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CHECK report for blacksheepr on riesling1

This page was generated on 2020-10-18 12:33:20 -0400 (Sun, 18 Oct 2020).

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 186/1874HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
blacksheepr 1.3.0
RugglesLab
Snapshot Date: 2020-10-17 14:41:49 -0400 (Sat, 17 Oct 2020)
URL: https://git.bioconductor.org/packages/blacksheepr
Branch: master
Last Commit: c938295
Last Changed Date: 2020-04-27 15:31:23 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: blacksheepr
Version: 1.3.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blacksheepr.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings blacksheepr_1.3.0.tar.gz
StartedAt: 2020-10-17 19:56:08 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 20:00:21 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 252.1 seconds
RetCode: 0
Status:  OK  
CheckDir: blacksheepr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:blacksheepr.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings blacksheepr_1.3.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/blacksheepr.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.3.0'
* 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
create_heatmap 6.37   2.07    8.46
deva           7.44   0.30    7.75
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
create_heatmap 5.47   1.92    7.39
deva           6.42   0.17    6.60
* 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_1.3.0.tar.gz && rm -rf blacksheepr.buildbin-libdir && mkdir blacksheepr.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=blacksheepr.buildbin-libdir blacksheepr_1.3.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL blacksheepr_1.3.0.zip && rm blacksheepr_1.3.0.tar.gz blacksheepr_1.3.0.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  40.9M      0 --:--:-- --:--:-- --:--:-- 40.9M

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_1.3.0.zip
* DONE (blacksheepr)
* installing to library 'D:/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(blacksheepr)
> 
> test_check("blacksheepr")
== testthat results  ===========================================================
[ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  20.76    0.48   21.23 

blacksheepr.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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(blacksheepr)
> 
> test_check("blacksheepr")
== testthat results  ===========================================================
[ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.65    0.57   19.21 

Example timings

blacksheepr.Rcheck/examples_i386/blacksheepr-Ex.timings

nameusersystemelapsed
annotationlist_builder000
comparison_groupings0.010.000.01
count_outliers3.030.143.17
create_heatmap6.372.078.46
deva7.440.307.75
deva_normalization0.060.000.06
deva_results4.500.064.57
make_comparison_columns000
make_outlier_table1.750.031.78
outlier_analysis4.090.004.09
outlier_heatmap4.360.044.39

blacksheepr.Rcheck/examples_x64/blacksheepr-Ex.timings

nameusersystemelapsed
annotationlist_builder0.390.020.41
comparison_groupings0.020.000.01
count_outliers2.810.142.95
create_heatmap5.471.927.39
deva6.420.176.60
deva_normalization0.080.000.08
deva_results3.930.094.03
make_comparison_columns000
make_outlier_table1.510.071.58
outlier_analysis3.140.043.19
outlier_heatmap3.300.023.31