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This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 127/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
barcodetrackR 1.12.0  (landing page)
Diego Alexander Espinoza
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/barcodetrackR
git_branch: RELEASE_3_19
git_last_commit: 586dd00
git_last_commit_date: 2024-04-30 11:32:45 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for barcodetrackR on kjohnson3

To the developers/maintainers of the barcodetrackR package:
- 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 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: barcodetrackR
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2024-06-10 08:03:50 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 08:08:48 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 298.5 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/barcodetrackR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘barcodetrackR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘barcodetrackR’ version ‘1.12.0’
* 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 ‘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 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 ... 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 5.274  0.063    7.41
* 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: 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/4.4-arm64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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(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 9 | SKIP 0 | PASS 31 ]

[ FAIL 0 | WARN 9 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 18.966   0.799  25.187 

Example timings

barcodetrackR.Rcheck/barcodetrackR-Ex.timings

nameusersystemelapsed
barcode_binary_heatmap0.4610.0130.475
barcode_ggheatmap1.4020.0282.444
barcode_ggheatmap_stat1.2050.0661.872
barcode_stat_test5.2740.0637.410
bias_histogram1.1310.0231.661
bias_lineplot0.2990.0070.399
bias_ridge_plot0.5520.0160.847
chord_diagram0.2610.0150.412
clonal_contribution0.2460.0080.370
clonal_count0.3180.0060.386
clonal_diversity0.2430.0050.248
cor_plot0.6990.0131.091
create_SE2.9720.0664.673
dist_plot0.1990.0070.314
estimate_barcode_threshold0.0010.0000.003
get_top_clones0.0090.0020.018
launchApp000
mds_plot0.1970.0050.304
rank_abundance_plot0.2170.0060.348
rank_abundance_stat_test0.3180.0170.421
scatter_plot0.1470.0090.156
stat_hist0.1800.0040.216
subset_SE0.0190.0020.025
threshold0.0410.0210.082
threshold_SE0.0420.0030.069