Package: Risa

Version: 1.22.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Risa.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Risa_1.22.0.tar.gz

StartedAt: 2018-10-16 03:18:20 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 03:21:03 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 163.0 seconds

RetCode: 0

Status:  OK

CheckDir: Risa.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Risa.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Risa_1.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/Risa.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.22.0’
* 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 ‘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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
readISAtab                  49.884  2.416   0.146
processAssayXcmsSet         46.972  2.316  13.646
processAssayXcmsSet.1factor  0.136  0.136  13.405
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/Risa.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL Risa
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘Risa’ ...
** 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
* DONE (Risa)

name	user	system	elapsed
AssayTab-class	0.004	0.000	0.004
ISAtab-class	0.000	0.000	0.002
Risa-package	0.484	0.084	1.021
getAnnotatedDataFrameAssay	0.164	0.012	0.218
getExpressionSet	0.068	0.000	0.068
getMIAMEMetadata	0.084	0.000	0.083
getMSAssayFilenames	0.024	0.000	0.022
getMicroarrayAssayFilenames	0.048	0.016	0.065
getStudyFilename	0.024	0.000	0.021
isMSAssay	0.020	0.000	0.021
isMicroarrayAssay	0.072	0.000	0.069
processAssayXcmsSet.1factor	0.136	0.136	13.405
processAssayXcmsSet	46.972	2.316	13.646
readISAtab	49.884	2.416	0.146
updateAssayMetadata	0.076	0.008	0.082
write.assay.file	0.024	0.000	0.026
write.investigation.file	0.020	0.004	0.023
write.isatab	0.028	0.000	0.028
write.study.file	0.020	0.000	0.023