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This page was generated on 2024-03-27 11:37:18 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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 2173/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
treekoR 1.10.0  (landing page)
Adam Chan
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/treekoR
git_branch: RELEASE_3_18
git_last_commit: cd2ce9f
git_last_commit_date: 2023-10-24 11:32:14 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for treekoR on palomino4


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: 1.10.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:treekoR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings treekoR_1.10.0.tar.gz
StartedAt: 2024-03-26 06:03:50 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 06:09:27 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 336.6 seconds
RetCode: 0
Status:   OK  
CheckDir: treekoR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:treekoR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings treekoR_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/treekoR.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'treekoR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'treekoR' version '1.10.0'
* 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 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
plotInteractiveHeatmap 4.58   0.11    5.06
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/treekoR.Rcheck/00check.log'
for details.



Installation output

treekoR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL treekoR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  23.62    1.46   25.12 

Example timings

treekoR.Rcheck/treekoR-Ex.timings

nameusersystemelapsed
DeBiasi_COVID_CD8_samp1.010.171.19
colourTree3.500.223.72
getCellGMeans2.560.082.64
getCellProp1.390.011.41
getClusterTree0.890.070.97
getTreeResults1.990.001.98
hopachToPhylo0.930.040.99
plotInteractiveHeatmap4.580.115.06
runHOPACH0.890.050.96
testTree2.560.122.68