Package: flowMap

Version: 1.16.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flowMap_1.16.0.tar.gz

StartedAt: 2018-04-11 23:30:08 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 23:30:51 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 43.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowMap.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings flowMap_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/flowMap.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMap’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘ade4’ ‘doParallel’ ‘abind’ ‘reshape2’ ‘scales’ ‘Matrix’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘flowMap’ can be installed ... OK
* checking installed package size ... OK
* 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 ... WARNING
'library' or 'require' call not declared from: ‘igraph’
'library' or 'require' call to ‘Matrix’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘igraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘abind’ ‘ade4’ ‘doParallel’ ‘methods’ ‘reshape2’ ‘scales’
  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
getFR: no visible global function definition for ‘dist’
getFR: no visible global function definition for ‘pnorm’
getFRest: no visible global function definition for ‘detectCores’
getFRest: no visible global function definition for
  ‘registerDoParallel’
getFRest: no visible global function definition for ‘%dopar%’
getFRest: no visible global function definition for ‘foreach’
getFRest: no visible binding for global variable ‘i’
getFRest: no visible global function definition for ‘new’
makeDistmat: no visible global function definition for ‘forceSymmetric’
makeFRMST: no visible global function definition for ‘dist’
makeFRMST: no visible global function definition for ‘as.dist’
makeFRMST: no visible global function definition for ‘graph.adjacency’
makeFRMST: no visible global function definition for
  ‘set.edge.attribute’
makeFRMST: no visible global function definition for ‘E’
makeFRMST: no visible global function definition for ‘E<-’
makeFRMST: no visible global function definition for ‘V’
makeFRMST: no visible global function definition for ‘V<-’
makeFRMST: no visible global function definition for ‘pnorm’
statCrossLists: no visible global function definition for ‘abind’
Undefined global functions or variables:
  %dopar% E E<- V V<- abind as.dist detectCores dist forceSymmetric
  foreach graph.adjacency i new pnorm registerDoParallel
  set.edge.attribute
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.dist", "dist", "pnorm")
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 ... WARNING
Undocumented arguments in documentation object 'getFRest'
  ‘ncores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘gplots’
* 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 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/flowMap.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
frstats-class	0.000	0.000	0.001
getFR	0.000	0.000	0.001
getFRest	0	0	0