Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:42 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 2204/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
treekoR 1.12.0 (landing page) Adam Chan
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | NA | |||||||||
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. |
Package: treekoR |
Version: 1.12.0 |
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_1.12.0.tar.gz |
StartedAt: 2024-08-12 13:06:02 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 13:17:36 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 694.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: treekoR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/treekoR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘treekoR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘treekoR’ version ‘1.12.0’ * 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 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 8.369 0.615 10.973 colourTree 6.696 0.408 8.676 getCellGMeans 6.849 0.140 8.395 testTree 5.676 0.089 6.811 getTreeResults 4.962 0.085 6.134 * 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 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-3.19-bioc/meat/treekoR.Rcheck/00check.log’ for details.
treekoR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL treekoR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 48.169 2.185 62.915
treekoR.Rcheck/treekoR-Ex.timings
name | user | system | elapsed | |
DeBiasi_COVID_CD8_samp | 3.641 | 0.249 | 4.523 | |
colourTree | 6.696 | 0.408 | 8.676 | |
getCellGMeans | 6.849 | 0.140 | 8.395 | |
getCellProp | 3.380 | 0.063 | 4.194 | |
getClusterTree | 2.255 | 0.049 | 2.892 | |
getTreeResults | 4.962 | 0.085 | 6.134 | |
hopachToPhylo | 2.291 | 0.048 | 2.833 | |
plotInteractiveHeatmap | 8.369 | 0.615 | 10.973 | |
runHOPACH | 2.217 | 0.056 | 2.905 | |
testTree | 5.676 | 0.089 | 6.811 | |