Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 1954/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SeqVarTools 1.47.0 (landing page) Stephanie M. Gogarten
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / 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: 1.47.0 |
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqVarTools.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings SeqVarTools_1.47.0.tar.gz |
StartedAt: 2025-08-15 07:49:47 -0400 (Fri, 15 Aug 2025) |
EndedAt: 2025-08-15 07:54:25 -0400 (Fri, 15 Aug 2025) |
EllapsedTime: 278.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SeqVarTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SeqVarTools.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings SeqVarTools_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/SeqVarTools.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * 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 '1.47.0' * 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 ... 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 'F:/biocbuild/bbs-3.22-bioc/meat/SeqVarTools.Rcheck/00check.log' for details.
SeqVarTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL SeqVarTools ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'SeqVarTools' ... ** this is package 'SeqVarTools' version '1.47.0' ** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" Copyright (C) 2025 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 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: Seqinfo > 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: F:\biocbuild\bbs-3.22-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 starting worker pid=41128 on localhost:11207 at 07:52:51.129 starting worker pid=121312 on localhost:11207 at 07:52:51.134 starting worker pid=43220 on localhost:11207 at 07:52:51.145 starting worker pid=68172 on localhost:11207 at 07:52:51.173 starting worker pid=140532 on localhost:11207 at 07:52:51.190 starting worker pid=111512 on localhost:11207 at 07:52:51.202 starting worker pid=62100 on localhost:11207 at 07:52:51.228 starting worker pid=131512 on localhost:11207 at 07:52:51.229 starting worker pid=102916 on localhost:11207 at 07:52:51.240 starting worker pid=28296 on localhost:11207 at 07:52:51.287 starting worker pid=115872 on localhost:11207 at 07:52:51.327 starting worker pid=124024 on localhost:11207 at 07:52:51.394 starting worker pid=97312 on localhost:11207 at 07:52:51.421 starting worker pid=98392 on localhost:11207 at 07:52:51.440 starting worker pid=15004 on localhost:11207 at 07:52:51.443 starting worker pid=44532 on localhost:11207 at 07:52:51.445 starting worker pid=20552 on localhost:11207 at 07:52:51.448 starting worker pid=96320 on localhost:11207 at 07:52:51.461 starting worker pid=3200 on localhost:11207 at 07:52:51.491 starting worker pid=36576 on localhost:11207 at 07:52:51.509 starting worker pid=84740 on localhost:11207 at 07:52:51.512 starting worker pid=68656 on localhost:11207 at 07:52:51.515 starting worker pid=32936 on localhost:11207 at 07:52:51.512 starting worker pid=35300 on localhost:11207 at 07:52:51.525 starting worker pid=89968 on localhost:11207 at 07:52:51.530 starting worker pid=117800 on localhost:11207 at 07:52:51.532 starting worker pid=100032 on localhost:11207 at 07:52:51.550 starting worker pid=77048 on localhost:11207 at 07:52:51.552 starting worker pid=11008 on localhost:11207 at 07:52:51.648 starting worker pid=9144 on localhost:11207 at 07:52:51.651 starting worker pid=52472 on localhost:11207 at 07:52:51.660 starting worker pid=101024 on localhost:11207 at 07:53:01.811 starting worker pid=126396 on localhost:11207 at 07:53:01.852 starting worker pid=41976 on localhost:11207 at 07:53:01.895 starting worker pid=97104 on localhost:11207 at 07:53:01.896 starting worker pid=107448 on localhost:11207 at 07:53:01.961 starting worker pid=112496 on localhost:11207 at 07:53:02.067 starting worker pid=66596 on localhost:11207 at 07:53:02.085 starting worker pid=38856 on localhost:11207 at 07:53:02.098 starting worker pid=66936 on localhost:11207 at 07:53:02.149 starting worker pid=105328 on localhost:11207 at 07:53:02.159 starting worker pid=31968 on localhost:11207 at 07:53:02.159 starting worker pid=25364 on localhost:11207 at 07:53:02.178 starting worker pid=52036 on localhost:11207 at 07:53:02.227 starting worker pid=108588 on localhost:11207 at 07:53:02.227 starting worker pid=73776 on localhost:11207 at 07:53:02.229 starting worker pid=126992 on localhost:11207 at 07:53:02.231 starting worker pid=21284 on localhost:11207 at 07:53:02.234 starting worker pid=140276 on localhost:11207 at 07:53:02.238 starting worker pid=37064 on localhost:11207 at 07:53:02.246 starting worker pid=141672 on localhost:11207 at 07:53:02.254 starting worker pid=62992 on localhost:11207 at 07:53:02.256 starting worker pid=20204 on localhost:11207 at 07:53:02.260 starting worker pid=13584 on localhost:11207 at 07:53:02.261 starting worker pid=104544 on localhost:11207 at 07:53:02.264 starting worker pid=121716 on localhost:11207 at 07:53:02.271 starting worker pid=115060 on localhost:11207 at 07:53:02.277 starting worker pid=16708 on localhost:11207 at 07:53:02.277 starting worker pid=55940 on localhost:11207 at 07:53:02.290 starting worker pid=41620 on localhost:11207 at 07:53:02.301 starting worker pid=39500 on localhost:11207 at 07:53:02.309 starting worker pid=76732 on localhost:11207 at 07:53:02.463 starting worker pid=122520 on localhost:11207 at 07:53:20.789 starting worker pid=32092 on localhost:11207 at 07:53:20.822 starting worker pid=56308 on localhost:11207 at 07:53:20.881 starting worker pid=116272 on localhost:11207 at 07:53:20.962 starting worker pid=46356 on localhost:11207 at 07:53:20.973 starting worker pid=35640 on localhost:11207 at 07:53:20.979 starting worker pid=47440 on localhost:11207 at 07:53:21.091 starting worker pid=11392 on localhost:11207 at 07:53:21.154 starting worker pid=43568 on localhost:11207 at 07:53:21.158 starting worker pid=13764 on localhost:11207 at 07:53:21.179 starting worker pid=117928 on localhost:11207 at 07:53:21.192 starting worker pid=32564 on localhost:11207 at 07:53:21.193 starting worker pid=70176 on localhost:11207 at 07:53:21.199 starting worker pid=74764 on localhost:11207 at 07:53:21.199 starting worker pid=26640 on localhost:11207 at 07:53:21.216 starting worker pid=22252 on localhost:11207 at 07:53:21.224 starting worker pid=141456 on localhost:11207 at 07:53:21.240 starting worker pid=90436 on localhost:11207 at 07:53:21.241 starting worker pid=78332 on localhost:11207 at 07:53:21.249 starting worker pid=50760 on localhost:11207 at 07:53:21.253 starting worker pid=82968 on localhost:11207 at 07:53:21.254 starting worker pid=12012 on localhost:11207 at 07:53:21.259 starting worker pid=30672 on localhost:11207 at 07:53:21.266 starting worker pid=76076 on localhost:11207 at 07:53:21.277 starting worker pid=13496 on localhost:11207 at 07:53:21.281 starting worker pid=58344 on localhost:11207 at 07:53:21.286 starting worker pid=88284 on localhost:11207 at 07:53:21.291 starting worker pid=44424 on localhost:11207 at 07:53:21.295 starting worker pid=77740 on localhost:11207 at 07:53:21.304 starting worker pid=19932 on localhost:11207 at 07:53:21.328 starting worker pid=71360 on localhost:11207 at 07:53:21.427 starting worker pid=105640 on localhost:11207 at 07:53:30.853 starting worker pid=129424 on localhost:11207 at 07:53:30.884 starting worker pid=48260 on localhost:11207 at 07:53:30.948 starting worker pid=114684 on localhost:11207 at 07:53:30.995 starting worker pid=102976 on localhost:11207 at 07:53:31.027 starting worker pid=18408 on localhost:11207 at 07:53:31.057 starting worker pid=9292 on localhost:11207 at 07:53:31.083 starting worker pid=108440 on localhost:11207 at 07:53:31.101 starting worker pid=62712 on localhost:11207 at 07:53:31.110 starting worker pid=86852 on localhost:11207 at 07:53:31.115 starting worker pid=106520 on localhost:11207 at 07:53:31.165 starting worker pid=26012 on localhost:11207 at 07:53:31.165 starting worker pid=101108 on localhost:11207 at 07:53:31.182 starting worker pid=18804 on localhost:11207 at 07:53:31.184 starting worker pid=79164 on localhost:11207 at 07:53:31.200 starting worker pid=134012 on localhost:11207 at 07:53:31.205 starting worker pid=64684 on localhost:11207 at 07:53:31.205 starting worker pid=98180 on localhost:11207 at 07:53:31.220 starting worker pid=102300 on localhost:11207 at 07:53:31.226 starting worker pid=82544 on localhost:11207 at 07:53:31.242 starting worker pid=37692 on localhost:11207 at 07:53:31.269 starting worker pid=67064 on localhost:11207 at 07:53:31.306 starting worker pid=85260 on localhost:11207 at 07:53:31.319 starting worker pid=130772 on localhost:11207 at 07:53:31.359 starting worker pid=79360 on localhost:11207 at 07:53:31.395 starting worker pid=97472 on localhost:11207 at 07:53:31.397 starting worker pid=1540 on localhost:11207 at 07:53:31.406 starting worker pid=92984 on localhost:11207 at 07:53:31.454 starting worker pid=112148 on localhost:11207 at 07:53:31.461 starting worker pid=90668 on localhost:11207 at 07:53:31.466 starting worker pid=118740 on localhost:11207 at 07:53:31.482 starting worker pid=104112 on localhost:11207 at 07:53:49.493 starting worker pid=134028 on localhost:11207 at 07:53:49.274 starting worker pid=111184 on localhost:11207 at 07:53:49.518 starting worker pid=39332 on localhost:11207 at 07:53:49.565 starting worker pid=76084 on localhost:11207 at 07:53:49.571 starting worker pid=133312 on localhost:11207 at 07:53:49.599 starting worker pid=85256 on localhost:11207 at 07:53:49.624 starting worker pid=28476 on localhost:11207 at 07:53:49.633 starting worker pid=16884 on localhost:11207 at 07:53:49.633 starting worker pid=13420 on localhost:11207 at 07:53:49.636 starting worker pid=96876 on localhost:11207 at 07:53:49.711 starting worker pid=34256 on localhost:11207 at 07:53:49.736 starting worker pid=55868 on localhost:11207 at 07:53:49.741 starting worker pid=78432 on localhost:11207 at 07:53:49.781 starting worker pid=28812 on localhost:11207 at 07:53:49.871 starting worker pid=22504 on localhost:11207 at 07:53:49.896 starting worker pid=37528 on localhost:11207 at 07:53:49.898 starting worker pid=83252 on localhost:11207 at 07:53:49.904 starting worker pid=98148 on localhost:11207 at 07:53:49.911 starting worker pid=67068 on localhost:11207 at 07:53:49.935 starting worker pid=103680 on localhost:11207 at 07:53:49.936 starting worker pid=76564 on localhost:11207 at 07:53:49.940 starting worker pid=106676 on localhost:11207 at 07:53:49.954 starting worker pid=85464 on localhost:11207 at 07:53:49.978 starting worker pid=21924 on localhost:11207 at 07:53:49.979 starting worker pid=12008 on localhost:11207 at 07:53:49.991 starting worker pid=37456 on localhost:11207 at 07:53:50.001 starting worker pid=46156 on localhost:11207 at 07:53:50.006 starting worker pid=59904 on localhost:11207 at 07:53:50.015 starting worker pid=24968 on localhost:11207 at 07:53:50.021 starting worker pid=65696 on localhost:11207 at 07:53:50.064 # 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 Aug 15 07:54:12 2025 *********************************************** 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 28.57 2.34 106.64
SeqVarTools.Rcheck/SeqVarTools-Ex.timings
name | user | system | elapsed | |
Iterator-class | 0.72 | 0.00 | 0.72 | |
SeqVarData-class | 0.08 | 0.00 | 0.08 | |
allele-methods | 0.01 | 0.00 | 0.01 | |
alleleFrequency | 0.03 | 0.00 | 0.03 | |
alternateAlleleDetection | 0 | 0 | 0 | |
applyMethod | 0.25 | 0.05 | 0.30 | |
countSingletons | 0.02 | 0.00 | 0.01 | |
duplicateDiscordance | 0.17 | 0.00 | 0.17 | |
getGenotype | 0.02 | 0.03 | 0.05 | |
getVariableLengthData | 0 | 0 | 0 | |
heterozygosity | 0.17 | 0.00 | 0.17 | |
hwe | 0.06 | 0.02 | 0.08 | |
imputedDosage | 0.22 | 0.03 | 0.31 | |
inbreedCoeff | 0.17 | 0.00 | 0.18 | |
isSNV | 0.02 | 0.00 | 0.01 | |
isVariant | 0 | 0 | 0 | |
meanBySample | 0.03 | 0.01 | 0.05 | |
mendelErr | 0.01 | 0.00 | 0.01 | |
missingGenotypeRate | 0.04 | 0.00 | 0.03 | |
pca | 0.82 | 0.10 | 0.93 | |
pedigree | 0 | 0 | 0 | |
refFrac | 0.03 | 0.01 | 0.05 | |
regression | 0.11 | 0.02 | 0.12 | |
setVariantID | 0.00 | 0.02 | 0.05 | |
titv | 0.19 | 0.04 | 0.25 | |
variantInfo | 0.04 | 0.02 | 0.06 | |