Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:39 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for barcodetrackR on machv2


To the developers/maintainers of the barcodetrackR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/barcodetrackR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 114/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
barcodetrackR 1.2.0  (landing page)
Diego Alexander Espinoza
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/barcodetrackR
git_branch: RELEASE_3_14
git_last_commit: 29ecd67
git_last_commit_date: 2021-10-26 13:08:19 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: barcodetrackR
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:barcodetrackR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings barcodetrackR_1.2.0.tar.gz
StartedAt: 2022-04-12 10:32:24 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 10:37:14 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 289.6 seconds
RetCode: 0
Status:   OK  
CheckDir: barcodetrackR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:barcodetrackR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings barcodetrackR_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/barcodetrackR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘barcodetrackR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘barcodetrackR’ version ‘1.2.0’
* 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 ‘barcodetrackR’ 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 ... OK
* 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
barcode_stat_test 11.996  0.038   12.07
* 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: OK


Installation output

barcodetrackR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL barcodetrackR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘barcodetrackR’ ...
** 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 (barcodetrackR)

Tests output

barcodetrackR.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(barcodetrackR)
> 
> test_check("barcodetrackR")
No threshold supplied. All barcodes will be retained. Be aware that lower abundance barcodes are likely to be less reliable due to sampling bias. To estimate an appropriate threshold, please see the barcodetrackR function `estimate_barcode_threshold`. 
No threshold supplied. All barcodes will be retained. Be aware that lower abundance barcodes are likely to be less reliable due to sampling bias. To estimate an appropriate threshold, please see the barcodetrackR function `estimate_barcode_threshold`. 
Removed 0 barcodes from the supplied dataframe based on relative threshold of 1e-07 
Removed 0 barcodes from the supplied dataframe based on relative threshold of 1e-07 
Removed 71 barcodes from the supplied dataframe based on relative threshold of 0.005 
Removed 71 barcodes from the supplied dataframe based on relative threshold of 0.005 
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 31 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 24.681   0.929  25.614 

Example timings

barcodetrackR.Rcheck/barcodetrackR-Ex.timings

nameusersystemelapsed
barcode_binary_heatmap0.5040.0200.524
barcode_ggheatmap0.5120.0100.523
barcode_ggheatmap_stat2.6570.0932.754
barcode_stat_test11.996 0.03812.070
bias_histogram1.9930.0142.008
bias_lineplot0.8290.0070.837
bias_ridge_plot1.5610.0301.595
chord_diagram0.4820.0210.505
clonal_contribution0.3630.0180.382
clonal_count0.5620.0100.573
clonal_diversity0.4330.0040.439
cor_plot1.3200.0111.333
create_SE2.0340.0782.115
dist_plot0.2820.0040.287
estimate_barcode_threshold0.0000.0000.001
get_top_clones0.0160.0020.018
launchApp000
mds_plot0.2310.0030.235
rank_abundance_plot0.4230.0070.431
rank_abundance_stat_test1.1120.0351.148
scatter_plot0.1480.0020.151
stat_hist0.3170.0030.321
subset_SE0.0300.0020.032
threshold0.0850.0570.143
threshold_SE0.1100.0030.112