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CHECK report for blacksheepr on tokay1

This page was generated on 2021-05-06 12:30:04 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the blacksheepr package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 195/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
blacksheepr 1.4.0  (landing page)
RugglesLab
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/blacksheepr
Branch: RELEASE_3_12
Last Commit: 558236a
Last Changed Date: 2020-10-27 11:50:16 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: blacksheepr
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blacksheepr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings blacksheepr_1.4.0.tar.gz
StartedAt: 2021-05-06 00:57:57 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:04:42 -0400 (Thu, 06 May 2021)
EllapsedTime: 405.0 seconds
RetCode: 0
Status:   OK   
CheckDir: blacksheepr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blacksheepr.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings blacksheepr_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/blacksheepr.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'blacksheepr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'blacksheepr' version '1.4.0'
* 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 'blacksheepr' 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
deva             13.91   0.31   14.22
create_heatmap   11.30   0.20   27.86
count_outliers    7.03   0.36    7.39
outlier_analysis  6.93   0.11    7.05
deva_results      6.30   0.32    6.61
outlier_heatmap   6.23   0.01    6.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
deva             10.15   0.23   10.39
create_heatmap    8.44   0.32    8.75
outlier_heatmap   6.17   0.00    6.17
outlier_analysis  5.54   0.04    5.58
deva_results      5.30   0.08    5.37
* 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


Installation output

blacksheepr.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/blacksheepr_1.4.0.tar.gz && rm -rf blacksheepr.buildbin-libdir && mkdir blacksheepr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=blacksheepr.buildbin-libdir blacksheepr_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL blacksheepr_1.4.0.zip && rm blacksheepr_1.4.0.tar.gz blacksheepr_1.4.0.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 3773k  100 3773k    0     0  46.6M      0 --:--:-- --:--:-- --:--:-- 47.2M

install for i386

* installing *source* package 'blacksheepr' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'blacksheepr'
    finding HTML links ... done
    annotationlist_builder                  html  
    comparison_groupings                    html  
    count_outliers                          html  
    create_heatmap                          html  
    deva                                    html  
    deva_normalization                      html  
    deva_results                            html  
    make_comparison_columns                 html  
    make_outlier_table                      html  
    outlier_analysis                        html  
    outlier_heatmap                         html  
    sample_annotationdata                   html  
    sample_phosphodata                      html  
    sample_rnadata                          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 'blacksheepr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'blacksheepr' as blacksheepr_1.4.0.zip
* DONE (blacksheepr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'blacksheepr' successfully unpacked and MD5 sums checked

Tests output

blacksheepr.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(blacksheepr)
> 
> test_check("blacksheepr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  30.62    0.93   41.39 

blacksheepr.Rcheck/tests_x64/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(blacksheepr)
> 
> test_check("blacksheepr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
  32.60    0.65   34.36 

Example timings

blacksheepr.Rcheck/examples_i386/blacksheepr-Ex.timings

nameusersystemelapsed
annotationlist_builder0.010.000.02
comparison_groupings0.020.020.03
count_outliers7.030.367.39
create_heatmap11.30 0.2027.86
deva13.91 0.3114.22
deva_normalization0.160.000.15
deva_results6.300.326.61
make_comparison_columns0.000.010.02
make_outlier_table3.500.103.59
outlier_analysis6.930.117.05
outlier_heatmap6.230.016.25

blacksheepr.Rcheck/examples_x64/blacksheepr-Ex.timings

nameusersystemelapsed
annotationlist_builder0.010.000.01
comparison_groupings0.020.000.02
count_outliers4.200.144.34
create_heatmap8.440.328.75
deva10.15 0.2310.39
deva_normalization0.080.000.08
deva_results5.300.085.37
make_comparison_columns000
make_outlier_table2.410.042.46
outlier_analysis5.540.045.58
outlier_heatmap6.170.006.17