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CHECK report for Risa on celaya2

This page was generated on 2019-04-09 13:05:48 -0400 (Tue, 09 Apr 2019).

Package 1355/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.25.0
Alejandra Gonzalez-Beltran
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Risa
Branch: master
Last Commit: cba25f9
Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: Risa
Version: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2019-04-09 05:00:14 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:05:14 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 299.3 seconds
RetCode: 0
Status:  OK 
CheckDir: Risa.Rcheck
Warnings: 0

Command output

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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_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Risa.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.25.0’
* 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 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.1factor 80.138 16.193  27.446
readISAtab                  77.492 16.920   0.999
processAssayXcmsSet          0.224  0.091  25.685
* 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.



Installation output

Risa.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output


Example timings

Risa.Rcheck/Risa-Ex.timings

nameusersystemelapsed
AssayTab-class0.0060.0030.008
ISAtab-class0.0030.0010.003
Risa-package0.9160.4111.386
getAnnotatedDataFrameAssay0.2840.0700.364
getExpressionSet0.0980.0360.147
getMIAMEMetadata0.1330.0260.162
getMSAssayFilenames0.0420.0030.044
getMicroarrayAssayFilenames0.0990.0360.191
getStudyFilename0.0530.0020.094
isMSAssay0.0520.0020.100
isMicroarrayAssay0.1130.0360.257
processAssayXcmsSet.1factor80.13816.19327.446
processAssayXcmsSet 0.224 0.09125.685
readISAtab77.49216.920 0.999
updateAssayMetadata0.1960.0690.265
write.assay.file0.0520.0080.060
write.investigation.file0.0550.0090.064
write.isatab0.0690.0160.084
write.study.file0.0640.0120.076