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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 2204/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treekoR 1.12.0  (landing page)
Adam Chan
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/treekoR
git_branch: RELEASE_3_19
git_last_commit: 7408f62
git_last_commit_date: 2024-04-30 11:33:24 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for treekoR on nebbiolo1

To the developers/maintainers of the treekoR package:
- 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 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: treekoR
Version: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:treekoR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings treekoR_1.12.0.tar.gz
StartedAt: 2024-06-17 04:48:30 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 04:53:48 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 317.6 seconds
RetCode: 0
Status:   OK  
CheckDir: treekoR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:treekoR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings treekoR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/treekoR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘treekoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘treekoR’ version ‘1.12.0’
* 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 ‘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 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
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 ... 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’ ... 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/treekoR.Rcheck/00check.log’
for details.


Installation output

treekoR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL treekoR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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(treekoR)
> 
> test_check("treekoR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
 20.479   1.521  21.965 

Example timings

treekoR.Rcheck/treekoR-Ex.timings

nameusersystemelapsed
DeBiasi_COVID_CD8_samp1.9310.1762.107
colourTree2.9280.1483.068
getCellGMeans2.4210.0232.438
getCellProp1.3410.0231.358
getClusterTree0.9320.0200.946
getTreeResults1.9030.0631.959
hopachToPhylo0.9730.0040.970
plotInteractiveHeatmap3.0420.0553.094
runHOPACH0.9770.0200.990
testTree2.6090.1802.783