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This page was generated on 2023-02-04 11:05:13 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 singscore on nebbiolo1


To the developers/maintainers of the singscore package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/singscore.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 1879/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
singscore 1.19.0  (landing page)
Dharmesh D. Bhuva
Snapshot Date: 2023-02-03 14:00:22 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/singscore
git_branch: master
git_last_commit: 12a6f26
git_last_commit_date: 2022-11-01 11:17:48 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: singscore
Version: 1.19.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:singscore.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings singscore_1.19.0.tar.gz
StartedAt: 2023-02-04 00:03:42 -0500 (Sat, 04 Feb 2023)
EndedAt: 2023-02-04 00:08:03 -0500 (Sat, 04 Feb 2023)
EllapsedTime: 261.0 seconds
RetCode: 0
Status:   OK  
CheckDir: singscore.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:singscore.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings singscore_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/singscore.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘singscore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singscore’ version ‘1.19.0’
* 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 ...
  ‘singscore.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/singscore.Rcheck/00check.log’
for details.



Installation output

singscore.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL singscore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 19.612   0.888  20.491 

Example timings

singscore.Rcheck/singscore-Ex.timings

nameusersystemelapsed
generateNull3.6400.0843.724
getPvals0.0690.0000.069
getStableGenes0.7080.0880.795
multiScore0.0170.0000.017
plotDispersion0.8900.0720.962
plotNull0.6630.0240.688
plotRankDensity0.3620.0080.370
plotScoreLandscape0.1520.0000.152
rankGenes0.0710.0000.071
simpleScore0.0070.0000.007