Multiple platform build/check report for BioC 3.13 - CHECK results for BEARscc on tokay2

Package: BEARscc

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEARscc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BEARscc_1.12.0.tar.gz

StartedAt: 2021-10-14 20:01:10 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 20:06:08 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 297.2 seconds

RetCode: 0

Status: OK

CheckDir: BEARscc.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEARscc.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BEARscc_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BEARscc.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 'BEARscc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BEARscc' version '1.12.0'
* 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 'BEARscc' 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
estimate_noiseparameters 8.88   0.59    9.47
simulate_replicates      6.86   0.02    6.88
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
estimate_noiseparameters 8.95    0.1    9.04
simulate_replicates      7.82    0.0    7.81
* 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://155.52.207.165/BBS/3.13/bioc/src/contrib/BEARscc_1.12.0.tar.gz && rm -rf BEARscc.buildbin-libdir && mkdir BEARscc.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BEARscc.buildbin-libdir BEARscc_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BEARscc_1.12.0.zip && rm BEARscc_1.12.0.tar.gz BEARscc_1.12.0.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
 27 2207k   27  598k    0     0  1170k      0  0:00:01 --:--:--  0:00:01 1169k
100 2207k  100 2207k    0     0  1802k      0  0:00:01  0:00:01 --:--:-- 1804k

install for i386

* installing *source* package 'BEARscc' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BEARscc'
    finding HTML links ... done
    BEARscc-package                         html  
    BEARscc_examples                        html  
    analysis_examples                       html  
    cluster_consensus                       html  
    compute_consensus                       html  
    estimate_noiseparameters                html  
    report_cell_metrics                     html  
    report_cluster_metrics                  html  
    simulate_replicates                     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 'BEARscc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BEARscc' as BEARscc_1.12.0.zip
* DONE (BEARscc)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BEARscc' successfully unpacked and MD5 sums checked


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(BEARscc)
> 
> test_check("BEARscc")

[1] "Running BEARscc on example data to test for correct installation."

[1] "Fitting parameter alpha to establish spike-in derived noise model."
[1] "Estimating error for spike-ins with alpha = 0"
[1] "Estimating error for spike-ins with alpha = 0.25"
[1] "Estimating error for spike-ins with alpha = 0.5"
[1] "Estimating error for spike-ins with alpha = 0.75"
[1] "Estimating error for spike-ins with alpha = 1"
[1] "There are adequate spike-in drop-outs to build the drop-out model. Estimating the drop-out model now."

[1] "Injecting noise for testing..."
[1] "Creating a simulated replicated counts matrix: 1."
[1] "Creating a simulated replicated counts matrix: 2."
[1] "Creating a simulated replicated counts matrix: 3."

[1] "Creating consensus matrix for testing..."

[1] "Computing cluster and cell metrics for testing..."
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 25 ]
> 
> proc.time()
   user  system elapsed 
  19.29    0.78   20.12


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(BEARscc)
> 
> test_check("BEARscc")

[1] "Running BEARscc on example data to test for correct installation."

[1] "Fitting parameter alpha to establish spike-in derived noise model."
[1] "Estimating error for spike-ins with alpha = 0"
[1] "Estimating error for spike-ins with alpha = 0.25"
[1] "Estimating error for spike-ins with alpha = 0.5"
[1] "Estimating error for spike-ins with alpha = 0.75"
[1] "Estimating error for spike-ins with alpha = 1"
[1] "There are adequate spike-in drop-outs to build the drop-out model. Estimating the drop-out model now."

[1] "Injecting noise for testing..."
[1] "Creating a simulated replicated counts matrix: 1."
[1] "Creating a simulated replicated counts matrix: 2."
[1] "Creating a simulated replicated counts matrix: 3."

[1] "Creating consensus matrix for testing..."

[1] "Computing cluster and cell metrics for testing..."
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 25 ]
> 
> proc.time()
   user  system elapsed 
  17.98    0.40   18.37

name	user	system	elapsed
BEARscc_examples	0.04	0.00	0.05
analysis_examples	0.04	0.00	0.05
cluster_consensus	0.05	0.01	0.06
compute_consensus	0.09	0.02	0.11
estimate_noiseparameters	8.88	0.59	9.47
report_cell_metrics	0.39	0.05	0.43
report_cluster_metrics	0.73	0.03	0.77
simulate_replicates	6.86	0.02	6.88

name	user	system	elapsed
BEARscc_examples	0.04	0.00	0.04
analysis_examples	0.03	0.00	0.03
cluster_consensus	0.05	0.00	0.05
compute_consensus	0.11	0.00	0.11
estimate_noiseparameters	8.95	0.10	9.04
report_cell_metrics	0.44	0.01	0.46
report_cluster_metrics	0.79	0.02	0.81
simulate_replicates	7.82	0.00	7.81

CHECK results for BEARscc on tokay2

Summary

Command output

Installation output

Tests output

Example timings