Helen Lindsay
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CrispRVariants |
| git_branch: master |
| git_last_commit: d8ef937 |
| git_last_commit_date: 2021-10-26 12:24:29 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:17 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 424/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CrispRVariants 1.23.0 (landing page) Helen Lindsay
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CrispRVariants |
| Version: 1.23.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CrispRVariants.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CrispRVariants_1.23.0.tar.gz |
| StartedAt: 2022-03-17 18:50:12 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:54:17 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 245.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CrispRVariants.Rcheck |
| Warnings: 2 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CrispRVariants.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CrispRVariants_1.23.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CrispRVariants.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CrispRVariants/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CrispRVariants' version '1.23.0'
* 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 '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 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 6.46 0.17 6.63
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/CrispRVariants.Rcheck/00check.log'
for details.
CrispRVariants.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CrispRVariants
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
converting help for package 'CrispRVariants'
finding HTML links ... done
CrisprRun-class html
CrisprSet-class html
abifToFastq html
addClipped html
addCodonFrame html
alleleLabelsHelpers html
alleles html
alns html
annotateGenePlot html
arrangePlots html
barplotAlleleFreqs html
collapsePairs html
consensusSeqs html
dispatchDots html
excludeFromBam html
explodeCigarOpCombs html
findChimeras html
findSNVs html
getAxisCoords html
getChimeras html
getInsertionsTable html
gol_clutch1 html
indelCounts html
indelLabels html
intersperse html
makeAlignmentTilePlot html
mergeChimeras html
mergeCrisprSets html
mismatchLabels html
mutationEfficiency html
narrowAlignments html
plotAlignments html
plotChimeras html
plotFreqHeatmap html
plotVariants html
rcAlns html
readTargetBam html
readsByPCRPrimer html
readsToTarget html
refFromAlns html
reverseCigar html
rmMultiPCRChimera html
selectAlnRegionsHelpers html
selectOps html
seqsToAln html
setDNATileColours html
setMismatchTileColours html
transformAlnsToLong html
variantCounts html
writeFastq html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'ropls' is missing or broken
done
CrispRVariants.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
24.56 1.10 25.70
CrispRVariants.Rcheck/CrispRVariants-Ex.timings
| name | user | system | elapsed | |
| CrisprRun-class | 0.59 | 0.14 | 0.74 | |
| CrisprSet-class | 3.88 | 0.19 | 4.06 | |
| abifToFastq | 0.22 | 0.02 | 0.23 | |
| alleles | 0.09 | 0.00 | 0.10 | |
| alns | 0.16 | 0.00 | 0.15 | |
| barplotAlleleFreqs | 1.28 | 0.00 | 1.28 | |
| consensusSeqs | 0.41 | 0.00 | 0.41 | |
| dispatchDots | 0 | 0 | 0 | |
| findChimeras | 0.03 | 0.00 | 0.04 | |
| getChimeras | 0.03 | 0.00 | 0.03 | |
| indelCounts | 0.08 | 0.02 | 0.09 | |
| intersperse | 0 | 0 | 0 | |
| mergeCrisprSets | 4.34 | 0.03 | 4.39 | |
| mutationEfficiency | 0.02 | 0.02 | 0.03 | |
| narrowAlignments | 0.31 | 0.00 | 0.32 | |
| plotAlignments | 0.75 | 0.01 | 0.76 | |
| plotChimeras | 1.22 | 0.00 | 1.22 | |
| plotFreqHeatmap | 0.34 | 0.00 | 0.34 | |
| plotVariants | 6.46 | 0.17 | 6.63 | |
| readsToTarget | 3.95 | 0.03 | 3.98 | |
| selectAlnRegionsHelpers | 0 | 0 | 0 | |
| variantCounts | 0.05 | 0.00 | 0.05 | |