Package: BEARscc

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEARscc.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BEARscc_1.6.0.tar.gz

StartedAt: 2020-04-15 01:30:06 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:35:32 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 325.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BEARscc.Rcheck

Warnings: 3

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BEARscc.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings BEARscc_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/BEARscc.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.0'
* 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 ... WARNING
Object named '.Random.seed' found in datasets:
  'BEARscc_examples' 'analysis_examples'
Please remove it.
* 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' ... WARNING
Found the following significant warnings:

  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                          user system elapsed
estimate_noiseparameters 14.58   4.18   15.79
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                          user system elapsed
estimate_noiseparameters 14.95   2.38   14.61
* 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: 3 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/BEARscc.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/BEARscc_1.6.0.tar.gz && rm -rf BEARscc.buildbin-libdir && mkdir BEARscc.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BEARscc.buildbin-libdir BEARscc_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL BEARscc_1.6.0.zip && rm BEARscc_1.6.0.tar.gz BEARscc_1.6.0.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
100 2213k  100 2213k    0     0  32.5M      0 --:--:-- --:--:-- --:--:-- 34.8M

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_1.6.0.zip
* DONE (BEARscc)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'BEARscc' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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..."
== testthat results  ===========================================================
[ OK: 25 | SKIPPED: 0 | WARNINGS: 14 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  19.78    2.82   21.01 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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..."
== testthat results  ===========================================================
[ OK: 25 | SKIPPED: 0 | WARNINGS: 14 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  20.21    1.26   20.32