Stephanie M. Gogarten
| Snapshot Date: 2024-06-27 14:00 -0400 (Thu, 27 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/SeqVarTools |
| git_branch: devel |
| git_last_commit: dbb2b6c |
| git_last_commit_date: 2024-04-30 10:32:56 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-28 11:39 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4089 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
| 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 1900/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqVarTools 1.43.0 (landing page) Stephanie M. Gogarten
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the SeqVarTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SeqVarTools.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: 1.43.0 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqVarTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SeqVarTools_1.43.0.tar.gz |
| StartedAt: 2024-06-28 03:36:04 -0400 (Fri, 28 Jun 2024) |
| EndedAt: 2024-06-28 03:39:14 -0400 (Fri, 28 Jun 2024) |
| EllapsedTime: 189.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SeqVarTools.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqVarTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings SeqVarTools_1.43.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/SeqVarTools.Rcheck'
* using R version 4.4.1 (2024-06-14 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 '1.43.0'
* 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
'C:/Users/biocbuild/bbs-3.20-bioc/meat/SeqVarTools.Rcheck/00check.log'
for details.
SeqVarTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL SeqVarTools ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-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)
SeqVarTools.Rcheck/tests/test.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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: C:\Users\biocbuild\bbs-3.20-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
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# 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 -- Fri Jun 28 03:39:05 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
18.00 3.70 75.87
SeqVarTools.Rcheck/SeqVarTools-Ex.timings
| name | user | system | elapsed | |
| Iterator-class | 0.41 | 0.02 | 0.44 | |
| SeqVarData-class | 0.03 | 0.00 | 0.03 | |
| allele-methods | 0.00 | 0.01 | 0.02 | |
| alleleFrequency | 0.01 | 0.00 | 0.01 | |
| alternateAlleleDetection | 0 | 0 | 0 | |
| applyMethod | 0.13 | 0.02 | 0.16 | |
| countSingletons | 0.01 | 0.00 | 0.01 | |
| duplicateDiscordance | 0.10 | 0.01 | 0.11 | |
| getGenotype | 0.00 | 0.01 | 0.02 | |
| getVariableLengthData | 0.01 | 0.00 | 0.01 | |
| heterozygosity | 0.57 | 0.00 | 0.56 | |
| hwe | 0.04 | 0.00 | 0.05 | |
| imputedDosage | 0.16 | 0.02 | 0.19 | |
| inbreedCoeff | 0.09 | 0.00 | 0.09 | |
| isSNV | 0 | 0 | 0 | |
| isVariant | 0 | 0 | 0 | |
| meanBySample | 0.03 | 0.00 | 0.03 | |
| mendelErr | 0.00 | 0.02 | 0.02 | |
| missingGenotypeRate | 0.02 | 0.00 | 0.01 | |
| pca | 0.37 | 0.07 | 0.46 | |
| pedigree | 0.00 | 0.02 | 0.01 | |
| refFrac | 0.04 | 0.00 | 0.03 | |
| regression | 0.04 | 0.00 | 0.05 | |
| setVariantID | 0.02 | 0.01 | 0.03 | |
| titv | 0.09 | 0.05 | 0.14 | |
| variantInfo | 0.03 | 0.00 | 0.03 | |