Package: Risa

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Risa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Risa_1.26.0.tar.gz

StartedAt: 2019-10-16 06:16:46 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:21:40 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 293.9 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 --install=check:Risa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Risa_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Risa.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Risa/DESCRIPTION’ ... OK
* this is package ‘Risa’ version ‘1.26.0’
* 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 : : no visible global function definition
  for ‘read.table’
initialize,ISATab :  : : 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet         73.861 16.227  24.203
processAssayXcmsSet.1factor  2.069  0.179  24.412
* 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-3.9-bioc/meat/Risa.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Risa
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Risa’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Risa)

name	user	system	elapsed
AssayTab-class	0.009	0.003	0.011
ISAtab-class	0.003	0.001	0.004
Risa-package	1.019	0.426	1.499
getAnnotatedDataFrameAssay	0.248	0.044	0.303
getExpressionSet	0.098	0.033	0.133
getMIAMEMetadata	0.139	0.036	0.178
getMSAssayFilenames	0.049	0.004	0.053
getMicroarrayAssayFilenames	0.101	0.033	0.136
getStudyFilename	0.047	0.002	0.049
isMSAssay	0.045	0.001	0.046
isMicroarrayAssay	0.090	0.035	0.132
processAssayXcmsSet.1factor	2.069	0.179	24.412
processAssayXcmsSet	73.861	16.227	24.203
readISAtab	0.220	0.389	0.631
updateAssayMetadata	0.206	0.066	0.272
write.assay.file	0.049	0.009	0.058
write.investigation.file	0.070	0.013	0.084
write.isatab	0.058	0.013	0.070
write.study.file	0.063	0.011	0.074