BioC 3.4: CHECK report for RiboProfiling on malbec1

Package: RiboProfiling

Version: 1.4.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RiboProfiling_1.4.1.tar.gz

StartedAt: 2017-04-15 00:56:18 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:05:39 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 560.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RiboProfiling.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RiboProfiling_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RiboProfiling.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RiboProfiling/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RiboProfiling’ version ‘1.4.1’
* 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 ‘RiboProfiling’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
See ‘/home/biocbuild/bbs-3.4-bioc/meat/RiboProfiling.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... 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
applyShiftFeature: no visible global function definition for 'is'
aroundPromoter: no visible global function definition for 'is'
codonInfo: no visible global function definition for 'is'
countShiftReads: no visible global function definition for 'is'
histMatchLength: no visible global function definition for 'is'
orfRelativePos: no visible global function definition for 'is'
plotSummarizedCov: no visible global function definition for 'is'
readStartCov: no visible global function definition for 'is'
readsToStartOrEnd: no visible global function definition for 'is'
riboSeqFromBAM: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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
countsPlot      61.344  1.496  62.892
riboSeqFromBAM  53.808  1.224  55.041
orfRelativePos  33.576  0.352  33.950
countShiftReads 27.512  0.760  28.327
codonInfo       27.268  0.164  27.424
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/RiboProfiling.Rcheck/00check.log’
for details.

* installing *source* package ‘RiboProfiling’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’
* DONE (RiboProfiling)

name	user	system	elapsed
aroundPromoter	4.776	0.100	4.881
codonInfo	27.268	0.164	27.424
codonPCA	1.276	0.040	1.309
countShiftReads	27.512	0.760	28.327
countsPlot	61.344	1.496	62.892
histMatchLength	0.268	0.004	0.274
orfRelativePos	33.576	0.352	33.950
plotSummarizedCov	4.632	0.164	4.801
printPCA	1.816	0.080	1.886
readStartCov	3.236	0.036	3.281
readsToStartOrEnd	0.068	0.000	0.066
riboSeqFromBAM	53.808	1.224	55.041