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CHECK report for flowBeads on malbec1

This page was generated on 2019-04-16 11:50:04 -0400 (Tue, 16 Apr 2019).

Package 524/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowBeads 1.20.1
Nikolas Pontikos
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/flowBeads
Branch: RELEASE_3_8
Last Commit: f1f1b24
Last Changed Date: 2019-01-04 13:31:32 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowBeads
Version: 1.20.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:flowBeads.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings flowBeads_1.20.1.tar.gz
StartedAt: 2019-04-15 23:55:42 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:56:31 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 49.0 seconds
RetCode: 0
Status:  OK 
CheckDir: flowBeads.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:flowBeads.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings flowBeads_1.20.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/flowBeads.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowBeads/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowBeads’ version ‘1.20.1’
* 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 ‘flowBeads’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘rrcov’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rrcov’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘methods’ ‘rrcov’
  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
BeadFlowFrame: no visible binding for global variable ‘filename’
BeadFlowFrame: no visible global function definition for ‘read.csv2’
BeadFlowFrame: no visible global function definition for ‘new’
mefTransform: no visible global function definition for ‘new’
absoluteNormalise,GatedBeadFlowFrame-data.frame: no visible global
  function definition for ‘lm’
gateBeads,BeadFlowFrame: no visible global function definition for ‘as’
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for ‘quantile’
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for ‘kmeans’
gateBeads,BeadFlowFrame : <anonymous>: no visible global function
  definition for ‘median’
gateBeads,BeadFlowFrame: no visible binding for global variable ‘sd’
gateBeads,BeadFlowFrame: no visible global function definition for ‘lm’
plot,BeadFlowFrame-character: no visible global function definition for
  ‘par’
plot,BeadFlowFrame-character: no visible global function definition for
  ‘hist’
plot,BeadFlowFrame-character: no visible global function definition for
  ‘segments’
plot,BeadFlowFrame-character: no visible global function definition for
  ‘title’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘par’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘hist’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘abline’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘segments’
plot,GatedBeadFlowFrame-character: no visible global function
  definition for ‘title’
relativeNormalise,GatedBeadFlowFrame-GatedBeadFlowFrame: no visible
  global function definition for ‘lm’
Undefined global functions or variables:
  abline as filename hist kmeans lm median new par quantile read.csv2
  sd segments title
Consider adding
  importFrom("graphics", "abline", "hist", "par", "segments", "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "kmeans", "lm", "median", "quantile", "sd")
  importFrom("utils", "read.csv2")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/flowBeads.Rcheck/00check.log’
for details.



Installation output

flowBeads.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL flowBeads
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘flowBeads’ ...
** R
** data
** inst
** 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 (flowBeads)

Tests output


Example timings

flowBeads.Rcheck/flowBeads-Ex.timings

nameusersystemelapsed
gateBeads-methods0.5840.0200.623