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This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1937/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singscore 1.20.0  (landing page)
Malvika Kharbanda
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/singscore
git_branch: RELEASE_3_17
git_last_commit: 9638adf
git_last_commit_date: 2023-04-25 11:01:47 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for singscore on kjohnson2


To the developers/maintainers of the singscore package:
- 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: singscore
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singscore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singscore_1.20.0.tar.gz
StartedAt: 2023-10-19 01:50:07 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 01:57:45 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 457.7 seconds
RetCode: 0
Status:   OK  
CheckDir: singscore.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:singscore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings singscore_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/singscore.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘singscore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singscore’ version ‘1.20.0’
* package encoding: UTF-8
* 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 ‘singscore’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
 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
plotDispersion: no visible binding for global variable ‘Score’
plotDispersion: no visible binding for global variable ‘Dispersion’
plotDispersion: no visible binding for global variable ‘Class’
plotDispersion: no visible binding for global variable ‘SampleText’
plotDispersion: no visible binding for global variable ‘SampleLabel’
plotRankDensity_intl: no visible binding for global variable ‘Ranks’
plotRankDensity_intl: no visible binding for global variable ‘upDown’
plotRankDensity_intl: no visible binding for global variable
  ‘..density..’
plotRankDensity_intl: no visible binding for global variable ‘EntrezID’
plotScoreLandscape: no visible binding for global variable ‘sc1’
plotScoreLandscape: no visible binding for global variable ‘sc2’
projectScoreLandscape: no visible binding for global variable
  ‘SampleText’
projectScoreLandscape: no visible binding for global variable ‘Class’
projectScoreLandscape: no visible binding for global variable
  ‘SampleLabel’
Undefined global functions or variables:
  ..density.. Class Dispersion EntrezID Ranks SampleLabel SampleText
  Score sc1 sc2 upDown
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/singscore.Rcheck/00check.log’
for details.



Installation output

singscore.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘singscore’ ...
** using staged installation
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (singscore)

Tests output

singscore.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(singscore)
> 
> test_check("singscore")
[ FAIL 0 | WARN 41 | SKIP 0 | PASS 143 ]

[ FAIL 0 | WARN 41 | SKIP 0 | PASS 143 ]
> 
> proc.time()
   user  system elapsed 
 21.340   0.833  39.869 

Example timings

singscore.Rcheck/singscore-Ex.timings

nameusersystemelapsed
generateNull2.6040.0394.448
getPvals0.0890.0030.161
getStableGenes0.8030.0491.641
multiScore0.0200.0010.036
plotDispersion1.0610.1072.051
plotNull0.7300.0261.317
plotRankDensity0.4020.0080.707
plotScoreLandscape0.1430.0030.244
rankGenes0.0890.0020.154
simpleScore0.0070.0010.018