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This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1896/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqVarTools 1.38.0 (landing page) Stephanie M. Gogarten
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
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. |
| 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 |
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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
###
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* 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
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)
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
SeqVarTools.Rcheck/SeqVarTools-Ex.timings
| name | user | system | elapsed | |
| Iterator-class | 0.814 | 0.028 | 1.508 | |
| SeqVarData-class | 0.064 | 0.007 | 0.128 | |
| allele-methods | 0.010 | 0.002 | 0.021 | |
| alleleFrequency | 0.017 | 0.003 | 0.037 | |
| alternateAlleleDetection | 0 | 0 | 0 | |
| applyMethod | 0.675 | 0.018 | 1.232 | |
| countSingletons | 0.021 | 0.002 | 0.039 | |
| duplicateDiscordance | 0.154 | 0.009 | 0.297 | |
| getGenotype | 0.036 | 0.005 | 0.074 | |
| getVariableLengthData | 0.004 | 0.002 | 0.009 | |
| heterozygosity | 0.172 | 0.020 | 0.328 | |
| hwe | 0.084 | 0.011 | 0.158 | |
| imputedDosage | 0.099 | 0.050 | 0.246 | |
| inbreedCoeff | 0.126 | 0.012 | 0.236 | |
| isSNV | 0.002 | 0.001 | 0.004 | |
| isVariant | 0.004 | 0.003 | 0.012 | |
| meanBySample | 0.028 | 0.004 | 0.054 | |
| mendelErr | 0.014 | 0.003 | 0.029 | |
| missingGenotypeRate | 0.011 | 0.002 | 0.021 | |
| pca | 0.292 | 0.028 | 0.541 | |
| pedigree | 0.004 | 0.002 | 0.015 | |
| refFrac | 0.045 | 0.005 | 0.084 | |
| regression | 0.092 | 0.007 | 0.165 | |
| setVariantID | 0.006 | 0.005 | 0.015 | |
| titv | 0.229 | 0.013 | 0.424 | |
| variantInfo | 0.055 | 0.003 | 0.099 | |