Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:03 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2239/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VariantTools 1.48.0 (landing page) Michael Lawrence
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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: 1.48.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings VariantTools_1.48.0.tar.gz |
StartedAt: 2024-11-20 11:11:19 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 11:16:29 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 310.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: VariantTools.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:VariantTools.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings VariantTools_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/VariantTools.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘VariantTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘VariantTools’ version ‘1.48.0’ * 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 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 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 checkRd: (-1) callVariants.Rd:48: Lost braces 48 | \code{...}{Arguments for \code{VariantCallingFilters}, listed below.} | ^ ./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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed callGenotypes 49.614 16.637 49.676 callSampleSpecificVariants 3.373 4.674 2.959 * 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 5 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/VariantTools.Rcheck/00check.log’ for details.
VariantTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL VariantTools ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 0.098 0.041 0.125
VariantTools.Rcheck/VariantTools-Ex.timings
name | user | system | elapsed | |
FilterConstructors | 0.681 | 0.079 | 0.769 | |
annnotateWithControlDepth | 1.141 | 0.040 | 1.180 | |
callGenotypes | 49.614 | 16.637 | 49.676 | |
callSampleSpecificVariants | 3.373 | 4.674 | 2.959 | |
callVariants | 1.662 | 2.403 | 1.740 | |
callWildtype | 0.193 | 0.047 | 0.241 | |
pileupVariants | 0.131 | 0.308 | 0.438 | |
postFilterVariants | 0.193 | 0.030 | 0.223 | |
qaVariants | 0.126 | 0.024 | 0.151 | |
tallyVariants | 1.589 | 2.472 | 1.639 | |
variantGR2Vcf | 0 | 0 | 0 | |
vignette | 0.008 | 0.003 | 0.011 | |