Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-02-18 02:29:19 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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

Package 2032/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
staRank 1.45.0  (landing page)
Juliane Siebourg
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/staRank
git_branch: devel
git_last_commit: 7d1bd94
git_last_commit_date: 2023-10-24 09:50:13 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for staRank on merida1


To the developers/maintainers of the staRank package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: staRank
Version: 1.45.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:staRank.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings staRank_1.45.0.tar.gz
StartedAt: 2024-02-17 11:21:30 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 11:27:46 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 375.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: staRank.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:staRank.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings staRank_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/staRank.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘staRank/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘staRank’ version ‘1.45.0’
* 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 ‘staRank’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'cellHTS2' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/staRank.Rcheck/00install.out’ for details.
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/staRank.Rcheck/00check.log’
for details.



Installation output

staRank.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘staRank’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'cellHTS2' is deprecated and will be removed from Bioconductor
  version 3.20 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'cellHTS2' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning: Package 'cellHTS2' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (staRank)

Tests output


Example timings

staRank.Rcheck/staRank-Ex.timings

nameusersystemelapsed
RankSummary-class0.1490.0060.181
aggregRank0.2250.0210.270
dataFormatRSA0.1850.0310.244
getRankmatrix0.2720.0240.358
getSampleScores-methods0.1670.0040.200
getStability0.1760.0040.202
mwTest2samp0.0010.0000.001
runRSA0.1750.0040.199
staRank-package0.1720.0050.201
stabilityRanking-methods0.7580.0080.901
summary-methods0.1670.0040.193
summaryStats-methods0.1650.0040.190
uniqueRSARanking0.1660.0030.194