21:24.872
starting worker pid=22136 on localhost:11228 at 06:21:24.904
starting worker pid=19164 on localhost:11228 at 06:21:24.931
starting worker pid=64728 on localhost:11228 at 06:21:24.943
starting worker pid=127456 on localhost:11228 at 06:21:24.961
starting worker pid=29376 on localhost:11228 at 06:21:24.962
starting worker pid=128540 on localhost:11228 at 06:21:24.965
starting worker pid=125740 on localhost:11228 at 06:21:25.033
starting worker pid=17208 on localhost:11228 at 06:21:25.099
starting worker pid=141668 on localhost:11228 at 06:21:25.126
starting worker pid=14808 on localhost:11228 at 06:21:25.144
starting worker pid=14008 on localhost:11228 at 06:21:25.169
starting worker pid=2128 on localhost:11228 at 06:21:33.829
starting worker pid=141920 on localhost:11228 at 06:21:33.845
starting worker pid=24324 on localhost:11228 at 06:21:33.902
starting worker pid=23992 on localhost:11228 at 06:21:33.914
starting worker pid=127944 on localhost:11228 at 06:21:33.937
starting worker pid=29816 on localhost:11228 at 06:21:33.938
starting worker pid=128764 on localhost:11228 at 06:21:33.948
starting worker pid=22964 on localhost:11228 at 06:21:34.051
starting worker pid=15508 on localhost:11228 at 06:21:34.053
starting worker pid=11880 on localhost:11228 at 06:21:34.067
starting worker pid=123132 on localhost:11228 at 06:21:34.101
starting worker pid=100860 on localhost:11228 at 06:21:34.114
starting worker pid=136080 on localhost:11228 at 06:21:34.140
starting worker pid=130172 on localhost:11228 at 06:21:34.150
starting worker pid=22792 on localhost:11228 at 06:21:34.166
starting worker pid=111832 on localhost:11228 at 06:21:34.188
starting worker pid=56644 on localhost:11228 at 06:21:34.195
starting worker pid=139124 on localhost:11228 at 06:21:34.252
starting worker pid=138780 on localhost:11228 at 06:21:34.382
starting worker pid=75092 on localhost:11228 at 06:21:34.389
starting worker pid=19692 on localhost:11228 at 06:21:34.391
starting worker pid=78352 on localhost:11228 at 06:21:34.392
starting worker pid=74704 on localhost:11228 at 06:21:34.402
starting worker pid=132036 on localhost:11228 at 06:21:34.413
starting worker pid=24040 on localhost:11228 at 06:21:34.425
starting worker pid=19504 on localhost:11228 at 06:21:34.439
starting worker pid=20292 on localhost:11228 at 06:21:34.444
starting worker pid=136044 on localhost:11228 at 06:21:34.468
starting worker pid=20896 on localhost:11228 at 06:21:34.483
starting worker pid=48968 on localhost:11228 at 06:21:34.505
starting worker pid=4012 on localhost:11228 at 06:21:34.535
starting worker pid=18040 on localhost:11228 at 06:21:51.155
starting worker pid=110260 on localhost:11228 at 06:21:51.165
starting worker pid=34044 on localhost:11228 at 06:21:51.250
starting worker pid=142048 on localhost:11228 at 06:21:51.272
starting worker pid=125044 on localhost:11228 at 06:21:51.414
starting worker pid=115956 on localhost:11228 at 06:21:51.440
starting worker pid=141548 on localhost:11228 at 06:21:51.495
starting worker pid=27836 on localhost:11228 at 06:21:51.558
starting worker pid=102412 on localhost:11228 at 06:21:51.569
starting worker pid=30296 on localhost:11228 at 06:21:51.576
starting worker pid=82624 on localhost:11228 at 06:21:51.621
starting worker pid=40792 on localhost:11228 at 06:21:51.649
starting worker pid=112664 on localhost:11228 at 06:21:51.686
starting worker pid=83908 on localhost:11228 at 06:21:51.715
starting worker pid=98020 on localhost:11228 at 06:21:51.727
starting worker pid=124384 on localhost:11228 at 06:21:51.730
starting worker pid=11568 on localhost:11228 at 06:21:51.730
starting worker pid=32116 on localhost:11228 at 06:21:51.733
starting worker pid=27912 on localhost:11228 at 06:21:51.786
starting worker pid=23788 on localhost:11228 at 06:21:51.789
starting worker pid=13440 on localhost:11228 at 06:21:51.790
starting worker pid=119356 on localhost:11228 at 06:21:51.815
starting worker pid=31920 on localhost:11228 at 06:21:51.844
starting worker pid=22388 on localhost:11228 at 06:21:51.853
starting worker pid=131716 on localhost:11228 at 06:21:51.866
starting worker pid=118392 on localhost:11228 at 06:21:51.868
starting worker pid=132812 on localhost:11228 at 06:21:51.873
starting worker pid=142000 on localhost:11228 at 06:21:51.913
starting worker pid=70084 on localhost:11228 at 06:21:51.924
starting worker pid=12832 on localhost:11228 at 06:21:51.989
starting worker pid=134164 on localhost:11228 at 06:21:52.065
starting worker pid=72524 on localhost:11228 at 06:22:00.437
starting worker pid=27716 on localhost:11228 at 06:22:00.440
starting worker pid=141320 on localhost:11228 at 06:22:00.443
starting worker pid=114620 on localhost:11228 at 06:22:00.471
starting worker pid=6520 on localhost:11228 at 06:22:00.493
starting worker pid=85456 on localhost:11228 at 06:22:00.524
starting worker pid=16872 on localhost:11228 at 06:22:00.533
starting worker pid=131484 on localhost:11228 at 06:22:00.540
starting worker pid=27236 on localhost:11228 at 06:22:00.541
starting worker pid=10424 on localhost:11228 at 06:22:00.551
starting worker pid=88540 on localhost:11228 at 06:22:00.563
starting worker pid=99280 on localhost:11228 at 06:22:00.615
starting worker pid=61336 on localhost:11228 at 06:22:00.630
starting worker pid=139992 on localhost:11228 at 06:22:00.782
starting worker pid=24124 on localhost:11228 at 06:22:00.783
starting worker pid=31568 on localhost:11228 at 06:22:00.783
starting worker pid=11920 on localhost:11228 at 06:22:00.793
starting worker pid=61616 on localhost:11228 at 06:22:00.812
starting worker pid=18968 on localhost:11228 at 06:22:00.818
starting worker pid=24232 on localhost:11228 at 06:22:00.889
starting worker pid=104816 on localhost:11228 at 06:22:00.896
starting worker pid=124908 on localhost:11228 at 06:22:00.906
starting worker pid=114116 on localhost:11228 at 06:22:00.908
starting worker pid=114132 on localhost:11228 at 06:22:00.909
starting worker pid=125332 on localhost:11228 at 06:22:00.922
starting worker pid=11608 on localhost:11228 at 06:22:00.934
starting worker pid=24372 on localhost:11228 at 06:22:00.941
starting worker pid=74456 on localhost:11228 at 06:22:00.946
starting worker pid=128904 on localhost:11228 at 06:22:00.957
starting worker pid=26444 on localhost:11228 at 06:22:00.966
starting worker pid=13960 on localhost:11228 at 06:22:00.991
starting worker pid=131016 on localhost:11228 at 06:22:18.021
starting worker pid=89044 on localhost:11228 at 06:22:18.098
starting worker pid=25040 on localhost:11228 at 06:22:18.099
starting worker pid=45936 on localhost:11228 at 06:22:18.123
starting worker pid=136420 on localhost:11228 at 06:22:18.141
starting worker pid=13460 on localhost:11228 at 06:22:18.149
starting worker pid=81824 on localhost:11228 at 06:22:18.169
starting worker pid=15592 on localhost:11228 at 06:22:18.177
starting worker pid=124664 on localhost:11228 at 06:22:18.178
starting worker pid=121724 on localhost:11228 at 06:22:18.207
starting worker pid=139684 on localhost:11228 at 06:22:18.207
starting worker pid=12464 on localhost:11228 at 06:22:18.234
starting worker pid=24504 on localhost:11228 at 06:22:18.254
starting worker pid=12084 on localhost:11228 at 06:22:18.262
starting worker pid=130728 on localhost:11228 at 06:22:18.288
starting worker pid=140664 on localhost:11228 at 06:22:18.292
starting worker pid=31056 on localhost:11228 at 06:22:18.310
starting worker pid=23592 on localhost:11228 at 06:22:18.350
starting worker pid=9680 on localhost:11228 at 06:22:18.376
starting worker pid=23844 on localhost:11228 at 06:22:18.378
starting worker pid=22460 on localhost:11228 at 06:22:18.381
starting worker pid=126344 on localhost:11228 at 06:22:18.412
starting worker pid=34704 on localhost:11228 at 06:22:18.416
starting worker pid=141128 on localhost:11228 at 06:22:18.420
starting worker pid=106384 on localhost:11228 at 06:22:18.423
starting worker pid=141908 on localhost:11228 at 06:22:18.429
starting worker pid=125200 on localhost:11228 at 06:22:18.433
starting worker pid=121916 on localhost:11228 at 06:22:18.433
starting worker pid=37932 on localhost:11228 at 06:22:18.434
starting worker pid=4612 on localhost:11228 at 06:22:18.477
starting worker pid=121520 on localhost:11228 at 06:22:18.497
# 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 May 20 06:22:40 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 
  27.51    2.92   99.84