BioC 3.4: CHECK report for ibh on malbec1

Package: ibh

Version: 1.22.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ibh_1.22.0.tar.gz

StartedAt: 2017-04-14 23:14:57 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:15:13 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 15.9 seconds

RetCode: 0

Status:  OK

CheckDir: ibh.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ibh_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ibh.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ibh/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ibh’ version ‘1.22.0’
* 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 ‘ibh’ 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 ... NOTE
Package in Depends field not imported from: ‘simpIntLists’
  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
ibhBioGRID: no visible global function definition for
  ‘findInteractionList’
ibhForMultipleGeneListsBioGRID: no visible global function definition
  for ‘findInteractionList’
readDirectedInteractionsFromCsv: no visible global function definition
  for ‘read.csv’
readUndirectedInteractionsFromCsv: no visible global function
  definition for ‘read.csv’
Undefined global functions or variables:
  findInteractionList read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/ibh.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
findEntry	0.016	0.004	0.034
ibh-package	1.264	0.016	1.277
ibh	0.008	0.000	0.008
ibhBioGRID	0.280	0.000	0.279
ibhClusterEval	0.344	0.004	0.348
ibhClusterEvalBioGRID	0.596	0.004	0.598
ibhForMultipleGeneLists	0.012	0.000	0.010
ibhForMultipleGeneListsBioGRID	0.176	0.000	0.177
readDirectedInteractionsFromCsv	0	0	0
readUndirectedInteractionsFromCsv	0	0	0