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CHECK report for SeqVarTools on merida2

This page was generated on 2018-10-17 08:51:51 -0400 (Wed, 17 Oct 2018).

Package 1355/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqVarTools 1.18.0
Stephanie M. Gogarten
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SeqVarTools
Branch: RELEASE_3_7
Last Commit: 2fc39e9
Last Changed Date: 2018-04-30 10:35:31 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SeqVarTools
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SeqVarTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SeqVarTools_1.18.0.tar.gz
StartedAt: 2018-10-17 00:01:53 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 00:05:02 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 189.1 seconds
RetCode: 0
Status:  OK 
CheckDir: SeqVarTools.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SeqVarTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SeqVarTools_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/SeqVarTools.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 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


Installation output

SeqVarTools.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SeqVarTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SeqVarTools’ ...
** 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
* DONE (SeqVarTools)

Tests output

SeqVarTools.Rcheck/tests/test.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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: 85
# of selected variants: 9
# 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/3.5/Resources/library/SeqArray/extdata/CEU_Exon.gds (299.1K)
+    [  ] *
|--+ description   [  ] *
|--+ sample.id   { Str8 90 LZMA_ra(35.8%), 258B } *
|--+ variant.id   { Int32 1348 LZMA_ra(16.8%), 906B } *
|--+ position   { Int32 1348 LZMA_ra(64.6%), 3.4K } *
|--+ chromosome   { Str8 1348 LZMA_ra(4.63%), 158B } *
|--+ allele   { Str8 1348 LZMA_ra(16.7%), 902B } *
|--+ genotype   [  ] *
|  |--+ data   { Bit2 2x90x1348 LZMA_ra(26.3%), 15.6K } *
|  |--+ ˜data   { Bit2 2x1348x90 LZMA_ra(29.3%), 17.3K }
|  |--+ extra.index   { Int32 3x0 LZMA_ra, 19B } *
|  \--+ extra   { Int16 0 LZMA_ra, 19B }
|--+ phase   [  ]
|  |--+ data   { Bit1 90x1348 LZMA_ra(0.91%), 138B } *
|  |--+ ˜data   { Bit1 1348x90 LZMA_ra(0.91%), 138B }
|  |--+ extra.index   { Int32 3x0 LZMA_ra, 19B } *
|  \--+ extra   { Bit1 0 LZMA_ra, 19B }
|--+ annotation   [  ]
|  |--+ id   { Str8 1348 LZMA_ra(38.4%), 5.5K } *
|  |--+ qual   { Float32 1348 LZMA_ra(2.26%), 122B } *
|  |--+ filter   { Int32,factor 1348 LZMA_ra(2.26%), 122B } *
|  |--+ info   [  ]
|  |  |--+ AA   { Str8 1348 LZMA_ra(25.6%), 690B } *
|  |  |--+ AC   { Int32 1348 LZMA_ra(24.2%), 1.3K } *
|  |  |--+ AN   { Int32 1348 LZMA_ra(19.8%), 1.0K } *
|  |  |--+ DP   { Int32 1348 LZMA_ra(47.9%), 2.5K } *
|  |  |--+ HM2   { Bit1 1348 LZMA_ra(150.3%), 254B } *
|  |  |--+ HM3   { Bit1 1348 LZMA_ra(150.3%), 254B } *
|  |  |--+ OR   { Str8 1348 LZMA_ra(20.1%), 342B } *
|  |  |--+ GP   { Str8 1348 LZMA_ra(24.4%), 3.8K } *
|  |  \--+ BN   { Int32 1348 LZMA_ra(20.9%), 1.1K } *
|  \--+ format   [  ]
|     \--+ DP   [  ] *
|        |--+ data   { Int32 90x1348 LZMA_ra(25.1%), 118.8K } *
|        \--+ ˜data   { Int32 1348x90 LZMA_ra(24.1%), 114.2K }
\--+ sample.annotation   [  ]
   \--+ family   { Str8 90 LZMA_ra(57.1%), 222B }
# 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
# of selected samples: 4
# of selected variants: 10
subject 1 of 2
subject 2 of 2
# of selected samples: 90
# of selected variants: 1,348
# of selected variants: 10
subject 1 of 2
subject 2 of 2
Warning in SeqVarTools:::.samplePairs(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: 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: 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: 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
# 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: 63
# of selected samples: 68
# of selected samples: 22
# 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 -- Wed Oct 17 00:04:56 2018 
*********************************************** 
Number of test functions: 133 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SeqVarTools RUnit Tests - 133 test functions, 0 errors, 0 failures
Number of test functions: 133 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 30.729   1.406  32.351 

Example timings

SeqVarTools.Rcheck/SeqVarTools-Ex.timings

nameusersystemelapsed
Iterator-class0.8230.0320.862
SeqVarData-class0.1130.0040.119
allele-methods0.0190.0010.021
alleleFrequency0.0230.0020.025
alternateAlleleDetection0.0010.0000.002
applyMethod0.2520.0310.287
countSingletons0.0950.0100.106
duplicateDiscordance0.0900.0030.092
getGenotype0.0760.0040.083
getVariableLengthData0.0450.0030.048
heterozygosity0.2870.0350.323
hwe0.0770.0040.081
inbreedCoeff0.2290.0260.257
isSNV0.0060.0010.007
isVariant0.0080.0020.009
meanBySample0.0480.0030.051
mendelErr0.0340.0020.036
missingGenotypeRate0.0180.0010.020
pca0.5600.1540.721
pedigree0.0100.0020.011
refFrac0.0850.0050.095
regression0.1360.0030.140
setVariantID0.0130.0040.017
titv0.2870.0060.294
variantInfo0.1120.0040.118