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This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1896/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqVarTools 1.38.0  (landing page)
Stephanie M. Gogarten
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SeqVarTools
git_branch: RELEASE_3_17
git_last_commit: 5826906
git_last_commit_date: 2023-04-25 10:28:13 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for SeqVarTools on kjohnson2


To the developers/maintainers of the SeqVarTools package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SeqVarTools
Version: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2023-10-19 00:29:24 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 00:35:12 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 347.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SeqVarTools.Rcheck
Warnings: 0

Command output

##############################################################################
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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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SeqVarTools.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqVarTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqVarTools’ version ‘1.38.0’
* 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’
 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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)

Tests output

SeqVarTools.Rcheck/tests/test.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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-arm64/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
# 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: 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 Oct 19 00:34:51 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 
 26.900   2.081  51.257 

Example timings

SeqVarTools.Rcheck/SeqVarTools-Ex.timings

nameusersystemelapsed
Iterator-class0.8140.0281.508
SeqVarData-class0.0640.0070.128
allele-methods0.0100.0020.021
alleleFrequency0.0170.0030.037
alternateAlleleDetection000
applyMethod0.6750.0181.232
countSingletons0.0210.0020.039
duplicateDiscordance0.1540.0090.297
getGenotype0.0360.0050.074
getVariableLengthData0.0040.0020.009
heterozygosity0.1720.0200.328
hwe0.0840.0110.158
imputedDosage0.0990.0500.246
inbreedCoeff0.1260.0120.236
isSNV0.0020.0010.004
isVariant0.0040.0030.012
meanBySample0.0280.0040.054
mendelErr0.0140.0030.029
missingGenotypeRate0.0110.0020.021
pca0.2920.0280.541
pedigree0.0040.0020.015
refFrac0.0450.0050.084
regression0.0920.0070.165
setVariantID0.0060.0050.015
titv0.2290.0130.424
variantInfo0.0550.0030.099