Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:56 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1957/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
treekoR 1.0.0 (landing page) Adam Chan
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: treekoR |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:treekoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings treekoR_1.0.0.tar.gz |
StartedAt: 2021-10-15 00:54:50 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:00:24 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 333.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: treekoR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:treekoR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings treekoR_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/treekoR.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.0.0’ * 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 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 ‘statParent’ colourTree: no visible binding for global variable ‘x’ colourTree: no visible binding for global variable ‘y’ colourTree: no visible binding for global variable ‘statAll’ colourTree: no visible binding for global variable ‘label’ 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 ‘statAll’ plotSigScatter: no visible binding for global variable ‘statParent’ plotSigScatter: no visible binding for global variable ‘isTip’ plotSigScatter: no visible binding for global variable ‘label’ Undefined global functions or variables: . cluster_id freq freq_label isTip label node statAll statParent 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 DeBiasi_COVID_CD8_samp 5.520 0.328 5.851 plotInteractiveHeatmap 4.983 0.205 5.444 * 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/treekoR.Rcheck/00check.log’ for details.
treekoR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL treekoR ### ############################################################################## ############################################################################## * 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)
treekoR.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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 30 ] > > proc.time() user system elapsed 27.228 1.183 28.411
treekoR.Rcheck/treekoR-Ex.timings
name | user | system | elapsed | |
DeBiasi_COVID_CD8_samp | 5.520 | 0.328 | 5.851 | |
colourTree | 3.889 | 0.077 | 3.969 | |
getCellProp | 2.881 | 0.066 | 2.950 | |
getClusterTree | 1.617 | 0.026 | 1.644 | |
getTreeResults | 2.949 | 0.146 | 3.095 | |
hopachToPhylo | 1.585 | 0.018 | 1.604 | |
plotInteractiveHeatmap | 4.983 | 0.205 | 5.444 | |
runHOPACH | 1.706 | 0.037 | 1.745 | |
testTree | 2.029 | 0.036 | 2.068 | |