BioC 3.1: CHECK report for spotSegmentation on petty

Package: spotSegmentation

Version: 1.42.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spotSegmentation_1.42.0.tar.gz

StartedAt: 2015-10-09 02:11:59 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:12:42 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 42.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: spotSegmentation.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings spotSegmentation_1.42.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/spotSegmentation.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spotSegmentation/DESCRIPTION’ ... OK
* this is package ‘spotSegmentation’ version ‘1.42.0’
* 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 ... [2s/2s] 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
spotseg : spotseg1: no visible global function definition for
  ‘mclustBIC’
spotseg : spotseg1: no visible global function definition for ‘hcE’
* 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 ... [18s/18s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
spotseg         5.633  0.033   5.676
plot.spotseg    5.578  0.046   5.635
summary.spotseg 5.591  0.033   5.630
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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	5.578	0.046	5.635
plotBlockImage	0.292	0.022	0.318
spotgrid	0.276	0.019	0.299
spotseg	5.633	0.033	5.676
summary.spotseg	5.591	0.033	5.630