Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-18 11:08:34 -0400 (Thu, 18 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4379
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4161
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4169
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Risa on lconway


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? 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 1655/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.39.0  (landing page)
Alejandra Gonzalez-Beltran
Snapshot Date: 2022-08-17 14:00:04 -0400 (Wed, 17 Aug 2022)
git_url: https://git.bioconductor.org/packages/Risa
git_branch: master
git_last_commit: e897873
git_last_commit_date: 2022-04-26 11:12:03 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Risa
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Risa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Risa_1.39.0.tar.gz
StartedAt: 2022-08-17 22:14:53 -0400 (Wed, 17 Aug 2022)
EndedAt: 2022-08-17 22:18:38 -0400 (Wed, 17 Aug 2022)
EllapsedTime: 224.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Risa.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Risa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Risa_1.39.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/Risa.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Risa/DESCRIPTION’ ... OK
* this is package ‘Risa’ version ‘1.39.0’
* 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 (user + system) or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet         58.432  9.893  13.743
processAssayXcmsSet.1factor 24.330  3.788  15.493
readISAtab                  11.664  2.071   0.246
* 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-3.16-bioc/meat/Risa.Rcheck/00check.log’
for details.



Installation output

Risa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Risa
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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-class0.0030.0020.004
ISAtab-class0.0000.0010.002
Risa-package0.4980.2280.765
getAnnotatedDataFrameAssay0.0960.0320.132
getExpressionSet0.0440.0240.069
getMIAMEMetadata0.0580.0200.078
getMSAssayFilenames0.0150.0030.019
getMicroarrayAssayFilenames0.0520.0260.080
getStudyFilename0.6690.0040.677
isMSAssay0.0210.0020.022
isMicroarrayAssay0.0520.0280.083
processAssayXcmsSet.1factor24.330 3.78815.493
processAssayXcmsSet58.432 9.89313.743
readISAtab11.664 2.071 0.246
updateAssayMetadata0.0470.0210.067
write.assay.file0.0170.0040.020
write.investigation.file0.0160.0030.018
write.isatab0.0230.0060.036
write.study.file0.0170.0030.020