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BioC 3.6: CHECK report for esetVis on veracruz1

This page was generated on 2017-08-16 13:49:02 -0400 (Wed, 16 Aug 2017).

Package 421/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
esetVis 1.3.0
Laure Cougnaud
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/esetVis
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: esetVis
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings esetVis_1.3.0.tar.gz
StartedAt: 2017-08-16 02:49:52 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:52:06 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 133.8 seconds
RetCode: 0
Status:  OK 
CheckDir: esetVis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings esetVis_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/esetVis.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘esetVis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘esetVis’ version ‘1.3.0’
* 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 ‘esetVis’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
* 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
esetPlotWrapper: no visible global function definition for ‘:=’
esetPlotWrapper: no visible binding for global variable ‘fill’
getMethodsInputObjectEsetVis: no visible binding for global variable
  ‘rowData’
getMethodsInputObjectEsetVis: no visible binding for global variable
  ‘colData’
getMethodsInputObjectEsetVis: no visible binding for global variable
  ‘assay’
getMethodsInputObjectEsetVis : <anonymous>: no visible global function
  definition for ‘colData’
getMethodsInputObjectEsetVis : <anonymous>: no visible global function
  definition for ‘rowData’
Undefined global functions or variables:
  := assay colData fill rowData
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
getGeneSetsForPlot 42.306  3.981  47.656
esetLda             5.834  0.143   6.157
esetPlotWrapper     5.150  0.247   5.554
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/esetVis.Rcheck/00check.log’
for details.


esetVis.Rcheck/00install.out:

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

esetVis.Rcheck/esetVis-Ex.timings:

nameusersystemelapsed
esetLda5.8340.1436.157
esetPlotWrapper5.1500.2475.554
esetSpectralMap3.6400.2153.969
esetTsne3.8700.0934.099
getGeneSetsForPlot42.306 3.98147.656