Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:46 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1922/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SeqVarTools 1.45.0 (landing page) Stephanie M. Gogarten
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 1.45.0 |
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_1.45.0.tar.gz |
StartedAt: 2024-12-22 21:25:51 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 21:26:51 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 60.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SeqVarTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.45.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SeqVarTools.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SeqVarTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SeqVarTools’ version ‘1.45.0’ * 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 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: Iterator-class.Rd: GRanges, GRangesList, DataFrame, SeqVarGDSClass, seqSetFilter SeqVarData-class.Rd: SeqVarGDSClass, AnnotatedDataFrame, seqSetFilter, GRanges, seqVCF2GDS, seqOpen, seqGetData, seqApply, seqClose SeqVarTools-package.Rd: SeqArray allele-methods.Rd: SeqVarGDSClass alleleFrequency.Rd: SeqVarGDSClass, seqParallel alternateAlleleDetection.Rd: seqSetFilter, SeqVarGDSClass applyMethod.Rd: SeqVarGDSClass, seqSetFilter chromWithPAR.Rd: SeqVarGDSClass countSingletons.Rd: SeqVarGDSClass duplicateDiscordance.Rd: seqSetFilter getGenotype.Rd: SeqVarGDSClass, seqParallel, Matrix, seqBlockApply, seqGetData, seqSetFilter getVariableLengthData.Rd: SeqVarGDSClass, seqParallel, seqGetData heterozygosity.Rd: SeqVarGDSClass, seqParallel hwe.Rd: SeqVarGDSClass, seqParallel, HWExact, GWASExactHW imputedDosage.Rd: SeqVarGDSClass inbreedCoeff.Rd: SeqVarGDSClass, seqParallel isSNV.Rd: SeqVarGDSClass isVariant.Rd: SeqVarGDSClass, seqParallel meanBySample.Rd: SeqVarGDSClass, seqApply mendelErr.Rd: SeqVarGDSClass missingGenotypeRate.Rd: SeqVarGDSClass, seqParallel pca.Rd: SeqVarGDSClass refFrac.Rd: SeqVarGDSClass, seqParallel regression.Rd: logistf, seqParallel, seqSetFilter setVariantID.Rd: seqVCF2GDS, SeqVarGDSClass titv.Rd: SeqVarGDSClass variantInfo.Rd: SeqVarGDSClass Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/SeqVarTools.Rcheck/00check.log’ for details.
SeqVarTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SeqVarTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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/4.5-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 -- Sun Dec 22 21:26:48 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 7.732 1.388 8.609
SeqVarTools.Rcheck/SeqVarTools-Ex.timings
name | user | system | elapsed | |
Iterator-class | 0.386 | 0.007 | 0.395 | |
SeqVarData-class | 0.018 | 0.002 | 0.019 | |
allele-methods | 0.003 | 0.001 | 0.003 | |
alleleFrequency | 0.007 | 0.000 | 0.011 | |
alternateAlleleDetection | 0 | 0 | 0 | |
applyMethod | 0.062 | 0.007 | 0.069 | |
countSingletons | 0.006 | 0.001 | 0.008 | |
duplicateDiscordance | 0.051 | 0.004 | 0.059 | |
getGenotype | 0.012 | 0.002 | 0.014 | |
getVariableLengthData | 0.001 | 0.001 | 0.003 | |
heterozygosity | 0.057 | 0.009 | 0.070 | |
hwe | 0.027 | 0.004 | 0.032 | |
imputedDosage | 0.029 | 0.017 | 0.054 | |
inbreedCoeff | 0.039 | 0.005 | 0.045 | |
isSNV | 0.001 | 0.000 | 0.001 | |
isVariant | 0.001 | 0.000 | 0.002 | |
meanBySample | 0.011 | 0.002 | 0.012 | |
mendelErr | 0.004 | 0.001 | 0.006 | |
missingGenotypeRate | 0.004 | 0.001 | 0.005 | |
pca | 0.088 | 0.032 | 0.126 | |
pedigree | 0.002 | 0.001 | 0.002 | |
refFrac | 0.013 | 0.002 | 0.015 | |
regression | 0.030 | 0.003 | 0.033 | |
setVariantID | 0.002 | 0.002 | 0.005 | |
titv | 0.056 | 0.005 | 0.064 | |
variantInfo | 0.012 | 0.001 | 0.016 | |