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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SeqVarTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SeqVarTools_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SeqVarTools.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqVarTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqVarTools’ version ‘1.40.0’
* 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 for sufficient/correct file permissions ... 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’
 ERROR
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  Test files with failing tests
  
     test_hethom.R 
       test_hethom_sum 
  
     test_missingGenotypeRate.R 
       test_missingGenotypeRate 
  
     test_parallel.R 
       test_parallel_bysample 
  
  
  Error in BiocGenerics:::testPackage("SeqVarTools") : 
    unit tests failed for package SeqVarTools
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/SeqVarTools.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqVarTools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
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: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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
Timing stopped at: 0.303 0.021 0.329
Error in checkEquals(rep(nvar, nsamp), heterozygosity(gds, margin = "by.sample") *  : 
  Numeric: lengths (90, 0) differ

# 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
Timing stopped at: 0.027 0.004 0.033
Error in checkIdentical(rowSums(is.na(geno[1, , ]))/dim(geno)[3], missingGenotypeRate(gds,  : 
  FALSE 
 
# 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
Timing stopped at: 0.359 0.538 0.369
Error in checkEquals(miss1, miss2) : Numeric: lengths (0, 90) differ

# 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 28 08:56:58 2024 
*********************************************** 
Number of test functions: 152 
Number of errors: 0 
Number of failures: 3 

 
1 Test Suite : 
SeqVarTools RUnit Tests - 152 test functions, 0 errors, 3 failures
FAILURE in test_hethom_sum: Error in checkEquals(rep(nvar, nsamp), heterozygosity(gds, margin = "by.sample") *  : 
  Numeric: lengths (90, 0) differ

FAILURE in test_missingGenotypeRate: Error in checkIdentical(rowSums(is.na(geno[1, , ]))/dim(geno)[3], missingGenotypeRate(gds,  : 
  FALSE 
 
FAILURE in test_parallel_bysample: Error in checkEquals(miss1, miss2) : Numeric: lengths (0, 90) differ


Test files with failing tests

   test_hethom.R 
     test_hethom_sum 

   test_missingGenotypeRate.R 
     test_missingGenotypeRate 

   test_parallel.R 
     test_parallel_bysample 


Error in BiocGenerics:::testPackage("SeqVarTools") : 
  unit tests failed for package SeqVarTools
Execution halted