Adam Chan
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/treekoR |
| git_branch: RELEASE_3_13 |
| git_last_commit: 2b645b7 |
| git_last_commit_date: 2021-05-19 13:02:12 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:26 -0400 (Fri, 15 Oct 2021).
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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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:treekoR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings treekoR_1.0.0.tar.gz |
| StartedAt: 2021-10-15 06:54:14 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 07:00:34 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 380.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: treekoR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:treekoR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings treekoR_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/treekoR.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.13-bioc/meat/treekoR.Rcheck/00check.log' for details.
treekoR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/treekoR_1.0.0.tar.gz && rm -rf treekoR.buildbin-libdir && mkdir treekoR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=treekoR.buildbin-libdir treekoR_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL treekoR_1.0.0.zip && rm treekoR_1.0.0.tar.gz treekoR_1.0.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1114k 100 1114k 0 0 1966k 0 --:--:-- --:--:-- --:--:-- 1968k
install for i386
* installing *source* package 'treekoR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'treekoR'
finding HTML links ... done
DeBiasi_COVID_CD8_samp html
addFreqBars html
addHeatMap html
addTree html
colourTree html
findChildren html
getCellProp html
getClusterTree html
getTreeResults html
hopachToPhylo html
plotInteractiveHeatmap html
plotSigScatter html
runHOPACH html
testTree html
** 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
install for x64
* installing *source* package 'treekoR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'treekoR' as treekoR_1.0.0.zip
* DONE (treekoR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'treekoR' successfully unpacked and MD5 sums checked
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treekoR.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
16.37 1.87 18.25
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treekoR.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 30 ]
>
> proc.time()
user system elapsed
18.28 1.01 19.28
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treekoR.Rcheck/examples_i386/treekoR-Ex.timings
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treekoR.Rcheck/examples_x64/treekoR-Ex.timings
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