DAPAR 1.9.5
Samuel Wieczorek
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DAPAR | | Last Changed Rev: 131109 / Revision: 131943 | | Last Changed Date: 2017-07-11 10:06:16 -0400 (Tue, 11 Jul 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DAPAR_1.9.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DAPAR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.9.5’
* 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 ‘DAPAR’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
boxPlotD_HC: no visible binding for global variable ‘iris’
corrMatrixD_HC: no visible global function definition for ‘tbl_df’
corrMatrixD_HC: no visible global function definition for ‘gather’
corrMatrixD_HC: no visible global function definition for ‘mutate’
corrMatrixD_HC: no visible global function definition for ‘left_join’
corrMatrixD_HC: no visible global function definition for ‘data_frame’
corrMatrixD_HC: no visible global function definition for ‘select_’
fudge2LRT: no visible binding for global variable ‘mad’
mvTypePlot_HC: no visible global function definition for ‘str’
Undefined global functions or variables:
data_frame gather iris left_join mad mutate select_ str tbl_df
Consider adding
importFrom("datasets", "iris")
importFrom("stats", "mad")
importFrom("utils", "str")
to your NAMESPACE file.
* checking Rd files ... WARNING
fudge2LRT.Rd: non-ASCII input and no declared encoding
problem found in ‘fudge2LRT.Rd’
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘CVDistD_HC’ ‘boxPlotD_HC’ ‘compareNormalizationD_HC’
‘corrMatrixD_HC’ ‘densityPlotD_HC’ ‘getPaletteForLabels_HC’
‘getPaletteForReplicates_HC’ ‘mvTypePlot_HC’ ‘proportionConRev_HC’
‘wrapper.CVDistD_HC’ ‘wrapper.boxPlotD_HC’
‘wrapper.compareNormalizationD_HC’ ‘wrapper.corrMatrixD_HC’
‘wrapper.densityPlotD_HC’ ‘wrapper.mvTypePlot_HC’
Undocumented data sets:
‘testWithoutNA’ ‘test’ ‘UPSpep25’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
wrapper.dapar.impute.mi 20.948 0.032 20.989
* 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, 1 NOTE
See
‘/home/biocbuild/bbs-3.6-bioc/meat/DAPAR.Rcheck/00check.log’
for details.