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This page was generated on 2021-10-15 15:05:50 -0400 (Fri, 15 Oct 2021).

CHECK results for Risa on nebbiolo1

To the developers/maintainers of the Risa package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Risa.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1587/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.34.0  (landing page)
Alejandra Gonzalez-Beltran
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Risa
git_branch: RELEASE_3_13
git_last_commit: 681a687
git_last_commit_date: 2021-05-19 11:53:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Risa
Version: 1.34.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Risa.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Risa_1.34.0.tar.gz
StartedAt: 2021-10-14 11:20:27 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:24:13 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 225.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Risa.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:Risa.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings Risa_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/Risa.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.34.0’
* 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 (user + system) or elapsed time > 5s
                              user system elapsed
readISAtab                  41.082  4.178   0.210
processAssayXcmsSet.1factor 38.299  4.441  17.075
processAssayXcmsSet         26.589  2.996  15.070
* 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-3.13-bioc/meat/Risa.Rcheck/00check.log’
for details.



Installation output

Risa.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Risa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/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-class0.0050.0000.005
ISAtab-class0.0020.0000.002
Risa-package0.4190.1450.584
getAnnotatedDataFrameAssay0.1150.0160.134
getExpressionSet0.0670.0150.082
getMIAMEMetadata0.0930.0120.105
getMSAssayFilenames0.0260.0040.030
getMicroarrayAssayFilenames0.0880.0080.095
getStudyFilename0.0200.0000.019
isMSAssay0.0180.0000.019
isMicroarrayAssay0.0630.0000.062
processAssayXcmsSet.1factor38.299 4.44117.075
processAssayXcmsSet26.589 2.99615.070
readISAtab41.082 4.178 0.210
updateAssayMetadata0.0490.0280.077
write.assay.file0.020.000.02
write.investigation.file0.0150.0040.018
write.isatab0.0130.0080.021
write.study.file0.0170.0000.018