BioC 3.4: CHECK report for domainsignatures on morelia

Package: domainsignatures

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings domainsignatures_1.34.0.tar.gz

StartedAt: 2017-04-15 01:14:21 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:16:01 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 100.5 seconds

RetCode: 0

Status:  OK

CheckDir: domainsignatures.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings domainsignatures_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/domainsignatures.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘domainsignatures/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘domainsignatures’ version ‘1.34.0’
* 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 ‘domainsignatures’ 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
'library' or 'require' call to ‘prada’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KEGG.db’ ‘biomaRt’ ‘methods’ ‘prada’
  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
compSimilarities: no visible global function definition for ‘progress’
compSimilarities: no visible global function definition for
  ‘killProgress’
compSimilarities: no visible global function definition for
  ‘updateProgress’
dataSource: no visible global function definition for ‘useMart’
dataSource: no visible global function definition for ‘getBM’
dataSource: no visible global function definition for ‘listLen’
dataSource: no visible global function definition for ‘new’
getKEGGdata: no visible binding for global variable ‘KEGGPATHID2EXTID’
getKEGGdata: no visible global function definition for ‘useMart’
getKEGGdata: no visible global function definition for ‘getBM’
getKEGGdata: no visible global function definition for ‘new’
getKEGGdescription: no visible binding for global variable
  ‘KEGGPATHID2NAME’
resampleGeneLists: no visible global function definition for ‘listLen’
sage.test: no visible global function definition for ‘pbinom’
sage.test: no visible global function definition for ‘chisq.test’
sage.test: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  KEGGPATHID2EXTID KEGGPATHID2NAME chisq.test dbinom getBM killProgress
  listLen new pbinom progress updateProgress useMart
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "chisq.test", "dbinom", "pbinom")
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 sizes of PDF files under ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/domainsignatures.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
dataSource	0.000	0.000	0.001
getKEGGdata	0.000	0.001	0.000
getKEGGdescription	0.018	0.002	0.067
gseDomain	0.000	0.000	0.001