Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:51 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
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 CrispRVariants package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CrispRVariants.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 418/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CrispRVariants 1.22.0 (landing page) Helen Lindsay
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: CrispRVariants |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CrispRVariants_1.22.0.tar.gz |
StartedAt: 2022-04-12 12:03:03 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 12:09:49 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 406.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CrispRVariants.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CrispRVariants_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CrispRVariants.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 ‘CrispRVariants/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CrispRVariants’ version ‘1.22.0’ * 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 ‘CrispRVariants’ 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 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 ... WARNING '::' or ':::' import not declared from: ‘SummarizedExperiment’ There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘indelLabels’ * 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 ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'arrangePlots': arrangePlots Code: function(top.plot, left.plot, right.plot, fig.height = NULL, col.wdth.ratio = c(2, 1), row.ht.ratio = c(1, 6), left.plot.margin = grid::unit(c(0.1, 0.2, 3, 0.2), "lines")) Docs: function(top.plot, left.plot, right.plot, fig.height = NULL, col.wdth.ratio = c(2, 1), row.ht.ratio = c(1, 6), left.plot.margin = grid::unit(c(0.1, 0, 3, 0.2), "lines")) Mismatches in argument default values: Name: 'left.plot.margin' Code: grid::unit(c(0.1, 0.2, 3, 0.2), "lines") Docs: grid::unit(c(0.1, 0, 3, 0.2), "lines") Codoc mismatches from documentation object 'indelLabels': indelLabels Code: function(alns, rc = FALSE, genome.to.pos = NULL, keep.ops = c("I", "D", "N"), regions = NULL, as.string = TRUE, ...) Docs: function(alns, rc = FALSE, genome.to.pos = NULL, keep.ops = c("I", "D", "N"), regions = NULL, ...) Argument names in code not in docs: as.string Mismatches in argument names: Position: 6 Code: as.string Docs: ... * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotVariants 10.551 0.101 10.738 CrisprSet-class 8.602 0.178 8.805 mergeCrisprSets 8.175 0.033 8.215 readsToTarget 6.071 0.026 6.100 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 See ‘/Users/biocbuild/bbs-3.14-bioc/meat/CrispRVariants.Rcheck/00check.log’ for details.
CrispRVariants.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CrispRVariants ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘CrispRVariants’ ... ** 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 (CrispRVariants)
CrispRVariants.Rcheck/tests/testthat.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. > library(testthat) > test_check("CrispRVariants") Loading required package: CrispRVariants Loading required package: ggplot2 [ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ] ══ Skipped tests ═══════════════════════════════════════════════════════════════ • empty test (1) [ FAIL 0 | WARN 0 | SKIP 1 | PASS 75 ] > > proc.time() user system elapsed 37.760 0.994 38.755
CrispRVariants.Rcheck/CrispRVariants-Ex.timings
name | user | system | elapsed | |
CrisprRun-class | 1.175 | 0.074 | 1.251 | |
CrisprSet-class | 8.602 | 0.178 | 8.805 | |
abifToFastq | 0.444 | 0.018 | 0.463 | |
alleles | 0.293 | 0.007 | 0.300 | |
alns | 0.186 | 0.008 | 0.194 | |
barplotAlleleFreqs | 2.065 | 0.046 | 2.114 | |
consensusSeqs | 0.764 | 0.036 | 0.800 | |
dispatchDots | 0.005 | 0.002 | 0.006 | |
findChimeras | 0.070 | 0.006 | 0.076 | |
getChimeras | 0.073 | 0.003 | 0.076 | |
indelCounts | 0.185 | 0.002 | 0.188 | |
intersperse | 0.000 | 0.001 | 0.001 | |
mergeCrisprSets | 8.175 | 0.033 | 8.215 | |
mutationEfficiency | 0.053 | 0.002 | 0.055 | |
narrowAlignments | 0.521 | 0.003 | 0.525 | |
plotAlignments | 1.190 | 0.008 | 1.202 | |
plotChimeras | 1.792 | 0.006 | 1.802 | |
plotFreqHeatmap | 0.375 | 0.002 | 0.377 | |
plotVariants | 10.551 | 0.101 | 10.738 | |
readsToTarget | 6.071 | 0.026 | 6.100 | |
selectAlnRegionsHelpers | 0.000 | 0.000 | 0.001 | |
variantCounts | 0.038 | 0.002 | 0.040 | |