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CHECK report for spotSegmentation on merida1

This page was generated on 2019-04-16 11:54:14 -0400 (Tue, 16 Apr 2019).

Package 1499/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spotSegmentation 1.56.0
Chris Fraley
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/spotSegmentation
Branch: RELEASE_3_8
Last Commit: 20273de
Last Changed Date: 2018-10-30 11:41:42 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: spotSegmentation
Version: 1.56.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spotSegmentation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spotSegmentation_1.56.0.tar.gz
StartedAt: 2019-04-16 02:57:17 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:57:49 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 31.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: spotSegmentation.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:spotSegmentation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings spotSegmentation_1.56.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/spotSegmentation.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spotSegmentation/DESCRIPTION’ ... OK
* this is package ‘spotSegmentation’ version ‘1.56.0’
* 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 ... 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 ... 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘spotsegdoc.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/spotSegmentation.Rcheck/00check.log’
for details.



Installation output

spotSegmentation.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL spotSegmentation
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘spotSegmentation’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spotSegmentation)

Tests output


Example timings

spotSegmentation.Rcheck/spotSegmentation-Ex.timings

nameusersystemelapsed
plot.spotseg2.2690.0422.333
plotBlockImage0.1680.0130.183
spotgrid0.1560.0130.170
spotseg2.4030.0312.461
summary.spotseg2.3220.0272.362