BioC 3.4: CHECK report for spotSegmentation on malbec1

Package: spotSegmentation

Version: 1.48.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings spotSegmentation_1.48.0.tar.gz

StartedAt: 2017-04-15 01:27:44 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:28:08 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 23.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: spotSegmentation.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings spotSegmentation_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/spotSegmentation.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 ‘spotSegmentation/DESCRIPTION’ ... OK
* this is package ‘spotSegmentation’ version ‘1.48.0’
* 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 ‘spotSegmentation’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... WARNING
Subdirectory ‘inst’ contains no files.
* 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 ... NOTE
Package in Depends field not imported from: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot.spotseg : plotSpotImage: no visible global function definition for
  ‘par’
plot.spotseg : plotSpotImage: no visible global function definition for
  ‘image’
plot.spotseg: no visible global function definition for ‘postscript’
plotBlockImage: no visible global function definition for ‘par’
plotBlockImage: no visible global function definition for ‘image’
plotBlockImage: no visible global function definition for ‘gray’
spotgrid : spotgridPeaks: no visible global function definition for
  ‘runif’
spotgrid : spotgridPeaks: no visible global function definition for
  ‘embed’
spotgrid: no visible global function definition for ‘contour’
spotseg : spotseg1 : plotSpotImage: no visible global function
  definition for ‘par’
spotseg : spotseg1 : plotSpotImage: no visible global function
  definition for ‘image’
spotseg : spotseg1: no visible global function definition for
  ‘mclustBIC’
spotseg : spotseg1: no visible global function definition for ‘hcE’
spotseg : spotseg1: no visible global function definition for ‘frame’
spotseg: no visible global function definition for ‘par’
spotseg: no visible global function definition for ‘median’
Undefined global functions or variables:
  contour embed frame gray hcE image mclustBIC median par postscript
  runif
Consider adding
  importFrom("grDevices", "gray", "postscript")
  importFrom("graphics", "contour", "frame", "image", "par")
  importFrom("stats", "embed", "median", "runif")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: plot.spotseg.Rd:23: Dropping empty section \author
prepare_Rd: plotBlockImage.Rd:20: Dropping empty section \author
prepare_Rd: spotgrid.Rd:21: Dropping empty section \details
prepare_Rd: spotgrid.Rd:33: Dropping empty section \note
prepare_Rd: spotgrid.Rd:34: Dropping empty section \author
prepare_Rd: spotseg.Rd:45: Dropping empty section \author
prepare_Rd: summary.spotseg.Rd:27: Dropping empty section \author
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/spotSegmentation.Rcheck/00check.log’
for details.

* installing *source* package ‘spotSegmentation’ ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spotSegmentation)

name	user	system	elapsed
plot.spotseg	2.588	0.004	2.595
plotBlockImage	0.156	0.000	0.156
spotgrid	0.136	0.000	0.137
spotseg	2.548	0.004	2.551
summary.spotseg	2.432	0.000	2.432