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CHECK report for Risa on malbec2

This page was generated on 2018-10-17 08:24:36 -0400 (Wed, 17 Oct 2018).

Package 1246/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.22.0
Alejandra Gonzalez-Beltran
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Risa
Branch: RELEASE_3_7
Last Commit: 3b5358d
Last Changed Date: 2018-04-30 10:35:27 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### Running 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
###
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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.



Installation output

Risa.Rcheck/00install.out

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

Tests output


Example timings

Risa.Rcheck/Risa-Ex.timings

nameusersystemelapsed
AssayTab-class0.0040.0000.004
ISAtab-class0.0000.0000.002
Risa-package0.4840.0841.021
getAnnotatedDataFrameAssay0.1640.0120.218
getExpressionSet0.0680.0000.068
getMIAMEMetadata0.0840.0000.083
getMSAssayFilenames0.0240.0000.022
getMicroarrayAssayFilenames0.0480.0160.065
getStudyFilename0.0240.0000.021
isMSAssay0.0200.0000.021
isMicroarrayAssay0.0720.0000.069
processAssayXcmsSet.1factor 0.136 0.13613.405
processAssayXcmsSet46.972 2.31613.646
readISAtab49.884 2.416 0.146
updateAssayMetadata0.0760.0080.082
write.assay.file0.0240.0000.026
write.investigation.file0.0200.0040.023
write.isatab0.0280.0000.028
write.study.file0.0200.0000.023