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This page was generated on 2021-10-15 15:06:54 -0400 (Fri, 15 Oct 2021).

CHECK results for staRank on machv2

To the developers/maintainers of the staRank package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/staRank.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 1853/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
staRank 1.34.0  (landing page)
Juliane Siebourg
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/staRank
git_branch: RELEASE_3_13
git_last_commit: 7703706
git_last_commit_date: 2021-05-19 11:52:29 -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: staRank
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:staRank.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings staRank_1.34.0.tar.gz
StartedAt: 2021-10-15 00:27:15 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:30:50 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 214.7 seconds
RetCode: 0
Status:   OK  
CheckDir: staRank.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:staRank.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings staRank_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/staRank.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘staRank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘staRank’ 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘staRank’ 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
OPIScore : <anonymous>: no visible global function definition for
  ‘phyper’
aggregRank : <anonymous>: no visible global function definition for
  ‘median’
mwTest2samp: no visible global function definition for ‘pwilcox’
mwTest2samp: no visible global function definition for ‘pnorm’
show,RankSummary: no visible global function definition for ‘head’
stabilityRanking,cellHTS: no visible global function definition for
  ‘channelNames’
stabilityRanking,cellHTS: no visible global function definition for
  ‘sampleNames’
stabilityRanking,cellHTS: no visible global function definition for
  ‘featureNames’
stabilityRanking,numeric: no visible global function definition for
  ‘avrgRank<-’
stabilityRanking,numeric: no visible global function definition for
  ‘cor’
summaryStats,list : <anonymous>: no visible global function definition
  for ‘median’
summaryStats,list : <anonymous>: no visible global function definition
  for ‘t.test’
summaryStats,matrix : <anonymous>: no visible global function
  definition for ‘median’
summaryStats,matrix : <anonymous>: no visible global function
  definition for ‘t.test’
Undefined global functions or variables:
  avrgRank<- channelNames cor featureNames head median phyper pnorm
  pwilcox sampleNames t.test
Consider adding
  importFrom("stats", "cor", "median", "phyper", "pnorm", "pwilcox",
             "t.test")
  importFrom("utils", "head")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/staRank.Rcheck/00check.log’
for details.



Installation output

staRank.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL staRank
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘staRank’ ...
** using staged installation
** R
** data
** 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 (staRank)

Tests output


Example timings

staRank.Rcheck/staRank-Ex.timings

nameusersystemelapsed
RankSummary-class0.1070.0070.114
aggregRank0.1950.0110.207
dataFormatRSA0.1210.0030.125
getRankmatrix0.1050.0040.108
getSampleScores-methods0.1220.0100.131
getStability0.1220.0130.136
mwTest2samp000
runRSA0.1320.0180.150
staRank-package0.1430.0100.154
stabilityRanking-methods0.1110.0020.113
summary-methods0.0940.0020.097
summaryStats-methods0.1020.0020.104
uniqueRSARanking0.0920.0040.096