Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:36:29 -0400 (Wed, 17 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 2219/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VariantTools 1.44.0 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the VariantTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantTools.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: VariantTools |
Version: 1.44.0 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings VariantTools_1.44.0.tar.gz |
StartedAt: 2024-04-16 05:05:34 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 05:11:55 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 380.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: VariantTools.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings VariantTools_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/VariantTools.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘VariantTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantTools’ version ‘1.44.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘VariantTools’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: doc 5.4Mb * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Initial release (start date: 12 September, 2012) * 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 loading without being on the library search path ... OK * checking dependencies in R code ... WARNING Missing or unexported object: ‘GenomicRanges::genome’ Unexported objects imported by ':::' calls: ‘BiocGenerics:::testPackage’ ‘IRanges:::unlist_as_integer’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE LowerFrequencyInOtherFilter : <anonymous>: no visible binding for global variable ‘control.alt.depth’ LowerFrequencyInOtherFilter : <anonymous>: no visible binding for global variable ‘control.total.depth’ ReadPositionTTestFilter : <anonymous>: no visible binding for global variable ‘read.pos.mean’ ReadPositionTTestFilter : <anonymous>: no visible binding for global variable ‘read.pos.mean.ref’ ReadPositionTTestFilter : <anonymous>: no visible binding for global variable ‘read.pos.var’ ReadPositionTTestFilter : <anonymous>: no visible binding for global variable ‘read.pos.var.ref’ ReadPositionTTestFilter : <anonymous>: no visible global function definition for ‘rawDepth’ StrandFETFilter : <anonymous>: no visible binding for global variable ‘count.plus.ref’ StrandFETFilter : <anonymous>: no visible binding for global variable ‘count.minus.ref’ StrandFETFilter : <anonymous>: no visible binding for global variable ‘count.plus’ StrandFETFilter : <anonymous>: no visible binding for global variable ‘count.minus’ calculateConcordanceMatrix: no visible binding for global variable ‘x’ caseControlFET: no visible binding for global variable ‘control.alt.depth’ caseControlFET: no visible binding for global variable ‘control.total.depth’ variantGR2Vcf: no visible global function definition for ‘variantGRangesIsDeprecated’ variantGR2Vcf: no visible global function definition for ‘makeVRangesFromVariantGRanges’ callVariants,GenomicRanges: no visible global function definition for ‘variantGRangesIsDeprecated’ callVariants,GenomicRanges: no visible global function definition for ‘variantGRangesToVRanges’ Undefined global functions or variables: control.alt.depth control.total.depth count.minus count.minus.ref count.plus count.plus.ref makeVRangesFromVariantGRanges rawDepth read.pos.mean read.pos.mean.ref read.pos.var read.pos.var.ref variantGRangesIsDeprecated variantGRangesToVRanges x * checking Rd files ... WARNING ./man/tallyVariants.Rd: non-ASCII input and no declared encoding problem found in ‘tallyVariants.Rd’ * 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 data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... NOTE The following directories should probably not be installed: ‘fig’ Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. * checking files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: 'applyPileups' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed callGenotypes 66.093 3.667 46.506 callSampleSpecificVariants 4.949 2.945 2.910 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘VariantTools_unit_tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘VariantTools.Rnw’... failed WARNING Errors in running code in vignettes: when running code in ‘VariantTools.Rnw’ ... > bam <- bams$H1993 > if (requireNamespace("gmapR", quietly = TRUE)) { + p53 <- gmapR:::exonsOnTP53Genome("TP53") + tally.param <- TallyVariantsParam(gmapR::TP53G .... [TRUNCATED] When sourcing ‘VariantTools.R’: Error: there is no package called ‘org.Hs.eg.db’ Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘VariantTools.Rnw’ using Sweave Loading required package: S4Vectors 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 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: GenomicRanges Loading required package: GenomeInfoDb Loading required package: VariantAnnotation Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: SummarizedExperiment 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")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Attaching package: ‘VariantAnnotation’ The following object is masked from ‘package:base’: tabulate Error: processing vignette 'VariantTools.Rnw' failed with diagnostics: chunk 2 (label = callVariants) Error in loadNamespace(x) : there is no package called ‘org.Hs.eg.db’ --- failed re-building ‘VariantTools.Rnw’ SUMMARY: processing the following file failed: ‘VariantTools.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 4 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/VariantTools.Rcheck/00check.log’ for details.
VariantTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL VariantTools ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘VariantTools’ ... ** using staged installation ** R ** data ** 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 (VariantTools)
VariantTools.Rcheck/tests/VariantTools_unit_tests.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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. > ##require("VariantTools") || stop("unable to load VariantTools package") > ##VariantTools:::.test() > > proc.time() user system elapsed 0.147 0.033 0.168
VariantTools.Rcheck/VariantTools-Ex.timings
name | user | system | elapsed | |
FilterConstructors | 1.735 | 0.204 | 1.941 | |
annnotateWithControlDepth | 0.291 | 0.052 | 0.343 | |
callGenotypes | 66.093 | 3.667 | 46.506 | |
callSampleSpecificVariants | 4.949 | 2.945 | 2.910 | |
callVariants | 2.543 | 1.430 | 1.395 | |
callWildtype | 0.291 | 0.048 | 0.339 | |
pileupVariants | 0.192 | 0.052 | 0.243 | |
postFilterVariants | 0.275 | 0.091 | 0.367 | |
qaVariants | 0.161 | 0.043 | 0.206 | |
tallyVariants | 2.160 | 1.417 | 1.154 | |
variantGR2Vcf | 0 | 0 | 0 | |
vignette | 0.011 | 0.004 | 0.015 | |