Multiple platform build/check report for BioC 3.14 - CHECK results for barcodetrackR on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: barcodetrackR

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:barcodetrackR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings barcodetrackR_1.2.0.tar.gz

StartedAt: 2022-04-12 15:54:33 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 15:59:26 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 292.4 seconds

RetCode: 0

Status: OK

CheckDir: barcodetrackR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:barcodetrackR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings barcodetrackR_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/barcodetrackR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
barcode_stat_test 6.73   0.01    6.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
barcode_stat_test 8.25      0    8.25
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/barcodetrackR_1.2.0.tar.gz && rm -rf barcodetrackR.buildbin-libdir && mkdir barcodetrackR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=barcodetrackR.buildbin-libdir barcodetrackR_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL barcodetrackR_1.2.0.zip && rm barcodetrackR_1.2.0.tar.gz barcodetrackR_1.2.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 84 1069k   84  902k    0     0  1103k      0 --:--:-- --:--:-- --:--:-- 1102k
100 1069k  100 1069k    0     0  1196k      0 --:--:-- --:--:-- --:--:-- 1196k

install for i386

* installing *source* package 'barcodetrackR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'barcodetrackR'
    finding HTML links ... done
    barcode_binary_heatmap                  html  
    barcode_ggheatmap                       html  
    barcode_ggheatmap_stat                  html  
    barcode_stat_test                       html  
    bias_histogram                          html  
    bias_lineplot                           html  
    bias_ridge_plot                         html  
    build_index_html                        html  
    chord_diagram                           html  
    clonal_contribution                     html  
    clonal_count                            html  
    clonal_diversity                        html  
    cor_plot                                html  
    create_SE                               html  
    dist_plot                               html  
    estimate_barcode_threshold              html  
    get_top_clones                          html  
    launchApp                               html  
    mds_plot                                html  
    rank_abundance_plot                     html  
    rank_abundance_stat_test                html  
    scatter_plot                            html  
    stat_hist                               html  
    subset_SE                               html  
    threshold                               html  
    threshold_SE                            html  
    wu_subset                               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 'barcodetrackR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'barcodetrackR' as barcodetrackR_1.2.0.zip
* DONE (barcodetrackR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'barcodetrackR' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(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 
   16.6     1.1    17.7


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(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 
  15.93    0.45   16.48

name	user	system	elapsed
barcode_binary_heatmap	0.26	0.08	0.34
barcode_ggheatmap	0.38	0.07	0.44
barcode_ggheatmap_stat	1.35	0.03	1.37
barcode_stat_test	6.73	0.01	6.75
bias_histogram	1.12	0.03	1.15
bias_lineplot	0.52	0.02	0.53
bias_ridge_plot	0.51	0.01	0.54
chord_diagram	0.30	0.07	0.36
clonal_contribution	0.20	0.01	0.21
clonal_count	0.31	0.00	0.32
clonal_diversity	0.24	0.00	0.23
cor_plot	0.69	0.02	0.70
create_SE	1.54	0.09	1.82
dist_plot	0.24	0.02	0.25
estimate_barcode_threshold	0	0	0
get_top_clones	0.00	0.01	0.01
launchApp	0	0	0
mds_plot	0.25	0.00	0.25
rank_abundance_plot	0.30	0.00	0.29
rank_abundance_stat_test	0.72	0.00	0.72
scatter_plot	0.12	0.00	0.13
stat_hist	0.19	0.00	0.19
subset_SE	0.01	0.00	0.02
threshold	0.05	0.03	0.08
threshold_SE	0.08	0.00	0.07

name	user	system	elapsed
barcode_binary_heatmap	0.27	0.02	0.28
barcode_ggheatmap	0.28	0.03	0.31
barcode_ggheatmap_stat	1.52	0.00	1.52
barcode_stat_test	8.25	0.00	8.25
bias_histogram	1.28	0.00	1.28
bias_lineplot	0.48	0.00	0.48
bias_ridge_plot	0.54	0.00	0.53
chord_diagram	0.31	0.00	0.31
clonal_contribution	0.23	0.00	0.24
clonal_count	0.40	0.00	0.41
clonal_diversity	0.25	0.00	0.25
cor_plot	0.75	0.00	0.75
create_SE	1.63	0.05	1.67
dist_plot	0.17	0.00	0.17
estimate_barcode_threshold	0.02	0.00	0.02
get_top_clones	0	0	0
launchApp	0	0	0
mds_plot	0.79	0.01	0.81
rank_abundance_plot	0.33	0.00	0.33
rank_abundance_stat_test	0.72	0.02	0.74
scatter_plot	0.13	0.00	0.12
stat_hist	0.23	0.00	0.23
subset_SE	0.03	0.00	0.04
threshold	0.05	0.00	0.04
threshold_SE	0.06	0.00	0.07

CHECK results for barcodetrackR on tokay2

Summary

Command output

Installation output

Tests output

Example timings