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This page was generated on 2025-08-09 12:05 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 1646/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QRscore 1.1.1  (landing page)
Fanding Zhou
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/QRscore
git_branch: devel
git_last_commit: 609b666
git_last_commit_date: 2025-06-19 23:43:25 -0400 (Thu, 19 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for QRscore on nebbiolo2

To the developers/maintainers of the QRscore package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QRscore.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: QRscore
Version: 1.1.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:QRscore.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings QRscore_1.1.1.tar.gz
StartedAt: 2025-08-09 01:39:07 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 01:41:11 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 123.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: QRscore.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:QRscore.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings QRscore_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/QRscore.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘QRscore/DESCRIPTION’ ... OK
* this is package ‘QRscore’ version ‘1.1.1’
* 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 ‘QRscore’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 code 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 loading without being on the library search path ... 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
.add_test_result: no visible binding for global variable ‘var’
.estimate_nb_parameters: no visible global function definition for
  ‘coef’
.extract_and_format_results: no visible global function definition for
  ‘p.adjust’
.fit_and_validate_zinb: no visible global function definition for
  ‘pchisq’
.fit_and_validate_zinb: no visible global function definition for
  ‘logLik’
.pairwise_tests: no visible global function definition for ‘var’
.qrscore_flex_one_sample: no visible global function definition for
  ‘setNames’
.run_qrscore_two_sample: no visible global function definition for
  ‘wilcox.test’
QRscore_ZINB_nSamples: no visible global function definition for
  ‘pchisq’
computeweight_disp: no visible global function definition for ‘var’
computeweight_mean: no visible global function definition for ‘var’
rank_x: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef logLik p.adjust pchisq runif setNames var wilcox.test
Consider adding
  importFrom("stats", "coef", "logLik", "p.adjust", "pchisq", "runif",
             "setNames", "var", "wilcox.test")
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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘QRscore.Rmd’ ‘fig1.jpg’
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
QRscoreGenetest 147.541  1.527   80.41
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/QRscore.Rcheck/00check.log’
for details.


Installation output

QRscore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL QRscore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘QRscore’ ...
** this is package ‘QRscore’ version ‘1.1.1’
** 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 (QRscore)

Tests output

QRscore.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(QRscore)
> 
> test_check("QRscore") 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
  9.866   0.357  10.214 

Example timings

QRscore.Rcheck/QRscore-Ex.timings

nameusersystemelapsed
QRscoreGenetest147.541 1.527 80.410
QRscoreTest0.0970.0110.109
QRscore_Flex0.0440.0000.044
QRscore_ZINB0.9800.0851.065
QRscore_ZINB_nSamples0.0620.0060.067
computeweight_disp0.0020.0000.002
computeweight_mean0.0010.0010.000
example_dataset0.0220.0050.027
example_dataset_raw_3000_genes0.1770.0150.192
getCompositionPValue0.0110.0010.011
rank_x0.0010.0000.001
rzinbinom000