BioC 3.4: CHECK report for Risa on morelia

Package: Risa

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Risa_1.16.0.tar.gz

StartedAt: 2017-04-15 07:22:44 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 07:26:32 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 227.9 seconds

RetCode: 0

Status:  OK

CheckDir: Risa.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Risa_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Risa.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 ‘Risa/DESCRIPTION’ ... OK
* this is package ‘Risa’ version ‘1.16.0’
* 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 loading without being on the library search path ... 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 ... 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
Examples with CPU or elapsed time > 5s
                             user system elapsed
Risa-package                0.143  0.125  18.363
readISAtab                  0.090  0.122   9.480
processAssayXcmsSet.1factor 0.082  0.022  17.057
processAssayXcmsSet         0.064  0.030  15.193
* 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 NOTE
See
  ‘/Users/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	0.001	0.005
ISAtab-class	0.002	0.000	0.003
Risa-package	0.143	0.125	18.363
getAnnotatedDataFrameAssay	0.125	0.016	1.512
getExpressionSet	0.073	0.012	0.760
getMIAMEMetadata	0.103	0.012	0.813
getMSAssayFilenames	0.045	0.003	0.334
getMicroarrayAssayFilenames	0.074	0.014	0.949
getStudyFilename	0.035	0.000	0.036
isMSAssay	0.041	0.000	0.041
isMicroarrayAssay	0.063	0.012	0.993
processAssayXcmsSet.1factor	0.082	0.022	17.057
processAssayXcmsSet	0.064	0.030	15.193
readISAtab	0.090	0.122	9.480
updateAssayMetadata	0.101	0.017	0.118
write.assay.file	0.039	0.003	0.139
write.investigation.file	0.038	0.001	0.055
write.isatab	0.047	0.003	0.118
write.study.file	0.031	0.003	0.080