CHECK report for CrispRVariants on celaya2
This page was generated on 2020-01-09 13:52:06 -0500 (Thu, 09 Jan 2020).
CrispRVariants 1.15.0
Helen Lindsay
| Snapshot Date: 2020-01-08 16:46:10 -0500 (Wed, 08 Jan 2020) |
| URL: https://git.bioconductor.org/packages/CrispRVariants |
| Branch: master |
| Last Commit: d7bf5eb |
| Last Changed Date: 2019-10-29 13:40:16 -0500 (Tue, 29 Oct 2019) |
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
Summary
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CrispRVariants_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CrispRVariants.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.15.0’
* 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 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 12.967 0.340 13.520
CrisprSet-class 10.724 0.279 11.566
readsToTarget 7.933 0.111 8.070
mergeCrisprSets 7.865 0.064 8.087
* 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-3.11-bioc/meat/CrispRVariants.Rcheck/00check.log’
for details.
Installation output
CrispRVariants.Rcheck/00install.out
Tests output
CrispRVariants.Rcheck/tests/testthat.Rout
Example timings
CrispRVariants.Rcheck/CrispRVariants-Ex.timings