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CHECK report for spotSegmentation on malbec2

This page was generated on 2018-10-17 08:21:24 -0400 (Wed, 17 Oct 2018).

Package 1421/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spotSegmentation 1.54.0
Chris Fraley
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/spotSegmentation
Branch: RELEASE_3_7
Last Commit: 4545ded
Last Changed Date: 2018-04-30 10:35:01 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: spotSegmentation
Version: 1.54.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:spotSegmentation.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings spotSegmentation_1.54.0.tar.gz
StartedAt: 2018-10-16 03:59:01 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 03:59:23 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 22.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: spotSegmentation.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:spotSegmentation.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings spotSegmentation_1.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/spotSegmentation.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.54.0’
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/spotSegmentation.Rcheck/00check.log’
for details.



Installation output

spotSegmentation.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL spotSegmentation
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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.spotseg1.5240.0041.526
plotBlockImage0.1720.0080.177
spotgrid0.1280.0040.134
spotseg1.7720.0001.774
summary.spotseg1.5000.0001.501