Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:59 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the VariantTools package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2041/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VariantTools 1.36.0 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: VariantTools |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantTools_1.36.0.tar.gz |
StartedAt: 2022-04-12 19:50:56 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 19:59:54 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 537.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: VariantTools.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VariantTools_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/VariantTools.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VariantTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantTools’ version ‘1.36.0’ * 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 ... 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 ... NOTE 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 sizes of PDF files under ‘inst/doc’ ... 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 174.120 4.635 110.404 callSampleSpecificVariants 12.885 3.881 6.261 callVariants 6.097 1.980 2.749 tallyVariants 6.016 1.944 2.490 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/VariantTools.Rcheck/00check.log’ for details.
VariantTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VariantTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 ‘VariantTools.Rnw’ ** 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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 0.249 0.065 0.291
VariantTools.Rcheck/VariantTools-Ex.timings
name | user | system | elapsed | |
FilterConstructors | 2.946 | 0.127 | 3.079 | |
annnotateWithControlDepth | 0.726 | 0.082 | 0.807 | |
callGenotypes | 174.120 | 4.635 | 110.404 | |
callSampleSpecificVariants | 12.885 | 3.881 | 6.261 | |
callVariants | 6.097 | 1.980 | 2.749 | |
callWildtype | 0.640 | 0.068 | 0.707 | |
pileupVariants | 0.398 | 0.059 | 0.463 | |
postFilterVariants | 0.525 | 0.052 | 0.577 | |
qaVariants | 0.348 | 0.040 | 0.389 | |
tallyVariants | 6.016 | 1.944 | 2.490 | |
variantGR2Vcf | 0.000 | 0.001 | 0.000 | |
vignette | 0.015 | 0.004 | 0.020 | |