CHECK report for CrispRVariants on malbec2
This page was generated on 2019-04-09 11:44:25 -0400 (Tue, 09 Apr 2019).
CrispRVariants 1.11.1
Helen Lindsay
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CrispRVariants |
| Branch: master |
| Last Commit: 683dfe2 |
| Last Changed Date: 2019-01-04 13:27:29 -0400 (Fri, 04 Jan 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 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 | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
Summary
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CrispRVariants.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CrispRVariants_1.11.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CrispRVariants.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.11.1’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotVariants 6.601 0.020 6.818
mergeCrisprSets 5.321 0.004 5.325
* 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
‘/home/biocbuild/bbs-3.9-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