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This page was generated on 2022-04-13 12:08:57 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 treekoR on machv2


To the developers/maintainers of the treekoR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/treekoR.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 1996/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treekoR 1.2.1  (landing page)
Adam Chan
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/treekoR
git_branch: RELEASE_3_14
git_last_commit: 71e2a0a
git_last_commit_date: 2022-02-10 20:36:57 -0400 (Thu, 10 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: treekoR
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:treekoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings treekoR_1.2.1.tar.gz
StartedAt: 2022-04-12 19:35:24 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:43:27 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 483.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: treekoR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:treekoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings treekoR_1.2.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/treekoR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘treekoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘treekoR’ version ‘1.2.1’
* 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 ‘treekoR’ 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
addFreqBars: no visible binding for global variable ‘freq’
addFreqBars: no visible binding for global variable ‘xmax’
addFreqBars: no visible binding for global variable ‘y’
addFreqBars: no visible binding for global variable ‘xmin’
addFreqBars: no visible binding for global variable ‘ymin’
addFreqBars: no visible binding for global variable ‘ymax’
addFreqBars: no visible binding for global variable ‘x_label’
addFreqBars: no visible binding for global variable ‘freq_label’
addHeatMap: no visible binding for global variable ‘variable’
addHeatMap: no visible binding for global variable ‘value’
addHeatMap: no visible binding for global variable ‘y’
addHeatMap: no visible binding for global variable ‘label’
addHeatMap: no visible binding for global variable ‘.’
addHeatMap: no visible binding for global variable ‘x’
colourTree: no visible binding for global variable ‘stat_parent’
colourTree: no visible binding for global variable ‘x’
colourTree: no visible binding for global variable ‘y’
colourTree: no visible binding for global variable ‘stat_total’
colourTree: no visible binding for global variable ‘label’
getCellGMeans: no visible binding for global variable ‘cluster_id’
getCellGMeans: no visible binding for global variable ‘sample_id’
getCellProp: no visible binding for global variable ‘cluster_id’
getCellProp: no visible binding for global variable ‘sample_id’
getCellProp: no visible binding for global variable ‘.’
getClusterTree: no visible binding for global variable ‘cluster_id’
plotInteractiveHeatmap: no visible binding for global variable ‘label’
plotInteractiveHeatmap: no visible binding for global variable ‘node’
plotSigScatter: no visible binding for global variable ‘stat_total’
plotSigScatter: no visible binding for global variable ‘stat_parent’
plotSigScatter: no visible binding for global variable ‘isTip’
plotSigScatter: no visible binding for global variable ‘label’
runEdgeRTests: no visible binding for global variable ‘PValue’
runEdgeRTests: no visible binding for global variable ‘logFC’
runEdgeRTests: no visible binding for global variable ‘node’
runEdgeRTests: no visible binding for global variable ‘stat_parent’
runEdgeRTests: no visible binding for global variable ‘pval_parent’
runEdgeRTests: no visible binding for global variable ‘FDR_parent’
runEdgeRTests: no visible binding for global variable ‘PValue_total’
runEdgeRTests: no visible binding for global variable ‘logFC_total’
runEdgeRTests: no visible binding for global variable ‘stat_total’
runEdgeRTests: no visible binding for global variable ‘pval_total’
runEdgeRTests: no visible binding for global variable ‘FDR_total’
runGLMMTests: no visible binding for global variable ‘isTip’
runGLMMTests: no visible binding for global variable ‘node’
Undefined global functions or variables:
  . FDR_parent FDR_total PValue PValue_total cluster_id freq freq_label
  isTip label logFC logFC_total node pval_parent pval_total sample_id
  stat_parent stat_total value variable x x_label xmax xmin y ymax ymin
* 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 ... WARNING
Undocumented arguments in documentation object 'runEdgeRTests'
  ‘pos_class_name’

Undocumented arguments in documentation object 'runGLMMTests'
  ‘pos_class_name’ ‘neg_class_name’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plotInteractiveHeatmap 6.330  0.214   6.824
colourTree             5.221  0.170   5.394
getCellGMeans          5.137  0.076   5.216
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/treekoR.Rcheck/00check.log’
for details.



Installation output

treekoR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘treekoR’ ...
** 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 (treekoR)

Tests output

treekoR.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(treekoR)
> 
> test_check("treekoR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
 39.080   1.224  40.317 

Example timings

treekoR.Rcheck/treekoR-Ex.timings

nameusersystemelapsed
DeBiasi_COVID_CD8_samp1.7090.1761.887
colourTree5.2210.1705.394
getCellGMeans5.1370.0765.216
getCellProp2.5040.0262.532
getClusterTree1.6720.0191.692
getTreeResults4.5470.0394.588
hopachToPhylo1.8050.0261.832
plotInteractiveHeatmap6.3300.2146.824
runHOPACH1.7810.0231.805
testTree3.8330.0353.870