BioC 3.4: CHECK report for Risa on zin1

Package: Risa

Version: 1.15.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.15.0.tar.gz

StartedAt: 2016-09-20 11:50:40 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 11:52:31 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 110.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Risa.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Risa.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Risa/DESCRIPTION’ ... OK
* this is package ‘Risa’ version ‘1.15.0’
* 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 ‘Risa’ 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 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
getPackagesInBiocView: no visible global function definition for ‘data’
readISAtabZip: no visible global function definition for ‘unzip’
suggestBiocPackage: no visible global function definition for
  ‘read.csv’
write.assay.file: no visible global function definition for
  ‘write.table’
write.investigation.file: no visible global function definition for
  ‘write.table’
write.study.file: no visible global function definition for
  ‘write.table’
initialize,ISATab: no visible global function definition for
  ‘count.fields’
initialize,ISATab: no visible global function definition for
  ‘read.table’
initialize,ISATab : <anonymous>: no visible global function definition
  for ‘read.table’
initialize,ISATab : <anonymous> : <anonymous>: no visible global
  function definition for ‘read.table’
initialize,ISATab: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  count.fields data na.omit read.csv read.table unzip write.table
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "count.fields", "data", "read.csv", "read.table",
             "unzip", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'AssayTab,ANY,ANY,ANY'
  generic '[' and siglist 'ISATab,ANY,ANY,ANY'
  generic '[<-' and siglist 'AssayTab,ANY,ANY,ANY'
  generic '[<-' and siglist 'ISATab,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU or elapsed time > 5s
                             user system elapsed
processAssayXcmsSet.1factor 0.056  0.016  11.196
processAssayXcmsSet         0.032  0.028  11.198
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/Risa.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
AssayTab-class	0.004	0.000	0.003
ISAtab-class	0.004	0.000	0.001
Risa-package	0.116	0.040	0.395
getAnnotatedDataFrameAssay	0.124	0.004	0.127
getExpressionSet	0.068	0.004	0.072
getMIAMEMetadata	0.084	0.004	0.090
getMSAssayFilenames	0.028	0.000	0.025
getMicroarrayAssayFilenames	0.072	0.000	0.074
getStudyFilename	0.024	0.000	0.024
isMSAssay	0.024	0.000	0.024
isMicroarrayAssay	0.068	0.004	0.117
processAssayXcmsSet.1factor	0.056	0.016	11.196
processAssayXcmsSet	0.032	0.028	11.198
readISAtab	0.052	0.056	0.318
updateAssayMetadata	0.076	0.004	0.080
write.assay.file	0.028	0.000	0.028
write.investigation.file	0.024	0.000	0.025
write.isatab	0.032	0.000	0.032
write.study.file	0.028	0.000	0.026